Last modified by Dennis Segebarth on 2024/10/02 18:38
From version 1.10
edited by Susan Evans
on 2023/07/10 22:30
Change comment: (Autosaved)
To version 4.1
edited by Susan Evans
on 2023/07/11 13:04
Change comment: There is no comment for this version

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1 +{{box cssClass="floatinginfobox" title="Table of Contents"}}
2 +{{toc depth="2"/}}
3 +{{/box}}
4 +
1 1  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.
2 2  
3 3  = Data Stewardship =
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102 102  
103 103  3) Device Login Successful message will appear and your authentication browser window can be closed.
104 104  
105 -4) The output of the Command Line Tool will also be updated (see line 14 below) to notify you about the successful login:
109 +4) The output of the Command Line Tool will also be updated to notify you about the successful login:
106 106  
107 107  {{code language="none"}}
108 108  $ pilotcli user login
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338 338  
339 339  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
340 340  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
341 -* Requires the Project code, which can be retrieved via pilotcli project list.
345 +* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
342 342  * 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."
343 343  * pilotcli must have the permission to write a file in the directory, otherwise an error is returned.
344 344  )))
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721 721  File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
722 722  {{/code}}
723 723  
724 -----
728 +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:
725 725  
726 --
727 -{{code language="none"}}{{/code}}
730 +{{code language="none"}}
731 +$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 ~/Downloads
732 +Preparing status: READY_FOR_DOWNLOADING
733 +/home/uname/Downloads/sample_file2 already exist, file will be saved as /home/uname/Downloads/sample_file2 (1)
734 +start downloading...
735 +Downloading sample_file2 (1) |██████████████████████████████ 100% 00:00
736 +File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2 (1)
737 +Preparing status: READY_FOR_DOWNLOADING
738 +start downloading...
739 +Downloading sample_file7 |██████████████████████████████ 100% 00:00
740 +File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
741 +{{/code}}
728 728  
743 += Dataset Commands: pilotcli **dataset** =
744 +
745 +== Help ==
746 +
747 +{{code language="none"}}
748 +$ pilotcli dataset --help
749 +Usage: pilotcli dataset [OPTIONS] COMMAND [ARGS]...
750 +
751 +Options:
752 + --help Show this message and exit.
753 +
754 +Commands:
755 + download Download a dataset or a particular version of a dataset.
756 + list List datasets belonging to logged in user.
757 + show-detail Show details of a dataset.
758 +{{/code}}
759 +
760 +== Command: **list** ==
761 +
762 +* **Usage**: List all datasets for the logged in user
763 +* (((
764 +**Prerequisite**:
765 +
766 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
767 +)))
768 +
769 +{{code language="none"}}
770 +$ pilotcli dataset list --help
771 +Usage: pilotcli dataset list [OPTIONS]
772 +
773 + List datasets belonging to logged in user.
774 +
775 +Options:
776 + --page INTEGER The page to be listed [default: 0]
777 + --page-size INTEGER number of objects per page [default: 10]
778 + -d, --detached whether run in detached mode
779 + --help Show this message and exit.
780 +{{/code}}
781 +
782 +=== Examples ===
783 +
784 +List all datasets that are accessible for the user:
785 +
786 +{{code language="none"}}
787 +$ pilotcli dataset list
788 + Dataset Title Dataset Code
789 +---------------------------------------------------------------------------
790 + dataset2 aug24202102
791 + dataset-01 aug242021
792 +Page: 0, Number of datasets: 2
793 +{{/code}}
794 +
795 +== Command: **show-detail** ==
796 +
797 +* **Usage**: Show the detailed information of a dataset.
798 +* (((
799 +**Prerequisite**:
800 +
801 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
802 +)))
803 +
804 +{{code language="none"}}
805 +$ pilotcli dataset show-detail --help
806 +Usage: pilotcli dataset show-detail [OPTIONS] CODE
807 +
808 + Show details of a dataset.
809 +
810 +Options:
811 + --page INTEGER The page to be listed [default: 0]
812 + --page-size INTEGER number of objects per page [default: 10]
813 + -d, --detached whether run in detached mode
814 + --help Show this message and exit.
815 +{{/code}}
816 +
817 +=== Examples ===
818 +
819 +Show the details of the specified Dataset by providing the unique Dataset Code - “aug242021” in this case:
820 +
821 +{{code language="none"}}
822 +$ pilotcli dataset show-detail aug242021
823 +--------------------------------------------------------------------------------
824 +| Title | dataset-01 |
825 +--------------------------------------------------------------------------------
826 +| Code | aug242021 |
827 +--------------------------------------------------------------------------------
828 +| Authors | uname, cli |
829 +--------------------------------------------------------------------------------
830 +| Type | GENERAL |
831 +--------------------------------------------------------------------------------
832 +| Modality | neuroimaging, microscopy, histological approach |
833 +--------------------------------------------------------------------------------
834 +| Collection_method | import, test, upload |
835 +--------------------------------------------------------------------------------
836 +| Tags | tag1, tag2, tag3 |
837 +--------------------------------------------------------------------------------
838 +| Versions | 1.0, 1.1, 1.2 |
839 +--------------------------------------------------------------------------------
840 +{{/code}}
841 +
842 +== Command: **download** ==
843 +
844 +* **Usage**: Download a particular version of a dataset.
845 +* **Options**: -v ~-~-version
846 +* (((
847 +**Prerequisite**:
848 +
849 +* User login is required, otherwise error is returned: "The current login session is invalid. Please login to continue."
850 +)))
851 +
852 +{{code language="none"}}
853 +$ pilotcli dataset download --help
854 +Usage: pilotcli dataset download [OPTIONS] [CODE]... OUTPUT_PATH
855 +
856 + Download a dataset or a particular version of a dataset.
857 +
858 +Options:
859 + -v, --version TEXT Download a particular version of a dataset.
860 + --help Show this message and exit.
861 +{{/code}}
862 +
863 +
864 +=== Examples ===
865 +
866 +Download a Dataset with Code “aug242021”:
867 +
868 +{{code language="none"}}
869 +$ pilotcli dataset download aug242021 ~/Downloads/
870 +Pre downloading dataset
871 +Preparing status: READY_FOR_DOWNLOADING
872 +start downloading...
873 +Downloading aug242021_1632342868.882398.zip |██████████████████████████████ 100% 00:00
874 +File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_163234
875 +2868.882398.zip
876 +{{/code}}
877 +
878 +Download the version 1.1 of a Dataset with Code “aug242021”:
879 +
880 +{{code language="none"}}
881 +$ pilotcli dataset download aug242021 ~/Downloads/ -v 1.1
882 +Current dataset version: 1.1
883 +Pre downloading dataset
884 +start downloading...
885 +Downloading aug242021_2021-08-24 11:10:00.042277.zip |██████████████████████████████ 100% 00:00
886 +File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_2021-08-24 11:10:00.042277.zip
887 +{{/code}}
888 +
889 +
890 +
729 729  ----
730 730  
731 731  Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].