Last modified by Dennis Segebarth on 2024/10/02 18:38
From version 1.6
edited by Susan Evans
on 2023/07/10 22:22
Change comment: (Autosaved)
To version 1.10
edited by Susan Evans
on 2023/07/10 22:30
Change comment: (Autosaved)

Summary

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584 584  Upload a file with tags and/or attributes.
585 585  
586 586  * 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).
587 -* 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 -a cli_Manifest1_template.json, where “cli_Manifest1_template.json" points to the location of the attributes JSON-file on your local machine.
587 +* 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.
588 588  * 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:
589 589  
590 +{{code language="none"}}
591 +$ pilotcli file upload ./sample_folder/sample_file6 -p cli/admin -t tag1 -t tag2 -a cli_Manifest1_template.json
592 +File attribute validation passed: True
593 +Starting upload of: ./sample_folder/sample_file6
594 +Pre-upload complete.
595 +uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: bc47ec2a-1a4e-4f71-a37a-7ce6473e415a-1627499273 resumable_relative_path admin/
596 +
597 +Upload job is finalizing, please wait...
598 +Upload job complete.
599 +Attribute attached
600 +All files uploaded successfully.
601 +{{/code}}
590 590  
603 +Upload a file with specified number of threads, using the {{code}}-td <thread_number>{{/code}} option.
591 591  
605 +* 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:
592 592  
607 +{{code language="none"}}
608 +$ pilotcli file upload -p indoctestproject/admin/test20230306_3 /home/color/indoc/script/large_folder_test_data/gentoo_root_100M.img -td 3
609 +Target folder does not exist. Would you like to create a new folder? [y/N]: y
610 +Starting upload of: /home/color/indoc/script/large_folder_test_data/gentoo_root_100M.img
611 +Pre-upload complete.
612 +Uploading gentoo_root_100M.img , resumable_id: c68752372b42c85d, job_id: 56de3632-58df-445c-bcb9-bddfe6be5bf7: |██████████████████████████████ 100% 00:00
613 +Upload Time: 79.77s for 1 files
614 +All uploading jobs have finished.
615 +{{/code}}
616 +
617 +(10) upload with customized manifest name
618 +
619 +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:
620 +
621 +{{code language="none"}}
622 +$ pilotcli file upload -p <path> <file> --output-path test_manifest.json
623 +{{/code}}
624 +
625 +== Command: **resume** ==
626 +
627 +* **Options**: -td ~-~-thread, -r ~-~-resumable-manifest
628 +* **Usage**: Resume unfinished file uploading based on the manifest file.
629 +* (((
630 +**Prerequisite**:
631 +
632 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
633 +* Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
634 +* The resumable manifest JSON file is required, which is generated upon executing the {{code}}pilotcli file upload{{/code}} command.
635 +)))
636 +
637 +=== Example: ===
638 +
639 +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.
640 +
641 +{{code language="none"}}
642 +$ pilotcli file resume -r ./manifest.json
643 +Resume the upload for 10 files.
644 +Resumable upload check complete.
645 +Uploading aggregated.py: |██████████████████████████████ 100% 00:00
646 +Uploading __init__.py: |██████████████████████████████ 100% 00:00
647 +Uploading service_meta_class.py: |██████████████████████████████ 100% 00:00
648 +Uploading upload_form.py: |██████████████████████████████ 100% 00:00
649 +Uploading convert_type.py: |██████████████████████████████ 100% 00:00
650 +Uploading singleton.py: |██████████████████████████████ 100% 00:00
651 +Uploading __init__.py: |██████████████████████████████ 100% 00:00
652 +Uploading base_library.zip: |██████████████████████████████ 100% 00:00 0% ?
653 +Uploading EXE-00.toc: |██████████████████████████████ 100% 00:00
654 +Uploading xref-pilotcli_test20230227_3.html: |██████████████████████████████ 100% 00:00
655 +Upload Time: 11.13s for 10 files
656 +{{/code}}
657 +
658 +== Command: **sync** ==
659 +
660 +* **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.
661 +* (((
662 +**Options**: -z ~-~-zone, -i ~-~-geid, ~-~-zip
663 +
664 +* 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.
665 +)))
666 +* (((
667 +**Prerequisite**:
668 +
669 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
670 +* 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.”
671 +* 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.”
672 +)))
673 +
674 +{{code language="none"}}
675 +$ pilotcli file sync --help
676 +Usage: pilotcli file sync [OPTIONS] [PATHS]... OUTPUT_PATH
677 +
678 + Download files/folders from a given Project/folder/file in core zone.
679 +
680 +Options:
681 + -z, --zone TEXT Target Zone (i.e., core/greenroom)
682 + --zip Download files as a zip.
683 + -i, --geid Enable downloading by geid.
684 + --help Show this message and exit.
685 +{{/code}}
686 +
687 +=== Examples ===
688 +
689 +Download a file or a folder from the Core zone of a Project:
690 +
691 +{{code language="none"}}
692 +$ pilotcli file sync cli/admin/sample_file2 -z core ~/Downloads/
693 +Preparing status: READY_FOR_DOWNLOADING
694 +start downloading...
695 +Downloading sample_file2 |██████████████████████████████ 100% 00:00
696 +File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
697 +{{/code}}
698 +
699 +Download multiple files or folders as a compressed zip by simply providing all source files or folders and adding the {{code}}--zip{{/code}} option:
700 +
701 +{{code language="none"}}
702 +$ pilotcli file sync cli/admin/sample_file2 cli/admin/sample_file7 -z core ~/Downloads/ --zip
703 +Preparing downloading
704 +Preparing status: READY_FOR_DOWNLOADING
705 +start downloading...
706 +Downloading cli_1632340658.768384.zip |██████████████████████████████ 100% 00:00
707 +File has been downloaded successfully and saved to: /home/uname/Downloads/cli_1632340658.768384.zip
708 +{{/code}}
709 +
710 +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:
711 +
712 +{{code language="none"}}
713 +$ pilotcli file sync -i 6d89afd4-f86e-4df7-b6c5-01a9af4e828e-1627499957 7e8e2bac-97c6-4738-bc08-12139c9ba225-1627498854 ~/Downloads/
714 +Preparing status: READY_FOR_DOWNLOADING
715 +start downloading...
716 +Downloading sample_file7 |██████████████████████████████ 100% 00:00
717 +File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file7
718 +Preparing status: READY_FOR_DOWNLOADING
719 +start downloading...
720 +Downloading sample_file2 |██████████████████████████████ 100% 00:00
721 +File has been downloaded successfully and saved to: /home/uname/Downloads/sample_file2
722 +{{/code}}
723 +
593 593  ----
594 594  
595 595  -
... ... @@ -599,5 +599,4 @@
599 599  
600 600  Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
601 601  
602 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].~{~{/code}}
603 -~)~)~)
733 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].