mirror of
https://github.com/OMGeeky/google-apis-rs.git
synced 2026-01-23 11:44:55 +01:00
4843 lines
244 KiB
Rust
4843 lines
244 KiB
Rust
// DO NOT EDIT !
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// This file was generated automatically from 'src/mako/cli/main.rs.mako'
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// DO NOT EDIT !
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#![allow(unused_variables, unused_imports, dead_code, unused_mut)]
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#[macro_use]
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extern crate clap;
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extern crate yup_oauth2 as oauth2;
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extern crate yup_hyper_mock as mock;
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extern crate serde;
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extern crate serde_json;
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extern crate hyper;
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extern crate mime;
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extern crate strsim;
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extern crate google_genomics1 as api;
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use std::env;
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use std::io::{self, Write};
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use clap::{App, SubCommand, Arg};
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mod cmn;
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use cmn::{InvalidOptionsError, CLIError, JsonTokenStorage, arg_from_str, writer_from_opts, parse_kv_arg,
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input_file_from_opts, input_mime_from_opts, FieldCursor, FieldError, CallType, UploadProtocol,
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calltype_from_str, remove_json_null_values, ComplexType, JsonType, JsonTypeInfo};
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use std::default::Default;
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use std::str::FromStr;
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use oauth2::{Authenticator, DefaultAuthenticatorDelegate};
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use serde_json as json;
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use clap::ArgMatches;
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enum DoitError {
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IoError(String, io::Error),
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ApiError(api::Error),
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}
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struct Engine<'n> {
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opt: ArgMatches<'n>,
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hub: api::Genomics<hyper::Client, Authenticator<DefaultAuthenticatorDelegate, JsonTokenStorage, hyper::Client>>,
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gp: Vec<&'static str>,
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gpm: Vec<(&'static str, &'static str)>,
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}
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impl<'n> Engine<'n> {
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fn _callsets_create(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
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-> Result<(), DoitError> {
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let mut field_cursor = FieldCursor::default();
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let mut object = json::value::Value::Object(Default::default());
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for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let last_errc = err.issues.len();
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let (key, value) = parse_kv_arg(&*kvarg, err, false);
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let mut temp_cursor = field_cursor.clone();
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if let Err(field_err) = temp_cursor.set(&*key) {
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err.issues.push(field_err);
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}
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if value.is_none() {
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field_cursor = temp_cursor.clone();
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if err.issues.len() > last_errc {
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err.issues.remove(last_errc);
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}
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continue;
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}
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let type_info: Option<(&'static str, JsonTypeInfo)> =
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match &temp_cursor.to_string()[..] {
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"sample-id" => Some(("sampleId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
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"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"created" => Some(("created", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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_ => {
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let suggestion = FieldCursor::did_you_mean(key, &vec!["created", "id", "name", "sample-id", "variant-set-ids"]);
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err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
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None
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}
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};
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if let Some((field_cursor_str, type_info)) = type_info {
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FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
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}
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}
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let mut request: api::CallSet = json::value::from_value(object).unwrap();
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let mut call = self.hub.callsets().create(request);
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for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let (key, value) = parse_kv_arg(&*parg, err, false);
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match key {
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_ => {
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let mut found = false;
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for param in &self.gp {
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if key == *param {
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found = true;
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call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
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break;
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}
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}
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if !found {
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err.issues.push(CLIError::UnknownParameter(key.to_string(),
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{let mut v = Vec::new();
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v.extend(self.gp.iter().map(|v|*v));
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v } ));
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}
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}
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}
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}
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let protocol = CallType::Standard;
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if dry_run {
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Ok(())
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} else {
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assert!(err.issues.len() == 0);
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for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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call = call.add_scope(scope);
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}
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let mut ostream = match writer_from_opts(opt.value_of("out")) {
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Ok(mut f) => f,
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Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
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};
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match match protocol {
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CallType::Standard => call.doit(),
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_ => unreachable!()
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} {
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Err(api_err) => Err(DoitError::ApiError(api_err)),
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Ok((mut response, output_schema)) => {
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let mut value = json::value::to_value(&output_schema);
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remove_json_null_values(&mut value);
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json::to_writer_pretty(&mut ostream, &value).unwrap();
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ostream.flush().unwrap();
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Ok(())
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}
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}
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}
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}
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fn _callsets_delete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
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-> Result<(), DoitError> {
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let mut call = self.hub.callsets().delete(opt.value_of("call-set-id").unwrap_or(""));
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for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let (key, value) = parse_kv_arg(&*parg, err, false);
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match key {
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_ => {
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let mut found = false;
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for param in &self.gp {
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if key == *param {
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found = true;
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call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
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break;
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}
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}
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if !found {
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err.issues.push(CLIError::UnknownParameter(key.to_string(),
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{let mut v = Vec::new();
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v.extend(self.gp.iter().map(|v|*v));
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v } ));
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}
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}
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}
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}
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let protocol = CallType::Standard;
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if dry_run {
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Ok(())
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} else {
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assert!(err.issues.len() == 0);
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for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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call = call.add_scope(scope);
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}
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let mut ostream = match writer_from_opts(opt.value_of("out")) {
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Ok(mut f) => f,
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Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
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};
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match match protocol {
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CallType::Standard => call.doit(),
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_ => unreachable!()
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} {
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Err(api_err) => Err(DoitError::ApiError(api_err)),
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Ok((mut response, output_schema)) => {
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let mut value = json::value::to_value(&output_schema);
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remove_json_null_values(&mut value);
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json::to_writer_pretty(&mut ostream, &value).unwrap();
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ostream.flush().unwrap();
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Ok(())
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}
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}
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}
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}
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fn _callsets_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
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-> Result<(), DoitError> {
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let mut call = self.hub.callsets().get(opt.value_of("call-set-id").unwrap_or(""));
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for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let (key, value) = parse_kv_arg(&*parg, err, false);
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match key {
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_ => {
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let mut found = false;
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for param in &self.gp {
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if key == *param {
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found = true;
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call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
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break;
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}
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}
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if !found {
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err.issues.push(CLIError::UnknownParameter(key.to_string(),
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{let mut v = Vec::new();
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v.extend(self.gp.iter().map(|v|*v));
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v } ));
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}
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}
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}
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}
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let protocol = CallType::Standard;
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if dry_run {
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Ok(())
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} else {
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assert!(err.issues.len() == 0);
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for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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call = call.add_scope(scope);
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}
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let mut ostream = match writer_from_opts(opt.value_of("out")) {
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Ok(mut f) => f,
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Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
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};
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match match protocol {
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CallType::Standard => call.doit(),
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_ => unreachable!()
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} {
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Err(api_err) => Err(DoitError::ApiError(api_err)),
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Ok((mut response, output_schema)) => {
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let mut value = json::value::to_value(&output_schema);
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remove_json_null_values(&mut value);
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json::to_writer_pretty(&mut ostream, &value).unwrap();
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ostream.flush().unwrap();
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Ok(())
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}
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}
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}
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}
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fn _callsets_patch(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
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-> Result<(), DoitError> {
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let mut field_cursor = FieldCursor::default();
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let mut object = json::value::Value::Object(Default::default());
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for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let last_errc = err.issues.len();
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let (key, value) = parse_kv_arg(&*kvarg, err, false);
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let mut temp_cursor = field_cursor.clone();
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if let Err(field_err) = temp_cursor.set(&*key) {
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err.issues.push(field_err);
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}
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if value.is_none() {
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field_cursor = temp_cursor.clone();
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if err.issues.len() > last_errc {
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err.issues.remove(last_errc);
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}
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continue;
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}
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let type_info: Option<(&'static str, JsonTypeInfo)> =
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match &temp_cursor.to_string()[..] {
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"sample-id" => Some(("sampleId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
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"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"created" => Some(("created", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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_ => {
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let suggestion = FieldCursor::did_you_mean(key, &vec!["created", "id", "name", "sample-id", "variant-set-ids"]);
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err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
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None
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}
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};
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if let Some((field_cursor_str, type_info)) = type_info {
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FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
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}
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}
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let mut request: api::CallSet = json::value::from_value(object).unwrap();
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let mut call = self.hub.callsets().patch(request, opt.value_of("call-set-id").unwrap_or(""));
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for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let (key, value) = parse_kv_arg(&*parg, err, false);
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match key {
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"update-mask" => {
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call = call.update_mask(value.unwrap_or(""));
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},
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_ => {
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let mut found = false;
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for param in &self.gp {
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if key == *param {
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found = true;
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call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
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break;
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}
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}
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if !found {
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err.issues.push(CLIError::UnknownParameter(key.to_string(),
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{let mut v = Vec::new();
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v.extend(self.gp.iter().map(|v|*v));
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v.extend(["update-mask"].iter().map(|v|*v));
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v } ));
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}
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}
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}
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}
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let protocol = CallType::Standard;
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if dry_run {
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Ok(())
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} else {
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assert!(err.issues.len() == 0);
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for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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call = call.add_scope(scope);
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}
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let mut ostream = match writer_from_opts(opt.value_of("out")) {
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Ok(mut f) => f,
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Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
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};
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match match protocol {
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CallType::Standard => call.doit(),
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_ => unreachable!()
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} {
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Err(api_err) => Err(DoitError::ApiError(api_err)),
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Ok((mut response, output_schema)) => {
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let mut value = json::value::to_value(&output_schema);
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remove_json_null_values(&mut value);
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json::to_writer_pretty(&mut ostream, &value).unwrap();
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ostream.flush().unwrap();
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Ok(())
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}
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}
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}
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}
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fn _callsets_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
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-> Result<(), DoitError> {
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let mut field_cursor = FieldCursor::default();
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let mut object = json::value::Value::Object(Default::default());
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for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
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let last_errc = err.issues.len();
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let (key, value) = parse_kv_arg(&*kvarg, err, false);
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let mut temp_cursor = field_cursor.clone();
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if let Err(field_err) = temp_cursor.set(&*key) {
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err.issues.push(field_err);
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}
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if value.is_none() {
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field_cursor = temp_cursor.clone();
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if err.issues.len() > last_errc {
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err.issues.remove(last_errc);
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}
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continue;
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}
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let type_info: Option<(&'static str, JsonTypeInfo)> =
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match &temp_cursor.to_string()[..] {
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"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
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"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
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"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
_ => {
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|
let suggestion = FieldCursor::did_you_mean(key, &vec!["name", "page-size", "page-token", "variant-set-ids"]);
|
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err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
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None
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}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchCallSetsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.callsets().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_create(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"create-time" => Some(("createTime", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["create-time", "id", "name", "project-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::Dataset = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().create(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_delete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.datasets().delete(opt.value_of("dataset-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.datasets().get(opt.value_of("dataset-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_get_iam_policy(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec![]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::GetIamPolicyRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().get_iam_policy(request, opt.value_of("resource").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_list(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.datasets().list();
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"project-id" => {
|
|
call = call.project_id(value.unwrap_or(""));
|
|
},
|
|
"page-token" => {
|
|
call = call.page_token(value.unwrap_or(""));
|
|
},
|
|
"page-size" => {
|
|
call = call.page_size(arg_from_str(value.unwrap_or("-0"), err, "page-size", "integer"));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["project-id", "page-size", "page-token"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_patch(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"create-time" => Some(("createTime", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["create-time", "id", "name", "project-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::Dataset = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().patch(request, opt.value_of("dataset-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"update-mask" => {
|
|
call = call.update_mask(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["update-mask"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_set_iam_policy(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"policy.version" => Some(("policy.version", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
"policy.etag" => Some(("policy.etag", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["etag", "policy", "version"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SetIamPolicyRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().set_iam_policy(request, opt.value_of("resource").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_test_iam_permissions(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"permissions" => Some(("permissions", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["permissions"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::TestIamPermissionsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().test_iam_permissions(request, opt.value_of("resource").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _datasets_undelete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec![]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::UndeleteDatasetRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.datasets().undelete(request, opt.value_of("dataset-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _operations_cancel(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec![]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::CancelOperationRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.operations().cancel(request, opt.value_of("name").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _operations_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.operations().get(opt.value_of("name").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _operations_list(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.operations().list(opt.value_of("name").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"page-token" => {
|
|
call = call.page_token(value.unwrap_or(""));
|
|
},
|
|
"page-size" => {
|
|
call = call.page_size(arg_from_str(value.unwrap_or("-0"), err, "page-size", "integer"));
|
|
},
|
|
"filter" => {
|
|
call = call.filter(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["filter", "page-token", "page-size"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_coveragebuckets_list(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.readgroupsets().coveragebuckets_list(opt.value_of("read-group-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"target-bucket-width" => {
|
|
call = call.target_bucket_width(value.unwrap_or(""));
|
|
},
|
|
"start" => {
|
|
call = call.start(value.unwrap_or(""));
|
|
},
|
|
"reference-name" => {
|
|
call = call.reference_name(value.unwrap_or(""));
|
|
},
|
|
"page-token" => {
|
|
call = call.page_token(value.unwrap_or(""));
|
|
},
|
|
"page-size" => {
|
|
call = call.page_size(arg_from_str(value.unwrap_or("-0"), err, "page-size", "integer"));
|
|
},
|
|
"end" => {
|
|
call = call.end(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["end", "page-size", "page-token", "start", "target-bucket-width", "reference-name"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_delete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.readgroupsets().delete(opt.value_of("read-group-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_export(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-names" => Some(("referenceNames", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"export-uri" => Some(("exportUri", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["export-uri", "project-id", "reference-names"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::ExportReadGroupSetRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.readgroupsets().export(request, opt.value_of("read-group-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.readgroupsets().get(opt.value_of("read-group-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_import(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"source-uris" => Some(("sourceUris", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"partition-strategy" => Some(("partitionStrategy", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-id" => Some(("datasetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-id", "partition-strategy", "reference-set-id", "source-uris"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::ImportReadGroupSetsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.readgroupsets().import(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_patch(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"filename" => Some(("filename", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-id" => Some(("datasetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-id", "filename", "id", "name", "reference-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::ReadGroupSet = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.readgroupsets().patch(request, opt.value_of("read-group-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"update-mask" => {
|
|
call = call.update_mask(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["update-mask"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _readgroupsets_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-ids" => Some(("datasetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"name" => Some(("name", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-ids", "name", "page-size", "page-token"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchReadGroupSetsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.readgroupsets().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _reads_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"read-group-ids" => Some(("readGroupIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"read-group-set-ids" => Some(("readGroupSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["end", "page-size", "page-token", "read-group-ids", "read-group-set-ids", "reference-name", "start"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchReadsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.reads().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _reads_stream(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"read-group-set-id" => Some(("readGroupSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["end", "project-id", "read-group-set-id", "reference-name", "start"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::StreamReadsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.reads().stream(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _references_bases_list(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.references().bases_list(opt.value_of("reference-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"start" => {
|
|
call = call.start(value.unwrap_or(""));
|
|
},
|
|
"page-token" => {
|
|
call = call.page_token(value.unwrap_or(""));
|
|
},
|
|
"page-size" => {
|
|
call = call.page_size(arg_from_str(value.unwrap_or("-0"), err, "page-size", "integer"));
|
|
},
|
|
"end" => {
|
|
call = call.end(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["start", "end", "page-size", "page-token"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _references_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.references().get(opt.value_of("reference-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _references_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"md5checksums" => Some(("md5checksums", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"accessions" => Some(("accessions", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["accessions", "md5checksums", "page-size", "page-token", "reference-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchReferencesRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.references().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _referencesets_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.referencesets().get(opt.value_of("reference-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _referencesets_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"md5checksums" => Some(("md5checksums", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"assembly-id" => Some(("assemblyId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"accessions" => Some(("accessions", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["accessions", "assembly-id", "md5checksums", "page-size", "page-token"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchReferenceSetsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.referencesets().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_create(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"variant-set-id" => Some(("variantSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"created" => Some(("created", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-bases" => Some(("referenceBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"filter" => Some(("filter", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"names" => Some(("names", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"alternate-bases" => Some(("alternateBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"quality" => Some(("quality", JsonTypeInfo { jtype: JsonType::Float, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["alternate-bases", "created", "end", "filter", "id", "names", "quality", "reference-bases", "reference-name", "start", "variant-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::Variant = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variants().create(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_delete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.variants().delete(opt.value_of("variant-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.variants().get(opt.value_of("variant-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_import(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"variant-set-id" => Some(("variantSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"normalize-reference-names" => Some(("normalizeReferenceNames", JsonTypeInfo { jtype: JsonType::Boolean, ctype: ComplexType::Pod })),
|
|
"source-uris" => Some(("sourceUris", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"format" => Some(("format", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["format", "normalize-reference-names", "source-uris", "variant-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::ImportVariantsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variants().import(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_patch(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"variant-set-id" => Some(("variantSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"created" => Some(("created", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-bases" => Some(("referenceBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"filter" => Some(("filter", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"names" => Some(("names", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"alternate-bases" => Some(("alternateBases", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"quality" => Some(("quality", JsonTypeInfo { jtype: JsonType::Float, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["alternate-bases", "created", "end", "filter", "id", "names", "quality", "reference-bases", "reference-name", "start", "variant-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::Variant = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variants().patch(request, opt.value_of("variant-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"update-mask" => {
|
|
call = call.update_mask(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["update-mask"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"max-calls" => Some(("maxCalls", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"call-set-ids" => Some(("callSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"variant-name" => Some(("variantName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"variant-set-ids" => Some(("variantSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["call-set-ids", "end", "max-calls", "page-size", "page-token", "reference-name", "start", "variant-name", "variant-set-ids"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchVariantsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variants().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variants_stream(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"variant-set-id" => Some(("variantSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"end" => Some(("end", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"start" => Some(("start", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"call-set-ids" => Some(("callSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"reference-name" => Some(("referenceName", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["call-set-ids", "end", "project-id", "reference-name", "start", "variant-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::StreamVariantsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variants().stream(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_create(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-id" => Some(("datasetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-id", "id", "reference-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::VariantSet = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variantsets().create(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_delete(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.variantsets().delete(opt.value_of("variant-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_export(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"project-id" => Some(("projectId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"bigquery-table" => Some(("bigqueryTable", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"bigquery-dataset" => Some(("bigqueryDataset", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"call-set-ids" => Some(("callSetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"format" => Some(("format", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["bigquery-dataset", "bigquery-table", "call-set-ids", "format", "project-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::ExportVariantSetRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variantsets().export(request, opt.value_of("variant-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_get(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
let mut call = self.hub.variantsets().get(opt.value_of("variant-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_patch(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"reference-set-id" => Some(("referenceSetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"id" => Some(("id", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-id" => Some(("datasetId", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-id", "id", "reference-set-id"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::VariantSet = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variantsets().patch(request, opt.value_of("variant-set-id").unwrap_or(""));
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
"update-mask" => {
|
|
call = call.update_mask(value.unwrap_or(""));
|
|
},
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v.extend(["update-mask"].iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _variantsets_search(&self, opt: &ArgMatches<'n>, dry_run: bool, err: &mut InvalidOptionsError)
|
|
-> Result<(), DoitError> {
|
|
|
|
let mut field_cursor = FieldCursor::default();
|
|
let mut object = json::value::Value::Object(Default::default());
|
|
|
|
for kvarg in opt.values_of("kv").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let last_errc = err.issues.len();
|
|
let (key, value) = parse_kv_arg(&*kvarg, err, false);
|
|
let mut temp_cursor = field_cursor.clone();
|
|
if let Err(field_err) = temp_cursor.set(&*key) {
|
|
err.issues.push(field_err);
|
|
}
|
|
if value.is_none() {
|
|
field_cursor = temp_cursor.clone();
|
|
if err.issues.len() > last_errc {
|
|
err.issues.remove(last_errc);
|
|
}
|
|
continue;
|
|
}
|
|
|
|
let type_info: Option<(&'static str, JsonTypeInfo)> =
|
|
match &temp_cursor.to_string()[..] {
|
|
"page-token" => Some(("pageToken", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Pod })),
|
|
"dataset-ids" => Some(("datasetIds", JsonTypeInfo { jtype: JsonType::String, ctype: ComplexType::Vec })),
|
|
"page-size" => Some(("pageSize", JsonTypeInfo { jtype: JsonType::Int, ctype: ComplexType::Pod })),
|
|
_ => {
|
|
let suggestion = FieldCursor::did_you_mean(key, &vec!["dataset-ids", "page-size", "page-token"]);
|
|
err.issues.push(CLIError::Field(FieldError::Unknown(temp_cursor.to_string(), suggestion, value.map(|v| v.to_string()))));
|
|
None
|
|
}
|
|
};
|
|
if let Some((field_cursor_str, type_info)) = type_info {
|
|
FieldCursor::from(field_cursor_str).set_json_value(&mut object, value.unwrap(), type_info, err, &temp_cursor);
|
|
}
|
|
}
|
|
let mut request: api::SearchVariantSetsRequest = json::value::from_value(object).unwrap();
|
|
let mut call = self.hub.variantsets().search(request);
|
|
for parg in opt.values_of("v").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
let (key, value) = parse_kv_arg(&*parg, err, false);
|
|
match key {
|
|
_ => {
|
|
let mut found = false;
|
|
for param in &self.gp {
|
|
if key == *param {
|
|
found = true;
|
|
call = call.param(self.gpm.iter().find(|t| t.0 == key).unwrap_or(&("", key)).1, value.unwrap_or("unset"));
|
|
break;
|
|
}
|
|
}
|
|
if !found {
|
|
err.issues.push(CLIError::UnknownParameter(key.to_string(),
|
|
{let mut v = Vec::new();
|
|
v.extend(self.gp.iter().map(|v|*v));
|
|
v } ));
|
|
}
|
|
}
|
|
}
|
|
}
|
|
let protocol = CallType::Standard;
|
|
if dry_run {
|
|
Ok(())
|
|
} else {
|
|
assert!(err.issues.len() == 0);
|
|
for scope in self.opt.values_of("url").map(|i|i.collect()).unwrap_or(Vec::new()).iter() {
|
|
call = call.add_scope(scope);
|
|
}
|
|
let mut ostream = match writer_from_opts(opt.value_of("out")) {
|
|
Ok(mut f) => f,
|
|
Err(io_err) => return Err(DoitError::IoError(opt.value_of("out").unwrap_or("-").to_string(), io_err)),
|
|
};
|
|
match match protocol {
|
|
CallType::Standard => call.doit(),
|
|
_ => unreachable!()
|
|
} {
|
|
Err(api_err) => Err(DoitError::ApiError(api_err)),
|
|
Ok((mut response, output_schema)) => {
|
|
let mut value = json::value::to_value(&output_schema);
|
|
remove_json_null_values(&mut value);
|
|
json::to_writer_pretty(&mut ostream, &value).unwrap();
|
|
ostream.flush().unwrap();
|
|
Ok(())
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
fn _doit(&self, dry_run: bool) -> Result<Result<(), DoitError>, Option<InvalidOptionsError>> {
|
|
let mut err = InvalidOptionsError::new();
|
|
let mut call_result: Result<(), DoitError> = Ok(());
|
|
let mut err_opt: Option<InvalidOptionsError> = None;
|
|
match self.opt.subcommand() {
|
|
("callsets", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("create", Some(opt)) => {
|
|
call_result = self._callsets_create(opt, dry_run, &mut err);
|
|
},
|
|
("delete", Some(opt)) => {
|
|
call_result = self._callsets_delete(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._callsets_get(opt, dry_run, &mut err);
|
|
},
|
|
("patch", Some(opt)) => {
|
|
call_result = self._callsets_patch(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._callsets_search(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("callsets".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("datasets", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("create", Some(opt)) => {
|
|
call_result = self._datasets_create(opt, dry_run, &mut err);
|
|
},
|
|
("delete", Some(opt)) => {
|
|
call_result = self._datasets_delete(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._datasets_get(opt, dry_run, &mut err);
|
|
},
|
|
("get-iam-policy", Some(opt)) => {
|
|
call_result = self._datasets_get_iam_policy(opt, dry_run, &mut err);
|
|
},
|
|
("list", Some(opt)) => {
|
|
call_result = self._datasets_list(opt, dry_run, &mut err);
|
|
},
|
|
("patch", Some(opt)) => {
|
|
call_result = self._datasets_patch(opt, dry_run, &mut err);
|
|
},
|
|
("set-iam-policy", Some(opt)) => {
|
|
call_result = self._datasets_set_iam_policy(opt, dry_run, &mut err);
|
|
},
|
|
("test-iam-permissions", Some(opt)) => {
|
|
call_result = self._datasets_test_iam_permissions(opt, dry_run, &mut err);
|
|
},
|
|
("undelete", Some(opt)) => {
|
|
call_result = self._datasets_undelete(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("datasets".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("operations", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("cancel", Some(opt)) => {
|
|
call_result = self._operations_cancel(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._operations_get(opt, dry_run, &mut err);
|
|
},
|
|
("list", Some(opt)) => {
|
|
call_result = self._operations_list(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("operations".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("readgroupsets", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("coveragebuckets-list", Some(opt)) => {
|
|
call_result = self._readgroupsets_coveragebuckets_list(opt, dry_run, &mut err);
|
|
},
|
|
("delete", Some(opt)) => {
|
|
call_result = self._readgroupsets_delete(opt, dry_run, &mut err);
|
|
},
|
|
("export", Some(opt)) => {
|
|
call_result = self._readgroupsets_export(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._readgroupsets_get(opt, dry_run, &mut err);
|
|
},
|
|
("import", Some(opt)) => {
|
|
call_result = self._readgroupsets_import(opt, dry_run, &mut err);
|
|
},
|
|
("patch", Some(opt)) => {
|
|
call_result = self._readgroupsets_patch(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._readgroupsets_search(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("readgroupsets".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("reads", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("search", Some(opt)) => {
|
|
call_result = self._reads_search(opt, dry_run, &mut err);
|
|
},
|
|
("stream", Some(opt)) => {
|
|
call_result = self._reads_stream(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("reads".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("references", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("bases-list", Some(opt)) => {
|
|
call_result = self._references_bases_list(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._references_get(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._references_search(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("references".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("referencesets", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("get", Some(opt)) => {
|
|
call_result = self._referencesets_get(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._referencesets_search(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("referencesets".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("variants", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("create", Some(opt)) => {
|
|
call_result = self._variants_create(opt, dry_run, &mut err);
|
|
},
|
|
("delete", Some(opt)) => {
|
|
call_result = self._variants_delete(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._variants_get(opt, dry_run, &mut err);
|
|
},
|
|
("import", Some(opt)) => {
|
|
call_result = self._variants_import(opt, dry_run, &mut err);
|
|
},
|
|
("patch", Some(opt)) => {
|
|
call_result = self._variants_patch(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._variants_search(opt, dry_run, &mut err);
|
|
},
|
|
("stream", Some(opt)) => {
|
|
call_result = self._variants_stream(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("variants".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
("variantsets", Some(opt)) => {
|
|
match opt.subcommand() {
|
|
("create", Some(opt)) => {
|
|
call_result = self._variantsets_create(opt, dry_run, &mut err);
|
|
},
|
|
("delete", Some(opt)) => {
|
|
call_result = self._variantsets_delete(opt, dry_run, &mut err);
|
|
},
|
|
("export", Some(opt)) => {
|
|
call_result = self._variantsets_export(opt, dry_run, &mut err);
|
|
},
|
|
("get", Some(opt)) => {
|
|
call_result = self._variantsets_get(opt, dry_run, &mut err);
|
|
},
|
|
("patch", Some(opt)) => {
|
|
call_result = self._variantsets_patch(opt, dry_run, &mut err);
|
|
},
|
|
("search", Some(opt)) => {
|
|
call_result = self._variantsets_search(opt, dry_run, &mut err);
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingMethodError("variantsets".to_string()));
|
|
writeln!(io::stderr(), "{}\n", opt.usage()).ok();
|
|
}
|
|
}
|
|
},
|
|
_ => {
|
|
err.issues.push(CLIError::MissingCommandError);
|
|
writeln!(io::stderr(), "{}\n", self.opt.usage()).ok();
|
|
}
|
|
}
|
|
|
|
if dry_run {
|
|
if err.issues.len() > 0 {
|
|
err_opt = Some(err);
|
|
}
|
|
Err(err_opt)
|
|
} else {
|
|
Ok(call_result)
|
|
}
|
|
}
|
|
|
|
// Please note that this call will fail if any part of the opt can't be handled
|
|
fn new(opt: ArgMatches<'n>) -> Result<Engine<'n>, InvalidOptionsError> {
|
|
let (config_dir, secret) = {
|
|
let config_dir = match cmn::assure_config_dir_exists(opt.value_of("folder").unwrap_or("~/.google-service-cli")) {
|
|
Err(e) => return Err(InvalidOptionsError::single(e, 3)),
|
|
Ok(p) => p,
|
|
};
|
|
|
|
match cmn::application_secret_from_directory(&config_dir, "genomics1-secret.json",
|
|
"{\"installed\":{\"auth_uri\":\"https://accounts.google.com/o/oauth2/auth\",\"client_secret\":\"hCsslbCUyfehWMmbkG8vTYxG\",\"token_uri\":\"https://accounts.google.com/o/oauth2/token\",\"client_email\":\"\",\"redirect_uris\":[\"urn:ietf:wg:oauth:2.0:oob\",\"oob\"],\"client_x509_cert_url\":\"\",\"client_id\":\"620010449518-9ngf7o4dhs0dka470npqvor6dc5lqb9b.apps.googleusercontent.com\",\"auth_provider_x509_cert_url\":\"https://www.googleapis.com/oauth2/v1/certs\"}}") {
|
|
Ok(secret) => (config_dir, secret),
|
|
Err(e) => return Err(InvalidOptionsError::single(e, 4))
|
|
}
|
|
};
|
|
|
|
let auth = Authenticator::new( &secret, DefaultAuthenticatorDelegate,
|
|
if opt.is_present("debug-auth") {
|
|
hyper::Client::with_connector(mock::TeeConnector {
|
|
connector: hyper::net::HttpsConnector::<hyper::net::Openssl>::default()
|
|
})
|
|
} else {
|
|
hyper::Client::new()
|
|
},
|
|
JsonTokenStorage {
|
|
program_name: "genomics1",
|
|
db_dir: config_dir.clone(),
|
|
}, None);
|
|
|
|
let client =
|
|
if opt.is_present("debug") {
|
|
hyper::Client::with_connector(mock::TeeConnector {
|
|
connector: hyper::net::HttpsConnector::<hyper::net::Openssl>::default()
|
|
})
|
|
} else {
|
|
hyper::Client::new()
|
|
};
|
|
let engine = Engine {
|
|
opt: opt,
|
|
hub: api::Genomics::new(client, auth),
|
|
gp: vec!["$-xgafv", "access-token", "alt", "bearer-token", "callback", "fields", "key", "oauth-token", "pp", "pretty-print", "quota-user", "upload-type", "upload-protocol"],
|
|
gpm: vec![
|
|
("$-xgafv", "$.xgafv"),
|
|
("access-token", "access_token"),
|
|
("bearer-token", "bearer_token"),
|
|
("oauth-token", "oauth_token"),
|
|
("pretty-print", "prettyPrint"),
|
|
("quota-user", "quotaUser"),
|
|
("upload-type", "uploadType"),
|
|
("upload-protocol", "upload_protocol"),
|
|
]
|
|
};
|
|
|
|
match engine._doit(true) {
|
|
Err(Some(err)) => Err(err),
|
|
Err(None) => Ok(engine),
|
|
Ok(_) => unreachable!(),
|
|
}
|
|
}
|
|
|
|
fn doit(&self) -> Result<(), DoitError> {
|
|
match self._doit(false) {
|
|
Ok(res) => res,
|
|
Err(_) => unreachable!(),
|
|
}
|
|
}
|
|
}
|
|
|
|
fn main() {
|
|
let mut exit_status = 0i32;
|
|
let arg_data = [
|
|
("callsets", "methods: 'create', 'delete', 'get', 'patch' and 'search'", vec"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_create",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("delete",
|
|
Some(r##"Deletes a call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_delete",
|
|
vec![
|
|
(Some(r##"call-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the call set to be deleted."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a call set by ID. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_get",
|
|
vec![
|
|
(Some(r##"call-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the call set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("patch",
|
|
Some(r##"Updates a call set. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_patch",
|
|
vec![
|
|
(Some(r##"call-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the call set to be updated."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Gets a list of call sets matching the criteria. For the definitions of call sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchCallSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L178)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/callsets_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("datasets", "methods: 'create', 'delete', 'get', 'get-iam-policy', 'list', 'patch', 'set-iam-policy', 'test-iam-permissions' and 'undelete'", vec"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_create",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("delete",
|
|
Some(r##"Deletes a dataset. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_delete",
|
|
vec![
|
|
(Some(r##"dataset-id"##),
|
|
None,
|
|
Some(r##"The ID of the dataset to be deleted."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a dataset by ID. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_get",
|
|
vec![
|
|
(Some(r##"dataset-id"##),
|
|
None,
|
|
Some(r##"The ID of the dataset."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get-iam-policy",
|
|
Some(r##"Gets the access control policy for the dataset. This is empty if the policy or resource does not exist. See Getting a Policy for more information. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_get-iam-policy",
|
|
vec![
|
|
(Some(r##"resource"##),
|
|
None,
|
|
Some(r##"REQUIRED: The resource for which policy is being specified. Format is `datasets/`."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("list",
|
|
Some(r##"Lists datasets within a project. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_list",
|
|
vec![
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("patch",
|
|
Some(r##"Updates a dataset. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_patch",
|
|
vec![
|
|
(Some(r##"dataset-id"##),
|
|
None,
|
|
Some(r##"The ID of the dataset to be updated."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("set-iam-policy",
|
|
Some(r##"Sets the access control policy on the specified dataset. Replaces any existing policy. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) See Setting a Policy for more information."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_set-iam-policy",
|
|
vec![
|
|
(Some(r##"resource"##),
|
|
None,
|
|
Some(r##"REQUIRED: The resource for which policy is being specified. Format is `datasets/`."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("test-iam-permissions",
|
|
Some(r##"Returns permissions that a caller has on the specified resource. See Testing Permissions for more information. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_test-iam-permissions",
|
|
vec![
|
|
(Some(r##"resource"##),
|
|
None,
|
|
Some(r##"REQUIRED: The resource for which policy is being specified. Format is `datasets/`."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("undelete",
|
|
Some(r##"Undeletes a dataset by restoring a dataset which was deleted via this API. For the definitions of datasets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This operation is only possible for a week after the deletion occurred."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/datasets_undelete",
|
|
vec![
|
|
(Some(r##"dataset-id"##),
|
|
None,
|
|
Some(r##"The ID of the dataset to be undeleted."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("operations", "methods: 'cancel', 'get' and 'list'", vec![
|
|
("cancel",
|
|
Some(r##"Starts asynchronous cancellation on a long-running operation. The server makes a best effort to cancel the operation, but success is not guaranteed. Clients may use Operations.GetOperation or Operations.ListOperations to check whether the cancellation succeeded or the operation completed despite cancellation."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_cancel",
|
|
vec![
|
|
(Some(r##"name"##),
|
|
None,
|
|
Some(r##"The name of the operation resource to be cancelled."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets the latest state of a long-running operation. Clients can use this method to poll the operation result at intervals as recommended by the API service."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_get",
|
|
vec![
|
|
(Some(r##"name"##),
|
|
None,
|
|
Some(r##"The name of the operation resource."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("list",
|
|
Some(r##"Lists operations that match the specified filter in the request."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/operations_list",
|
|
vec![
|
|
(Some(r##"name"##),
|
|
None,
|
|
Some(r##"The name of the operation collection."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("readgroupsets", "methods: 'coveragebuckets-list', 'delete', 'export', 'get', 'import', 'patch' and 'search'", vec Coverage is defined as the number of reads which are aligned to a given base in the reference sequence. Coverage buckets are available at several precomputed bucket widths, enabling retrieval of various coverage 'zoom levels'. The caller must have READ permissions for the target read group set."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_coveragebuckets-list",
|
|
vec![
|
|
(Some(r##"read-group-set-id"##),
|
|
None,
|
|
Some(r##"Required. The ID of the read group set over which coverage is requested."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("delete",
|
|
Some(r##"Deletes a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_delete",
|
|
vec![
|
|
(Some(r##"read-group-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the read group set to be deleted. The caller must have WRITE permissions to the dataset associated with this read group set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("export",
|
|
Some(r##"Exports a read group set to a BAM file in Google Cloud Storage. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. See [ImportReadGroupSets](google.genomics.v1.ReadServiceV1.ImportReadGroupSets) for caveats."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_export",
|
|
vec![
|
|
(Some(r##"read-group-set-id"##),
|
|
None,
|
|
Some(r##"Required. The ID of the read group set to export. The caller must have READ access to this read group set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a read group set by ID. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_get",
|
|
vec![
|
|
(Some(r##"read-group-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the read group set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("import",
|
|
Some(r##"Creates read group sets by asynchronously importing the provided information. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The caller must have WRITE permissions to the dataset. ## Notes on [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) import - Tags will be converted to strings - tag types are not preserved - Comments (`@CO`) in the input file header will not be preserved - Original header order of references (`@SQ`) will not be preserved - Any reverse stranded unmapped reads will be reverse complemented, and their qualities (also the "BQ" and "OQ" tags, if any) will be reversed - Unmapped reads will be stripped of positional information (reference name and position)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_import",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("patch",
|
|
Some(r##"Updates a read group set. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_patch",
|
|
vec![
|
|
(Some(r##"read-group-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the read group set to be updated. The caller must have WRITE permissions to the dataset associated with this read group set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Searches for read group sets matching the criteria. For the definitions of read group sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReadGroupSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L135)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/readgroupsets_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("reads", "methods: 'search' and 'stream'", vec Reads search operates over a genomic coordinate space of reference sequence & position defined over the reference sequences to which the requested read group sets are aligned. If a target positional range is specified, search returns all reads whose alignment to the reference genome overlap the range. A query which specifies only read group set IDs yields all reads in those read group sets, including unmapped reads. All reads returned (including reads on subsequent pages) are ordered by genomic coordinate (by reference sequence, then position). Reads with equivalent genomic coordinates are returned in an unspecified order. This order is consistent, such that two queries for the same content (regardless of page size) yield reads in the same order across their respective streams of paginated responses. Implements [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/reads_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("stream",
|
|
Some(r##"Returns a stream of all the reads matching the search request, ordered by reference name, position, and ID."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/reads_stream",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("references", "methods: 'bases-list', 'get' and 'search'", vec Implements [GlobalAllianceApi.getReferenceBases](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L221)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_bases-list",
|
|
vec![
|
|
(Some(r##"reference-id"##),
|
|
None,
|
|
Some(r##"The ID of the reference."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a reference. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_get",
|
|
vec![
|
|
(Some(r##"reference-id"##),
|
|
None,
|
|
Some(r##"The ID of the reference."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Searches for references which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/references_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("referencesets", "methods: 'get' and 'search'", vec Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/referencesets_get",
|
|
vec![
|
|
(Some(r##"reference-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the reference set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/referencesets_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("variants", "methods: 'create', 'delete', 'get', 'import', 'patch', 'search' and 'stream'", vec"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_create",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("delete",
|
|
Some(r##"Deletes a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_delete",
|
|
vec![
|
|
(Some(r##"variant-id"##),
|
|
None,
|
|
Some(r##"The ID of the variant to be deleted."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a variant by ID. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_get",
|
|
vec![
|
|
(Some(r##"variant-id"##),
|
|
None,
|
|
Some(r##"The ID of the variant."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("import",
|
|
Some(r##"Creates variant data by asynchronously importing the provided information. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) The variants for import will be merged with any existing variant that matches its reference sequence, start, end, reference bases, and alternative bases. If no such variant exists, a new one will be created. When variants are merged, the call information from the new variant is added to the existing variant, and other fields (such as key/value pairs) are discarded. In particular, this means for merged VCF variants that have conflicting INFO fields, some data will be arbitrarily discarded. As a special case, for single-sample VCF files, QUAL and FILTER fields will be moved to the call level; these are sometimes interpreted in a call-specific context. Imported VCF headers are appended to the metadata already in a variant set."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_import",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("patch",
|
|
Some(r##"Updates a variant. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) This method supports patch semantics. Returns the modified variant without its calls."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_patch",
|
|
vec![
|
|
(Some(r##"variant-id"##),
|
|
None,
|
|
Some(r##"The ID of the variant to be updated."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Gets a list of variants matching the criteria. For the definitions of variants and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchVariants](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L126)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("stream",
|
|
Some(r##"Returns a stream of all the variants matching the search request, ordered by reference name, position, and ID."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variants_stream",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
("variantsets", "methods: 'create', 'delete', 'export', 'get', 'patch' and 'search'", vec The provided variant set must have a valid `datasetId` set - all other fields are optional. Note that the `id` field will be ignored, as this is assigned by the server."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_create",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("delete",
|
|
Some(r##"Deletes the contents of a variant set. The variant set object is not deleted. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_delete",
|
|
vec![
|
|
(Some(r##"variant-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the variant set to be deleted."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("export",
|
|
Some(r##"Exports variant set data to an external destination. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_export",
|
|
vec![
|
|
(Some(r##"variant-set-id"##),
|
|
None,
|
|
Some(r##"Required. The ID of the variant set that contains variant data which should be exported. The caller must have READ access to this variant set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("get",
|
|
Some(r##"Gets a variant set by ID. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_get",
|
|
vec![
|
|
(Some(r##"variant-set-id"##),
|
|
None,
|
|
Some(r##"Required. The ID of the variant set."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("patch",
|
|
Some(r##"Updates a variant set using patch semantics. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)"##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_patch",
|
|
vec![
|
|
(Some(r##"variant-set-id"##),
|
|
None,
|
|
Some(r##"The ID of the variant to be updated (must already exist)."##),
|
|
Some(true),
|
|
Some(false)),
|
|
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
("search",
|
|
Some(r##"Returns a list of all variant sets matching search criteria. For the definitions of variant sets and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchVariantSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/variantmethods.avdl#L49)."##),
|
|
"Details at http://byron.github.io/google-apis-rs/google_genomics1_cli/variantsets_search",
|
|
vec![
|
|
(Some(r##"kv"##),
|
|
Some(r##"r"##),
|
|
Some(r##"Set various fields of the request structure, matching the key=value form"##),
|
|
Some(true),
|
|
Some(true)),
|
|
|
|
(Some(r##"v"##),
|
|
Some(r##"p"##),
|
|
Some(r##"Set various optional parameters, matching the key=value form"##),
|
|
Some(false),
|
|
Some(true)),
|
|
|
|
(Some(r##"out"##),
|
|
Some(r##"o"##),
|
|
Some(r##"Specify the file into which to write the program's output"##),
|
|
Some(false),
|
|
Some(false)),
|
|
]),
|
|
]),
|
|
|
|
];
|
|
|
|
let mut app = App::new("genomics1")
|
|
.author("Sebastian Thiel <byronimo@gmail.com>")
|
|
.version("0.3.3+20160124")
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.about("An API to store, process, explore, and share genomic data. It supports reference-based alignments, genetic variants, and reference genomes. This API provides an implementation of the Global Alliance for Genomics and Health (GA4GH) v0.5.1 API as well as several extensions.")
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.after_help("All documentation details can be found at http://byron.github.io/google-apis-rs/google_genomics1_cli")
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.arg(Arg::with_name("url")
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.long("scope")
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.help("Specify the authentication a method should be executed in. Each scope requires the user to grant this application permission to use it.If unset, it defaults to the shortest scope url for a particular method.")
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.multiple(true)
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.takes_value(true))
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.arg(Arg::with_name("folder")
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.long("config-dir")
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.help("A directory into which we will store our persistent data. Defaults to a user-writable directory that we will create during the first invocation.[default: ~/.google-service-cli")
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.multiple(false)
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.takes_value(true))
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.arg(Arg::with_name("debug")
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.long("debug")
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.help("Output all server communication to standard error. `tx` and `rx` are placed into the same stream.")
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.multiple(false)
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.takes_value(false))
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.arg(Arg::with_name("debug-auth")
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.long("debug-auth")
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.help("Output all communication related to authentication to standard error. `tx` and `rx` are placed into the same stream.")
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.multiple(false)
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.takes_value(false));
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for &(main_command_name, about, ref subcommands) in arg_data.iter() {
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let mut mcmd = SubCommand::with_name(main_command_name).about(about);
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for &(sub_command_name, ref desc, url_info, ref args) in subcommands {
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let mut scmd = SubCommand::with_name(sub_command_name);
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if let &Some(desc) = desc {
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scmd = scmd.about(desc);
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}
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scmd = scmd.after_help(url_info);
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for &(ref arg_name, ref flag, ref desc, ref required, ref multi) in args {
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let arg_name_str =
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match (arg_name, flag) {
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(&Some(an), _ ) => an,
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(_ , &Some(f)) => f,
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_ => unreachable!(),
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};
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let mut arg = Arg::with_name(arg_name_str)
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.empty_values(false);
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if let &Some(short_flag) = flag {
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arg = arg.short(short_flag);
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}
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if let &Some(desc) = desc {
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arg = arg.help(desc);
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}
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if arg_name.is_some() && flag.is_some() {
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arg = arg.takes_value(true);
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}
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if let &Some(required) = required {
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arg = arg.required(required);
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}
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if let &Some(multi) = multi {
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arg = arg.multiple(multi);
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}
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scmd = scmd.arg(arg);
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}
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mcmd = mcmd.subcommand(scmd);
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}
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app = app.subcommand(mcmd);
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}
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let matches = app.get_matches();
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let debug = matches.is_present("debug");
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match Engine::new(matches) {
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Err(err) => {
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exit_status = err.exit_code;
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writeln!(io::stderr(), "{}", err).ok();
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},
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Ok(engine) => {
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if let Err(doit_err) = engine.doit() {
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exit_status = 1;
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match doit_err {
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DoitError::IoError(path, err) => {
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writeln!(io::stderr(), "Failed to open output file '{}': {}", path, err).ok();
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},
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DoitError::ApiError(err) => {
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if debug {
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writeln!(io::stderr(), "{:#?}", err).ok();
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} else {
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writeln!(io::stderr(), "{}", err).ok();
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}
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}
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}
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}
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}
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}
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std::process::exit(exit_status);
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} |