Rc/staging release 20240221

[colorzzr]

Summary

staging release 20240221:

• optimize resumable upload logic:
  • update cli logic to allow resume an upload with different chuck size @hugoantunes
  • change the log name to resumable_upload_log.log @colorzzr
• add new command file metadata to download metadata/tags/attributes of a specific file @colorzzr
• add proper handler to invalid token error @colorzzr
• update logic of configuration@colorzzr:
  • unify configuration for multi-tenancy
  • make config_path as env variable for nextflow pipeline
• update cli logic to adopt project folder implementation @colorzzr
• add new command file move to allow moving and renaming a file or folder @colorzzr

JIRA Issues

(What JIRA issues this merge request is related to)

Type of Change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update
• Refactor or reformatting

Testing

Are there any new or updated tests to validate the changes?

• Yes
• No

Test Directions

(Additional instructions for how to run tests or validate functionality if not covered by unit tests)

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
__init__.py	0	0	100%
pilotcli.py	0	31	0%	5, 7–8, 10–14, 17–21, 23–28, 31–39, 42–44
commands
__init__.py	0	0	100%
container_registry.py	0	19	59%	16, 22–24, 31–33, 41–44, 50–53, 62–65
dataset.py	0	48	44%	19, 36–38, 41–48, 50–60, 78–80, 83–91, 93–103, 123, 127
entry_point.py	0	10	85%	39, 45, 89–91, 93–97
file.py	0	41	83%	40, 137, 146–148, 152, 157, 160–162, 179–180, 222, 307–314, 316, 318, 332–338, 340, 369, 371, 374, 420, 423, 440–442, 448–449
project.py	0	1	97%	17
user.py	0	6	85%	23, 40, 48, 56, 72–73
configs
__init__.py	0	0	100%
app_config.py	0	0	100%
config.py	0	0	100%
user_config.py	0	17	84%	61, 70, 114, 124, 131, 135, 139, 143, 147, 151, 155, 159, 163, 167, 171, 175, 179
models
__init__.py	0	0	100%
enums.py	0	0	100%
service_meta_class.py	0	1	80%	9
singleton.py	0	0	100%
upload_form.py	0	6	25%	30, 42–46
resources
custom_error.py	0	0	100%
custom_help.py	0	0	100%
services
__init__.py	0	0	100%
services/container_registry_manager
container_registry_manager.py	0	108	17%	19–20, 23–26, 29–33, 36–44, 48–60, 62–64, 68–82, 84–86, 90–99, 101–103, 107–110, 125–136, 140–143, 147–162, 164, 166–169
services/crypto
__init__.py	0	0	100%
crypto.py	0	19	40%	35, 43–47, 49, 59–61, 69–75, 77, 79
services/dataset_manager
dataset_detail.py	0	23	70%	42, 44, 61, 68–73, 75–77, 79–88, 90
dataset_download.py	0	19	83%	56, 72–73, 84, 96, 98–99, 101–102, 104, 106–108, 116–119, 153, 165
dataset_list.py	0	8	78%	37, 43–46, 48–50
model.py	0	0	100%
services/file_manager
__init__.py	0	0	100%
file_list.py	0	17	75%	29, 54, 56, 70–72, 80–83, 85, 91–96
file_manifests.py	0	95	25%	19–24, 39–43, 47–48, 51–59, 61, 65–68, 71–75, 77, 81–82, 85–87, 91–92, 95–102, 104, 107, 109–110, 112–113, 115–118, 123–129, 134–139, 142–148, 150–152, 155–161, 163–165, 167–170
file_tag.py	0	39	31%	23, 27–31, 33, 36–48, 50–52, 54–55, 59–61, 64–68, 70–73, 75–76
services/file_manager/file_download
__init__.py	0	0	100%
download_client.py	0	174	23%	44–45, 47–53, 56–57, 59–60, 69, 71–72, 76–79, 86, 91–94, 96, 98–106, 108, 110, 114–119, 121, 124–125, 128–130, 132–134, 136–137, 139–141, 145–153, 156–161, 165–174, 182–184, 186–193, 195–199, 204–214, 216–217, 220–221, 226–227, 231–236, 240–241, 244–246, 248–259, 263–266, 269–273, 275–277, 279–281, 283–284, 286, 290–292, 294–307, 309
model.py	0	1	87%	15
services/file_manager/file_metadata
__init__.py	0	0	100%
file_metadata_client.py	0	3	95%	97–99
services/file_manager/file_move
__init__.py	0	0	100%
file_move_client.py	0	5	93%	79–81, 83, 110
services/file_manager/file_upload
__init__.py	0	0	100%
exception.py	0	1	75%	10
file_upload.py	0	28	84%	35–42, 99–101, 113, 144–145, 149, 154, 191, 211–213, 254–255, 257–259, 333, 336, 340
models.py	0	5	91%	24, 44, 150–152
upload_client.py	0	77	60%	101–104, 207–209, 223–229, 231–235, 237–249, 251, 295, 298, 302, 304–306, 308–311, 315–319, 321, 325, 327, 329, 331, 350, 380–381, 386, 390–393, 397, 413, 415–417, 424, 429–430, 432, 434–435, 437–440, 442
upload_validator.py	0	21	56%	29–31, 34–39, 42–48, 51–52, 57, 59, 61
services/logger_services
__init__.py	0	0	100%
log_functions.py	0	0	100%
services/output_manager
__init__.py	0	0	100%
error_handler.py	0	0	100%
help_page.py	0	0	100%
message_handler.py	0	57	70%	23, 45, 50, 65–67, 72, 82, 87, 100, 105, 112, 117, 122, 126, 142, 177, 187, 196, 214, 224, 243, 265–276, 287–292, 294–300, 311, 315–316, 320–321, 323–324, 328, 332, 336
services/project_manager
__init__.py	0	0	100%
project.py	0	8	78%	38, 44–47, 49–51
services/user_authentication
__init__.py	0	0	100%
decorator.py	0	2	93%	27, 30
token_manager.py	0	9	86%	26, 41–42, 73, 76, 91, 96, 100, 105
user_login_logout.py	0	42	66%	30–31, 41, 122, 126–132, 134–136, 140–141, 145–152, 154–156, 160–161, 168–173, 175–177, 181–184
utils
__init__.py	0	0	100%
aggregated.py	0	40	68%	50, 62, 102, 115–117, 119–120, 127–128, 130, 134–137, 139–140, 154–161, 163–164, 168–175, 177–179, 194–195
TOTAL	3079	981	68%