CoolFace
Datasetpublic

SciCodePile/SciCode-Domain-Code

DATA1: Domain-Specific Code Dataset Dataset Overview DATA1 is a large-scale domain-specific code dataset focusing on code samples from interdisciplinary fields such as biology, chemistry, materials science, and related areas. The dataset is collected and organized from GitHub repositories, covering 178 different domain topics with over 1.1 billion lines of code. Dataset Statistics Total Datasets: 178 CSV files Total Data Size: ~115 GB Total Lines… See the full description on the dataset page: https://huggingface.co/datasets/SciCodePile/SciCode-Domain-Code.

sourceHugging Faceapache-2.0updated 6mo agoView on Hugging Face
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rootdatadataset_Assay.csv
dataset_Assay.csv64176 linesDownload Raw Back to data
1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"Assay","FDA/precisionFDA","LOCAL_INSTALL.md",".md","3325","99","# Localhost setup on OSX 10.11.63 4## Overview5 6To develop on pFDA locally you need to manually add a new user and organization.7Because when you first get started in a new system,8there is no existing user. So you can't log in to provision new accounts.9This requires manually ""bootstrapping"" the situation in steps described in10[pFDA localhost user](#pFDA-localhost-user).11 12## Install13 14### Setup for localhost development on MacOS15 16* Install XCode17    * Search and install XCode from the App Store.18* Install Apple Command Line Tools19    * Open XCode (this just needs to run once to initialize it) and close it.20    * Install XCode command line tools by running `xcode-select --install` in21    the terminal.22* Install [Homebrew](http://brew.sh/)23    * `/usr/bin/ruby -e ""$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)""`24    * Run `brew update` to make sure all your formulas are current25* Install RVM26    * `gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3`27    * `\curl -sSL https://get.rvm.io | bash -s stable`28* Install ruby29    * `rvm install 2.2.3`30* Install bundler31    * `gem install bundler`32    * to keep the current bundler version from Gemfile.lock:33        * `gem install bundler -v 1.16.6`34* Update the `libv8` gem before `bundle i`:35    * `gem install libv8 -v '3.16.14.13' -- --with-system-v8`36* Install git37    * `brew install git`38* Set up git ssh39    * `ssh-keygen -t rsa -b 4096 -C ""your_email@dnanexus.com""`40    * Use `pbcopy < ~/.ssh/id_rsa.pub` to add SSH key to github [here](https://github.com/settings/keys)41* Set up git config42    * `git config --global core.editor ""vim""`43    * `git config --global user.email “your_email@dnanexus.com”`44    * `git config --global user.name “FirstName LastName”`45    * `git config --global push.default simple`46 47### Docker setup48 49* Install Docker and Docker-Compose. See [instructions](https://docs.docker.com/compose/install/)50* Install gems51  * `docker-compose run web bundle install`52* Prepare db53  * `docker-compose run web bundle exec rake db:create`54  * `docker-compose run web bundle exec rake db:schema:load`55* start rails server56  * `docker-compose up`57* start rails console58  * `docker compose exec web bundle exec rails c`  59 60## pFDA setup61 62* Clone Repo63    * `git clone git@github.com:dnanexus/precision-fda.git`64* `bundle install`65* `bundle exec rake db:schema:load`66 67### Issues68 69On your first `bundle`, you may have issues installing the libv8 and70therubyracer gems. See [here](https://github.com/cowboyd/libv8/issues/205) for71potential solutions. Try `bundle update libv8`.72 73Create a User and Org, and other required records by running74 75 76The _dxuser_ of the user record must match your DNAnexus username, and the _handle_ of the org record must77match the DNAnexus org handle without the pfda.. prefix, i.e. floranteorg.78 79## pFDA running80 81* start rails server82    * `bundle exec thin --ssl start`83    * **You must use https, ex: [https://localhost:3000](https://localhost:3000)**84* start rails console85    * `bundle exec rails c`86 87## Dev team Backend Testing88 89* Run all tests90    * `bundle exec rspec`91 92* Run tests with Rspec Guard93    * `bundle exec guard`94    95* To exit from Guard mode:96    * `exit`97 98* Check current code coverage:99    * `open coverage/index.html`100","Markdown"
101"Assay","FDA/precisionFDA","packages/cli/pfda_test.go",".go","25574","803","package main102 103import (104	""flag""105	""os""106	""testing""107 108	""dnanexus.com/precision-fda-cli/precisionfda""109	""dnanexus.com/precision-fda-cli/precisionfda/test""110)111 112func TestMain(m *testing.M) {113	// Not the most elegant way of avoiding usage spew in unit test output114	// but works since main uses the default flagset115	flag.Usage = func() {}116 117	// Run tests118	exitVal := m.Run()119 120	// Teardown121 122	// Exit with exit value from tests123	os.Exit(exitVal)124}125 126type InputFlags struct {127	InputFilePath    *string128	FilePaths        *[]string129	FolderID         *string130	SpaceID          *string131	AssetFolderPath  *string132	AssetName        *string133	ReadmeFilePath   *string134	FileID           *string135	Args             *[]string136	Arg              *string137	OutputFilePath   *string138	EntityID         *string139	EntityType       *string140	Overwrite        *string141	FlagWithProgress bool142 143	// optional flags for ls, list-spaces, download, mkdir, head144	FlagRecursive     bool145	FlagHelp          bool146	FlagBrief         bool147	FlagJson          bool148	FlagFoldersOnly   bool149	FlagFilesOnly     bool150	FlagLocked        bool151	FlagUnactivated   bool152	FlagPhiProtected  bool153	FlagGroups        bool154	FlagReview        bool155	FlagPrivate       bool156	FlagAdministrator bool157	FlagGovernment    bool158	FlagParents       bool159	FlagPublic		  bool160	FlagLines         int161}162 163func (f *InputFlags) Reset() {164	f.InputFilePath = nil165	f.FilePaths = nil166	f.FolderID = nil167	f.SpaceID = nil168	f.AssetFolderPath = nil169	f.AssetName = nil170	f.ReadmeFilePath = nil171	f.FileID = nil172	f.Args = nil173	f.Arg = nil174	f.OutputFilePath = nil175	f.EntityID = nil176	f.EntityType = nil177	f.FlagRecursive = false178	f.FlagWithProgress = true179	// optional flags - default to false180	f.FlagHelp = false181	f.FlagJson = false182	f.FlagFoldersOnly = false183	f.FlagFilesOnly = false184	f.FlagBrief = false185	f.FlagLocked = false186	f.FlagUnactivated = false187	f.FlagReview = false188	f.FlagGroups = false189	f.FlagPrivate = false190	f.FlagAdministrator = false191	f.FlagGovernment = false192	f.FlagParents = false193	f.FlagPublic = false194	f.FlagLines = 10195}196 197func runMainInternal(surpressStdout bool) int {198	var originalStdout = os.Stdout199	if surpressStdout {200		os.Stdout, _ = os.Open(os.DevNull)201	}202	returnCode := mainInternal()203	if surpressStdout {204		os.Stdout = originalStdout205	}206	return returnCode207}208 209func TestMainNoArgs(t *testing.T) {210	oldArgs := os.Args211	defer func() { os.Args = oldArgs }()212 213	os.Args = []string{""pfda""}214	returnCode := runMainInternal(true)215	test.Equals(t, 1, returnCode)216}217 218func TestWrongCmdError(t *testing.T) {219	oldArgs := os.Args220	defer func() { os.Args = oldArgs }()221 222	os.Args = []string{""pfda"", ""--cmd"", ""foobar""}223	returnCode := runMainInternal(true)224	test.Equals(t, 1, returnCode)225}226 227func TestPositionalCmdInWrongPlace(t *testing.T) {228	oldArgs := os.Args229	defer func() { os.Args = oldArgs }()230 231	var funcWasCalled = false232	invokeDownload = func(client precisionfda.IPFDAClient, args *[]string, folderID *string, spaceID *string, public bool, recursive bool, outputFilePath *string, overwriteFile *string) error {233		funcWasCalled = true234		return nil235	}236 237	os.Args = []string{""pfda"", ""--file-id"", ""file-12345"", ""--key"", ""HELLO"", ""download""}238	returnCode := runMainInternal(true)239	test.Equals(t, 1, returnCode)240	test.Equals(t, false, funcWasCalled)241 242	invokeUploadFile = func(client precisionfda.IPFDAClient, inputFilePath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {243		funcWasCalled = true244		return nil245	}246 247	os.Args = []string{""pfda"", ""--file"", ""./README.md"", ""--key"", ""HELLO"", ""upload-file""}248	returnCode = runMainInternal(true)249	test.Equals(t, 1, returnCode)250	test.Equals(t, false, funcWasCalled)251}252 253func TestPositionalCmdAndCommandBothSpecified(t *testing.T) {254	oldArgs := os.Args255	defer func() { os.Args = oldArgs }()256 257	var funcWasCalled = false258	invokeUploadFile = func(client precisionfda.IPFDAClient, inputFilePath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {259		funcWasCalled = true260		return nil261	}262	os.Args = []string{""pfda"", ""upload-file"", ""--cmd"", ""upload-file"", ""--file"", ""./README.md"", ""--key"", ""HELLO""}263	returnCode := runMainInternal(true)264	test.Equals(t, 1, returnCode)265	test.Equals(t, false, funcWasCalled)266}267 268func TestInvokeUploadFile(t *testing.T) {269	oldArgs := os.Args270	defer func() { os.Args = oldArgs }()271 272	var funcWasCalled = false273	input := &InputFlags{}274	var reset = func() {275		funcWasCalled = false276		input.Reset()277	}278 279	invokeUploadFile = func(client precisionfda.IPFDAClient, inputFilePath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {280		funcWasCalled = true281		input.InputFilePath = inputFilePath282		input.FolderID = folderID283		input.SpaceID = spaceID284		return nil285	}286 287	// Case: --file is missing288	os.Args = []string{""pfda"", ""--cmd"", ""upload-file""}289	returnCode := runMainInternal(true)290	test.Equals(t, 1, returnCode)291	test.Equals(t, false, funcWasCalled)292	reset()293 294	// Case: --file does not exist295	os.Args = []string{""pfda"", ""upload-file"", ""--file"", ""./IDoNot.Exist""}296	returnCode = runMainInternal(true)297	test.Equals(t, 1, returnCode)298	test.Equals(t, false, funcWasCalled)299	test.Equals(t, (*string)(nil), input.InputFilePath)300	reset()301 302	// Case: --file does not exist with --cmd303	os.Args = []string{""pfda"", ""--cmd"", ""upload-file"", ""--file"", ""./IDoNot.Exist""}304	returnCode = runMainInternal(true)305	test.Equals(t, 1, returnCode)306	test.Equals(t, false, funcWasCalled)307	test.Equals(t, (*string)(nil), input.InputFilePath)308	reset()309 310	// Case: upload-file upload success311	os.Args = []string{""pfda"", ""--cmd"", ""upload-file"", ""--file"", ""./README.md"", ""--key"", ""HELLO""}312	returnCode = runMainInternal(false)313	test.Equals(t, 0, returnCode)314	test.Equals(t, true, funcWasCalled)315	test.Equals(t, ""README.md"", *input.InputFilePath)316	reset()317 318	// Case: upload-file success with folder and space319	os.Args = []string{""pfda"", ""upload-file"", ""--file"", ""./Dockerfile"", ""--key"", ""HELLO"", ""--folder-id"", ""test-folder"", ""--space-id"", ""test-space""}320	returnCode = runMainInternal(false)321	test.Equals(t, 0, returnCode)322	test.Equals(t, true, funcWasCalled)323	test.Equals(t, ""Dockerfile"", *input.InputFilePath)324	test.Equals(t, ""test-folder"", *input.FolderID)325	test.Equals(t, ""test-space"", *input.SpaceID)326	reset()327 328	invokeUploadMultipleFiles = func(client precisionfda.IPFDAClient, filePaths *[]string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {329		funcWasCalled = true330		input.FilePaths = filePaths331		input.FolderID = folderID332		input.SpaceID = spaceID333		return nil334	}335 336	// Case: upload-file success with multiple files/folders separated by commas337	os.Args = []string{""pfda"", ""upload-file"", ""file1.csv"", ""file2.xlsx"", ""./src/file123.txt"", ""./src/folder123"", ""--key"", ""HELLO""}338	returnCode = runMainInternal(false)339	test.Equals(t, 0, returnCode)340	test.Equals(t, true, funcWasCalled)341	test.Equals(t, []string{""file1.csv"", ""file2.xlsx"", ""./src/file123.txt"", ""./src/folder123""}, *input.FilePaths)342	reset()343 344	// Case: upload-file success with folder and space with --cmd345	os.Args = []string{""pfda"", ""--cmd"", ""upload-file"", ""--file"", ""./Dockerfile"", ""--key"", ""HELLO"", ""--folder-id"", ""test-folder"", ""--space-id"", ""test-space""}346	returnCode = runMainInternal(false)347	test.Equals(t, 0, returnCode)348	test.Equals(t, true, funcWasCalled)349	test.Equals(t, ""Dockerfile"", *input.InputFilePath)350	test.Equals(t, ""test-folder"", *input.FolderID)351	test.Equals(t, ""test-space"", *input.SpaceID)352	reset()353 354	invokeUploadFolder = func(client precisionfda.IPFDAClient, inputFilePath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {355		funcWasCalled = true356		input.InputFilePath = inputFilePath357		input.FolderID = folderID358		input.SpaceID = spaceID359		return nil360	}361 362	// Case: upload-file with single folder363	os.Args = []string{""pfda"", ""upload-file"", ""helpers/"", ""--key"", ""HELLO""}364	returnCode = runMainInternal(false)365	test.Equals(t, 0, returnCode)366	test.Equals(t, true, funcWasCalled)367	test.Equals(t, ""helpers"", *input.InputFilePath)368	reset()369 370}371 372func TestInvokeUploadAsset(t *testing.T) {373	oldArgs := os.Args374	defer func() { os.Args = oldArgs }()375 376	var funcWasCalled = false377	input := &InputFlags{}378	var reset = func() {379		funcWasCalled = false380		input.Reset()381	}382 383	invokeUploadAsset = func(client precisionfda.IPFDAClient, assetFolderPath *string, assetName *string, readmeFilePath *string, inputChunkSize *int, inputNumRoutines *int) error {384		funcWasCalled = true385		input.AssetFolderPath = assetFolderPath386		input.AssetName = assetName387		input.ReadmeFilePath = readmeFilePath388		return nil389	}390 391	// Case: upload-asset with folder and space392	os.Args = []string{""pfda"", ""upload-asset"", ""--name"", ""test-asset.tar.gz"", ""--key"", ""HELLO"", ""--root"", ""./precisionfda"", ""--readme"", ""./README.md""}393	returnCode := runMainInternal(false)394	test.Equals(t, 0, returnCode)395	test.Equals(t, true, funcWasCalled)396	test.Equals(t, ""./precisionfda"", *input.AssetFolderPath)397	test.Equals(t, ""test-asset.tar.gz"", *input.AssetName)398	test.Equals(t, ""./README.md"", *input.ReadmeFilePath)399	reset()400 401	// Case: upload-asset with folder and space with --cmd402	os.Args = []string{""pfda"", ""--cmd"", ""upload-asset"", ""--name"", ""test-asset.tar.gz"", ""--key"", ""HELLO"", ""--root"", ""./precisionfda"", ""--readme"", ""./README.md""}403	returnCode = runMainInternal(false)404	test.Equals(t, 0, returnCode)405	test.Equals(t, true, funcWasCalled)406	test.Equals(t, ""./precisionfda"", *input.AssetFolderPath)407	test.Equals(t, ""test-asset.tar.gz"", *input.AssetName)408	test.Equals(t, ""./README.md"", *input.ReadmeFilePath)409	reset()410 411	// Case: upload-asset fails if --root doesn't exist412	os.Args = []string{""pfda"", ""upload-asset"", ""--name"", ""test-asset.tar.gz"", ""--key"", ""HELLO"", ""--root"", ""root-folder"", ""--readme"", ""./README.md""}413	returnCode = runMainInternal(false)414	test.Equals(t, 1, returnCode)415	test.Equals(t, false, funcWasCalled)416	test.Equals(t, (*string)(nil), input.AssetFolderPath)417	test.Equals(t, (*string)(nil), input.AssetName)418	test.Equals(t, (*string)(nil), input.ReadmeFilePath)419	reset()420 421	// Case: upload-asset fails if --file doesn't exist422	os.Args = []string{""pfda"", ""upload-asset"", ""--name"", ""test-asset.tar.gz"", ""--key"", ""HELLO"", ""--root"", ""./i-do-not-exist"", ""--readme"", ""./README.md""}423	returnCode = runMainInternal(false)424	test.Equals(t, 1, returnCode)425	test.Equals(t, false, funcWasCalled)426	test.Equals(t, (*string)(nil), input.AssetFolderPath)427	test.Equals(t, (*string)(nil), input.AssetName)428	test.Equals(t, (*string)(nil), input.ReadmeFilePath)429	reset()430 431	// Case: upload-asset with all parameters432	os.Args = []string{""pfda"", ""--cmd"", ""upload-asset"", ""--name"", ""test-asset.tar.gz"", ""--key"", ""HELLO"", ""--root"", ""./"", ""--readme"", ""./README.md""}433	returnCode = runMainInternal(false)434	test.Equals(t, 0, returnCode)435	test.Equals(t, true, funcWasCalled)436	test.Equals(t, ""./"", *input.AssetFolderPath)437	test.Equals(t, ""test-asset.tar.gz"", *input.AssetName)438	test.Equals(t, ""./README.md"", *input.ReadmeFilePath)439	reset()440}441 442func TestInvokeDownloadFile(t *testing.T) {443	oldArgs := os.Args444	defer func() { os.Args = oldArgs }()445 446	var funcWasCalled = false447	input := &InputFlags{}448	var reset = func() {449		funcWasCalled = false450		input.Reset()451	}452 453	invokeDownload = func(client precisionfda.IPFDAClient, args *[]string, folderID *string, spaceID *string, public bool, recursive bool, outputFilePath *string, overwriteFile *string) error {454		funcWasCalled = true455		input.Args = args456		input.FolderID = folderID457		input.SpaceID = spaceID458		input.FlagRecursive = recursive459		input.OutputFilePath = outputFilePath460		input.Overwrite = overwriteFile461		return nil462	}463 464	// Case: download with --cmd465	os.Args = []string{""pfda"", ""--cmd"", ""download"", ""--file-id"", ""file-12345"", ""--key"", ""HELLO""}466	returnCode := runMainInternal(false)467	test.Equals(t, 0, returnCode)468	test.Equals(t, true, funcWasCalled)469	test.Equals(t, []string{""file-12345""}, *input.Args)470	reset()471 472	// Case: download without --cmd, with outputFilePath473	os.Args = []string{""pfda"", ""download"", ""--file-id"", ""file-23456"", ""--key"", ""HELLO"", ""--output"", ""/tmp/canyoupleaseworksoicanbedonefortheday.argh""}474	returnCode = runMainInternal(false)475	test.Equals(t, 0, returnCode)476	test.Equals(t, true, funcWasCalled)477	test.Equals(t, []string{""file-23456""}, *input.Args)478	reset()479 480	// Case: download without --cmd, with -overwrite flag481	os.Args = []string{""pfda"", ""download"", ""--file-id"", ""file-23456"", ""--key"", ""HELLO"", ""--overwrite"", ""true""}482	returnCode = runMainInternal(false)483	test.Equals(t, 0, returnCode)484	test.Equals(t, true, funcWasCalled)485	test.Equals(t, []string{""file-23456""}, *input.Args)486	test.Equals(t, ""true"", *input.Overwrite)487	reset()488 489	// Case: download whole folder with -overwrite and recursive flag490	os.Args = []string{""pfda"", ""download"", ""-folder-id"", ""12223"", ""-key"", ""HELLO"", ""-overwrite"", ""true"", ""-recursive""}491	returnCode = runMainInternal(false)492	test.Equals(t, 0, returnCode)493	test.Equals(t, true, funcWasCalled)494	test.Equals(t, ""12223"", *input.FolderID)495	test.Equals(t, ""true"", *input.Overwrite)496	test.Equals(t, true, input.FlagRecursive)497	reset()498 499	// Case: download without --cmd, with -overwrite flag500	os.Args = []string{""pfda"", ""download"", ""file-23456"", ""file-2221"", ""file-11111"", ""-key"", ""HELLO"", ""-overwrite"", ""true""}501	returnCode = runMainInternal(false)502	test.Equals(t, 0, returnCode)503	test.Equals(t, true, funcWasCalled)504	test.Equals(t, []string{""file-23456"", ""file-2221"", ""file-11111""}, *input.Args)505	test.Equals(t, ""true"", *input.Overwrite)506	reset()507 508}509 510func TestInvokeListing(t *testing.T) {511	oldArgs := os.Args512	defer func() { os.Args = oldArgs }()513 514	var funcWasCalled = false515	input := &InputFlags{}516	var reset = func() {517		funcWasCalled = false518		input.Reset()519	}520 521	invokeListing = func(client precisionfda.IPFDAClient, folderID *string, spaceID *string, flags map[string]bool) error {522		funcWasCalled = true523		input.FolderID = folderID524		input.SpaceID = spaceID525		input.FlagBrief = flags[""brief""]526		input.FlagFilesOnly = flags[""files_only""]527		input.FlagFoldersOnly = flags[""folders_only""]528		input.FlagJson = flags[""json""]529		return nil530	}531 532	// Case: ls without folderID and spaceID and no flags533	os.Args = []string{""pfda"", ""ls"", ""--key"", ""AUTH_KEY""}534	returnCode := runMainInternal(false)535	test.Equals(t, 0, returnCode)536	test.Equals(t, true, funcWasCalled)537	test.Equals(t, false, input.FlagBrief)538	test.Equals(t, false, input.FlagFilesOnly)539	test.Equals(t, false, input.FlagFoldersOnly)540	test.Equals(t, false, input.FlagJson)541	reset()542 543	// Case: ls with help - only show help and do not call the func544	os.Args = []string{""pfda"", ""ls"", ""--help""}545	returnCode = runMainInternal(false)546	test.Equals(t, 1, returnCode)547	test.Equals(t, false, funcWasCalled)548	test.Equals(t, false, input.FlagBrief)549	test.Equals(t, false, input.FlagFilesOnly)550	test.Equals(t, false, input.FlagFoldersOnly)551	test.Equals(t, false, input.FlagJson)552	reset()553 554	// Case: ls return only files in json format555	os.Args = []string{""pfda"", ""ls"", ""--key"", ""AUTH_KEY"", ""--json"", ""--files""}556	returnCode = runMainInternal(false)557	test.Equals(t, 0, returnCode)558	test.Equals(t, true, funcWasCalled)559	test.Equals(t, false, input.FlagBrief)560	test.Equals(t, true, input.FlagFilesOnly)561	test.Equals(t, false, input.FlagFoldersOnly)562	test.Equals(t, true, input.FlagJson)563	reset()564 565	// Case: ls return only folders in brief format566	os.Args = []string{""pfda"", ""ls"", ""--key"", ""AUTH_KEY"", ""--brief"", ""--folders""}567	returnCode = runMainInternal(false)568	test.Equals(t, 0, returnCode)569	test.Equals(t, true, funcWasCalled)570	test.Equals(t, true, input.FlagBrief)571	test.Equals(t, false, input.FlagFilesOnly)572	test.Equals(t, true, input.FlagFoldersOnly)573	test.Equals(t, false, input.FlagJson)574	reset()575}576 577func TestInvokeListSpaces(t *testing.T) {578	oldArgs := os.Args579	defer func() { os.Args = oldArgs }()580 581	var funcWasCalled = false582	input := &InputFlags{}583	var reset = func() {584		funcWasCalled = false585		input.Reset()586	}587 588	invokeListSpaces = func(client precisionfda.IPFDAClient, flags map[string]bool) error {589		funcWasCalled = true590		input.FlagJson = flags[""json""]591		input.FlagLocked = flags[""locked""]592		input.FlagUnactivated = flags[""unactivated""]593		input.FlagReview = flags[""review""]594		input.FlagGroups = flags[""groups""]595		input.FlagPrivate = flags[""private_type""]596		input.FlagAdministrator = flags[""administrator""]597		input.FlagGovernment = flags[""government""]598		return nil599	}600 601	// Case: list-spaces with no flags602	os.Args = []string{""pfda"", ""list-spaces"", ""--key"", ""AUTH_KEY""}603	returnCode := runMainInternal(false)604	test.Equals(t, 0, returnCode)605	test.Equals(t, true, funcWasCalled)606	test.Equals(t, false, input.FlagLocked)607	test.Equals(t, false, input.FlagUnactivated)608	test.Equals(t, false, input.FlagReview)609	test.Equals(t, false, input.FlagGroups)610	test.Equals(t, false, input.FlagPrivate)611	test.Equals(t, false, input.FlagAdministrator)612	test.Equals(t, false, input.FlagGovernment)613	test.Equals(t, false, input.FlagJson)614	reset()615 616	// Case: list-spaces with help - only show help and do not call the func617	os.Args = []string{""pfda"", ""list-spaces"", ""--help""}618	returnCode = runMainInternal(false)619	test.Equals(t, 1, returnCode)620	test.Equals(t, false, funcWasCalled)621	test.Equals(t, false, input.FlagLocked)622	test.Equals(t, false, input.FlagUnactivated)623	test.Equals(t, false, input.FlagReview)624	test.Equals(t, false, input.FlagGroups)625	test.Equals(t, false, input.FlagPrivate)626	test.Equals(t, false, input.FlagAdministrator)627	test.Equals(t, false, input.FlagGovernment)628	test.Equals(t, false, input.FlagJson)629	reset()630 631	// Case: list-spaces only locked and in json format632	os.Args = []string{""pfda"", ""list-spaces"", ""--key"", ""AUTH_KEY"", ""--locked"", ""--json""}633	returnCode = runMainInternal(false)634	test.Equals(t, 0, returnCode)635	test.Equals(t, true, funcWasCalled)636	test.Equals(t, true, input.FlagLocked)637	test.Equals(t, false, input.FlagUnactivated)638	test.Equals(t, false, input.FlagReview)639	test.Equals(t, false, input.FlagGroups)640	test.Equals(t, false, input.FlagPrivate)641	test.Equals(t, false, input.FlagAdministrator)642	test.Equals(t, false, input.FlagGovernment)643	test.Equals(t, true, input.FlagJson)644	reset()645 646	// Case: list spaces - multi-type filter647	os.Args = []string{""pfda"", ""list-spaces"", ""--key"", ""AUTH_KEY"", ""--groups"", ""--private"", ""--administrator"", ""--review"", ""--government""}648	returnCode = runMainInternal(false)649	test.Equals(t, 0, returnCode)650	test.Equals(t, true, funcWasCalled)651	test.Equals(t, false, input.FlagLocked)652	test.Equals(t, false, input.FlagUnactivated)653	test.Equals(t, true, input.FlagReview)654	test.Equals(t, true, input.FlagGroups)655	test.Equals(t, true, input.FlagPrivate)656	test.Equals(t, true, input.FlagAdministrator)657	test.Equals(t, true, input.FlagGovernment)658	test.Equals(t, false, input.FlagJson)659	reset()660}661 662func TestInvokeDescribeEntity(t *testing.T) {663	oldArgs := os.Args664	defer func() { os.Args = oldArgs }()665 666	var funcWasCalled = false667	input := &InputFlags{}668	var reset = func() {669		funcWasCalled = false670		input.Reset()671	}672 673	invokeDescribe = func(client precisionfda.IPFDAClient, entityID *string, entityType *string) error {674		funcWasCalled = true675		input.EntityID = entityID676		input.EntityType = entityType677		return nil678	}679 680	// Case: describe-app entity - old syntax681	os.Args = []string{""pfda"", ""describe-app"", ""--app-id"", ""APP_ID"", ""--key"", ""AUTH_KEY""}682	returnCode := runMainInternal(false)683	test.Equals(t, 0, returnCode)684	test.Equals(t, true, funcWasCalled)685	test.Equals(t, ""APP_ID"", *input.EntityID)686	test.Equals(t, ""app"", *input.EntityType)687	reset()688 689	// Case: describe-app entity - new syntax690	os.Args = []string{""pfda"", ""describe-app"", ""APP_ID"", ""--key"", ""AUTH_KEY""}691	returnCode = runMainInternal(false)692	test.Equals(t, 0, returnCode)693	test.Equals(t, true, funcWasCalled)694	test.Equals(t, ""APP_ID"", *input.EntityID)695	test.Equals(t, ""app"", *input.EntityType)696	reset()697 698	// Case: describe-workflow entity - old syntax699	os.Args = []string{""pfda"", ""describe-workflow"", ""--workflow-id"", ""WORKFLOW_ID"", ""--key"", ""AUTH_KEY""}700	returnCode = runMainInternal(false)701	test.Equals(t, 0, returnCode)702	test.Equals(t, true, funcWasCalled)703	test.Equals(t, ""WORKFLOW_ID"", *input.EntityID)704	test.Equals(t, ""workflow"", *input.EntityType)705	reset()706 707	// Case: describe-workflow entity - new syntax708	os.Args = []string{""pfda"", ""describe-workflow"", ""WORKFLOW_ID"", ""--key"", ""AUTH_KEY""}709	returnCode = runMainInternal(false)710	test.Equals(t, 0, returnCode)711	test.Equals(t, true, funcWasCalled)712	test.Equals(t, ""WORKFLOW_ID"", *input.EntityID)713	test.Equals(t, ""workflow"", *input.EntityType)714	reset()715}716 717func TestInvokeMkdir(t *testing.T) {718	oldArgs := os.Args719	defer func() { os.Args = oldArgs }()720 721	var funcWasCalled = false722	input := &InputFlags{}723	var reset = func() {724		funcWasCalled = false725		input.Reset()726	}727 728	invokeMkdir = func(client precisionfda.IPFDAClient, names *[]string, folderID *string, spaceID *string, parents bool) error {729		funcWasCalled = true730		input.Args = names731		input.FolderID = folderID732		input.SpaceID = spaceID733		input.FlagParents = parents734		return nil735	}736 737	// Case: simple mkdir738	os.Args = []string{""pfda"", ""mkdir"", ""dir1"", ""--key"", ""AUTH_KEY""}739	returnCode := runMainInternal(false)740	test.Equals(t, 0, returnCode)741	test.Equals(t, true, funcWasCalled)742	test.Equals(t, []string{""dir1""}, *input.Args)743	reset()744 745	// Case: mkdir with multiple args746	os.Args = []string{""pfda"", ""mkdir"", ""dir1"",""dir2"", ""dir3"", ""-folder-id"",""123"", ""-space-id"",""333"", ""--key"", ""AUTH_KEY""}747	returnCode = runMainInternal(false)748	test.Equals(t, 0, returnCode)749	test.Equals(t, true, funcWasCalled)750	test.Equals(t, []string{""dir1"", ""dir2"",""dir3""}, *input.Args)751	test.Equals(t, ""123"", *input.FolderID)752	test.Equals(t, ""333"", *input.SpaceID)753	test.Equals(t, false, input.FlagParents)754	reset()755 756	// Case: mkdir nested folders with parents flag757	os.Args = []string{""pfda"", ""mkdir"", ""dir1/dir2/dir3"", ""-p"", ""--key"", ""AUTH_KEY""}758	returnCode = runMainInternal(false)759	test.Equals(t, 0, returnCode)760	test.Equals(t, true, funcWasCalled)761	test.Equals(t, []string{""dir1/dir2/dir3""}, *input.Args)762	test.Equals(t, true, input.FlagParents)763	reset()764}765 766func TestInvokeRmdir(t *testing.T) {767	oldArgs := os.Args768	defer func() { os.Args = oldArgs }()769 770	var funcWasCalled = false771	input := &InputFlags{}772	var reset = func() {773		funcWasCalled = false774		input.Reset()775	}776 777	invokeRmdir = func(client precisionfda.IPFDAClient, args *[]string) error {778		funcWasCalled = true779		input.Args = args780		return nil781	}782 783	// Case: simple mkdir784	os.Args = []string{""pfda"", ""rmdir"", ""123"", ""--key"", ""AUTH_KEY""}785	returnCode := runMainInternal(false)786	test.Equals(t, 0, returnCode)787	test.Equals(t, true, funcWasCalled)788	test.Equals(t, []string{""123""}, *input.Args)789	reset()790 791	// Case: mkdir with multiple args792	os.Args = []string{""pfda"", ""rmdir"", ""123"", ""333"", ""--key"", ""AUTH_KEY""}793	returnCode = runMainInternal(false)794	test.Equals(t, 0, returnCode)795	test.Equals(t, true, funcWasCalled)796	test.Equals(t, []string{""123"", ""333""}, *input.Args)797 798	test.Equals(t, false, input.FlagParents)799	reset()800}801 802func TestInvokeRm(t *testing.T) {803	oldArgs := os.Args804	defer func() { os.Args = oldArgs }()805 806	var funcWasCalled = false807	input := &InputFlags{}808	var reset = func() {809		funcWasCalled = false810		input.Reset()811	}812 813	invokeRm = func(client precisionfda.IPFDAClient, args *[]string,folderID *string, spaceID *string) error {814		funcWasCalled = true815		input.Args = args816		return nil817	}818 819	// Case: simple mkdir820	os.Args = []string{""pfda"", ""rm"", ""123"", ""--key"", ""AUTH_KEY""}821	returnCode := runMainInternal(false)822	test.Equals(t, 0, returnCode)823	test.Equals(t, true, funcWasCalled)824	test.Equals(t, []string{""123""}, *input.Args)825	reset()826 827	// Case: mkdir with multiple args828	os.Args = []string{""pfda"", ""rm"", ""123*"", ""333"", ""--key"", ""AUTH_KEY""}829	returnCode = runMainInternal(false)830	test.Equals(t, 0, returnCode)831	test.Equals(t, true, funcWasCalled)832	test.Equals(t, []string{""123*"", ""333""}, *input.Args)833 834	test.Equals(t, false, input.FlagParents)835	reset()836}837 838func TestInvokeHead(t *testing.T) {839	oldArgs := os.Args840	defer func() { os.Args = oldArgs }()841 842	var funcWasCalled = false843	input := &InputFlags{}844	var reset = func() {845		funcWasCalled = false846		input.Reset()847	}848 849	invokeHead = func(client precisionfda.IPFDAClient, arg *string, lines int) error {850		funcWasCalled = true851		input.Arg = arg852		input.FlagLines = lines853		return nil854	}855 856	// Case: simple mkdir857	os.Args = []string{""pfda"", ""head"", ""testfile.txt"", ""--key"", ""AUTH_KEY""}858	returnCode := runMainInternal(false)859	test.Equals(t, 0, returnCode)860	test.Equals(t, true, funcWasCalled)861	test.Equals(t, ""testfile.txt"", *input.Arg)862	test.Equals(t, 10, input.FlagLines)863	reset()864 865	// Case: mkdir with multiple args866	os.Args = []string{""pfda"", ""head"", ""testfile.txt"", ""-lines"", ""222"", ""--key"", ""AUTH_KEY""}867	returnCode = runMainInternal(false)868	test.Equals(t, 0, returnCode)869	test.Equals(t, true, funcWasCalled)870	test.Equals(t, ""testfile.txt"", *input.Arg)871	test.Equals(t, 222, input.FlagLines)872	reset()873}874 875func TestInvokeCat(t *testing.T) {876	oldArgs := os.Args877	defer func() { os.Args = oldArgs }()878 879	var funcWasCalled = false880	input := &InputFlags{}881	var reset = func() {882		funcWasCalled = false883		input.Reset()884	}885 886	invokeCat = func(client precisionfda.IPFDAClient, arg *string) error {887		funcWasCalled = true888		input.Arg = arg889		input.FlagLines = -1890		return nil891	}892 893	// Case: simple mkdir894	os.Args = []string{""pfda"", ""cat"", ""testfile.txt"", ""--key"", ""AUTH_KEY""}895	returnCode := runMainInternal(false)896	test.Equals(t, 0, returnCode)897	test.Equals(t, true, funcWasCalled)898	test.Equals(t, ""testfile.txt"", *input.Arg)899	test.Equals(t, -1, input.FlagLines)900	reset()901 902}903","Go"
904"Assay","FDA/precisionFDA","packages/cli/build-dist.sh",".sh","1132","45","#!/bin/sh905#906# N.B. run from precision-fda/go907 908VERSION=2.8.0909COMMITID=`git rev-parse HEAD`910 911BuildAndPackage() {912    PLATFORM=$1913    ARCH=$2914    BUILDTIME=$(date +%Y-%m-%d-%H%M%S)915    echo ""Building pfda CLI (v$VERSION) for $PLATFORM $ARCH""916    docker run --rm --mount type=bind,source=""$(pwd)"",target=/go/src/dnanexus.com/precision-fda-cli \917           -e GOOS=""$PLATFORM"" -e GOARCH=""$ARCH"" -e COMMITID=""$COMMITID"" \918           -e VERSION=""$VERSION"" -e BUILDTIME=""$BUILDTIME"" precisionfda-cli919    cd ./dist920 921    OUT_FILE=pfda_${PLATFORM}_${ARCH}922    if [ ! -f ""$OUT_FILE"" ]; then923        echo924        echo ""$OUT_FILE does not exist. Exiting""925        exit 1926    fi927 928    EXEC_NAME=""pfda""929    if [ $PLATFORM = ""windows"" ]; then930        EXEC_NAME=""pfda.exe""931    fi932 933    mv ${OUT_FILE} ${EXEC_NAME}934 935    if [ $PLATFORM = ""windows"" ]; then936        zip -rj pfda-${PLATFORM}-${VERSION}.zip ${EXEC_NAME}937    else938        tar -czvf pfda-${PLATFORM}-${VERSION}.tar.gz ${EXEC_NAME}939    fi940    rm ${EXEC_NAME}941 942    cd ..943}944 945BuildAndPackage 'linux' 'amd64'946BuildAndPackage 'darwin' 'amd64' # N.B. darwin is macOS947BuildAndPackage 'windows' 'amd64'948","Shell"
949"Assay","FDA/precisionFDA","packages/cli/pfda.go",".go","31100","967","// PrecisionFDA CLI950// Version 2.8.0951package main952 953import (954	""crypto/tls""955	""encoding/json""956	""flag""957	""fmt""958	""net/http""959	""os""960	""path/filepath""961	""runtime""962	""strconv""963	""strings""964 965	_ ""crypto/tls/fipsonly""966	""dnanexus.com/precision-fda-cli/helpers""967	""dnanexus.com/precision-fda-cli/precisionfda""968	""rsc.io/goversion/version""969)970 971// CONSTANTS972const defaultNumRoutines = 10973const defaultChunkSize = 1 << 26 // default 64MB (min. 16MB)974const defaultSkipVerify = ""false""975const usageString = `976****************************977PFDA COMMAND LINE TOOL v2.8.0978****************************979 980All available commands:981   pfda cat982   pfda describe983   pfda download984   pfda get-scope985   pfda head986   pfda ls987   pfda ls-apps988   pfda ls-assets989   pfda ls-discussions990   pfda ls-executions991   pfda ls-members992   pfda ls-spaces993   pfda ls-workflows994   pfda mkdir995   pfda rm996   pfda rmdir997   pfda upload-asset998   pfda upload-file999   pfda view-link1000 1001Command specific help section with description, examples and available flags:1002   pfda <COMMAND> -help1003 1004To print version info and exit:1005   pfda -version1006 1007Full documentation can be found in the Docs section of the precisionFDA website - https://precision.fda.gov/docs/cli1008`1009 1010//1011// N.B. the -cmd flag exists and is now deprecated, but the following should all work1012//1013// # Testing upload to localhost1014// $ ./pfda upload-file -server localhost:3000 -skipverify true -key $KEY -file fileYouWantToUpload.pdf1015// $ ./pfda -cmd upload-file -server localhost:3000 -skipverify true -key $KEY -file fileYouWantToUpload.pdf1016//1017// # Testing download from localhost1018// $ ./pfda download -server localhost:3000 -skipverify true -key $KEY -file file-yourfileuuid-11019// $ ./pfda -cmd download -server localhost:3000 -skipverify true -key $KEY -file file-yourfileuuid-11020//1021// # Testing the API for file download1022// $ ./pfda api -server localhost:3000 -skipverify true -key $KEY -route ""files/file-G70fbKj0qp9YGkg24kGxQvF4-1/download"" -json '{ ""format"": ""json"" }'1023// $ ./pfda -cmd api -server localhost:3000 -skipverify true -key $KEY -route ""files/file-G70fbKj0qp9YGkg24kGxQvF4-1/download"" -json '{ ""format"": ""json"" }'1024 1025// GLOBAL VARIABLES1026var defaultURL = ""precision.fda.gov""1027 1028// these varaibles are populated by -ldflags -X command line options1029var (1030	commitID  string1031	Version   string1032	BuildTime string1033	OsArch    string1034)1035 1036// ACTION FUNCTIONS1037// Wrapping calls to pfdaclient allow us to replace these functions in pfda_test.go with mocks1038var invokeUploadFile = func(client precisionfda.IPFDAClient, inputFilePath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {1039	client.SetChunkSize(*inputChunkSize)1040	client.SetNumRoutines(*inputNumRoutines)1041	return client.UploadFile(*inputFilePath, *folderID, *spaceID, true)1042}1043 1044var invokeUploadStdinFile = func(client precisionfda.IPFDAClient, fileName *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {1045	client.SetChunkSize(*inputChunkSize)1046	client.SetNumRoutines(*inputNumRoutines)1047	return client.UploadStdin(*fileName, *folderID, *spaceID, true)1048 1049}1050 1051var invokeUploadMultipleFiles = func(client precisionfda.IPFDAClient, filePaths *[]string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {1052	client.SetChunkSize(*inputChunkSize)1053	client.SetNumRoutines(*inputNumRoutines)1054	return client.UploadMultipleFiles(*filePaths, *folderID, *spaceID)1055}1056 1057var invokeUploadFolder = func(client precisionfda.IPFDAClient, inputPath *string, folderID *string, spaceID *string, inputChunkSize *int, inputNumRoutines *int) error {1058	client.SetChunkSize(*inputChunkSize)1059	client.SetNumRoutines(*inputNumRoutines)1060	return client.UploadFolder(*inputPath, *folderID, *spaceID)1061}1062 1063var invokeUploadAsset = func(client precisionfda.IPFDAClient, assetFolderPath *string, assetName *string, readmeFilePath *string, inputChunkSize *int, inputNumRoutines *int) error {1064	client.SetChunkSize(*inputChunkSize)1065	client.SetNumRoutines(*inputNumRoutines)1066	return client.UploadAsset(*assetFolderPath, *assetName, *readmeFilePath)1067}1068 1069var invokeDownload = func(client precisionfda.IPFDAClient, args *[]string, folderID *string, spaceID *string, public bool, recursive bool, outputFilePath *string, overwriteFile *string) error {1070	return client.Download(*args, *folderID, *spaceID, public, recursive, *outputFilePath, *overwriteFile)1071}1072 1073var invokeFileViewLink = func(client precisionfda.IPFDAClient, fileID *string, preauthenticated bool, duration int64) error {1074	return client.FileViewLink(*fileID, preauthenticated, duration)1075}1076 1077var invokeUploadResources = func(client precisionfda.IPFDAClient, args *[]string, portalID *string) error {1078	return client.UploadResources(*args, *portalID)1079}1080 1081var invokeDescribe = func(client precisionfda.IPFDAClient, entityID *string) error {1082	return client.DescribeEntity(*entityID)1083}1084 1085var invokeLsSpaces = func(client precisionfda.IPFDAClient, flags map[string]bool) error {1086	return client.LsSpaces(flags)1087}1088 1089var invokeListing = func(client precisionfda.IPFDAClient, folderID *string, spaceID *string, flags map[string]bool) error {1090	return client.Ls(*folderID, *spaceID, flags)1091}1092 1093var invokeLsApps = func(client precisionfda.IPFDAClient, spaceID *string, flags map[string]bool) error {1094	return client.LsApps(*spaceID, flags)1095}1096 1097var invokeLsAssets = func(client precisionfda.IPFDAClient, spaceID *string, flags map[string]bool) error {1098	return client.LsAssets(*spaceID, flags)1099}1100 1101var invokeLsWorkflows = func(client precisionfda.IPFDAClient, spaceID *string, flags map[string]bool) error {1102	return client.LsWorkflows(*spaceID, flags)1103}1104 1105var invokeLsExecutions = func(client precisionfda.IPFDAClient, spaceID *string, flags map[string]bool) error {1106	return client.LsExecutions(*spaceID, flags)1107}1108 1109var invokeLsMembers = func(client precisionfda.IPFDAClient, spaceID *string) error {1110	return client.LsMembers(*spaceID)1111}1112 1113var invokeLsDiscussions = func(client precisionfda.IPFDAClient, spaceID *string) error {1114	return client.LsDiscussions(*spaceID, map[string]bool{})1115}1116 1117var invokeMkdir = func(client precisionfda.IPFDAClient, names *[]string, folderID *string, spaceID *string, parents bool) error {1118	return client.Mkdir(*names, *folderID, *spaceID, parents)1119}1120 1121var invokeRmdir = func(client precisionfda.IPFDAClient, args *[]string) error {1122	return client.Rmdir(*args)1123}1124 1125var invokeRm = func(client precisionfda.IPFDAClient, args *[]string, folderID *string, spaceID *string) error {1126	return client.Rm(*args, *folderID, *spaceID)1127}1128 1129var invokeHead = func(client precisionfda.IPFDAClient, arg *string, lines int) error {1130	return client.Head(*arg, lines)1131}1132 1133var invokeCat = func(client precisionfda.IPFDAClient, arg *string) error {1134	// reusing head command with unreachable limit1135	return client.Head(*arg, -1)1136}1137 1138var invokeGetScope = func(client precisionfda.IPFDAClient) error {1139	return client.GetScope()1140}1141 1142var invokeCreateDiscussion = func(client precisionfda.IPFDAClient, spaceID *string, jsonBody *string) error {1143	return client.CreateDiscussion(*spaceID, *jsonBody)1144}1145 1146var invokeCreateReply = func(client precisionfda.IPFDAClient, jsonBody *string) error {1147	return client.CreateReply(*jsonBody)1148}1149 1150var invokeEditDiscussion = func(client precisionfda.IPFDAClient, jsonBody *string) error {1151	return client.EditDiscussion(*jsonBody)1152}1153 1154var invokeEditReply = func(client precisionfda.IPFDAClient, jsonBody *string) error {1155	return client.EditReply(*jsonBody)1156}1157 1158var invokeRefreshToken = func(client precisionfda.IPFDAClient, autoRefresh bool) (string, error) {1159	return client.RefreshToken(autoRefresh)1160}1161 1162var invokeGetLatestVersion = func(client precisionfda.IPFDAClient) (string, error) {1163	return client.GetLatestVersion()1164}1165 1166func main() {1167	returnCode := mainInternal()1168	os.Exit(returnCode)1169}1170 1171func mainInternal() int {1172	// This isn't necessary for the CLI to run correctly, but we define command line flags1173	// inside mainInternal so that they can be unit tested1174	flag.CommandLine = flag.NewFlagSet(os.Args[0], flag.ExitOnError)1175 1176	command := flag.String(""cmd"", """", ""[Deprecated - please use the format ./pfda <cmd>] Command to execute."")1177	authKey := flag.String(""key"", """", ""Authorization key. Required if a previous config doesn't exist."")1178	apiRoute := flag.String(""route"", """", ""Name of precisionFDA API route to call."")1179	jsonInput := flag.String(""json-payload"", """", ""JSON payload for specified API call (if any)."")1180	inputFilePath := flag.String(""file"", """", ""Path to file for 'upload-file'"")1181	assetFolderPath := flag.String(""root"", """", ""Path to root folder for 'upload-asset'"")1182	fileName := flag.String(""name"", """", ""Name of uploaded file."")1183	readmeFilePath := flag.String(""readme"", """", ""Readme file for uploaded asset. Must end with '.txt' or '.md'."")1184	fileID := flag.String(""file-id"", """", ""File ID of the file to be downloaded"")1185	appID := flag.String(""app-id"", """", ""App ID of the app to be described"")1186	workflowID := flag.String(""workflow-id"", """", ""Workflow ID of the workflow to be described"")1187	folderID := flag.String(""folder-id"", """", ""Folder ID of the target folder"")1188	spaceID := flag.String(""space-id"", """", ""Space ID of the target space"")1189	portalID := flag.String(""portal-id"", """", ""Slug or ID of the target portal"")1190	outputFilePath := flag.String(""output"", """", ""[optional] File path to write api call response data. Defaults to stdout."")1191	inputChunkSize := flag.Int(""chunksize"", defaultChunkSize, ""[optional] Size of each upload chunk in bytes (Min 5MB,/Max 2GB)."")1192	inputNumRoutines := flag.Int(""threads"", defaultNumRoutines, ""[optional] Maximum number of upload threads to spawn (Max 100)."")1193	server := flag.String(""server"", defaultURL, ""[optional] Server to connect and make requests to."")1194	skipVerify := flag.String(""skipverify"", defaultSkipVerify, ""[optional] Boolean string to skip certificate verification."")1195	pfda_version := flag.Bool(""version"", false, ""[optional] Print version"")1196 1197	// help flag - does not run any command just prints help info1198	flagHelp := flag.Bool(""help"", false, ""[optional] Print help info for the particular command"")1199	flagHelpShort := flag.Bool(""h"", false, ""[optional] Print help info for the particular command"") // is there a better way to have aliases ??1200

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