John Davis
43500cf656
Fix SA2.0 usage in tool_shed.util.commit_util
2023-10-12 10:57:59 -04:00
John Chilton
698d58eed4
WIP: Implement dry_run in upload API.
2023-09-26 13:46:58 -04:00
John Chilton
5a4e950f08
metadata_generator: Typing has improved to the point that we can annotate this.
2023-09-26 13:46:56 -04:00
John Chilton
55564b67d7
Remove upload_point upload logic in tool shed.
...
Not used by planemo and not tested by any tests.
2023-09-26 13:46:56 -04:00
John Chilton
2fa165781b
Use repository manager to capture more of the upload process.
2023-09-26 13:46:55 -04:00
John Chilton
86d5ab6bb3
Typing for various tool shed utilities.
2023-02-03 13:47:38 -05:00
Nicola Soranzo
14b1730eb2
Combine "as" imports with other "from" imports
2022-06-20 20:06:30 +01:00
Nicola Soranzo
df08de7fbc
Merge branch 'release_22.01' into dev
2022-02-22 14:04:17 +00:00
mvdbeek
907130d772
Fix repository uploads with remove_repo_files_not_in_tar
...
This fixes erroneously deleting the just uploaded files, which otherwise
happens in
```
if full_name not in filenames_in_archive:
files_to_remove.append(full_name)
```
2022-02-21 10:28:41 +01:00
Dannon Baker
623a5e165a
Apply black formatting.
...
Apply isort.
2022-02-03 07:42:20 -05:00
mvdbeek
2d70fa5466
Fix one usage of hg_util.remove_file
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I missed this one in https://github.com/galaxyproject/galaxy/pull/13230
2022-01-26 16:54:45 +01:00
mvdbeek
956ad8143f
Fix adding new files via tarball upload
...
The API of `repo.dirstate.write` has changed and takes a `tr` parameter
now. I've removed the whole fallback since it fails and uses internals
of mercurial that we should probably not be using anyway.
Instead we're going to delete untracked files in hg_util.remove_file()
2022-01-24 11:58:30 +01:00
Dannon Baker
22e7601653
First pass fstring conversion
2021-05-11 13:47:00 -04:00
mvdbeek
aa6e1dcc05
Merge branch 'release_21.01' into dev
2021-04-01 16:52:11 +02:00
mvdbeek
1a12c3df9e
Revert "Fix usage of email_alerts column"
...
This reverts commit c9dc398bf0
2021-03-31 14:02:37 +02:00
mvdbeek
d5607fd65c
Drop legacy-ish use of model.context.current
2021-02-11 16:01:34 +01:00
mvdbeek
c9dc398bf0
Fix usage of email_alerts column
2021-02-04 20:41:21 +01:00
mvdbeek
ccdb6c3f10
Replace usage of mkstemp with NamedTemporaryFile
2020-12-07 22:31:53 +01:00
Dannon Baker
3de5d7ac5d
Merge remote-tracking branch 'upstream/dev' into py3-compat-drop
2020-07-20 11:40:25 -04:00
Nicola Soranzo
ec7107dd42
Fix issues reported by flake8-bugbear and W504 errors
2020-06-30 17:28:24 +01:00
Dannon Baker
e2461e5c5b
Remainder of py3-only feature updates.
2020-06-26 08:26:00 -04:00
Nicola Soranzo
d1863e7b3f
Full Python dependencies update
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using `make update-dependencies`.
Also:
- Drop dependencies on `bz2file` and `ipaddress`
2020-06-24 19:15:57 +01:00
mvdbeek
d304711066
Don't need to pass into Repository.is_new
2020-04-01 16:48:29 +02:00
mvdbeek
3fd4b71390
Avoid repeated calls to get_repo_for_repository
...
by creating the `hg_repo` property on the `Repository` object. This is
only used in the toolshed, meaning we can move get_repo_for_repository
to lib/tool_shed/util/hg_util.py.
`get_repo_for_repository` takes up considerable time when hitting the
`/api/repositories/updates` route in the tool shed. This is hit at
least whice per call
(https://gist.github.com/mvdbeek/6a58b5f4fe9489dd9a15109da74a0c86#file-gistfile1-txt-L7 ),
so making this a cached property should result in a nice speedup.
2020-04-01 11:16:51 +02:00
Nicola Soranzo
f4203ca051
Fix errors reported by flake8 3.6.0
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Ignore W504.
2018-10-24 23:22:19 +01:00
Nicola Soranzo
0ca83cbc7c
Use Mercurial CLI instead of API for remove_file()
2018-06-08 16:08:19 +01:00
Nicola Soranzo
1831dbe3f3
Use Mercurial CLI instead of API for add_changeset()
2018-06-08 16:08:18 +01:00
Nicola Soranzo
6c56467641
Use Mercurial CLI instead of API for commit_changeset()
2018-06-08 16:08:18 +01:00
Nicola Soranzo
17d7c0fb1f
Consolidate use of get_repo_for_repository()
2018-06-05 12:08:29 +01:00
mvdbeek
7df9dce63d
Rename the ToolDataTableManager that deals with repository data to ShedToolDataTableManager to avoid confusion
2017-12-01 14:58:04 +01:00
Nate Coraor
30266c5221
Merge remote-tracking branch 'origin/dev' into job-handler-mules
2017-11-09 13:11:46 -05:00
mvdbeek
cccf79ac5f
Make bz2file dependency conditional on python being below version 3.3
2017-09-05 18:30:25 +02:00
mvdbeek
46c85ffa98
Allow working with pbzip2 compressed files
...
This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html ). The problem was reported by
@alpapan in #4538 and this commit should fix #4538 .
Depends on https://github.com/galaxyproject/starforge/pull/147 for the
bz2file wheel.
2017-09-05 16:54:34 +02:00
Nate Coraor
09feaf6f4d
- Do all logging configuration other than paste fileConfig logging from
...
dictConfig. Default log message format varies by stack.
- Refactor a lot of file extension handling in to galaxy.util.path.
- Simplify and improve config file finding.
- Simplify and improve native app creation.
- Integrate uWSGI argument generation with @jmchilton's improvements to
the startup scripts.
- Fix starting without a config file under uWSGI
2017-09-01 01:08:16 -04:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
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using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Dannon Baker
d43d7aa140
Fix E241, F841 from exception refactoring.
2017-04-14 08:02:33 -04:00
Dannon Baker
c46e36bdee
Overhaul string templating in log.exception statements -- should apply to all logs, eventually.
2017-04-13 15:03:28 -04:00
Dannon Baker
d303cf5ffb
Strip exception strings from being included in log.exception statements across the project.
2017-04-13 14:06:11 -04:00
Dannon Baker
aba34eecda
Update to 'new' except style.
2016-05-16 13:37:53 -04:00
Nate Coraor
3a006766d3
Security fixes for tool shed hg push and capsule/tarball uploads
2016-02-24 11:18:24 -05:00
John Chilton
50e531aa59
Refactor galaxy.datatypes.checkers into galaxy.util.checkers.
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- Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not.
- This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library.
2015-12-17 15:41:06 +00:00
Nate Coraor
97ad53f570
Merge remote-tracking branch 'upstream/dev' into smash_eggs
...
Conflicts:
eggs.ini
lib/galaxy/__init__.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/eggs/__init__.py
lib/galaxy/eggs/dist.py
lib/galaxy/eggs/scramble.py
lib/galaxy/exceptions/__init__.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/check.py
lib/galaxy/model/orm/__init__.py
lib/galaxy/model/tool_shed_install/migrate/check.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/web/framework/helpers/__init__.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/framework/openid_manager.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/reports/controllers/workflows.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/search/repo_search.py
lib/galaxy/webapps/tool_shed/search/tool_search.py
lib/galaxy_ext/metadata/set_metadata.py
lib/pulsar/client/config_util.py
lib/tool_shed/galaxy_install/install_manager.py
lib/tool_shed/galaxy_install/migrate/check.py
lib/tool_shed/grids/admin_grids.py
lib/tool_shed/grids/repository_grids.py
lib/tool_shed/repository_types/repository_suite_definition.py
lib/tool_shed/repository_types/tool_dependency_definition.py
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
lib/tool_shed/scripts/check_repositories_for_functional_tests.py
lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
lib/tool_shed/util/basic_util.py
lib/tool_shed/util/encoding_util.py
lib/tool_shed/util/hg_util.py
scripts/check_eggs.py
scripts/dist-scramble.py
scripts/fetch_eggs.py
scripts/make_egg_packager.py
scripts/scramble.py
scripts/scramble/lib/scramble_lib.py
scripts/scramble/scripts/DRMAA_python-macosx.py
scripts/scramble/scripts/DRMAA_python-solaris.py
scripts/scramble/scripts/DRMAA_python.py
scripts/scramble/scripts/MySQL_python-solaris.py
scripts/scramble/scripts/MySQL_python.py
scripts/scramble/scripts/PyRods.py
scripts/scramble/scripts/bx_python-solaris.py
scripts/scramble/scripts/generic.py
scripts/scramble/scripts/pbs_python.py
scripts/scramble/scripts/psycopg2-linux.py
scripts/scramble/scripts/psycopg2-macosx.py
scripts/scramble/scripts/psycopg2-solaris.py
scripts/scramble/scripts/psycopg2.py
scripts/scramble/scripts/pysam-solaris.py
scripts/scramble/scripts/pysqlite.py
scripts/test_dist_egg.py
2015-09-21 15:02:47 -04:00
Nicola Soranzo
df808d0c1e
flake8 lib/tool_shed/ .
...
Also:
- use sys.exit() instead of exit()
- fix sys.path manipulations.
2015-09-09 19:57:41 +01:00
Dannon Baker
b639bc0638
Correct bug in incorrect usage of log.exception, pep8 commit_util
2015-03-04 02:08:10 -05:00
Dannon Baker
6102edf5ba
Add missing bz2 import in toolshed.commit_util
2015-03-04 02:05:47 -05:00
Björn Grüning
6b7634011e
Add planemo test files to the tool shed upload blacklist.
2015-01-09 19:02:42 +00:00
Greg Von Kuster
0760ab25ea
Add a ToolDataTableManager for managing tool data tables in the Tool Shed.
2014-07-22 15:12:40 -04:00
Greg Von Kuster
38c0d78979
Move 2 Tool Shed utility functions into the middleware hg class.
2014-06-22 08:00:57 -04:00
Greg Von Kuster
88d6c68201
Add a dependency manager with tag attribute handler classes to manage the process of populating and unpopulating the toolshed and changeset_revision attributes for <repository> tag sets when uploading and importing / exporting repositories from the tool shed.
2014-06-21 14:15:20 -04:00
John Davis