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Commit Graph
88 Commits
Author SHA1 Message Date
mvdbeek bab12662a9 Drop old sqlalchemy patterns 2021-12-16 12:30:49 +01:00
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
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
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
Nuwan Goonasekera c9f29aa888 Refactor toolshed password validation 2020-05-25 23:39:52 +05:30
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 f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
Nicola Soranzo 2fcbe0afa3 changectx() method was dropped in mercurial 4.6 
in favour of `__getitem__()`.
 2019-12-05 18:31:26 +00:00
Martin Cech 5a18a486bd when building ts index log parse errors as debug level 2019-11-22 17:27:07 -05:00
Nicola Soranzo 72186b40a1 Merge branch 'release_19.09' into dev 2019-11-19 23:30:02 +01:00
Martin CechandMarius van den Beek fc8b832888 Apply suggestions from code review @mvdbeek 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-11-19 09:32:15 -05:00
Martin Cech 0c075f73b4 set logging level according to the argument 
also report the run summary as 'info' level
 2019-11-18 12:05:02 -05:00
Martin Cech 5c495d6514 refactor logging 2019-11-18 11:25:47 -05:00
Martin Cech 19c56c725b add exec timer 2019-11-18 09:56:15 -05:00
Martin Cech c9d9009299 refactor and modernize toolshed search indexes build script 
mainly so it can read yml config
 2019-11-14 18:07:06 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Martin Cech a48c7420d7 Merge pull request #8956 from jmchilton/remove_ts_api 
Remove tool shed API examples.
 2019-11-11 10:41:22 -05:00
Nicola Soranzo 6b1bacc2b8 Merge pull request #8957 from jmchilton/remove_legacy_shed 
Remove script for migrating tools to the tool shed...
 2019-11-11 10:54:27 +00:00
John Chilton d4196b61a4 Remove tool shed API examples. 
These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html), and we should be encouraging TS interactions to be done through Planemo and not raw API calls.

Excluding scripts used by bootstrap.
 2019-11-11 02:55:26 -05:00
John Chilton a27beb0fd8 Remove script for migrating tools to the tool shed... 
from an older tool shed? I completely forgot there even was an older tool shed.
 2019-11-11 02:50:12 -05:00
John Chilton fbe21f94bf Remove tool dependency scripts. 2019-11-11 02:35:31 -05:00
Nicola Soranzo 85f7f91206 Fix script shebangs 
Improve tools.
 2019-10-26 20:20:01 +01:00
John Chilton 4287bb787f Merge pull request #8621 from martenson/ux-ts-installer 
[19.09] allow the TS search API to bypass wildcard search
 2019-09-12 13:35:01 -04:00
Martin Cech 99ec4ecf75 adjust indexing and searching of special keywords to be case-insensitive 2019-09-11 16:39:14 -04:00
Martin Cech 02a3342bd6 regenerate ts search indexes in tmp directory 2019-09-10 16:06:21 -04:00
Sergey Golitsynskiy 1694b79185 Update import paths for loader_directory 2019-07-06 00:52:45 +02:00
Nicola Soranzo 90a6c6d46b Fix issues reported by ShellCheck 2019-06-13 12:53:26 +01:00
Martin Cech d6a26e1ba5 enhance repository search API capabilities 
* include categories as keywords for repository index
* allow filtering on category/owner using github-like wildards "category:name"
* only log metadtaa like matched terms, do not return in http response
* refactoring
 2019-05-29 16:17:09 -04:00
Martin Cech fd82ec013b repo search - prefix hash with changeset number, stringify as list 2019-05-28 11:38:16 -04:00
Martin Cech 0706a7ea24 add repo lineage to search results, lower limit to 1 char 2019-05-24 16:05:15 -04:00
Martin Cech 93609f4e68 include repo changeset history in the search index 
unicodify the lineage string
 2019-05-24 16:05:09 -04:00
John Chilton 528497f7c4 Refactor galaxy.web.security into galaxy.security.idencoding. 
I want to be able to use this class in galaxy.model and it doesn't have any dependnecies on "web" stuff so I'd like to move it out of galaxy.model and into galaxy.security. galaxy.model shouldn't have dependencies on galaxy.web (and doesn't after the recent 976f5ad367), so this pre-emptively ensures it doesn't require these dependencies for https://github.com/galaxyproject/galaxy/pull/7367.

This has the benefit of also eliminating any galaxy.web dependencies from the generic test base file (test/base/testcase.py) which has long been a goal of mine as well.

There are places we legimately use ID encoding and decoding for security (i.e. job files API) but for the most part it doesn't provide security for API endpoints and this causes confusion repeatedly, so I've started the process of renaming the contained class SecurityHelper to something I feel makes it clearer this is just about encoding and decoding IDs.
 2019-03-19 14:28:31 -04:00
Nicola Soranzo f4203ca051 Fix errors reported by flake8 3.6.0 
Ignore W504.
 2018-10-24 23:22:19 +01:00
Nicola Soranzo 949dcfdbc3 Do not log exceptions twice 
`logging.exception()` already adds the the exception information after
the supplied message.

Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.

xref. https://github.com/galaxyproject/galaxy/issues/1715
 2018-10-24 12:57:05 +01:00
Nate Coraor 44c291bc66 Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config 2018-01-18 12:30:05 -05:00
Nicola Soranzo 14259b11d9 Python3: finish first pass on whole codebase 2017-12-14 12:01:01 +00:00
John Chilton 7bae23e105 yaml_config - update code base for converting galaxy.ini.sample to YAML. 2017-12-06 20:28:20 -05:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nicola Soranzo b956406c4d Fix Python3 compatibility and import order for 21 files 2017-10-16 19:43:01 +01:00
Nicola Soranzo d1bc98dfcb Python3: fix remaining print statements 
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
 2017-10-12 18:34:29 +01:00
Nicola Soranzo 9b1832abb1 Fix import order for cron/, scripts/ and test/ 2017-09-25 23:44:39 +01:00
E Rasche 290971ca7a more review comments 2017-09-25 11:39:15 +02:00
E Rasche 9b8e76f9d9 Convert urllib to requests 
Which has built-in protection against urls like "file:///tmp/a"
 2017-09-25 11:39:13 +02:00
Martin Cech 095c1045b6 add logging to ts index building 2017-09-06 14:05:05 -04:00
Nicola Soranzo a8d7b2df8b Fix more indentation errors 2017-08-17 11:35:39 +01:00
Nicola Soranzo a353b2e88f Fix E127 errors introduced by previous commit 
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