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Author SHA1 Message Date
Martin Cech cc19fc76ef Merge pull request #9940 from mvdbeek/20.05_release_notes 
[20.05] Update 20.05 release notes with later PRs
 2020-06-30 17:53:51 +02:00
Nicola Soranzo ba3a07a736 Small fixes 2020-06-30 16:23:13 +01:00
mvdbeek c6830137e8 Merge branch 'release_20.01' into release_20.05 2020-06-30 16:58:03 +02:00
DannonandNicola Soranzo aadc914069 Update lib/galaxy/web/framework/base.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-30 16:37:35 +02:00
Dannon Baker 56b40e24ba Fix, split imports 2020-06-30 16:37:35 +02:00
Dannon Baker 9911c59782 Drop paste usage in cookie handling 2020-06-30 16:37:35 +02:00
Dannon Baker 2f12a20ee5 Initial hack to fix cookie handling that changed with py3. Cookie handling used to be more robust, allowing invalid values to be set without breaking the whole thing. 2020-06-30 16:37:35 +02:00
mvdbeek 93e02008a3 Update release notes with later PRs 2020-06-30 16:32:37 +02:00
Nicola Soranzo 31579298e2 Merge pull request #9936 from mvdbeek/backport_sqlite_sniffing_fix 2020-06-30 13:31:17 +01:00
Marius van den Beek 38e1c381a8 Merge pull request #9921 from dannon/fix-py3-cookie-robustitude 
[20.01] Make cookie handling more robust
 2020-06-30 13:32:05 +02:00
mvdbeek 6fe1ce3e2e Fix Chira sniffer 2020-06-30 11:48:09 +02:00
Marius van den Beek 7fb4fc8acf Merge pull request #9925 from blankenberg/regex-valid-list-20.05 
[20.05] Enable regex validator to validate lists of values.
 2020-06-30 11:46:49 +02:00
John Chilton 34b4fcca1d Merge pull request #9931 from almahmoud/patch-1 
[20.05] Explicitly cast oidc providers to a list
 2020-06-29 16:21:49 -04:00
John Chilton fb8cf65961 Merge pull request #9932 from nsoranzo/release_20.05_fix_9929 
[20.05] Move the `--debug` flag after the conda subcommand
 2020-06-29 16:20:44 -04:00
Nicola Soranzo 95d8ede5fa Merge branch 'release_20.01' into release_20.05 2020-06-29 19:38:36 +01:00
Nicola Soranzo 6f2bf92bdd Move the --debug flag after the conda subcommand 
Fix https://github.com/galaxyproject/galaxy/issues/9929 .

Also:
- Better variable names
- Do not use list as argument default
 2020-06-29 19:33:40 +01:00
Marius van den Beek a37af154c2 Merge pull request #9920 from nsoranzo/release_20.01_fix_check_html 
[20.01] Rewrite `check_html()` and `Text.count_data_lines()` to read a chunk of each line
 2020-06-29 20:31:10 +02:00
Alexandru MahmoudandNicola Soranzo 4b6e61196d explicitly cast oidc providers to a list 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-29 13:57:37 -04:00
Daniel Blankenberg b195db8778 Add unit test to regex validator 2020-06-29 09:23:19 -04:00
Daniel Blankenberg daa6715a56 Enable regex validator to validate lists of values. 2020-06-26 16:25:07 -04:00
Nicola Soranzo 975ba9166d Read a chunk of each line in Text.count_data_lines() 
Prevent out-of-memory issues when setting metadata of files with
very long lines, e.g.
ftp://ftp.ensembl.org/pub/current_json/homo_sapiens/homo_sapiens.json
 2020-06-26 18:14:49 +01:00
John Chilton a9b7a4aa79 Merge pull request #9907 from dannon/handler_assignment_bugfix 
[20.01] Fix incorrect variable assignment
 2020-06-26 08:43:46 -04:00
DannonandNicola Soranzo 3d2eae565a Update lib/galaxy/web/framework/base.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-26 07:59:11 -04:00
Nicola Soranzo 663b7931a1 Rewrite check_html() to read a chunk of each line 
Fix the following traceback during upload of files with very long lines
(e.g. JSON from Ensembl):

```
Traceback (most recent call last):
  File "/srv/galaxy/tools/data_source/upload.py", line 326, in <module>
    __main__()
  File "/srv/galaxy/tools/data_source/upload.py", line 319, in __main__
    metadata.append(add_file(dataset, registry, output_path))
  File "/srv/galaxy/tools/data_source/upload.py", line 128, in add_file
    convert_spaces_to_tabs=dataset.space_to_tab,
  File "/srv/galaxy/lib/galaxy/datatypes/upload_util.py", line 54, in handle_upload
    convert_spaces_to_tabs=convert_spaces_to_tabs,
  File "/srv/galaxy/lib/galaxy/datatypes/sniff.py", line 749, in handle_uploaded_dataset_file_internal
    if not is_binary and check_content and check_html(converted_path):
  File "/srv/galaxy/lib/galaxy/util/checkers.py", line 42, in check_html
    line = util.unicodify(line)
  File "/srv/galaxy/lib/galaxy/util/__init__.py", line 1042, in unicodify
    raise Exception(msg)
Exception: Value '...' could not be coerced to Unicode: MemoryError('')
```

Also:
- Use `with` statement to open/close files inside archives
- Add tests
 2020-06-26 03:08:27 +01:00
Dannon Baker 9b56449399 Fix, split imports 2020-06-25 18:29:04 -04:00
Dannon Baker cb94255e5c Drop paste usage in cookie handling 2020-06-25 18:28:51 -04:00
Dannon Baker b418b17bea Initial hack to fix cookie handling that changed with py3. Cookie handling used to be more robust, allowing invalid values to be set without breaking the whole thing. 2020-06-25 17:49:23 -04:00
Nicola Soranzo 9b757c0040 Add original exception details in error message 2020-06-25 22:47:31 +01:00
Nicola Soranzo aeb92db070 Merge branch 'release_20.01' into release_20.05 2020-06-24 21:30:10 +01:00
Nicola Soranzo 6d29cb3b47 Merge pull request #9913 from nuwang/fix_user_prefs_leak 
[20.01] Fix extra preference values leaking between requests
 2020-06-24 20:22:15 +01:00
Nuwan Goonasekera 780f8606a8 Fix extra preference values leaking between requests 2020-06-24 23:14:47 +05:30
Nuwan Goonasekera 9a8be72e5f Fix incorrect variable assignment 2020-06-23 18:28:22 -04:00
Dannon 580c36af87 Merge pull request #9892 from mvdbeek/tsv_sra_manifest 
[20.05] Output SRA manifest as tabular dataset
 2020-06-23 11:45:26 -04:00
mvdbeek 845b02cf91 Allow sra_manifest upload, so that we can test with planemo 2020-06-23 17:25:06 +02:00
mvdbeek b8dc6d79f4 Set comment_lines to 1 for SraManifest 2020-06-23 16:24:12 +02:00
Marius van den Beek 049956b4f4 Merge pull request #9897 from nsoranzo/release_20.05_py3_only 
[20.05] Python 2.7 is officially unsupported on 20.05
 2020-06-23 10:14:03 +02:00
John Chilton f39f6bd6c4 Merge pull request #9898 from dannon/fix-webpack-import-proxy-prefix 
[20.05] Fix webpack import proxy prefix
 2020-06-22 15:44:25 -04:00
Dannon Baker 2a2957def4 Eslint global declaration and unused-vars conflict; simply disable rule for a single line instead of declaring. 2020-06-22 11:50:03 -04:00
Marius van den Beek eaaf0cb161 Merge pull request #9896 from nsoranzo/release_20.05_flake8_fixes 
[20.05] Fixes for flake8 3.8 and bugbear
 2020-06-22 17:06:21 +02:00
mvdbeek 278a033372 Add SraManifest datatype 
This datatype auto-generates its column_names from the first line of the
dataset, since the user can choose which columns to include.
 2020-06-22 17:03:26 +02:00
mvdbeek c9942e3d0a Display up to 100 columns 
Bumping this up from 50 so that we can display the manifest coming from
the SRA nicely.
 2020-06-22 17:01:36 +02:00
mvdbeek 52138db431 Allow datatypes to specify data_line_offset 
If set, the first ``data_line_offset`` lines won't be rendered.
This is useful if the column_names are specified in the first line.
Otherwise these would be rendered twice, once as the header and once
as the data.
 2020-06-22 17:01:36 +02:00
mvdbeek ee8d9f0877 Update sra_source tool to outut sra_manifest.tabular 2020-06-22 17:01:36 +02:00
John Chilton 693e115202 Merge pull request #9894 from dannon/custos_wording_tweak 
[20.05] Custos login notice wording tweak
 2020-06-22 08:58:07 -04:00
Dannon Baker 5ee0a0061d Declare webpack global for linting, swap to explicit <root>/static/dist, which should always be correct. 2020-06-22 07:49:02 -04:00
Dannon Baker bf2df2ac0f Move publicPath setting to its own module 2020-06-20 21:18:51 -04:00
Dannon Baker bc553e3331 Prettier.? 2020-06-20 14:44:40 -04:00
Dannon Baker 919d919d31 Fix webpack dynamic imports when serving Galaxy at a prefix 2020-06-20 14:44:11 -04:00
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Nicola Soranzo f1f5beaa6a Drop use of removed config option 
In commit c8c34fa2f7
`enable_beta_mulled_containers` was replaced by
`enable_mulled_containers`, which defaults to `true`.

xref. https://github.com/galaxyproject/galaxy/pull/8195#pullrequestreview-284244354
 2020-06-20 18:16:30 +01:00