John Chilton
dd6b185ab8
Implement composite uploads on arbitrary datatypes.
...
Prior to this, composite uploads were only allowed for select data types. As far as I can tell, the framework itself allows arbitrary datatypes to have extra files. This allows the upload API to take in extra files for datatypes that aren't explicitly annotated has having extra files.
These may be specified one at a time or in directory structures via tar files.
2018-10-24 09:55:25 -04:00
Pierrick ROGER
35093e38fc
Remove spaces in blank line.
2018-10-18 11:16:29 +02:00
Pierrick ROGER
efc7864cab
Merge branch 'dev' into feature/isa_data_type
2018-10-18 10:36:49 +02:00
Nicola Soranzo
6b3f672770
Replace deprecated assertEquals() method
...
Fix warnings during py34-unit tests like:
```
/home/travis/build/galaxyproject/galaxy/test/unit/workflows/test_extract_summary.py:46: DeprecationWarning: Please use assertEqual instead.
self.assertEquals(job_dict[hda.job], [('out1', derived_hda_2)])
```
See e.g. https://travis-ci.org/galaxyproject/galaxy/jobs/438829277
2018-10-09 12:37:15 +01:00
mvdbeek
70e325574c
Use with statement for all file uploads
2018-09-27 22:20:00 +02:00
mvdbeek
53b062f804
Add bam upload test
...
`test_upload_bam_file` fails on release_18.09 but passes on 18.05.
2018-09-27 20:31:33 +02:00
Martin Cech
9b5724d62d
add back the unstable flags for bed.gz datasets
...
I expect the datatypes_conf.xml bed compress default will change in near future
2018-08-30 13:09:32 -04:00
Martin Cech
4a21ac30ea
Merge branch 'rename-and-document-config-value' of github.com:martenson/galaxy into rename-and-document-config-value
2018-08-30 10:41:44 -04:00
Martin Cech
e1b3236802
fix tests for the bed.gz dtaatype
...
compressed beds are not part of the datatypes_conf.xml.sample
2018-08-30 10:40:24 -04:00
mvdbeek
7c339c9bff
Use uses_test_history for selected upload tests
2018-08-29 22:41:55 +02:00
Martin Cech
0acdc8a1a3
adjust test definitions for compressed handling
...
so it tests the new defaults
2018-08-29 13:54:06 -04:00
John Chilton
f9ba8d3823
Allow setting tags on targets & contents in data fetch API.
...
Rebased with default argument handling improvements suggested by Marius.
2018-07-16 08:46:57 -04:00
djcomlab
a98cc55db2
Fix upload test for isa-tab datatype
2018-06-29 07:15:46 -07:00
Pierrick Roger
87cdd2156d
Start writing upload test for isa-tab.
...
Do not know how to read zip file content and submit it to uploader for a
composite type.
2018-06-07 12:07:35 +01:00
John Chilton
03a815a2c3
Some more upload/sniff tests.
2018-05-24 10:31:28 -04:00
John Chilton
cdbae706e6
Respect auto_decompress in fetch API, synchronize upload APIs.
2018-05-15 07:39:14 -04:00
John Chilton
35b96475a1
Missing upload tests.
...
Lots of upload and datatype behavior changes conflicting in 18.05 - these tests would have helped a lot.
2018-05-11 16:23:35 -04:00
Nicola Soranzo
39d7e2e739
Close file handles
2018-03-14 18:53:22 +00:00
John Chilton
d651348da6
More upload tests and fixes.
2018-03-08 10:33:42 -05:00
John Chilton
90ba35a9a4
Merge remote-tracking branch 'jmchilton/release_17.09' into merge_1709
2017-12-15 12:02:07 -05:00
John Chilton
005f9d70f3
Improve error handling for incorrect datatype upload.
2017-11-02 16:21:21 -04:00
John Chilton
bce4da7bc8
Add another upload test this time with no dbkey param.
...
Works fine...
2017-10-11 15:09:03 -04:00
John Chilton
108e94c9c2
FTP upload integration tests.
...
Test various configuration options (ftp_upload_dir, ftp_upload_identifier, ftp_upload_dir_template) and various upload API parameters (space_to_tab, to_posix_lines, auto_decompress).
2017-10-04 09:16:19 -04:00
John Chilton
8eac80a51b
More upload API tests.
2017-10-04 09:16:19 -04:00
John Chilton
78d1dda69e
Refactor API upload tests into their own test class.
2017-10-04 09:16:19 -04:00
John Chilton