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Commit Graph
19058 Commits
Author SHA1 Message Date
Nicola Soranzo f9a84b0ffe Merge pull request #6972 from Slugger70/biom_datatype_changes 
Added a metadata element to the biom1 datatype
 2018-11-08 11:36:28 +00:00
Nicola Soranzo e4c00af38d Merge branch 'release_18.09' into dev 2018-11-08 09:32:30 +00:00
Martin Cech d28ce7686d Merge pull request #6898 from martenson/no-sanitization-db 
prevent sanitized history names being saved in database
 2018-11-07 16:31:50 -05:00
John Chilton 5e1fb9a7a2 Merge pull request #6983 from mvdbeek/schema_amamdment_tags_in_collection 
[18.09] List tags as attribute of TestCollection
 2018-11-07 14:37:56 -05:00
Nicola Soranzo 6dd098f747 Simplify code 2018-11-07 18:57:06 +00:00
mvdbeek bff5d51245 Use comma-separated instead of comma separated 2018-11-07 19:34:40 +01:00
Nicola Soranzo be87d2402d Merge branch 'release_18.09' into dev 2018-11-07 17:19:16 +00:00
mvdbeek 0ecb4e7c59 List tags as attribute of TestCollection 2018-11-07 11:13:02 +01:00
Slugger70 0bc6e35ad6 Minor alteration for flake8 2018-11-07 10:23:31 +11:00
Enis Afgan 2f2153292b Merge pull request #6583 from VJalili/cloud_download_tool 
Send data to cloud
 2018-11-06 16:36:19 -05:00
Dannon 6487d52d51 Merge pull request #6978 from nsoranzo/release_18.09_paste 
[18.09] Fix traceback when starting under Python3 with ``galaxy.ini``
 2018-11-06 10:16:41 -05:00
John Chilton 82a8eb05d6 Merge remote-tracking branch 'jmchilton/release_18.09' into dev_merge_1 2018-11-06 09:10:22 -05:00
Nicola Soranzo dc9128213f Fix traceback when starting under Python3 with `galaxy.ini` 
Update `paste` requirement to 3.0.4 to include:

https://github.com/cdent/paste/pull/14

to fix the following traceback:

```
Starting server in PID 6792.
Traceback (most recent call last):
  File "./scripts/paster.py", line 27, in <module>
    serve.run()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run
    invoke(command, command_name, options, args[1:])
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke
    exit_code = runner.run(args)
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run
    result = self.command()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command
    serve()
  File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve
    server(app)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper
    **context.local_conf)
  File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call
    val = callable(*args, **kw)
  File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner
    for name, value in kwargs.items():
RuntimeError: dictionary changed size during iteration
galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down
```
 2018-11-06 12:49:44 +00:00
Slugger70 fc53123a94 Changes as per review 2018-11-06 22:28:00 +11:00
Slugger70 258ada862e Added a metadata element to the biom1 datatype 2018-11-06 17:50:12 +11:00
John Chilton ccb1e08000 In enqueue, always set an object_store_id if one isn't set. 
Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode.
 2018-11-05 18:50:51 -05:00
Dannon e9f2693933 Merge pull request #6729 from scrathat/admin.data.manager.vue.steps 
Vue rewrite of admin data manager (local data) in steps
 2018-11-05 15:00:20 -05:00
Martin Cech 61bda3d11a Merge pull request #6960 from dannon/collection_ext_dl 
[18.09] Allow deferring 'to_ext' extension to the server
 2018-11-05 10:11:11 -05:00
Nicola Soranzo 2deb302ae7 Merge pull request #6951 from bernt-matthias/topic/test-colouts-backport 
[18.09] Backport: tests need to count data sets and collections
 2018-11-05 13:43:36 +00:00
Marius van den Beek c1e4b0111a Merge pull request #6911 from jmchilton/workflow_mapping_refactor 
Refactor collection mapping workflows toward independence from tools.
 2018-11-05 14:04:09 +01:00
Marius van den Beek a3f213e3c5 Merge pull request #6962 from bernt-matthias/topic/rma 
add RMA6 data type (MEGAN6 read-match archive)
 2018-11-05 13:04:37 +01:00
mvdbeek f8b160535c Some minor fixes for the blast datatype 
The signature for Data.display_data wasn't quite correct,
and the description of display_data was also a little misleading.
 2018-11-05 11:28:45 +01:00
mvdbeek 3be8d66d71 Remove unncecessary implementations of display_data 
These were not updated to use `_download_filename`,
and so this fixes the download name for collection elements
to include the element identifier.
Note that the Data class should handle composite data just
fine.
 2018-11-05 10:04:52 +01:00
M Bernt 562b10b7ef rma: renamed test data to rma6 2018-11-05 09:26:33 +01:00
Marius van den Beek 0ede377925 Merge pull request #6957 from bernt-matthias/topic/empty-data-table 
Topic/empty data table
 2018-11-04 22:13:12 +01:00
Sebastian Kapust 91df3971be DataManagerRouter, DataManager, DataManagerJobs: Fix routing problem 
* Forward path following the data manager url to DataManagerRouter
* encode id in DataManager and DataManagerJobs
 2018-11-03 14:06:46 +01:00
Sebastian Kapust 8789713b95 Merge branch 'dev' into admin.data.manager.vue.steps 2018-11-03 09:59:36 +01:00
M Bernt 09de6fe496 rma: fix test 2018-11-02 09:44:26 +01:00
M Bernt 0beac8fdf4 rma: add RMA6 data type (MEGAN6 read-match archive) 2018-11-01 23:46:41 +01:00
Dannon Baker 69b447169f Allow deferring 'to_ext' extension to the server, implement for collections. 2018-11-01 15:22:52 -04:00
M Bernt 13a4238510 removed debug output 2018-11-01 19:10:02 +01:00
M Bernt cc8e1c211e fix empty loc file bug 2018-11-01 19:06:46 +01:00
mvdbeek 30aaa296dd Fix sniffing of readname sorted BAM files 
This fixes https://github.com/galaxyproject/galaxy/issues/6949.
The problem is that `super` would fall back to the BamInputSorted
sniffer, which prevents sniffing. Includes a test file for the new
datatype upload testing framework.
 2018-11-01 12:00:38 -04:00
John Chilton f035d642ce Merge pull request #6844 from jmchilton/compressed_types_and_extra_files 
Infrastructure/API Support for Composite Uploads/Downloads
 2018-11-01 10:57:09 -04:00
John Chilton c312c1014d Merge pull request #6937 from natefoo/shed-tools-relocate 
Default shed tool installation to database/shed_tools
 2018-11-01 10:22:05 -04:00
John Chilton f40bb68141 Merge pull request #6950 from mvdbeek/qname_sorted_sniffer 
Fix sniffing of readname sorted BAM files
 2018-10-31 10:40:10 -04:00
M Bernt 20cecd2a68 galaxy test needs to count data sets and collection outputs 2018-10-31 12:52:25 +01:00
mvdbeek c78f704c23 Add two test files that exercise json and txt sniffing 2018-10-31 10:03:50 +01:00
mvdbeek ddeef3fbc2 Fix sniffing of readname sorted BAM files 
This fixes https://github.com/galaxyproject/galaxy/issues/6949.
The problem is that `super` would fall back to the BamInputSorted
sniffer, which prevents sniffing. Includes a test file for the new
datatype upload testing framework.
 2018-10-31 09:59:41 +01:00
Nicola Soranzo b47efd4ade Merge branch 'release_18.09' into dev 2018-10-31 09:38:34 +01:00
mvdbeek 49d9409f00 Bam index is only available for coordinate sorted bam files 2018-10-30 18:09:37 +01:00
Marius van den Beek 1482cacee5 Merge pull request #6886 from ilveroluca/fix/k8s_error_handling 
Improve k8s job error handling
 2018-10-30 12:01:18 +01:00
mvdbeek 16962ad6a1 Add newline to lib/galaxy/datatypes/test/5e5z.pqr 2018-10-30 10:32:19 +01:00
mvdbeek ba5d76eb93 Avoid exception if no match 
This fixes the sniffing unit test, the datatype framework would just
continue anyway.
 2018-10-30 09:27:26 +01:00
mvdbeek ecc02bb659 Fix UploadProblemException 2018-10-30 09:27:26 +01:00
mvdbeek 0fae117e67 Use raw strings in regex and allow lowercase fastq sequences 2018-10-30 09:27:26 +01:00
mvdbeek c50a0fccac Don't sniff simple json types 
These should instead be text.
 2018-10-30 09:27:26 +01:00
mvdbeek 1a407429ba Tighten up mothur and phylip sniffers 2018-10-30 09:27:26 +01:00
mvdbeek 738bde0127 Fix check_html on python 3 
We can open the file in binary mode and then use unicodify on the lines,
as we have to do that anyway if `chunks` is provided.
Also adds the unicode flag to re.compile.
 2018-10-30 09:27:26 +01:00
mvdbeek d168042b36 Fix newline conversion on python 3 if no encoding is set 2018-10-30 09:27:25 +01:00