Last modified by Dennis Segebarth on 2024/10/02 18:38
From version 9.1
edited by Dennis Segebarth
on 2023/09/13 18:09
Change comment: There is no comment for this version
To version 1.10
edited by Susan Evans
on 2023/07/10 22:30
Change comment: (Autosaved)

Summary

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1 -XWiki.dsegebarth
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1 -{{box cssClass="floatinginfobox" title="Table of Contents"}}
2 -{{toc depth="2"/}}
3 -{{/box}}
4 -
5 5  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.
6 6  
7 7  = Data Stewardship =
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12 12  
13 13  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.
14 14  
15 -= Using the Pilot Command Line Interface in Guacamole VMs =
16 -
17 -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.
18 -
19 19  = Downloading the Pilot Command Line Interface =
20 20  
21 21  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.
... ... @@ -110,7 +110,7 @@
110 110  
111 111  3) Device Login Successful message will appear and your authentication browser window can be closed.
112 112  
113 -4) The output of the Command Line Tool will also be updated to notify you about the successful login:
105 +4) The output of the Command Line Tool will also be updated (see line 14 below) to notify you about the successful login:
114 114  
115 115  {{code language="none"}}
116 116  $ pilotcli user login
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346 346  
347 347  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
348 348  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
349 -* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
341 +* Requires the Project code, which can be retrieved via pilotcli project list.
350 350  * 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."
351 351  * pilotcli must have the permission to write a file in the directory, otherwise an error is returned.
352 352  )))
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414 414  
415 415  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
416 416  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
417 -* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
409 +* Requires the Project code, which can be retrieved via pilotcli project list.
418 418  )))
419 419  
420 420  {{code language="none"}}
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622 622  All uploading jobs have finished.
623 623  {{/code}}
624 624  
625 -Upload with customized manifest name
617 +(10) upload with customized manifest name
626 626  
627 627  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:
628 628  
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729 729  File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
730 730  {{/code}}
731 731  
732 -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:
724 +----
733 733  
734 -{{code language="none"}}
735 -$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 ~/Downloads
736 -Preparing status: READY_FOR_DOWNLOADING
737 -/home/uname/Downloads/sample_file2 already exist, file will be saved as /home/uname/Downloads/sample_file2 (1)
738 -start downloading...
739 -Downloading sample_file2 (1) |██████████████████████████████ 100% 00:00
740 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2 (1)
741 -Preparing status: READY_FOR_DOWNLOADING
742 -start downloading...
743 -Downloading sample_file7 |██████████████████████████████ 100% 00:00
744 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
745 -{{/code}}
726 +-
727 +{{code language="none"}}{{/code}}
746 746  
747 -= Dataset Commands: pilotcli **dataset** =
748 -
749 -== Help ==
750 -
751 -{{code language="none"}}
752 -$ pilotcli dataset --help
753 -Usage: pilotcli dataset [OPTIONS] COMMAND [ARGS]...
754 -
755 -Options:
756 - --help Show this message and exit.
757 -
758 -Commands:
759 - download Download a dataset or a particular version of a dataset.
760 - list List datasets belonging to logged in user.
761 - show-detail Show details of a dataset.
762 -{{/code}}
763 -
764 -== Command: **list** ==
765 -
766 -* **Usage**: List all datasets for the logged in user
767 -* (((
768 -**Prerequisite**:
769 -
770 -* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
771 -)))
772 -
773 -{{code language="none"}}
774 -$ pilotcli dataset list --help
775 -Usage: pilotcli dataset list [OPTIONS]
776 -
777 - List datasets belonging to logged in user.
778 -
779 -Options:
780 - --page INTEGER The page to be listed [default: 0]
781 - --page-size INTEGER number of objects per page [default: 10]
782 - -d, --detached whether run in detached mode
783 - --help Show this message and exit.
784 -{{/code}}
785 -
786 -=== Examples ===
787 -
788 -List all datasets that are accessible for the user:
789 -
790 -{{code language="none"}}
791 -$ pilotcli dataset list
792 - Dataset Title Dataset Code
793 ----------------------------------------------------------------------------
794 - dataset2 aug24202102
795 - dataset-01 aug242021
796 -Page: 0, Number of datasets: 2
797 -{{/code}}
798 -
799 -== Command: **show-detail** ==
800 -
801 -* **Usage**: Show the detailed information of a dataset.
802 -* (((
803 -**Prerequisite**:
804 -
805 -* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
806 -)))
807 -
808 -{{code language="none"}}
809 -$ pilotcli dataset show-detail --help
810 -Usage: pilotcli dataset show-detail [OPTIONS] CODE
811 -
812 - Show details of a dataset.
813 -
814 -Options:
815 - --page INTEGER The page to be listed [default: 0]
816 - --page-size INTEGER number of objects per page [default: 10]
817 - -d, --detached whether run in detached mode
818 - --help Show this message and exit.
819 -{{/code}}
820 -
821 -=== Examples ===
822 -
823 -Show the details of the specified Dataset by providing the unique Dataset Code - “aug242021” in this case:
824 -
825 -{{code language="none"}}
826 -$ pilotcli dataset show-detail aug242021
827 ---------------------------------------------------------------------------------
828 -| Title | dataset-01 |
829 ---------------------------------------------------------------------------------
830 -| Code | aug242021 |
831 ---------------------------------------------------------------------------------
832 -| Authors | uname, cli |
833 ---------------------------------------------------------------------------------
834 -| Type | GENERAL |
835 ---------------------------------------------------------------------------------
836 -| Modality | neuroimaging, microscopy, histological approach |
837 ---------------------------------------------------------------------------------
838 -| Collection_method | import, test, upload |
839 ---------------------------------------------------------------------------------
840 -| Tags | tag1, tag2, tag3 |
841 ---------------------------------------------------------------------------------
842 -| Versions | 1.0, 1.1, 1.2 |
843 ---------------------------------------------------------------------------------
844 -{{/code}}
845 -
846 -== Command: **download** ==
847 -
848 -* **Usage**: Download a particular version of a dataset.
849 -* **Options**: -v ~-~-version
850 -* (((
851 -**Prerequisite**:
852 -
853 -* User login is required, otherwise error is returned: "The current login session is invalid. Please login to continue."
854 -)))
855 -
856 -{{code language="none"}}
857 -$ pilotcli dataset download --help
858 -Usage: pilotcli dataset download [OPTIONS] [CODE]... OUTPUT_PATH
859 -
860 - Download a dataset or a particular version of a dataset.
861 -
862 -Options:
863 - -v, --version TEXT Download a particular version of a dataset.
864 - --help Show this message and exit.
865 -{{/code}}
866 -
867 -
868 -=== Examples ===
869 -
870 -Download a Dataset with Code “aug242021”:
871 -
872 -{{code language="none"}}
873 -$ pilotcli dataset download aug242021 ~/Downloads/
874 -Pre downloading dataset
875 -Preparing status: READY_FOR_DOWNLOADING
876 -start downloading...
877 -Downloading aug242021_1632342868.882398.zip |██████████████████████████████ 100% 00:00
878 -File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_163234
879 -2868.882398.zip
880 -{{/code}}
881 -
882 -Download the version 1.1 of a Dataset with Code “aug242021”:
883 -
884 -{{code language="none"}}
885 -$ pilotcli dataset download aug242021 ~/Downloads/ -v 1.1
886 -Current dataset version: 1.1
887 -Pre downloading dataset
888 -start downloading...
889 -Downloading aug242021_2021-08-24 11:10:00.042277.zip |██████████████████████████████ 100% 00:00
890 -File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_2021-08-24 11:10:00.042277.zip
891 -{{/code}}
892 -
893 -
894 -
895 895  ----
896 896  
897 -Copyright © 2023 [[Indoc Systems>>url:https://www.indocsystems.com]].
731 +Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
898 898  
899 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
733 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].