Dannon Baker
623a5e165a
Apply black formatting.
...
Apply isort.
2022-02-03 07:42:20 -05:00
Nicola Soranzo
7b67cea7d0
Remove unnecessary list creations
2021-11-29 16:33:05 +00:00
Nicola Soranzo
90a729e431
New pyupgrade fixes
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Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
2021-10-24 12:10:34 +01:00
Nicola Soranzo
d26b3d9848
Fix all E203, E741 and W504 flake8 errors
2021-01-18 10:35:41 +00:00
Nicola Soranzo
452aba9ee3
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
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
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
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