John Chilton
57ff68edd0
Merge pull request #4539 from mvdbeek/purge_source
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Prevent in-place editing of uploaded files if files are imported from the FTP folder
2017-09-07 10:11:04 -04:00
Dannon Baker
d887cb17f0
Merge join_header into dev.
2017-09-06 20:35:33 -04:00
mvdbeek
cccf79ac5f
Make bz2file dependency conditional on python being below version 3.3
2017-09-05 18:30:25 +02:00
mvdbeek
46c85ffa98
Allow working with pbzip2 compressed files
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This adds supprt for uploading and uncompressing pbzip2 compressed
files by exchanging the bz2 module with bz2file (recommended as workaround in
https://docs.python.org/2/library/bz2.html ). The problem was reported by
@alpapan in #4538 and this commit should fix #4538 .
Depends on https://github.com/galaxyproject/starforge/pull/147 for the
bz2file wheel.
2017-09-05 16:54:34 +02:00
mvdbeek
06db29413e
Move instead of copying converted datasets when possible
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shutil.move tries to move files by renaming them. If that fails with
OSError (due to permission or cross-filesystem rename) it falls back to
copying files followed by removing them
(https://github.com/python/cpython/blob/2.7/Lib/shutil.py#L279 ). By
using shutil.move and catching permission problems we avoid an
unnecessary copy if source and destination are on the same filesystem.
Also avoids shutil.move if the upload tool is run as real-user which
should fix https://github.com/galaxyproject/galaxy/issues/4300 .
2017-09-03 12:03:36 +02:00
mvdbeek
62ef8b52ae
Fix sniffing for non-binary files
2017-09-03 10:49:23 +02:00
mvdbeek
14497719ba
Prevent in-place editing if purge_source is false
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When importing files from the FTP folder the admin can choose to prevent
purging of imported files. In this case the source file should not be
modified in-place by galaxy.
This also modifies relevant bare `except:` statements and modifies
the meaning of `in_place` in upload.py from no external chown script to
do not edit files in place if we keep the source file.
This fixes https://github.com/galaxyproject/galaxy/issues/4527 .
2017-09-03 09:48:39 +02:00
John Chilton
5a7a15d161
Test and clarifications for composite uploads.
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- Add an API test for datatype-defined composite uploads - including exercising newline conversion and the space_to_tab parameter.
- Add a test decorator skip_without_datatype to mirror skip_without_tool for this test, improve both decorators.
- The ftype parameter in the composite test tools does nothing - drop it and drop it from the XSD spec.
- Slightly improve the documentation for these composite_data elements in the XSD.
2017-08-31 12:47:40 -04:00
Nuwan Goonasekera
52b26f45a2
Registered genomespace_importer as a tool needing Galaxy's python env
2017-08-19 00:38:08 +05:30
Nuwan Goonasekera
3e8bf3c4e7
Moved genomespace token to environment variable
2017-08-19 00:38:08 +05:30
Nuwan Goonasekera
46dc4a252c
Fixed template formatting according to review comments
2017-08-19 00:38:08 +05:30
Nuwan Goonasekera
b73e21b584
Formatting and linting fixes for GenomeSpace tool
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
517fd23fc8
Fixed typo in exporter help text
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
678d575a7a
Improved recognition of compressed files
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
46c04dcbd4
Fix incorrect reference when determining file type through file ext
2017-08-19 00:38:07 +05:30
Nuwan Goonasekera
cb1b086324
Fixed pylint errors
2017-08-19 00:38:07 +05:30
slugger70
b04ccbe55b
Fixed genomespace_importer.xml command block
2017-08-19 00:38:06 +05:30
Nuwan Goonasekera
ad1b613445
Added support for pushing multiple files from GenomeSpace to Galaxy.
2017-08-19 00:38:06 +05:30
Nuwan Goonasekera
e39901ef06
Moved back some code to wrapper and added back data type sniffing.
2017-08-19 00:38:06 +05:30
Nuwan Goonasekera
1342c2bd70
Integrated File Browsing and Workflow support for GenomeSpace
2017-08-19 00:38:06 +05:30
John Chilton
0fa287f76a
Add autopep8 script to help rebasing branches after #4440 .
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Fixes a few more PEP8 issues as part of the autopep8'ing as well.
2017-08-17 13:47:03 -04:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
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using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
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using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
John Chilton
fec1eab82d
Add ability to arbitrarily not decompress files on upload via API.
2017-08-12 06:36:50 -04:00
John Chilton
59aa11864a
Add configuration option to disable upload content checking.
2017-08-12 06:36:50 -04:00
Björn Grüning
46dbf8d10c
Merge pull request #3076 from peterjc/gff3_filter_by_attribute
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GFF3 support in filter by attribute
2017-06-26 18:00:45 +02:00
lecorguille
530827f654
join with header: flake import order fix
2017-06-26 17:16:15 +02:00
lecorguille
222a7502e7
join header: fix tool syntax
2017-06-26 15:55:41 +02:00
lecorguille
f8bc407617
join with header: add a use case with a fill value
2017-06-26 15:12:21 +02:00
lecorguille
712a7045e5
join with header: add a regression test
2017-06-26 15:12:15 +02:00
lecorguille
406c71acab
join with header: test passed
2017-06-26 15:12:12 +02:00
lecorguille
5cf405902b
join with header: add test
2017-06-26 15:11:51 +02:00
Devon Ryan
8a6ef05858
Single quote file names
2017-06-26 13:56:56 +02:00
peterjc
005f3d9f98
Defensive code in case standard GFF fields missing
2017-06-26 11:16:14 +01:00
peterjc
c87e0eedb7
Cope with GFF3 as well as legacy GFF.
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In GFF3 have key=value rather than space separated
as in legacy GFF and GTF format. Closes #3068 .
2017-06-26 11:16:06 +01:00
peterjc
cb40b01db8
Ignore blank lines and comments in GFF files
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Previously would wrongly issue warnings about valid # lines.
Closes #3067
2017-06-26 11:15:08 +01:00
Devon Ryan
4ee1848992
Running a word count on a compressed fastq file now runs wc on the uncompressed file
2017-06-26 12:03:57 +02:00
guerler
7a6961e30d
Undo dataset renaming
2017-05-01 11:57:07 -04:00
Nicola Soranzo
d1974a42e5
Use detect_errors="exit_code" in Trim tool
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Prevent job failures due to spurious messages on stderr from the cluster
scheduler.
2017-04-04 18:47:55 +01:00
Nate Coraor
f645259dd0
Only keep the last path element when naming files uploaded via the URL
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paste method
2017-02-27 10:59:21 -05:00
Nicola Soranzo
03a807e374
Lint some tools
2017-01-23 21:11:43 +00:00
John Chilton
45bf7ad8c4
Make requirement tags in bar_chart.xml functional with default dependency resolver.
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I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose.
xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening
2017-01-19 17:05:53 -05:00
John Chilton
52e4b6e89e
Remove seemingly unused file sort_gtf.py.
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Added in df28aec040
2016-12-23 10:21:15 -05:00
John Chilton
58a3a5b71b
Fix linting of gff_filter_by_attribute.
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Broken during security patching - Travis tests are failing now against dev.
2016-12-16 10:10:44 -05:00
Nate Coraor
74923463cf
Merge branch 'release_16.10' into dev
2016-12-15 13:08:22 -05:00
Nate Coraor
42cda96928
Merge branch 'release_16.07' into release_16.10
2016-12-15 13:07:39 -05:00
Nate Coraor
22fda449f9
Merge branch 'release_16.04' into release_16.07
2016-12-15 13:05:22 -05:00
Nate Coraor
4cf70aea79
Merge branch 'release_16.01' into release_16.04
2016-12-15 13:04:29 -05:00
Nate Coraor
4c07734f57
Merge branch 'release_15.10' into release_16.01
2016-12-15 12:55:39 -05:00
Nate Coraor
95daf69b37
Merge branch 'release_15.07' into release_15.10
2016-12-15 12:49:39 -05:00
John Chilton