Last modified by Dennis Segebarth on 2024/10/02 18:38
From version 11.1
edited by Susan Evans
on 2023/09/22 18:38
Change comment: There is no comment for this version
To version 1.9
edited by Susan Evans
on 2023/07/10 22:28
Change comment: (Autosaved)

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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 =
... ... @@ -8,18 +8,10 @@
8 8  
9 9  Users are reminded to abide by the Platform Terms of Use and any Project-specific restrictions when using the Command Line Interface to access data and code.
10 10  
11 -{{warning}}
12 -⚠ If you are using pilotcli in an environment or system where other users can access and read all your files, please make sure to always run {{code language="none"}}pilotcli user logout{{/code}} as soon as you are done using pilotcli. This could be, for instance, if you are using pilotcli on a shared computer in your local institute, with system administrators of your University or Hospital having superuser privileges. You should not use pilotcli in an environment where users with such privileges are from an entity that is not trusted.e your warning message here.
13 -{{/warning}}
14 -
15 15  = Using the Pilot Command Line Interface in JupyterHub =
16 16  
17 17  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.
18 18  
19 -= Using the Pilot Command Line Interface in Guacamole VMs =
20 -
21 -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.
22 -
23 23  = Downloading the Pilot Command Line Interface =
24 24  
25 25  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.
... ... @@ -114,7 +114,7 @@
114 114  
115 115  3) Device Login Successful message will appear and your authentication browser window can be closed.
116 116  
117 -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:
118 118  
119 119  {{code language="none"}}
120 120  $ pilotcli user login
... ... @@ -350,7 +350,7 @@
350 350  
351 351  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
352 352  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
353 -* 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.
354 354  * 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."
355 355  * pilotcli must have the permission to write a file in the directory, otherwise an error is returned.
356 356  )))
... ... @@ -418,7 +418,7 @@
418 418  
419 419  * User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
420 420  * Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
421 -* 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.
422 422  )))
423 423  
424 424  {{code language="none"}}
... ... @@ -626,7 +626,7 @@
626 626  All uploading jobs have finished.
627 627  {{/code}}
628 628  
629 -Upload with customized manifest name
617 +(10) upload with customized manifest name
630 630  
631 631  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:
632 632  
... ... @@ -708,196 +708,17 @@
708 708  File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
709 709  {{/code}}
710 710  
711 -Download multiple files or folders as a compressed zip by simply providing all source files or folders and adding the {{code}}--zip{{/code}} option:
699 +Download multiple files or folders as a compressed zip by simply providing all source files or folders and adding the ~-~-zip option:
712 712  
713 -{{code language="none"}}
714 -$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 -z core ~/Downloads/ --zip
715 -Preparing downloading
716 -Preparing status: READY_FOR_DOWNLOADING
717 -start downloading...
718 -Downloading cli_1632340658.768384.zip |██████████████████████████████ 100% 00:00
719 -File has been downloaded successfully and saved to: /home/uname/Downloads/cli_1632340658.768384.zip
720 -{{/code}}
721 721  
722 -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:
702 +----
723 723  
724 -{{code language="none"}}
725 -$ pilotcli file sync -i 6d89afd4-f86e-4df7-b6c5-01a9af4e828e-1627499957 7e8e2bac-97c6-4738-bc08-12139c9ba225-1627498854 ~/Downloads/
726 -Preparing status: READY_FOR_DOWNLOADING
727 -start downloading...
728 -Downloading sample_file7 |██████████████████████████████ 100% 00:00
729 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
730 -Preparing status: READY_FOR_DOWNLOADING
731 -start downloading...
732 -Downloading sample_file2 |██████████████████████████████ 100% 00:00
733 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
734 -{{/code}}
704 +-
705 +{{code language="none"}}{{/code}}
735 735  
736 -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:
737 -
738 -{{code language="none"}}
739 -$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 ~/Downloads
740 -Preparing status: READY_FOR_DOWNLOADING
741 -/home/uname/Downloads/sample_file2 already exist, file will be saved as /home/uname/Downloads/sample_file2 (1)
742 -start downloading...
743 -Downloading sample_file2 (1) |██████████████████████████████ 100% 00:00
744 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2 (1)
745 -Preparing status: READY_FOR_DOWNLOADING
746 -start downloading...
747 -Downloading sample_file7 |██████████████████████████████ 100% 00:00
748 -File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
749 -{{/code}}
750 -
751 -= Dataset Commands: pilotcli **dataset** =
752 -
753 -== Help ==
754 -
755 -{{code language="none"}}
756 -$ pilotcli dataset --help
757 -Usage: pilotcli dataset [OPTIONS] COMMAND [ARGS]...
758 -
759 -Options:
760 - --help Show this message and exit.
761 -
762 -Commands:
763 - download Download a dataset or a particular version of a dataset.
764 - list List datasets belonging to logged in user.
765 - show-detail Show details of a dataset.
766 -{{/code}}
767 -
768 -== Command: **list** ==
769 -
770 -* **Usage**: List all datasets for the logged in user
771 -* (((
772 -**Prerequisite**:
773 -
774 -* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
775 -)))
776 -
777 -{{code language="none"}}
778 -$ pilotcli dataset list --help
779 -Usage: pilotcli dataset list [OPTIONS]
780 -
781 - List datasets belonging to logged in user.
782 -
783 -Options:
784 - --page INTEGER The page to be listed [default: 0]
785 - --page-size INTEGER number of objects per page [default: 10]
786 - -d, --detached whether run in detached mode
787 - --help Show this message and exit.
788 -{{/code}}
789 -
790 -=== Examples ===
791 -
792 -List all datasets that are accessible for the user:
793 -
794 -{{code language="none"}}
795 -$ pilotcli dataset list
796 - Dataset Title Dataset Code
797 ----------------------------------------------------------------------------
798 - dataset2 aug24202102
799 - dataset-01 aug242021
800 -Page: 0, Number of datasets: 2
801 -{{/code}}
802 -
803 -== Command: **show-detail** ==
804 -
805 -* **Usage**: Show the detailed information of a dataset.
806 -* (((
807 -**Prerequisite**:
808 -
809 -* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
810 -)))
811 -
812 -{{code language="none"}}
813 -$ pilotcli dataset show-detail --help
814 -Usage: pilotcli dataset show-detail [OPTIONS] CODE
815 -
816 - Show details of a dataset.
817 -
818 -Options:
819 - --page INTEGER The page to be listed [default: 0]
820 - --page-size INTEGER number of objects per page [default: 10]
821 - -d, --detached whether run in detached mode
822 - --help Show this message and exit.
823 -{{/code}}
824 -
825 -=== Examples ===
826 -
827 -Show the details of the specified Dataset by providing the unique Dataset Code - “aug242021” in this case:
828 -
829 -{{code language="none"}}
830 -$ pilotcli dataset show-detail aug242021
831 ---------------------------------------------------------------------------------
832 -| Title | dataset-01 |
833 ---------------------------------------------------------------------------------
834 -| Code | aug242021 |
835 ---------------------------------------------------------------------------------
836 -| Authors | uname, cli |
837 ---------------------------------------------------------------------------------
838 -| Type | GENERAL |
839 ---------------------------------------------------------------------------------
840 -| Modality | neuroimaging, microscopy, histological approach |
841 ---------------------------------------------------------------------------------
842 -| Collection_method | import, test, upload |
843 ---------------------------------------------------------------------------------
844 -| Tags | tag1, tag2, tag3 |
845 ---------------------------------------------------------------------------------
846 -| Versions | 1.0, 1.1, 1.2 |
847 ---------------------------------------------------------------------------------
848 -{{/code}}
849 -
850 -== Command: **download** ==
851 -
852 -* **Usage**: Download a particular version of a dataset.
853 -* **Options**: -v ~-~-version
854 -* (((
855 -**Prerequisite**:
856 -
857 -* User login is required, otherwise error is returned: "The current login session is invalid. Please login to continue."
858 -)))
859 -
860 -{{code language="none"}}
861 -$ pilotcli dataset download --help
862 -Usage: pilotcli dataset download [OPTIONS] [CODE]... OUTPUT_PATH
863 -
864 - Download a dataset or a particular version of a dataset.
865 -
866 -Options:
867 - -v, --version TEXT Download a particular version of a dataset.
868 - --help Show this message and exit.
869 -{{/code}}
870 -
871 -
872 -=== Examples ===
873 -
874 -Download a Dataset with Code “aug242021”:
875 -
876 -{{code language="none"}}
877 -$ pilotcli dataset download aug242021 ~/Downloads/
878 -Pre downloading dataset
879 -Preparing status: READY_FOR_DOWNLOADING
880 -start downloading...
881 -Downloading aug242021_1632342868.882398.zip |██████████████████████████████ 100% 00:00
882 -File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_163234
883 -2868.882398.zip
884 -{{/code}}
885 -
886 -Download the version 1.1 of a Dataset with Code “aug242021”:
887 -
888 -{{code language="none"}}
889 -$ pilotcli dataset download aug242021 ~/Downloads/ -v 1.1
890 -Current dataset version: 1.1
891 -Pre downloading dataset
892 -start downloading...
893 -Downloading aug242021_2021-08-24 11:10:00.042277.zip |██████████████████████████████ 100% 00:00
894 -File has been downloaded successfully and saved to: /home/uname/Downloads/aug242021_2021-08-24 11:10:00.042277.zip
895 -{{/code}}
896 -
897 -
898 -
899 899  ----
900 900  
901 -Copyright © 2023 [[Indoc Systems>>url:https://www.indocsystems.com]].
709 +Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
902 902  
903 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
711 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].{{/code}}
712 +