John Chilton
915948a305
Hide to_posix_lines in UI by default.
...
Galaxy still completely supports this option on backend - API tests still completely work and will hopefully ensure this functionality continues running. Any Galaxy deployements that wish to enable this option simply have to switch this one param from hidden to select. This is a ugly workaround - but it is a very small workaround - and will hopefully alleviate any potential fears Gert Hulselmans has of Galaxy diverging from his changes. This is only a stop gap until the Galaxy upload UI supports more advanced options.
I have previously outlined my concerns with the visual clutter on the upload.xml page - this is why I am hiding it by default. If anyone with commit access disagrees - please by all means backout of this individual changeset and restore the full functionality of pull request 171 (I have a terrible eye for this sort of GUI design stuff).
2014-01-17 00:03:26 -06:00
Gert Hulselmans
fb01c3cc96
Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.
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Add an option in the upload tool to disable the conversion of universal
line endings to Posix line endings.
This is useful for avoiding corruption of uploaded files when a binary
file is contained inside a gzip, bz2 and zip archive.
This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702
2013-05-27 20:55:52 +02:00
John Chilton
262413f7c0
Based on input from natefoo, replace root tool tag "upload" with inverse tag "workflow_compatible". Adjust logic in tools module accordingly.
2013-02-13 10:45:56 -06:00
John Chilton
7e6ee45bb0
Add optional "upload" attribute to tool definitions.
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When extracting workflows, such tools are treated as inputs. This eliminates the need for the hack of hardcoding 'upload1' in tools.py and allows multiple upload tools to exist and function properly when extracting workflows.
2013-02-10 11:13:51 -06:00
Daniel Blankenberg
a273960126
Backout 3189a1bf18af
2013-02-04 06:43:35 -05:00
Daniel Blankenberg
bab984ed69
Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py
2013-02-04 06:33:19 -05:00
Brad Chapman
cf1407d471
Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API
2012-10-04 15:31:16 -04:00
Nate Coraor
03c4fa3689
The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.
2011-12-06 11:42:12 -05:00
Kanwei Li
a9370f1b72
Spacing fix
2011-08-20 02:56:33 -04:00
Nate Coraor
1026641425
Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes issue #533 .
2011-06-08 13:25:45 -04:00
Nate Coraor
15aa3cba69
Highlight the futility of uploading files >2GB via a browser.
2011-01-14 23:52:31 -05:00
Nate Coraor
c9a881e114
Add a new "Files uploaded via FTP" grid to the upload form and related parameter types, form fields, etc.
2010-11-05 11:04:50 -04:00
Nate Coraor
4ca447aa70
Add support for bz2 compressed uploads.
2010-09-10 14:07:16 -04:00
Nate Coraor
8a66864aee
Stop ignoring the sniff order set in the datatypes config file.
2010-08-18 14:56:10 -04:00
Nate Coraor
7c71894533
Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani.
2010-06-23 16:48:13 -04:00
Nate Coraor
ca066cef04
Add a tip to the upload tool about using url paste for big files
2010-05-04 10:18:42 -04:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Greg Von Kuster
dd32491716
A bit of code cleanup in genetics.py, and add all rgenetics data types to datatypes_conf.xml.sample. Also include the new Sff data type in the upload config help section.
2009-11-13 16:24:00 -05:00
Nate Coraor
e8cbb18a87
Make Galaxy attempt to honor the user's umask and primary group (output datasets can have the wrong primary group if the primary group differs on the cluster). Also fixed a composite datatype files_path bug in the upload tool.
2009-10-23 14:33:23 -04:00
Nate Coraor
d14eb4d653
Reintroduce nginx upload module support.
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http://www.grid.net.ru/nginx/upload.en.html
The following config variables are added to universe_wsgi.ini:
nginx_upload_store = Path to nginx upload store
ex: = database/upload_store
nginx_upload_path = URL (from root of the Galaxy server) to direct upload POSTs to
ex: = /_upload
The following nginx config supports such a configuration:
location /_upload {
upload_store /path/to/galaxy/database/upload_store;
upload_pass_form_field "tool_id";
upload_pass_form_field "tool_state";
upload_pass_form_field "async_datasets";
upload_pass_form_field "^files_[0-9]+\|.*";
upload_pass_form_field "file_type";
upload_pass_form_field "dbkey";
upload_pass_form_field "runtool_btn";
upload_pass_form_field "ajax_upload";
upload_pass_form_field "upload_option";
upload_pass_form_field "library_id";
upload_pass_form_field "folder_id";
upload_pass_form_field "message";
upload_pass_form_field "roles";
upload_set_form_field "__${upload_field_name}__is_composite" "true";
upload_set_form_field "__${upload_field_name}__keys" "name path";
upload_set_form_field "${upload_field_name}_name" "$upload_file_name";
upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path";
upload_pass_args on;
upload_pass /_upload_done;
}
location /_upload_done {
set $dst /tool_runner/index;
if ($args ~ nginx_redir=([^&]+)) {
set $dst $1;
}
rewrite "" $dst;
}
2009-09-29 17:14:20 -04:00
Kanwei Li
3531212ff6
typo fixes for tools in folders A-M
2009-09-27 23:11:43 -04:00
Nate Coraor
6f3a169b01
Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally
2009-09-10 14:52:38 -04:00
Nate Coraor
3f5da01132
Real Job(tm) upload support
2009-08-20 10:49:54 -04:00
Daniel Blankenberg
cc22aee3cb
Initial pass at allowing the setting of certain metadata parameters on upload (controlled via a flag). This allows the user to specify the 'base_name' to be used for Rgenetics datatypes, etc. Bunch of cleanup needed in upload.
2009-07-15 14:11:35 -04:00
James Taylor
db9c0a9870
Commenting out 'other dbkey' in upload
2009-06-11 15:41:57 -04:00
James Taylor
537f8952ef
Merging Ian's trackster update with current head
2009-06-11 12:20:03 -04:00
Daniel Blankenberg
c0d797e00d
Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged.
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A more structured way of storing these files (rather than dumping in a directory) is worth considering.
2009-06-08 12:49:26 -04:00
Ian Schenck
feda672ffa
- Performance of indexers much improved.
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- Indexing for tracks done in background with a visual treatment done to Trackster
- DB builds can be uploaded by a user (chromInfo/len extension).
- TODO: Add ability to change the dbkey of a dataset to any arbitrary string value.
2009-04-23 13:46:52 -04:00
Nate Coraor
86eb5e62b2
Asynchronous uploads. Currently disabled in IE, since IE throws
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occasional 'permission denied' errors when jquery attempts to set the
form target. Compatible with the nginx upload module, but interrupted
uploads will remain in the 'upload' state indefinitely.
2009-03-13 13:48:59 -04:00
Greg Von Kuster
666de20b4d
Cleanup for fastqsolexa data type converters. We are currently supporting only the Solexa variant and will add support for other variants when the formats stabilize.
2008-06-09 20:15:04 +00:00
Wen-Yu Chung
782d7db6be
Update fastq format.
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Now we only support FastqSolexa variants.
If the quality scores are presented as characters,
the integer values are obtained by their ascii code subtract 64.
2008-06-06 18:52:11 +00:00
Greg Von Kuster
1a23f9e55d
Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.
2008-05-29 19:12:36 +00:00
Daniel Blankenberg
11a2c767c3
Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.
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MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
2008-05-29 17:38:46 +00:00
Greg Von Kuster
84c5c4387d
Add support ( sans sniffer ) for FASTQ data type.
2008-05-27 19:25:54 +00:00
Greg Von Kuster
737bdf23f9
Enhanced upload to handle certain binary and zip files. Cleaned up the upload config. Added 4 new data types: ab1, scf, binseq.zip and txtseq.zip. Added Regional Variation section to tool_conf.xml.main.
2007-12-14 21:07:11 +00:00
Greg Von Kuster
ab1d867915
More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores.
2007-11-30 20:08:21 +00:00
Greg Von Kuster
79745f4012
Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py.
2007-11-29 17:04:42 +00:00
Greg Von Kuster
b3aa4efa6f
Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.
2007-10-03 14:17:41 +00:00
Greg Von Kuster
4c6dab39eb
Enhanced upload utility to dynamically load the File Format select list using values from the registry's datatypes_by_extension dictionary.
2007-09-27 14:12:01 +00:00
Chinmay Rao
18e2c28a45
Added support for gff3 datatype
2007-09-18 15:43:44 +00:00
Greg Von Kuster
a7336bfaa5
Support for Gff version 3 which will be coming from GMOD applications (wormbase, hapmap, etc).
2007-06-26 15:43:57 +00:00
Greg Von Kuster
401e30e2c5
Requires db schema change. Enhance upload tool to default to the last build used in the "current" history.
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Database changes required:
alter table history add genome_build varchar(40);
There is now a new tool ToolParameter named GenomeBuildParameter which should be useful in several existing tools.
Also took care of some other miscellaneous items.
2007-04-19 20:53:16 +00:00
Greg Von Kuster
e34fff8ff8
Added a corner-case fix for auto-detect file formats. Updated info displayed to user on upload and filter tools and added more valid words to filter tool.
2007-03-23 17:46:06 +00:00
Daniel Blankenberg
74784e1755
Pushing my changes from james-wsgi branch onto the trunk.
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Biomart doesn't work on the trunk yet (Before or after this commit).
axt to lav tool won't be functional until multiple datasets per history item is available on trunk - although I could
make it so that only the lav file is generated and no fasta files, in which case it wouldn't be an issue.
2006-12-14 21:02:17 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
John Chilton