Changes for page Working with HDC Project Files in the Command Line Interface

Last modified by Dennis Segebarth on 2024/10/02 18:38

From 1.3 to 1.4 From 9.1 to 10.1

From version 1.4

edited by Susan Evans
on 2023/07/10 22:18

Change comment: (Autosaved)

To version 9.1

edited by Dennis Segebarth
on 2023/09/13 18:09

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--XWiki.sgevans
++XWiki.dsegebarth

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++{{box cssClass="floatinginfobox" title="Table of Contents"}}
++{{toc depth="2"/}}
++{{/box}}
++
  The Pilot Command Line Interface (pilotcli) is a binary executable program that provides a convenient way for users to perform file actions and platform-related tasks programmatically. The Pilot Command Line Interface can be downloaded and run on on your local Linux and Linux subsystems (as Windows user, see for instance the [[Windows Subsystem for Linux installation guide>>url:https://learn.microsoft.com/en-us/windows/wsl/install]]) to support large file uploads. For convenience, pilotcli is also pre-deployed and installed in the users JupyterHub accessible via worskpace tools.
  = Data Stewardship =
@@ -8,6 +8,10 @@
  To get started with the Pilot Command Line Interface in the HDC JupyterHub workspace tool, see the article //Using JupyterHub in HDC //and refer to the remaining sections in this article for a full description of the pilotcli commands.
++= Using the Pilot Command Line Interface in Guacamole VMs =
++
++To get started with the Pilot Command Line Interface in the HDC Guacamole workspace tool, see //Using Guacamole in HDC// on how to launch a terminal, either in a Desktop VM or directly by establishing a connection to a Command Line VM. The Pilot Command Line Interface will be installed, configured, and ready to be used. Please refer to the remaining sections in this article for a full description of the pilotcli commands.
++
  = Downloading the Pilot Command Line Interface =
  If you wish to use the Pilot Command Line Interface to upload large files from your local environment, it is necessary to download Pilot Command Line Interface tool on your Linux system. The recommended Linux version is Ubuntu 20.04.
@@ -102,7 +102,7 @@
 ) Device Login Successful message will appear and your authentication browser window can be closed.
--4) The output of the Command Line Tool will also be updated (see line 14 below) to notify you about the successful login:
++4) The output of the Command Line Tool will also be updated to notify you about the successful login:
  {{code language="none"}}
  $ pilotcli user login
@@ -338,7 +338,7 @@
  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
--* Requires the Project code, which can be retrieved via pilotcli project list.
++* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
  * Requires the Attribute template name. If the attribute template name does not exist or is spelled incorrectly, an error is returned: "Attribute 'sample-template' not found in Project. Please verify and try again."
  * pilotcli must have the permission to write a file in the directory, otherwise an error is returned.
  )))
@@ -406,7 +406,7 @@
  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
--* Requires the Project code, which can be retrieved via pilotcli project list.
++* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
  )))
  {{code language="none"}}
@@ -453,16 +453,439 @@
  * When uploading file to the Project Core, the user must have access to the Core (Project Contributors cannot upload files/folders to the Project Core).
  )))
++{{code language="none"}}
++$ pilotcli file upload --help
++Usage: pilotcli file upload [OPTIONS] [PATHS]...
++  Upload files/folders to a given Project path.
------
++Options:
++  -p, --project-path TEXT    Project folder path starting from Project code.
++                             (i.e., indoctestproject/user/folder)  [required]
---
--{{code language="none"}}{{/code}}
++  -a, --attribute TEXT       File Attribute Template used for annotating files
++                             during upload.
++  -t, --tag TEXT             Add a tag to the file. This option could be used
++                             multiple times for adding multiple tags.
++
++  -z, --zone TEXT            Target Zone (i.e., core/greenroom)  [default:
++                             greenroom]  [default: greenroom]
++
++  -m, --upload-message TEXT  The message used to comment on the purpose of
++                             uploading your processed file  [default: ]
++
++  -s, --source-file TEXT     The Project path of the source file of your
++                             processed files.
++
++  --zip                      Upload folder as a compressed zip file.
++  -td, --thread INTEGER      The number of thread for upload a file  [default:
++                             1]
++
++  -o, --output-path TEXT     The output path for the manifest file of
++                             resumable upload  [default: ./manifest.json]
++
++  --help                     Show this message and exit.
++{{/code}}
++
++=== Examples ===
++
++Upload a file (or folder) to a specified directory of a Project’s Green Room, in this case the file located at {{code}}./sample_folder/sample_file1{{/code}} will be uploaded to the folder “admin” in the Project with the Project Code “cli” {{code}}(-p cli/admin){{/code}}:
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/sample_file1 -p cli/admin
++Starting upload of: ./sample_folder/sample_file1
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: e958247c-ce05-48b2-9038-78b774836256-1627498771 resumable_relative_path admin/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++All files uploaded successfully.
++{{/code}}
++
++In case the specified destination directory does not exist yet, you will be prompted to confirm its creation by entering “y”, or to abort the command by entering “N”:
++
++{{code language="none"}}
++Target folder does not exist. Would you like to create a new folder? [y/N]: y
++{{/code}}
++
++In order to upload a file (or folder) to a destination directory in a Project's Core, core must be specified as corresponding zone {{code}}(-z core){{/code}} and you will be required to provide a message to that should describe the files` content and why you are uploading it directly into the Core {{code}}(-m "sample message"){{/code}}. Moreover, you will be reminded about the Terms of Use of the Platform and additional considerations regarding the direct upload of data into the Core zone, and are prompted to confirm your intention to proceed with the upload by entering “y” or “Yes”:
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/sample_file2 -p cli/admin -z core -m "sample message"
++You are about to transfer data directly to the Core! In accordance with the Terms of Use, please confirm that you
++have made your best efforts to pseudonymize or anonymize the data and that you have the legal authority to transfer and make this
++data available for dissemination and use within the Platform.To review the Terms of Use, please the Portal. If you
++need to process the data to remove sensitive identifiers, please cancel this transfer and upload the data to the Green Room to
++perform these actions.
++To cancel this transfer, enter [n/No]
++To confirm and proceed with the data transfer, enter [y/Yes]
++  [y/N]: y
++Starting upload of: ./sample_folder/sample_file2
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: fa807a0f-ceb0-4fff-9c9e-563bdcbb309f-1627498851 resumable_relative_path admin/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++All files uploaded successfully.
++{{/code}}
++
++Upload a folder to Project Green Room
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/example_folder -p cli/admin
++Starting upload of: ./sample_folder/example_folder
++Current version does not support folder tagging, any selected tags will be ignored
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: 4f0eee2e-70f4-4b03-9e72-040544ec7d3a-1627498907 resumable_relative_path admin/example_folder/
++
++Starting finalization...
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: 41ec70e2-0859-4aba-9009-06e700c7c79e-1627498907 resumable_relative_path admin/example_folder/
++
++Starting finalization...
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: 28454c51-ec9a-4dc5-ab3c-0f7e80e3050d-1627498907 resumable_relative_path admin/example_folder/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++All files uploaded successfully.
++{{/code}}
++
++Upload file to existing folder in Green Room
++
++* Specify a target folder to upload files by inputting folder name after the Project code separated by the '/'.
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/sample_file5 -p cli/admin/example_folder
++Starting upload of: ./sample_folder/sample_file5
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: 7ef58005-d408-4ad9-a741-fa938f58e67f-1627498977 resumable_relative_path admin/example_folder/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++All files uploaded successfully.
++{{/code}}
++
++Upload folder as zip to a specified directory of a Project's Green Room by adding the ~-~-zip option.
++
++* The specified folder will then be compressed as a zip file and subsequently be uploaded to the specified destination. Once the upload is completed, the compressed zip file will be removed from the directory. Note: pilotcli must have the permission to create and delete zip files in the corresponding directory of your local machine:
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/example_folder -p cli/admin --zip
++Starting upload of: ./sample_folder/example_folder
++Started zipping files.
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 3595 total_chunks: 1 uniq_identifier: 61a729ce-cdd6-4a87-82b5-3f8ea63e6c4a-1627499012 resumable_relative_path admin/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++All files uploaded successfully.
++{{/code}}
++
++Upload a file with tags and/or attributes.
++
++* When entering the upload command, the user can add a maximum of ten tags to the file. For example, in order to add “sample_tag1” and “sample_tag2” to your file, simply add {{code}}-t sample_tag1{{/code}} {{code}}-t sample_tag2{{/code}} to the command (see example below using {{code}}tag1{{/code}} and {{code}}tag2{{/code}} as tags).
++* In addition, you can also use attribute templates for a more enriched annotation of your files. Please note, that the corresponding attribute template file needs to be edited & saved prior to uploading. To get the blank template, see the **attribute-export** instructions above for more details. To attach a attribute JSON-file to your file upon uploading, use {{code}}-a cli_Manifest1_template.json{{/code}}, where “{{code}}cli_Manifest1_template.json{{/code}}" points to the location of the attributes JSON-file on your local machine.
++* Upon uploading, pilotcli will also validate the content of the attached attribute JSON-file. Whenever a template is invalid, including missing non-optional fields, non-existing choice in multiple choice attribute, exceeding length text field and so on, pilotcli will raise error to user and user must update the attribute template and upload again:
++
++{{code language="none"}}
++$ pilotcli file upload ./sample_folder/sample_file6 -p cli/admin -t tag1 -t tag2 -a cli_Manifest1_template.json
++File attribute validation passed: True
++Starting upload of: ./sample_folder/sample_file6
++Pre-upload complete.
++uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: bc47ec2a-1a4e-4f71-a37a-7ce6473e415a-1627499273 resumable_relative_path admin/
++
++Upload job is finalizing, please wait...
++Upload job complete.
++Attribute attached
++All files uploaded successfully.
++{{/code}}
++
++Upload a file with specified number of threads, using the {{code}}-td <thread_number>{{/code}} option.
++
++* By default, the number of threads is 1. There will no UI difference when using threads. The maximal number of threads depends on your local machine and the recommend thread number is 3:
++
++{{code language="none"}}
++$ pilotcli file upload -p indoctestproject/admin/test20230306_3 /home/color/indoc/script/large_folder_test_data/gentoo_root_100M.img -td 3
++Target folder does not exist. Would you like to create a new folder? [y/N]: y
++Starting upload of: /home/color/indoc/script/large_folder_test_data/gentoo_root_100M.img
++Pre-upload complete.
++Uploading gentoo_root_100M.img , resumable_id: c68752372b42c85d, job_id: 56de3632-58df-445c-bcb9-bddfe6be5bf7:  |██████████████████████████████ 100% 00:00
++Upload Time: 79.77s for 1 files
++All uploading jobs have finished.
++{{/code}}
++
++Upload with customized manifest name
++
++When you upload a file using pilotcli, a JSON file with the details of your specific upload job will be created automatically and allows you to resume the upload at a later time, in case the process is aborted due to any reason. By default, this JSON file will be created as “manifest.json” in the current working directory (see //Command: **resume**// below for more details on how to resume the file upload). However, you can use the {{code}}--output-path{{/code}} option to specify the filepath and, thus, the filename of this JSON file:
++
++{{code language="none"}}
++$ pilotcli file upload -p <path> <file> --output-path test_manifest.json
++{{/code}}
++
++== Command: **resume** ==
++
++* **Options**: -td ~-~-thread, -r ~-~-resumable-manifest
++* **Usage**: Resume unfinished file uploading based on the manifest file.
++* (((
++**Prerequisite**:
++
++* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
++* Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
++* The resumable manifest JSON file is required, which is generated upon executing the {{code}}pilotcli file upload{{/code}} command.
++)))
++
++=== Example: ===
++
++For instance upon disconnecting from the internet, or by accidentally closing the terminal, a currently running uploading process can be aborted. You can use the {{code}}pilotcli file resume{{/code}} command in order to resume the uploading process right where you left off. Simply point to the manifest JSON file that was created upon executing the original upload command. Please note that the source files still have to be in the same location, otherwise resuming the uploading process will fail.
++
++{{code language="none"}}
++$ pilotcli file resume -r  ./manifest.json
++Resume the upload for 10 files.
++Resumable upload check complete.
++Uploading aggregated.py:  |██████████████████████████████ 100% 00:00
++Uploading __init__.py:  |██████████████████████████████ 100% 00:00
++Uploading service_meta_class.py:  |██████████████████████████████ 100% 00:00
++Uploading upload_form.py:  |██████████████████████████████ 100% 00:00
++Uploading convert_type.py:  |██████████████████████████████ 100% 00:00
++Uploading singleton.py:  |██████████████████████████████ 100% 00:00
++Uploading __init__.py:  |██████████████████████████████ 100% 00:00
++Uploading base_library.zip:  |██████████████████████████████ 100% 00:00         0% ?
++Uploading EXE-00.toc:  |██████████████████████████████ 100% 00:00
++Uploading xref-pilotcli_test20230227_3.html:  |██████████████████████████████ 100% 00:00
++Upload Time: 11.13s for 10 files
++{{/code}}
++
++== Command: **sync** ==
++
++* **Usage**: Download a file or a folder from a Project. If pilotcli is used outside of the Platform, e.g. the users local machine, users can only download from Project’s Core. When pilotcli is used within the Platform, e.g. from one of the workspace tools, users will also be able to download from the Green Room of a Project as well.
++* (((
++**Options**: -z ~-~-zone, -i ~-~-geid, ~-~-zip
++
++* To look up a file’s geid, or unique file ID, open the Project File Explorer in the Portal and inspect the File Properties for the ID.
++)))
++* (((
++**Prerequisite**:
++
++* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
++* The specified file or folder must exist, otherwise an error is returned: “File does not exist or source file provided is invalid: folder_name/file_name.”
++* If the user has no access to the specified file or folder on the Portal, an error is returned: “Permission denied. Please verify that your role in the Project has permission to perform this action.”
++)))
++
++{{code language="none"}}
++$ pilotcli file sync --help
++Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH
++
++  Download files/folders from a given Project/folder/file in core zone.
++
++Options:
++  -z, --zone TEXT  Target Zone (i.e., core/greenroom)
++  --zip            Download files as a zip.
++  -i, --geid       Enable downloading by geid.
++  --help           Show this message and exit.
++{{/code}}
++
++=== Examples ===
++
++Download a file or a folder from the Core zone of a Project:
++
++{{code language="none"}}
++$ pilotcli file sync cli/admin/sample_file2 -z core ~/Downloads/
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading sample_file2 |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
++{{/code}}
++
++Download multiple files or folders as a compressed zip by simply providing all source files or folders and adding the {{code}}--zip{{/code}} option:
++
++{{code language="none"}}
++$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 -z core ~/Downloads/ --zip
++Preparing downloading
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading cli_1632340658.768384.zip |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/cli_1632340658.768384.zip
++{{/code}}
++
++Download files or folders by their geid, instead of their location. To enable this, add {{code}}-i{{/code}} or {{code}}--geid{{/code}} to the command:
++
++{{code language="none"}}
++$ pilotcli file sync -i 6d89afd4-f86e-4df7-b6c5-01a9af4e828e-1627499957 7e8e2bac-97c6-4738-bc08-12139c9ba225-1627498854  ~/Downloads/
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading sample_file7 |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading sample_file2 |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
++{{/code}}
++
++Download a file or folder from the Green Room of a Project. This will only be possible if pilotcli is used within the Platform, e.g. in one of the Workspace tools. It works the same way as downloading from Core, including all the additional options like zipping, by either adding {{code}}-z greenroom{{/code}} or by omitting the {{code}}-z{{/code}}  option entirely, as “greenroom” is the default value:
++
++{{code language="none"}}
++$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 ~/Downloads
++Preparing status: READY_FOR_DOWNLOADING
++/home/uname/Downloads/sample_file2 already exist, file will be saved as /home/uname/Downloads/sample_file2 (1)
++start downloading...
++Downloading sample_file2 (1) |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2 (1)
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading sample_file7 |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
++{{/code}}
++
++= Dataset Commands: pilotcli **dataset** =
++
++== Help ==
++
++{{code language="none"}}
++$ pilotcli dataset --help
++Usage: pilotcli dataset [OPTIONS] COMMAND [ARGS]...
++
++Options:
++  --help  Show this message and exit.
++
++Commands:
++  download     Download a dataset or a particular version of a dataset.
++  list         List datasets belonging to logged in user.
++  show-detail  Show details of a dataset.
++{{/code}}
++
++== Command: **list** ==
++
++* **Usage**: List all datasets for the logged in user
++* (((
++**Prerequisite**:
++
++* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
++)))
++
++{{code language="none"}}
++$ pilotcli dataset list --help
++Usage: pilotcli dataset list [OPTIONS]
++
++  List datasets belonging to logged in user.
++
++Options:
++  --page INTEGER       The page to be listed  [default: 0]
++  --page-size INTEGER  number of objects per page  [default: 10]
++  -d, --detached       whether run in detached mode
++  --help               Show this message and exit.
++{{/code}}
++
++=== Examples ===
++
++List all datasets that are accessible for the user:
++
++{{code language="none"}}
++$ pilotcli dataset list
++             Dataset Title                            Dataset Code
++---------------------------------------------------------------------------
++               dataset2                               aug24202102
++              dataset-01                               aug242021
++Page: 0, Number of datasets: 2
++{{/code}}
++
++== Command: **show-detail** ==
++
++* **Usage**: Show the detailed information of a dataset.
++* (((
++**Prerequisite**:
++
++* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
++)))
++
++{{code language="none"}}
++$ pilotcli dataset show-detail --help
++Usage: pilotcli dataset show-detail [OPTIONS] CODE
++
++  Show details of a dataset.
++
++Options:
++  --page INTEGER       The page to be listed  [default: 0]
++  --page-size INTEGER  number of objects per page  [default: 10]
++  -d, --detached       whether run in detached mode
++  --help               Show this message and exit.
++{{/code}}
++
++=== Examples ===
++
++Show the details of the specified Dataset by providing the unique Dataset Code - “aug242021” in this case:
++
++{{code language="none"}}
++$ pilotcli dataset show-detail aug242021
++--------------------------------------------------------------------------------
++|        Title        |                        dataset-01                      |
++--------------------------------------------------------------------------------
++|         Code        |                        aug242021                       |
++--------------------------------------------------------------------------------
++|       Authors       |                     uname, cli                         |
++--------------------------------------------------------------------------------
++|         Type        |                         GENERAL                        |
++--------------------------------------------------------------------------------
++|       Modality      |     neuroimaging, microscopy, histological approach    |
++--------------------------------------------------------------------------------
++|  Collection_method  |                   import, test, upload                 |
++--------------------------------------------------------------------------------
++|         Tags        |                     tag1, tag2, tag3                   |
++--------------------------------------------------------------------------------
++|       Versions      |                      1.0, 1.1, 1.2                     |
++--------------------------------------------------------------------------------
++{{/code}}
++
++== Command: **download** ==
++
++* **Usage**: Download a particular version of a dataset.
++* **Options**: -v ~-~-version
++* (((
++**Prerequisite**:
++
++* User login is required, otherwise error is returned: "The current login session is invalid. Please login to continue."
++)))
++
++{{code language="none"}}
++$ pilotcli dataset download --help
++Usage: pilotcli dataset download [OPTIONS] [CODE]... OUTPUT_PATH
++
++  Download a dataset or a particular version of a dataset.
++
++Options:
++  -v, --version TEXT  Download a particular version of a dataset.
++  --help              Show this message and exit.
++{{/code}}
++
++
++=== Examples ===
++
++Download a Dataset with Code “aug242021”:
++
++{{code language="none"}}
++$ pilotcli dataset download aug242021 ~/Downloads/
++Pre downloading dataset
++Preparing status: READY_FOR_DOWNLOADING
++start downloading...
++Downloading aug242021_1632342868.882398.zip |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_163234
++2868.882398.zip
++{{/code}}
++
++Download the version 1.1 of a Dataset with Code “aug242021”:
++
++{{code language="none"}}
++$ pilotcli dataset download aug242021 ~/Downloads/ -v 1.1
++Current dataset version: 1.1
++Pre downloading dataset
++start downloading...
++Downloading aug242021_2021-08-24 11:10:00.042277.zip |██████████████████████████████ 100% 00:00
++File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_2021-08-24 11:10:00.042277.zip
++{{/code}}
++
++
++
  ----
--Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
++Copyright © 2023 [[Indoc Systems>>url:https://www.indocsystems.com]].
--HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].~{~{/code}}
--~)~)~)
++HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].