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Author SHA1 Message Date
mvdbeek b8dc6d79f4 Set comment_lines to 1 for SraManifest 2020-06-23 16:24:12 +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
Marius van den Beek bc99000d6a Merge pull request #9890 from OlegZharkov/release_20.05 
[20.05] hide expression tools
 2020-06-19 13:17:14 +02:00
Dannon 4185a43293 Merge pull request #9889 from dannon/custos-tweaks 
[20.05] Custos spec fixes
 2020-06-18 13:21:25 -04:00
Dannon Baker 251821d556 Minor verbiage tweaks 2020-06-18 10:46:36 -04:00
Oleg Zharkov ed535ab55e hide expression tools 2020-06-18 16:35:53 +02:00
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 6684f7062d Formatting of test data 2020-06-18 09:36:42 -04:00
Dannon Baker fc324f73fc Fix custos authnz tests with more request mocks 2020-06-18 09:29:51 -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
Nicola Soranzo 79e5634409 Merge pull request #9884 from dannon/fix-workflow-input-format-spec 
[20.01] Input dataset module format filtering fix;
 2020-06-17 16:57:05 +01:00
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 aeed0f7b47 Adjust unit test cases to match reality. 2020-06-17 08:34:55 -04:00
Dannon Baker 482131a542 Add lookup of keycloak/custos backends instead of using ors everywhere 2020-06-17 08:18:35 -04:00
Marius van den Beek eb69186429 Merge pull request #9870 from mvdbeek/fix_tool_not_getting_update 
[20.05] Only cache xml tool files
 2020-06-17 13:19:47 +02:00
Dannon Baker 674b6bea41 Backport a small bit of an InteractiveTools test fix to get things green (8d2d8bbc4d) 2020-06-16 18:20:07 -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
Martin Cech 3bed89490e Merge pull request #9838 from galaxyproject/20.05_release_notes 
Release notes for 20.05
 2020-06-16 18:21:33 +02:00
Martin Cech 7b99755029 include RN in index and add minor changes to them 2020-06-16 12:06:13 +02:00
John Chilton ccb6657507 Merge pull request #9878 from mvdbeek/9869_backport 
[20.05] Improved UploadModal state handling during initialization.
 2020-06-15 08:37:52 -04:00
John Chilton f566c87b3c Improved UploadModal state handling during initialization. 
Track whether datatypes and genomes have been set and use the LoadingSpan component to display information about this wait if the component is not yet ready.
 2020-06-15 12:24:47 +02:00
mvdbeek 9bc4c53343 Only cache xml files 2020-06-12 13:33:05 +02:00
Nicola Soranzo 9de73a8353 Merge pull request #9866 from mvdbeek/fix_tool_not_getting_update 
[20.05] Invalidate tool cache when tool modified outside of Galaxy
 2020-06-12 01:59:37 +01:00
mvdbeek ff492b652f Add source_path property to YamlToolSource and CwlToolSource 2020-06-11 19:23:34 +02:00
mvdbeek cdf103667d Make tool_source and macro_path properties, move paths_and_modtimes to interface 2020-06-11 17:38:08 +02:00
Nicola Soranzo 72f7f14918 Fix typo 2020-06-11 16:00:51 +01:00
mvdbeek bcc7cc6bf1 Don't store path_and_modtimes since we don't re-use it 2020-06-11 16:50:12 +02:00
Marius van den BeekandNicola Soranzo 753db45019 Use method call to get macro paths 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-11 16:25:03 +02:00
mvdbeek a264cfc9b4 Invalidate tool cache when tool modified outside of Galaxy 
We store modtime and if the modtime changes we regenerate the cache
entry. Fixes https://github.com/galaxyproject/galaxy/issues/9863
 2020-06-11 13:54:30 +02:00
Marius van den BeekandNicola Soranzo e687b463f1 Typo fix 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-09 12:41:21 +02:00
mvdbeek ec55c42ae3 Update main announcement 2020-06-09 12:30:11 +02:00
Marius van den BeekandNicola Soranzo 9ba04d3aa5 IT announcement 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-09 11:23:11 +02:00
Marius van den Beek c377ee13b1 Merge pull request #9854 from astrovsky01/remotes/origin/20.05_release_notes 
blurb
 2020-06-05 18:57:36 +02:00
Alexander OSTROVSKY 45d71df053 blurb 2020-06-05 09:43:45 -07:00