opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
46,573 Commits 63 Branches 243 Tags
cc19fc76efd513d742d63bc075049de644e68e19
Commit Graph
23662 Commits
Author SHA1 Message Date
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 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
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
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
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
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
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Nicola Soranzo 41af684cc2 Fixes for flake8 3.8 and bugbear 2020-06-20 18:10:54 +01:00
Dannon Baker 2894cf52a2 Drop idphint from custos sample; allowlist will provide this functionality in the future. 2020-06-18 10:31:56 -04:00
Dannon Baker 48aae69e3e Icon isn't used for custos 2020-06-18 10:25:36 -04:00
Dannon Baker 778d79d52c Swap enable_idp_logout in sample to default (false) 2020-06-18 10:23:21 -04:00
Dannon Baker 1b184ac49e Update sample to include default custos url 2020-06-18 08:46:52 -04:00
Dannon Baker 94c55bab58 Refactor credential loading for custos, compose credential URL instead 
of requiring specification (TODO: Should be in well-known eventually?)
 2020-06-18 08:41:59 -04:00
Dannon Baker a14f282df1 Swap custos to use composed well-known URL 2020-06-18 08:41:26 -04:00
Dannon c0db660e33 Merge pull request #9730 from dannon/fix-authnz-provider-naming 
[20.05] oidc-based authnz provider overhaul; breaking changes for keycloak
 2020-06-17 14:31:15 -04:00
Dannon Baker b490eafa00 Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 2020-06-17 12:05:25 -04:00
Dannon Baker 29018e0cb6 Minor tweak. 2020-06-17 09:03:37 -04:00
Dannon Baker f6f579f34c Refactor fetching/loading well-known oidc config for custos/keycloak 2020-06-17 09:02:33 -04:00
Dannon Baker 78c934f601 Input dataset module format filtering fix; this would previously turn fasta into f,,,,a,,,,s,,,... and so on when you actually tried to run a workflow using this functionality. It would increasingly proliferate commas on runs to the point where it crashed a webserver. 2020-06-17 08:41:08 -04:00
Nicola Soranzo b56ca26f38 Split imports for future additions 2020-06-17 13:37:22 +01:00
Dannon Baker 482131a542 Add lookup of keycloak/custos backends instead of using ors everywhere 2020-06-17 08:18:35 -04:00
Dannon Baker e915c787bc Minor typo in oidc backends sample 2020-06-16 18:20:07 -04:00
Dannon Baker 32fbd22783 Drop commented code related to oidc config loading 2020-06-16 18:20:07 -04:00
almahmoud 7b5effa3f4 Adding Keycloak provider to sample oidc backends 2020-06-16 18:20:07 -04:00
almahmoud ebabfd3bf4 Add Keycloak IDP and standardize URL and well-known formation for Keycloak and Custos 2020-06-16 18:20:07 -04:00
Dannon Baker ab46011b04 Consistently use provider.lower in configuration. Custos != custos. 2020-06-16 18:20:07 -04:00
mvdbeek 9bc4c53343 Only cache xml files 2020-06-12 13:33:05 +02:00
mvdbeek ff492b652f Add source_path property to YamlToolSource and CwlToolSource 2020-06-11 19:23:34 +02:00