John Chilton
044eb906cf
Lint and spelling fixes.
2020-12-22 11:18:31 +01:00
John Chilton
16951e4176
Add FastAPI roles controller, de-duplicate app initialization for FastAPI.
2020-12-22 11:18:31 +01:00
mvdbeek
e865741092
Adjust galaxy-main script so we can import from it for easy app setup
2020-12-22 11:18:00 +01:00
Nicola Soranzo
e40e5aef7e
Upgrade syntax using pyupgrade --py36-plus
2020-11-18 16:16:46 +00:00
Sergey Golitsynskiy
31b908226a
Set uwsgi's honor-stdin when in debug mode
2020-10-28 14:08:25 -04:00
Dannon Baker
434d406bde
Cleanout communication server.
...
I don't think anyone's actively using this anymore, and most
communication has moved to (also embeddable) things like Gitter, etc.
2020-10-22 09:58:34 -04:00
mvdbeek
36d6eaa9e8
Lint release_diff script
2020-10-14 10:43:04 +02:00
Dannon
8959aa9213
Merge pull request #10258 from hexylena/release-diff
...
Add script to diff two release config files.
2020-10-09 16:39:47 -04:00
Marius van den Beek
65718c9d30
Merge pull request #10350 from ic4f/dev_missing_indexes_script
...
Script for finding missing db indexes
2020-10-08 16:24:08 +02:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
Sergey Golitsynskiy and Marius van den Beek
574fa4cb1f
Let get_config() handle env override
...
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2020-10-04 23:25:23 -04:00
Sergey Golitsynskiy
f27b4e50f6
Add github workflow; env var to override db uri
2020-10-03 02:26:40 -04:00
Sergey Golitsynskiy
20c7cdb2cb
Rename missing_index > index_tuple
2020-10-03 02:26:40 -04:00
Sergey Golitsynskiy and Nicola Soranzo
b9093e33da
Update scripts/check_model.py
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2020-10-03 02:26:40 -04:00
Sergey Golitsynskiy and Nicola Soranzo
7719f53bca
Update scripts/check_model.py
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2020-10-03 02:26:40 -04:00
Sergey Golitsynskiy
2dbfdce295
Add script + wrapper
2020-10-03 02:26:40 -04:00
Helena Rasche
483b21d906
remove trailing commas
2020-09-22 12:10:04 +02:00
Helena Rasche
cac94a0f24
output
2020-09-22 12:06:06 +02:00
Helena Rasche
01a2aa4bd9
small bug
2020-09-22 12:01:07 +02:00
Helena Rasche
721ad64a61
improvements
2020-09-22 11:59:36 +02:00
Helena Rasche
64892baf5c
add new files
2020-09-22 11:46:29 +02:00
Helena Rasche
6a1edfdb35
make it loop over yml
2020-09-22 11:39:35 +02:00
Helena Rasche
f7f44371f6
Add script to diff two release config files.
2020-09-22 11:11:30 +02:00
Kaivan Kamali
eb6129a3ac
Another import re-ordering :(
2020-09-11 16:49:24 -04:00
Kaivan Kamali
1894248a5f
Sorted imports
2020-09-11 16:05:55 -04:00
Kaivan Kamali
5b77b57e28
Fixed import orders
2020-09-11 11:44:00 -04:00
Kaivan Kamali
1f12c7e42c
Made some changes based on code review feedback.
2020-09-08 12:17:17 -04:00
Kaivan Kamali
9191f20d42
Fixed an issue in copy folders to irods
2020-09-01 13:16:01 -04:00
Kaivan Kamali
3b342389d8
Removed some prit statements.
2020-09-01 12:32:30 -04:00
Kaivan Kamali
e00e4fd127
Tape resource used based on a cuttoff date
2020-09-01 12:00:56 -04:00
Kaivan Kamali
12f4529f70
irods resource selected based on the last time the dataset was used in a job as input or output. Any dataset used prior to a cuttoff date will be sent to tape resource. Otherewise, the dataset is sent to the regular (non-tape) resource.
2020-08-31 14:17:24 -04:00
Kaivan Kamali
244fc677f4
Initial vesion of SQL statement to get the last usage time of all datasets.
2020-08-28 16:19:30 -04:00
Kaivan Kamali
d88e955e8a
Fixed a typo
2020-08-27 09:48:43 -04:00
Kaivan Kamali
fcf5a997bf
Revised help message (added list of packages to install, needed to run the script).
2020-08-26 13:02:33 -04:00
Kaivan Kamali
64dec6390f
Minor revision to documentation
2020-08-26 10:54:27 -04:00
Kaivan Kamali
220c97850e
Cleaned up script, added documentation to help.
2020-08-26 10:47:12 -04:00
Kaivan Kamali
7f811424ae
Removing redundant script. Minor change in copy script
2020-08-26 09:07:16 -04:00
Kaivan Kamali
35d4e77015
Merged both scripts into one. The same script does the copy or checksum/delete depending on a new input parmater. Will delete the second script later.
2020-08-25 16:42:33 -04:00
Kaivan Kamali
08b9ea521c
Fixed a bug
2020-08-25 15:40:15 -04:00
Kaivan Kamali
43a3cadb80
Now comparing the checksum with irods checksum for all files in extra folder
2020-08-25 14:39:25 -04:00
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
John Chilton