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1508 Commits
Author SHA1 Message Date
Kaivan Kamali aced6baee3 Broke the script into two scripts: One script copies files from disk to irods, and another script verifies the checksum, then updated the object store id in dataset table and deletes the file on disk. 2020-08-25 09:17:59 -04:00
Kaivan Kamali 063588a997 Irods calculates checksum now when a file is added to it. Also, calculating the checksum locally, so can comapre to irods checksum after getting the file. 2020-08-24 15:31:06 -04:00
Kaivan Kamali 2e267ef55b Formatted the json file 2020-08-21 16:32:52 -04:00
Kaivan Kamali d96fe5db10 Revised script so that it now updates dataset table's object_store_id after file is copied to irods. Added script input json files. 2020-08-21 16:31:38 -04:00
Kaivan Kamali 0e00d24c1d Added function to display the required input parameters, incase caller does not provide all of them. 2020-08-21 14:20:58 -04:00
Kaivan Kamali 2b8aad8ccf irods and DB connection info passed in as json files 2020-08-21 14:06:13 -04:00
Kaivan Kamali 2cc093e938 object store info pased in as a json file 2020-08-21 13:42:54 -04:00
Kaivan Kamali 4ec2c98a1c iput works now 2020-08-20 18:54:19 -04:00
Kaivan Kamali b77e75d79c iputalmost works -- debugging 2020-08-20 16:41:43 -04:00
Kaivan Kamali 9fe92f8388 Updated dynamic sql per code review feedback. 2020-08-20 11:54:19 -04:00
Kaivan Kamali 1dec4af804 python irods client successfully puts filer in irods. Added partial capability to parse input parameters. 2020-08-20 11:16:23 -04:00
Kaivan Kamali 672eafad4d Using a single SQL statement to get all data instead of multiple SQL statements to get data one row at a time. 2020-08-19 14:28:49 -04:00
Kaivan Kamali 3193b51065 Applied some of the code review changes. 2020-08-19 13:26:43 -04:00
Kaivan Kamali a3699d05c2 Added wrapper method to call the method that adds file to irods in a loop for a range of object IDs. Also pulled out the DB connection object into the wrapper to no create/destroy it for every call. 2020-08-18 16:11:56 -04:00
Kaivan Kamali ed2d7633a5 Made revision based on self review. 2020-08-18 14:46:01 -04:00
Kaivan Kamali d5f26a72d3 More revision to script copying files to irods 2020-08-18 09:57:30 -04:00
Dannon Baker 0538f3bcf1 Update static-safe mappings to match new layout, rebuild client. 2020-08-11 10:26:06 -04:00
Dannon Baker 3de5d7ac5d Merge remote-tracking branch 'upstream/dev' into py3-compat-drop 2020-07-20 11:40:25 -04:00
John Chilton 2c2ed3f288 Decouple API and Selenium tests from galaxy-test-driver (and the whole app!) 
I've been refactoring toward this for at least half a decade. Being able to pip install the API and Selenium tests without bringing in the whole app is important to make them usable outside the context of the app - for testing remote, running servers for instance.

If galaxy-test-driver is available the test cases will still spawn a Galaxy instance if needed, but this is not longer required for import or use.
 2020-07-06 13:57:48 -04:00
Dannon Baker 8d17fafa4e Missed one new style class here. 2020-06-26 08:20:49 -04:00
Nicola Soranzo 7ded4170ce Merge branch 'release_20.05' into dev 2020-06-23 10:25:25 +01:00
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Dannon Baker 0c3a81b0d2 Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-06-17 12:05:55 -04:00
Martin Cech 3bed89490e Merge pull request #9838 from galaxyproject/20.05_release_notes 
Release notes for 20.05
 2020-06-16 18:21:33 +02:00
Nicola Soranzo a3c423873d Merge branch 'release_20.05' into dev 2020-06-05 10:22:05 +01:00
Nicola Soranzo 089e11ce65 Small refactor to `validate_password()`. Add back deleted line 
Follow-up on https://github.com/galaxyproject/galaxy/pull/9587
 2020-06-04 18:52:59 +01:00
Helena Rasche bb903c60cf shorten url 2020-06-03 13:54:48 +02:00
Helena Rasche 039a3d0233 And ensure not forgotten in future 2020-06-03 12:10:00 +02:00
mvdbeek 81abd93658 Merge branch 'release_20.05' into dev 2020-06-02 12:30:41 +02:00
Marius van den Beek 0fe6be60ea Merge pull request #9587 from nuwang/set_password_if_null 
[20.05] Assign random password in user manager if none specified
 2020-06-02 12:04:50 +02:00
Matthias Bernt d22fe1f3b4 release process: merge IUC/devteam CI and PR update 2020-05-26 11:31:57 +02:00
Nuwan Goonasekera c9f29aa888 Refactor toolshed password validation 2020-05-25 23:39:52 +05:30
Matthias Bernt 2b0e419a59 switch branch of IUC CI earlier in release process 2020-05-22 11:33:30 +02:00
Nate Coraor 8cf33be81f Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-05-13 10:56:53 -04:00
mvdbeek f219fa6d82 Switch to lxml for xml parsing 2020-05-12 15:00:27 +02:00
mvdbeek 6a0653affc Skip check for branch protection 2020-05-05 22:45:39 +02:00
John Chilton 705669a783 Merge pull request #9610 from mvdbeek/store_tool_source 
Startup speedups (XML doc cache, delay non-essential tool param parsing & indexing)
 2020-04-27 14:54:32 -04:00
Nicola Soranzo 7118b4fa11 Hide "python: not found" error when Python 2 is not installed 2020-04-27 02:32:06 +01:00
mvdbeek 51549d0391 Only build toolbox index for webapps, delay until after startup 2020-04-25 20:40:26 +02:00
Nicola Soranzo b481e0c2c8 Merge pull request #9637 from mvdbeek/fix_issue_creation 2020-04-21 13:01:25 +01:00
mvdbeek 3c0f22d451 Use pygithub for issue creation 2020-04-21 12:55:39 +02:00
mvdbeek a36b4486bf Merge branch 'release_20.01' into dev 2020-03-26 10:51:46 +01:00
mvdbeek 7105de2fb0 Fix import order 2020-03-21 13:27:53 +01:00
mvdbeek 159a94b95d Move index logic to lib.tool_shed.util.shed_index 
Since we need the index for browsing repos in the new client
we should incrementally build the index with every repo update.
Having this in tool_shed will make re-use easier.
 2020-03-21 13:27:53 +01:00
mvdbeek afce65249f Implement incremental indexing 2020-03-21 13:27:53 +01:00
mvdbeek 2bb2f0989f Make build_ts_whoosh_index.py py3 compatible 2020-03-21 13:27:53 +01:00
Nicola Soranzo 56450de8a9 Print help if no action is selected 2020-03-05 13:26:28 +01:00
Dannon Baker e183cc1f7b Merge remote-tracking branch 'upstream/release_20.01' into dev 2020-02-29 09:55:46 -05:00
Nicola Soranzo 088653e2cb Add missing pygithub dev-requirement 
Follow-up to https://github.com/galaxyproject/galaxy/pull/9271

Also move GitHub client initialisation and check for `requests` closer to where they
are used to prevent error messages when running `make`.
 2020-02-29 01:55:05 +00:00
mvdbeek a02480f35b Merge branch 'release_20.01' into dev 2020-02-27 17:51:34 +01:00