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cr-connect-workflow
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1598 Commits

Author SHA1 Message Date
mike cullerton c6b1fd4e52 Fix for failing tests. Q_COMPLETE is no longer a column in the PB Mock study table. 2021-04-05 13:18:56 -04:00
mike cullerton 61f37ff894 Changed the order of imports so I could debug a failing test 2021-04-05 13:16:43 -04:00
mike cullerton f0f5cff8d7 Added some checks to do_task to look for valid irb_doc_code and whether or not we found a file 
Added code for do_task_validate
 2021-04-05 13:15:09 -04:00
mike cullerton 9317e49e65 Merge branch 'dev' into delete-uploaded-file-script-283 2021-04-05 10:40:33 -04:00
Kelly McDonald 9f66a938f2 Update pip 2021-04-05 10:19:29 -04:00
mike cullerton d81497f8cb Test and workflow for new script to delete IRB documents 2021-04-05 08:55:41 -04:00
mike cullerton 0eb6291740 Script to delete an IRB document. Takes an `irb_document` argument. 
Deletes all files associated with the workflow with that IRB document code
 2021-04-05 08:55:02 -04:00
Dan Funk 7ef43fd477
Merge pull request #279 from sartography/263-optimize-dashboard 
263 optimize dashboard
 2021-04-02 18:54:56 -04:00
Dan 9dca220089 updating package.lock 2021-04-02 17:58:43 -04:00
Dan dcb4e7b736 fixing an error by taking a bit of the magic out of one of Mike's regex hinting tools. I figure the hint is still good, and a little less bittle, and all the information is already there if people need to dig. 2021-04-02 17:58:27 -04:00
Dan 3ad3a086ba Merge branch 'dev' into 263-optimize-dashboard 2021-04-02 17:12:02 -04:00
Dan 8edcb4fbc0 Merge remote-tracking branch 'origin/dev' into 263-optimize-dashboard 2021-04-02 17:11:21 -04:00
Dan Funk c7a07af88b
Merge pull request #276 from sartography/dependabot/pip/lxml-4.6.3 
Bump lxml from 4.6.2 to 4.6.3
 2021-04-02 17:10:53 -04:00
Dan 2100f27976 fixing the api.yml file which was starting to throw errors when updating the libraries. 
Seems that sqlalchemy now has a hard time incrementing sequences, so putting in a fix for this.
Upgrading many of our libraries, to avoid any disconnects as we try to handle security patches from these automated bumps.
 2021-04-02 17:10:05 -04:00
Dan 51b8b4f52c Merge remote-tracking branch 'origin/dev' into dependabot/pip/lxml-4.6.3 2021-04-02 15:11:09 -04:00
Dan 33a87f6c35 Merge branch 'dev' into dependabot/pip/lxml-4.6.3 2021-04-02 14:55:59 -04:00
Dan Funk 6083cacc4a
Merge pull request #268 from sartography/dependabot/pip/deploy/urllib3-1.26.3 
Bump urllib3 from 1.26.2 to 1.26.3 in /deploy
 2021-04-02 14:55:34 -04:00
Dan Funk ae1e847d73
Merge pull request #278 from sartography/dependabot/pip/deploy/pygments-2.7.4 
Bump pygments from 2.7.2 to 2.7.4 in /deploy
 2021-04-02 14:35:36 -04:00
Dan cfa8003173 Merge branch 'dev' into dependabot/pip/deploy/urllib3-1.26.3 2021-04-02 14:32:03 -04:00
mike cullerton d7894f43b6 These changes relate to changes in PB Mock ticket 273, where we removed Q_COMPLETE as a column in the PB Mock Study table. It is now a relationship. 
Here, we removed Q_COMPLETE from ProtocolBuilderStudy and ProtocolBuilderStudySchema definitions to accommodate the PB Mock changes.

***This push will need to be coordinated with ticket 273***
 2021-04-02 12:01:00 -04:00
Kelly McDonald 116bf5e7aa Merge branch 'dev' into 263-optimize-dashboard 
# Conflicts:
#	crc/services/study_service.py
 2021-03-31 10:20:33 -04:00
Kelly McDonald 9084866015 Update error message - it may be that we should spend a bit and see if we can make the Box error 2021-03-31 10:17:08 -04:00
Kelly McDonald 60f5be1aef Check in - pending change from @cullerton 2021-03-30 12:10:49 -04:00
dependabot[bot] 0feee28ba1
Bump pygments from 2.7.2 to 2.7.4 in /deploy 
Bumps [pygments](https://github.com/pygments/pygments) from 2.7.2 to 2.7.4.
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](https://github.com/pygments/pygments/compare/2.7.2...2.7.4)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-29 23:39:17 +00:00
Dan Funk b5d4df595f
Merge pull request #271 from sartography/master-workflow-status-messages-222 
Master workflow status messages 222
 2021-03-26 20:52:24 -04:00
Dan ded11ddd82 fixing a code smell 2021-03-26 20:25:34 -04:00
Dan 14f3c5b413 Merge branch 'dependabot/pip/lxml-4.6.3' of github.com:sartography/cr-connect-workflow into dependabot/pip/lxml-4.6.3 2021-03-26 20:07:48 -04:00
dependabot[bot] a28f1f3750
Bump lxml from 4.6.2 to 4.6.3 
Bumps [lxml](https://github.com/lxml/lxml) from 4.6.2 to 4.6.3.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.6.2...lxml-4.6.3)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-26 23:56:10 +00:00
Dan 00bdeb17c0 Merge remote-tracking branch 'origin/dev' into dependabot/pip/lxml-4.6.3 2021-03-26 19:55:46 -04:00
Dan Funk 8176d7e2b6
Merge pull request #275 from sartography/dependabot/pip/deploy/lxml-4.6.3 
Bump lxml from 4.6.2 to 4.6.3 in /deploy
 2021-03-26 19:50:43 -04:00
Dan Funk e79e810ae1
Merge pull request #273 from sartography/modify-email-template-215 
Change location of `CR Connect` string. Move it left, closer to the logo
 2021-03-26 19:50:16 -04:00
Dan Funk 123ec50912
Merge pull request #272 from sartography/infinite-validations-262 
Infinite validations 262
 2021-03-26 19:49:42 -04:00
Dan b64b52e7cb Assure that we properly return the new status message over the api calls. 2021-03-26 19:47:31 -04:00
Dan ac4877fecf Merge remote-tracking branch 'origin/dev' into master-workflow-status-messages-222 2021-03-26 17:47:57 -04:00
dependabot[bot] 02995da699
Bump lxml from 4.6.2 to 4.6.3 
Bumps [lxml](https://github.com/lxml/lxml) from 4.6.2 to 4.6.3.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.6.2...lxml-4.6.3)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-26 21:47:31 +00:00
dependabot[bot] 115f9db5d9
Bump lxml from 4.6.2 to 4.6.3 in /deploy 
Bumps [lxml](https://github.com/lxml/lxml) from 4.6.2 to 4.6.3.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.6.2...lxml-4.6.3)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-26 21:42:47 +00:00
Dan Funk 89077c4e59
Merge pull request #270 from sartography/dependabot/pip/deploy/jinja2-2.11.3 
Bump jinja2 from 2.11.2 to 2.11.3 in /deploy
 2021-03-26 17:42:33 -04:00
Dan Funk fbd516bdb9
Merge pull request #274 from sartography/dependabot/pip/deploy/pyyaml-5.4 
Bump pyyaml from 5.3.1 to 5.4 in /deploy
 2021-03-26 17:42:20 -04:00
dependabot[bot] 6334b0afa0
Bump pyyaml from 5.3.1 to 5.4 in /deploy 
Bumps [pyyaml](https://github.com/yaml/pyyaml) from 5.3.1 to 5.4.
- [Release notes](https://github.com/yaml/pyyaml/releases)
- [Changelog](https://github.com/yaml/pyyaml/blob/master/CHANGES)
- [Commits](https://github.com/yaml/pyyaml/compare/5.3.1...5.4)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-25 23:46:10 +00:00
mike cullerton d9bf2a8a81 Change location of `CR Connect` string. Move it left, closer to the logo 2021-03-23 13:12:13 -04:00
Kelly McDonald f1ca44a0e1 Add primitive cache on the fileservice is_review, halves the time of loading the list on the primary dashboard 2021-03-23 10:17:48 -04:00
mike cullerton 3ee8109535 Tests for the changes to master workflow status dictionary 
Test for each valid WorkflowState
Test for all three failure states; not in status, not a dictionary, not a valid state.
 2021-03-22 17:52:14 -04:00
mike cullerton a201e49d21 The master workflow now generates a dictionary of dictionaries, rather than a dictionary of strings. 
Each entry in status is a dictionary with 'status' and 'message' keys.
We updated the StudyService._update_status_of_workflow_meta method to accommodate the master workflow changes.

Changed the order of some if statements so we move forward while we have good data, and run all the error states at the end.
Added some comments to explain the cascading if statements

We changed the names of private methods to begin with one underscore, so they work in the test environment.
Changed  some internal calls to accommodate the underscore change.
 2021-03-22 17:46:39 -04:00
dependabot[bot] 24b6b5c7e7
Bump jinja2 from 2.11.2 to 2.11.3 in /deploy 
Bumps [jinja2](https://github.com/pallets/jinja) from 2.11.2 to 2.11.3.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/master/CHANGES.rst)
- [Commits](https://github.com/pallets/jinja/compare/2.11.2...2.11.3)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-20 04:01:34 +00:00
dependabot[bot] 491a7de879
Bump urllib3 from 1.26.2 to 1.26.3 in /deploy 
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.2 to 1.26.3.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/1.26.2...1.26.3)

Signed-off-by: dependabot[bot] <support@github.com>
 2021-03-19 19:54:34 +00:00
Dan Funk 6ab98c1dee
Merge pull request #267 from sartography/get-study-associates-validation-242 
The `do_task_validate_only` method in the `get_study_associates` scri…
 2021-03-19 15:41:46 -04:00
Dan Funk 544f4a4418
Merge pull request #266 from sartography/study-associated-email-207-223 
We now perform an LDAP lookup for the associated user email addresses…
 2021-03-19 15:40:31 -04:00
mike cullerton 47ff29e3ab Added a test for dictionary output from a decision table. 
Will need dictionary output for master workflow status messages.
 2021-03-18 12:25:27 -04:00
mike cullerton c4b52f85af Test and workflow for testing infinite loop code. 2021-03-17 14:52:50 -04:00
mike cullerton 938079cf59 Lowered count ceiling to 100, from 1000. This significantly increased validation time, from about 3 minutes to about 10 seconds. 
Changed ApiError call to from_task, instead of from_workflow_exception.
 2021-03-17 14:52:19 -04:00