mvdbeek
2d70fa5466
Fix one usage of hg_util.remove_file
...
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.
...
- 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
Greg Von Kuster
e17ad656ac
Fix for handling complex repository dependency definitions that contain recipes that include <package> tag sets that define dependencies needed only for compiling the dependent package.
2014-06-19 17:46:04 -04:00
Greg Von Kuster
4297b7054a
Eliminate the use of the Galaxy web transaction object in Tool Shed utility functions related to importing a repository capsule into a Tool Shed and move som hg related functions from the commit_util module to the hg_util module.
2014-06-18 15:28:20 -04:00
Greg Von Kuster
390d05bbd1
Eliminate the Tool Shed's td_common_util.py module by moving the functions to appropriate classes.
2014-05-28 15:49:02 -04:00
Greg Von Kuster
b2f3d6a551
Continued down-sizing of the Tool Shed's shed_util_common module by moving certain functions to more appropriate locations. Some fixes for adding and removing entries to the Tool Shed's repository registry.
2014-05-28 11:17:50 -04:00
Greg Von Kuster
ec1688d1da
Clarify problematic members of tar archives being uploaded to Tool Shed repositories.
2014-05-27 11:13:05 -04:00
Greg Von Kuster
7238ba2304
Use the new hg_util.get_repo_for_repository() function to retrieve a mercurial repo for a repository.
2014-05-21 12:22:16 -04:00
Greg Von Kuster
f6b05fea77
Change function signatures for several utility functions that used to require trans but now only need app.
2014-05-21 09:55:12 -04:00
Greg Von Kuster
f4fee7d3cb
Add a repository registry to the Tool Shed to keep in-memory information about repositories. This will significantly improve some page rendering in the tool shed, specifically the current main Categories splash page. This registry will provide filtered certification information for the planned Tool Shed splash page which will be rendered with Javascript. The Tool Shed's install and test framework still needs to be enhanced to update this registry during install and test runs.
2014-05-20 17:18:14 -04:00
Trevor Wennblom
268dae876e
selected_file -> repo_file
2014-04-29 19:24:47 -05:00
Greg Von Kuster
8bce650dda
Add a new tool shed mercurial utility module named hg_util.py and begin to extract hg related utility functions out of the shed_util_common.py module. Enhance the functions that display the mercurial changeset rev and hash string to display one or the other or both. Display only the rev and not the hash string on the prominent grids in the tool shed, but continue to display the hash string on admin grids.
2014-04-10 17:11:01 -04:00
mvdbeek