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https://github.com/C3BI-pasteur-fr/ReGaTE
05 April 2024, 23:39:51 UTC
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Revision Author Date Message Commit Date
5c32495 fmareuil 07 January 2019, 12:28:57 UTC Update README.md Travis badge 07 January 2019, 12:28:57 UTC
110ba34 fmareuil 07 January 2019, 12:19:21 UTC Update requirements.txt update requirement requests from requests/2.7.0 to requests/2.21.0 07 January 2019, 12:19:21 UTC
d44afb2 fmareuil 07 January 2019, 12:14:29 UTC Update requirements.txt update requirement pyaml from PYAML to ruamel.yaml 07 January 2019, 12:14:29 UTC
d474786 Hervé MENAGER 15 December 2016, 16:15:40 UTC use ruamel instead of pyyaml 15 December 2016, 16:15:40 UTC
75885d8 Hervé MENAGER 15 December 2016, 15:56:11 UTC correct CI tests call 15 December 2016, 15:56:11 UTC
9adbeb4 Hervé MENAGER 15 December 2016, 15:50:22 UTC add additional data files required for tests 15 December 2016, 15:50:22 UTC
23656d0 Hervé MENAGER 15 December 2016, 15:49:33 UTC add tests in CI and specify additional dependency for it. 15 December 2016, 15:49:33 UTC
3d15866 Hervé MENAGER 15 December 2016, 15:46:43 UTC update tests for regate 15 December 2016, 15:46:43 UTC
f082e88 Hervé MENAGER 15 December 2016, 15:44:46 UTC modify JSON comply with the new bio.tools format, and refactor/gardening 15 December 2016, 15:44:46 UTC
cf68fdb Hervé MENAGER 15 December 2016, 15:43:44 UTC save yml data downloaded from the Galaxy instance 15 December 2016, 15:43:44 UTC
edf0857 odoppelt 12 December 2016, 16:00:54 UTC Update configuration.rst 12 December 2016, 16:00:54 UTC
2227f77 odoppelt 12 December 2016, 15:52:24 UTC Update configuration.rst 12 December 2016, 15:52:24 UTC
7482ebb odoppelt 12 December 2016, 15:48:12 UTC Update configuration.rst 12 December 2016, 15:48:12 UTC
2a68e19 Hervé MENAGER 05 December 2016, 14:05:25 UTC turn off smartypants to avoid turning double dash to endash 05 December 2016, 14:05:25 UTC
7003fdb Hervé Ménager 05 December 2016, 13:58:06 UTC correct double-dashes in CL syntax example 05 December 2016, 13:58:06 UTC
8b0ff5b Hervé Ménager 05 December 2016, 13:55:01 UTC update README to add a setup and run howto 05 December 2016, 13:55:01 UTC
69c6a33 Hervé MENAGER 05 December 2016, 13:02:29 UTC more code gardening 05 December 2016, 13:02:29 UTC
8beb678 Hervé MENAGER 05 December 2016, 12:39:57 UTC reformat code 05 December 2016, 12:39:57 UTC
a874061 Hervé MENAGER 05 December 2016, 12:33:10 UTC sensible values for homepage URL, and "uses", plus code gardening 05 December 2016, 12:33:10 UTC
659faf0 Hervé MENAGER 04 December 2016, 21:02:27 UTC correct a few old lines of code that crept back in with last merge 04 December 2016, 21:02:27 UTC
afb9753 Hervé MENAGER 04 December 2016, 20:54:14 UTC Merge branch 'master' of https://github.com/C3BI-pasteur-fr/ReGaTE 04 December 2016, 20:54:14 UTC
2b48546 Hervé MENAGER 04 December 2016, 20:52:35 UTC upgrade ReGaTE to be compliant with BioToolsSchema 2.0.0 (as available in dev.bio.tools on Dec 4, 2016) 04 December 2016, 20:52:35 UTC
2f47b6a Olivia Doppelt-Azeroual 02 December 2016, 15:36:05 UTC url (usesHomepage) bug fixed 02 December 2016, 15:36:05 UTC
722aa08 Hervé MENAGER 30 November 2016, 21:41:53 UTC update README.md 30 November 2016, 21:41:53 UTC
254ae29 Hervé MENAGER 30 November 2016, 21:36:50 UTC add myself as an author in remag 30 November 2016, 21:36:50 UTC
23712e2 Hervé MENAGER 30 November 2016, 21:23:39 UTC Merge branch 'master' of https://github.com/C3BI-pasteur-fr/ReGaTE 30 November 2016, 21:23:39 UTC
7202b1b Hervé MENAGER 30 November 2016, 21:23:08 UTC add sensible defaults to the configuration file 30 November 2016, 21:23:08 UTC
5e08ea4 Hervé MENAGER 30 November 2016, 21:20:00 UTC update and simplify documentation 30 November 2016, 21:20:00 UTC
e0c0a44 odoppelt 30 November 2016, 15:58:23 UTC Update regate.ini 30 November 2016, 15:58:23 UTC
887f87f Hervé MENAGER 30 November 2016, 13:48:27 UTC restructure tool_dir code 30 November 2016, 13:48:27 UTC
d4091c7 Hervé MENAGER 25 November 2016, 15:39:35 UTC Add Hervé as an author 25 November 2016, 15:39:35 UTC
4951461 Hervé Ménager 24 November 2016, 21:28:56 UTC update installation instructions 24 November 2016, 21:28:56 UTC
70d2135 Hervé MENAGER 24 November 2016, 21:04:11 UTC improve EDAM data/format terms lookup 24 November 2016, 21:04:11 UTC
667a82b Hervé MENAGER 24 November 2016, 20:47:05 UTC correct indentation error 24 November 2016, 20:47:05 UTC
b5a31bd Hervé MENAGER 24 November 2016, 20:45:38 UTC recreate JSON directory when running ReGaTE this is to avoid trying to upload old JSON files... 24 November 2016, 20:45:38 UTC
5e578e0 Hervé MENAGER 21 November 2016, 15:28:03 UTC Better handling of resource removal - handle error due to current version!=versionID discrepancy in bio.tools - only remove entries for the declared collection - skip and log entry on error 21 November 2016, 15:28:03 UTC
14cfce3 Hervé MENAGER 21 November 2016, 15:20:01 UTC minor refactor in code 21 November 2016, 15:20:01 UTC
999eb47 Hervé MENAGER 21 November 2016, 15:18:35 UTC escape special characters in entry names 21 November 2016, 15:18:35 UTC
a3d9a87 Hervé MENAGER 21 November 2016, 15:15:06 UTC add undeclared Galaxy datatypes to the reference mapping this should probably lead to: - corrections in Tool XML files (e.g. uppercased datatypes) - or addition of missing datatypes in Galaxy (e.g. agp) 21 November 2016, 15:15:06 UTC
065177b Hervé MENAGER 18 November 2016, 13:17:31 UTC update YAML mapping file to the new format, add "text" pseudo-format 18 November 2016, 13:17:31 UTC
66cb584 Hervé MENAGER 17 November 2016, 22:16:56 UTC improve logging 17 November 2016, 22:16:56 UTC
023daa1 Hervé MENAGER 17 November 2016, 22:15:42 UTC improve tool duplicates detection 17 November 2016, 22:15:42 UTC
f27ba50 Hervé MENAGER 17 November 2016, 21:35:51 UTC do not try to conver to URIs EDAM formats if they are set to None 17 November 2016, 21:35:51 UTC
54dbe33 Hervé MENAGER 17 November 2016, 21:34:45 UTC correct source mappings for data handles and descriptions 17 November 2016, 21:34:45 UTC
0960c7b Hervé MENAGER 17 November 2016, 21:31:58 UTC manage outputs which refer to input datatypes with a quickfix we currently do not give them meaningful EDAM references, until the Galaxy API provides the necessary format source information from the XML. 17 November 2016, 21:31:58 UTC
3a87169 Hervé MENAGER 17 November 2016, 21:29:36 UTC simplify debug print 17 November 2016, 21:29:36 UTC
a6a2034 Hervé MENAGER 17 November 2016, 21:28:07 UTC ask again the password if authentication fails 17 November 2016, 21:28:07 UTC
dd73cb0 Hervé MENAGER 17 November 2016, 21:25:26 UTC escape tool IDs when building the home URL 17 November 2016, 21:25:26 UTC
603e251 Hervé MENAGER 17 November 2016, 21:24:15 UTC add versionID which is the one used by bio.tools DB 17 November 2016, 21:24:15 UTC
8d448a7 Hervé MENAGER 17 November 2016, 21:23:15 UTC fix missing descriptions in Galaxy tools with a dummy one. 17 November 2016, 21:23:15 UTC
0746eb6 Hervé MENAGER 15 November 2016, 10:41:58 UTC only delete the bio.tools descriptions belonging to 'resourcename' - leave the bio.tools descriptions which do not belong to the collection 'resourcename' - ressourcename->resourcename 15 November 2016, 10:41:58 UTC
394dd31 Hervé MENAGER 15 November 2016, 10:38:53 UTC correct error logging statement 15 November 2016, 10:38:53 UTC
4480acd Hervé MENAGER 14 November 2016, 16:07:52 UTC log delete responses 14 November 2016, 16:07:52 UTC
6d478c1 Hervé MENAGER 14 November 2016, 16:00:54 UTC modify delete url due to a bio.tools bug the one specified before should work, but not anymore, so I'm copying the one used in the JS code. 14 November 2016, 16:00:54 UTC
6bfb166 Hervé Ménager 21 October 2016, 19:04:12 UTC modify regate and remag to include term labels EDAM terms should be replaced by the bio.tools server but we provide it for JSON readability purpose. 21 October 2016, 19:04:12 UTC
7710ca1 Hervé Ménager 19 October 2016, 15:43:35 UTC more package setup work here goal is `pip install regate` 19 October 2016, 15:43:35 UTC
23110e2 Hervé Ménager 19 October 2016, 14:02:04 UTC multiple packaging improvements, plus start pip-ing the package (test) 19 October 2016, 14:02:04 UTC
b368159 Hervé Ménager 17 October 2016, 14:23:10 UTC Merge branch 'master' into dev_bio_tools 17 October 2016, 14:23:10 UTC
bcfacc2 Hervé Ménager 17 October 2016, 14:17:16 UTC upgrade setuptools before installing requirements 17 October 2016, 14:17:16 UTC
40a962c Hervé Ménager 17 October 2016, 14:14:46 UTC setuptools has to be upgraded before to launch pip of course :( 17 October 2016, 14:14:46 UTC
831847e Hervé Ménager 17 October 2016, 14:09:59 UTC add minimal version of setuptools required by html5lib required by rdflib 17 October 2016, 14:09:59 UTC
f7a0baa Hervé Ménager 17 October 2016, 11:25:41 UTC upload the JSON instead of XML because there is currently no support for XML in bio.tools. 17 October 2016, 11:25:41 UTC
69f09ec Hervé Ménager 17 October 2016, 11:25:21 UTC tool ID is mandatory. 17 October 2016, 11:25:21 UTC
6d02488 Hervé Ménager 17 October 2016, 11:21:54 UTC do not specify the sourceRegistry sourceRegistry is a string of 50 chars or less now... FIXME: find the right string. 17 October 2016, 11:21:54 UTC
604e53c Hervé Ménager 17 October 2016, 11:17:54 UTC colons aren't authorized anymore in tool names. 17 October 2016, 11:17:54 UTC
bd32564 Hervé Ménager 17 October 2016, 11:14:03 UTC "platform" format has changed. 17 October 2016, 11:14:03 UTC
151aa8f Hervé Ménager 17 October 2016, 11:11:28 UTC disable "unsecure https" messages generated by requests library. 17 October 2016, 11:11:28 UTC
a67a641 Hervé Ménager 13 October 2016, 22:05:15 UTC update upload to continue to next tool if current one is not valid. 13 October 2016, 22:05:15 UTC
a88ff0e Hervé Ménager 13 October 2016, 22:04:13 UTC update "delete all existing services" part to new API 13 October 2016, 22:04:13 UTC
b73d70e Hervé Ménager 13 October 2016, 22:03:20 UTC update authentication to use rest-auth 13 October 2016, 22:03:20 UTC
ad7680f Hervé Ménager 13 October 2016, 22:02:16 UTC allow inputs with no clear data types (for now) 13 October 2016, 22:02:16 UTC
af96d7a Hervé Ménager 13 October 2016, 22:01:03 UTC correct the construction of the Galaxy link in tool description 13 October 2016, 22:01:03 UTC
0224d68 Hervé Ménager 12 September 2016, 13:48:14 UTC add minimal Travis config file. 12 September 2016, 13:48:14 UTC
bfa4dac Olivia Doppelt-Azeroual 12 September 2016, 08:51:10 UTC debug xml file format 12 September 2016, 08:51:10 UTC
cd50439 Olivia Doppelt-Azeroual 08 September 2016, 15:47:17 UTC documentation addons 08 September 2016, 15:47:17 UTC
fc7cdbe Olivia Doppelt-Azeroual 08 September 2016, 15:46:18 UTC documentation addons 08 September 2016, 15:46:18 UTC
c749d31 Olivia Doppelt-Azeroual 08 September 2016, 15:44:42 UTC documentation addons 08 September 2016, 15:44:42 UTC
66c71c2 Hervé Ménager 05 August 2016, 11:47:56 UTC correct python path in regate.py script 05 August 2016, 11:47:56 UTC
d36e14b Hervé Ménager 05 August 2016, 08:39:56 UTC correct syntax error in regate.py script 05 August 2016, 08:39:56 UTC
4fe8188 Olivia Doppelt-Azeroual 22 June 2016, 14:03:59 UTC adaptation for XML validation based on bio.tools xsd version 1.4 22 June 2016, 14:03:59 UTC
bc5a166 Olivia Doppelt-Azeroual 22 June 2016, 10:11:56 UTC modification of the accessibility variable 22 June 2016, 10:11:56 UTC
9a8d8cc Olivia Doppelt-Azeroual 03 June 2016, 13:33:09 UTC warning addition if same tool id and same version are detected in a galaxy instance 03 June 2016, 13:33:09 UTC
0108db7 odoppelt 03 June 2016, 10:27:05 UTC remove suffix value from regate.ini 03 June 2016, 10:27:05 UTC
55a434b Olivia Doppelt-Azeroual 01 June 2016, 16:01:45 UTC code cleanup 01 June 2016, 16:01:45 UTC
c7bd410 odoppelt 01 June 2016, 15:17:26 UTC Update regate.ini 01 June 2016, 15:17:26 UTC
942889f Olivia Doppelt-Azeroual 01 June 2016, 15:23:12 UTC modification of the section for prefix and suffix conf variables 01 June 2016, 15:23:12 UTC
5cd0cfc Olivia Doppelt-Azeroual 01 June 2016, 15:19:07 UTC resolve conflict with data/regate.ini 01 June 2016, 15:19:07 UTC
63a76cf Olivia Doppelt-Azeroual 01 June 2016, 15:11:45 UTC Merge branch 'master' of https://github.com/C3BI-pasteur-fr/ReGaTE 01 June 2016, 15:11:45 UTC
dbbcff5 Olivia Doppelt-Azeroual 01 June 2016, 15:03:52 UTC 1/addition of prefix and suffix for biotools name tag. They are not mandatory but are aimed to tag tools from galaxys 2/the xml and json filenames are now toolname_version 01 June 2016, 15:03:52 UTC
c82580b odoppelt 01 June 2016, 07:57:41 UTC Update regate.ini 01 June 2016, 07:57:41 UTC
223516c Olivia Doppelt-Azeroual 31 May 2016, 09:03:10 UTC adaptation of galaxy biotools.py in regate 31 May 2016, 09:03:10 UTC
79e6b74 fmareuil 17 March 2016, 16:07:03 UTC typo 17 March 2016, 16:07:03 UTC
3b147b7 Fabien Mareuil 19 January 2016, 10:28:40 UTC correction of the get_source_registry function 19 January 2016, 10:28:40 UTC
8e57478 Fabien Mareuil 19 January 2016, 09:06:14 UTC bug correction json to xml in the push_to_elixir function 19 January 2016, 09:06:14 UTC
39ab754 Fabien Mareuil 18 January 2016, 21:26:41 UTC documentation for requirement installation 18 January 2016, 21:26:41 UTC
0fd6c7d Fabien Mareuil 18 January 2016, 12:51:22 UTC add lxml requirement 18 January 2016, 12:51:22 UTC
c851ab3 fmareuil 09 December 2015, 15:04:39 UTC bug correction: xml name is now a mapping of the uniq galaxy id 09 December 2015, 15:04:39 UTC
79b44a8 fmareuil 09 December 2015, 10:22:40 UTC new template XML and verification schema with xsd 09 December 2015, 10:22:40 UTC
663f86c fmareuil 04 December 2015, 09:43:13 UTC documentation requirement modification 04 December 2015, 09:43:13 UTC
a57f088 fmareuil 04 December 2015, 09:34:13 UTC correction version number 04 December 2015, 09:34:13 UTC
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