Last modified by Dennis Segebarth on 2024/10/02 18:38
From version 1.1
edited by Susan Evans
on 2023/07/10 22:12
Change comment: (Autosaved)
To version 1.5
edited by Susan Evans
on 2023/07/10 22:20
Change comment: (Autosaved)

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252 252  
253 253  * **Options**: -p ~-~-project-code
254 254  * **Usage**: List all attributes from a specified Project.
255 +* **Prerequisite**:
256 +
257 +* User login is required, otherwise an error is returned: ‘The current login session is invalid. Please login to continue.’
258 +* Requires the Project code, which can be retrieved via {{code}}pilotcli project list{{/code}}.
259 +
260 +{{code language="none"}}
261 +$ pilotcli file attribute-list --help
262 +Usage: pilotcli file attribute-list [OPTIONS]
263 +
264 + List attribute templates of a given Project.
265 +
266 +Options:
267 + -p, --project-code TEXT Project Code
268 + --help Show this message and exit.
269 +{{/code}}
270 +
271 +=== Examples ===
272 +
273 +List attributes from a given Project by providing the Project Code at the prompt. In this example, “cli” is the corresponding Project Code:
274 +
275 +{{code language="none"}}
276 +$ pilotcli file attribute-list
277 +ProjectCode: cli
278 +
279 +Manifest1
280 +--------------------------------------------------------------------------
281 +| Attribute Name | Type | Value | Optional |
282 +--------------------------------------------------------------------------
283 +| attr1 | multiple_choice | a1,a2,a3,a4,a5 | False |
284 +--------------------------------------------------------------------------
285 +| attr2 | text | None | False |
286 +--------------------------------------------------------------------------
287 +| attr3 | multiple_choice | t1,t2,t3,t4,t5 | True |
288 +--------------------------------------------------------------------------
289 +
290 +Manifest2
291 +--------------------------------------------------------------------------
292 +| Attribute Name | Type | Value | Optional |
293 +--------------------------------------------------------------------------
294 +| attr1 | multiple_choice | a1,a2,a3,a4 | True |
295 +--------------------------------------------------------------------------
296 +| attr2 | text | None | False |
297 +--------------------------------------------------------------------------
298 +| attr3 | multiple_choice | t1,t2,t3 | True |
299 +--------------------------------------------------------------------------
300 +All Attributes fetched successfully.
301 +{{/code}}
302 +
303 +List attributes from given a Project and provide the Project Code “cli” as an option in the same line {{code}}-p cli{{/code}}:
304 +
305 +{{code language="none"}}
306 +$ pilotcli file attribute-list -p cli
307 +
308 +Manifest1
309 +--------------------------------------------------------------------------
310 +| Attribute Name | Type | Value | Optional |
311 +--------------------------------------------------------------------------
312 +| attr1 | multiple_choice | a1,a2,a3,a4,a5 | False |
313 +--------------------------------------------------------------------------
314 +| attr2 | text | None | False |
315 +--------------------------------------------------------------------------
316 +| attr3 | multiple_choice | t1,t2,t3,t4,t5 | True |
317 +--------------------------------------------------------------------------
318 +
319 +Manifest2
320 +--------------------------------------------------------------------------
321 +| Attribute Name | Type | Value | Optional |
322 +--------------------------------------------------------------------------
323 +| attr1 | multiple_choice | a1,a2,a3,a4 | True |
324 +--------------------------------------------------------------------------
325 +| attr2 | text | None | False |
326 +--------------------------------------------------------------------------
327 +| attr3 | multiple_choice | t1,t2,t3 | True |
328 +--------------------------------------------------------------------------
329 +All Attributes fetched successfully.
330 +{{/code}}
331 +
332 +== Command: **attribute-export** ==
333 +
334 +* **Options**: -p ~-~-project-code, -n ~-~-attribute-name
335 +* **Usage**: Export an attribute template as JSON-file from a given Project
255 255  * (((
256 256  **Prerequisite**:
257 257  
258 -* User login is required, otherwise an error is returned: ‘The current login session is invalid. Please login to continue.’
259 -* Requires the Project code, which can be retrieved via `pilotcli project list.
339 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
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.
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 +* pilotcli must have the permission to write a file in the directory, otherwise an error is returned.
260 260  )))
261 261  
346 +{{code language="none"}}
347 +$ pilotcli file attribute-export --help
348 +Usage: pilotcli file attribute-export [OPTIONS]
262 262  
350 + Export attribute template from a given Project.
263 263  
352 +Options:
353 + -p, --project-code TEXT Project Code
354 + -n, --attribute-name TEXT Attribute Template Name
355 + --help Show this message and exit.
356 +{{/code}}
264 264  
358 +=== Examples ===
359 +
360 +Export an attribute template from a given Project. The user is prompted to provide the Project Code (“cli”) and the Attribute Template Name (“Manifest1”):
361 +
362 +{{code language="none"}}
363 +$ pilotcli file attribute-export
364 +ProjectCode: cli
365 +AttributeName: Manifest1
366 +
367 +Manifest1
368 +--------------------------------------------------------------------------
369 +| Attribute Name | Type | Value | Optional |
370 +--------------------------------------------------------------------------
371 +| attr1 | multiple_choice | a1,a2,a3,a4,a5 | False |
372 +--------------------------------------------------------------------------
373 +| attr2 | text | None | False |
374 +--------------------------------------------------------------------------
375 +| attr3 | multiple_choice | t1,t2,t3,t4,t5 | True |
376 +--------------------------------------------------------------------------
377 +Template saved successfully: cli_Manifest1_template.json
378 +Attribute definition saved successfully: cli_Manifest1_definition.json
379 +{{/code}}
380 +
381 +Export an attribute template from a given Project using options to provide both the Project Code {{code}}(-p cli){{/code}} and the Attribute Template Name {{code}}(-n Manifest1){{/code}}, “cli” and “Manifest1” in this case, respectively:
382 +
383 +{{code language="none"}}
384 +$ pilotcli file attribute-export -p cli -n Manifest1
385 +
386 +Manifest1
387 +--------------------------------------------------------------------------
388 +| Attribute Name | Type | Value | Optional |
389 +--------------------------------------------------------------------------
390 +| attr1 | multiple_choice | a1,a2,a3,a4,a5 | False |
391 +--------------------------------------------------------------------------
392 +| attr2 | text | None | False |
393 +--------------------------------------------------------------------------
394 +| attr3 | multiple_choice | t1,t2,t3,t4,t5 | True |
395 +--------------------------------------------------------------------------
396 +Template saved successfully: cli_Manifest1_template.json
397 +Attribute definition saved successfully: cli_Manifest1_definition.json
398 +{{/code}}
399 +
400 +== Command: **list** ==
401 +
402 +* **Options**: -z ~-~-zone
403 +* **Usage**: List files and folders in the specified directory within the Platform. Folders will be displayed in blue and files will be displayed in white (or black, depending on the background of your terminal). If no zone (i.e. Green Room or Core) is specified, Green Room will be used as default.
404 +* (((
405 +**Prerequisite**:
406 +
407 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
408 +* Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
409 +* Requires the Project code, which can be retrieved via pilotcli project list.
410 +)))
411 +
412 +{{code language="none"}}
413 +$ pilotcli file list --help
414 +Usage: pilotcli file list [OPTIONS] PATHS
415 +
416 + List files and folders inside a given Project/folder.
417 +
418 +Options:
419 + -z, --zone TEXT Target Zone (i.e., core/greenroom) [default:
420 + greenroom] [default: greenroom]
421 +
422 + --page INTEGER The page to be listed [default: 0]
423 + --page-size INTEGER number of objects per page [default: 10]
424 + -d, --detached whether run in detached mode
425 + --help Show this message and exit.
426 +{{/code}}
427 +
428 +=== Examples ===
429 +
430 +List folders in the directory “admin” in the Project with the Project Code “indoctestproject”. Since no zone was specified, the corresponding directory in the Green Room will be queried:
431 +
432 +{{code language="none"}}
433 +$ pilotcli file list indoctestproject/admin
434 +test_folder1 test_folder2 file1 file2 file3
435 +{{/code}}
436 +
437 +To list the corresponding elements in the “indoctestproject/admin” directory in the Projects' Core, the zone needs to be specified {{code}}(-z core){{/code}}:
438 +
439 +{{code language="none"}}
440 +$ pilotcli file list indoctestproject/admin -z core
441 +folder1 folder2 test_folder.zip file.txt sample.txt large-file.json
442 +{{/code}}
443 +
444 +== Command: **upload** ==
445 +
446 +* **Options**: -p ~-~-project, -a ~-~-attribute, -t ~-~-tag, -z ~-~-zone, -m ~-~-upload-message, -s ~-~-source-file, ~-~-zip, -td ~-~-thread, -o ~-~-output path
447 +* **Usage**: Upload files/folders to the given project, with optional tags and attributes, to the target folder.
448 +* (((
449 +**Prerequisite**:
450 +
451 +* User login is required, otherwise an error is returned: "The current login session is invalid. Please login to continue."
452 +* Project must be accessible to the user, otherwise an error is returned: "Project Code not found in list. Please verify and try again."
453 +* 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).
454 +)))
455 +
456 +{{code language="none"}}
457 +$ pilotcli file upload --help
458 +Usage: pilotcli file upload [OPTIONS] [PATHS]...
459 +
460 + Upload files/folders to a given Project path.
461 +
462 +Options:
463 + -p, --project-path TEXT Project folder path starting from Project code.
464 + (i.e., indoctestproject/user/folder) [required]
465 +
466 + -a, --attribute TEXT File Attribute Template used for annotating files
467 + during upload.
468 +
469 + -t, --tag TEXT Add a tag to the file. This option could be used
470 + multiple times for adding multiple tags.
471 +
472 + -z, --zone TEXT Target Zone (i.e., core/greenroom) [default:
473 + greenroom] [default: greenroom]
474 +
475 + -m, --upload-message TEXT The message used to comment on the purpose of
476 + uploading your processed file [default: ]
477 +
478 + -s, --source-file TEXT The Project path of the source file of your
479 + processed files.
480 +
481 + --zip Upload folder as a compressed zip file.
482 + -td, --thread INTEGER The number of thread for upload a file [default:
483 + 1]
484 +
485 + -o, --output-path TEXT The output path for the manifest file of
486 + resumable upload [default: ./manifest.json]
487 +
488 + --help Show this message and exit.
489 +{{/code}}
490 +
491 +=== Examples ===
492 +
493 +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}}:
494 +
495 +{{code language="none"}}
496 +$ pilotcli file upload ./sample_folder/sample_file1 -p cli/admin
497 +Starting upload of: ./sample_folder/sample_file1
498 +Pre-upload complete.
499 +uploader: admin container_id: 18061 total_size: 1048576 total_chunks: 1 uniq_identifier: e958247c-ce05-48b2-9038-78b774836256-1627498771 resumable_relative_path admin/
500 +
501 +Upload job is finalizing, please wait...
502 +Upload job complete.
503 +All files uploaded successfully.
504 +{{/code}}
505 +
506 +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”:
507 +
508 +{{code language="none"}}
509 +Target folder does not exist. Would you like to create a new folder? [y/N]: y
510 +{{/code}}
511 +
512 +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”:
513 +
514 +
515 +
516 +
517 +
265 265  ----
266 266  
267 267  -
... ... @@ -271,4 +271,5 @@
271 271  
272 272  Copyright © 2023 [[Indoc Research>>url:https://www.indocresearch.org/]].
273 273  
274 -HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].
527 +HealthDataCloud is powered by Pilot technology, a product of [[Indoc Research>>url:https://www.indocresearch.org/]].~{~{/code}}
528 +~)~)~)