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Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Sep 20 20:53:45 2010 UTC (9 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0928, rast_rel_2010_1206
Changes since 1.25: +3 -1 lines
Diff to previous 1.25
Support -determineFamily

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 18 16:58:49 2010 UTC (9 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0827
Changes since 1.24: +20 -8 lines
Diff to previous 1.24
Update parser for new html format.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 2 19:02:19 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.23: +2 -1 lines
Diff to previous 1.23
Allow anyone with access to the job to be able to upload data.
Unlink the spooled tarfile upon successful extraction.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 1 20:25:29 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.22: +59 -8 lines
Diff to previous 1.22
Add chunked upload and directory support.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 30 21:53:54 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
bugfix

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 30 21:50:10 2010 UTC (9 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.20: +73 -0 lines
Diff to previous 1.20
First working version of copy code

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 22 22:15:17 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.19: +1 -1 lines
Diff to previous 1.19
bugfix

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 22 22:05:24 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.18: +1 -1 lines
Diff to previous 1.18
bugfix

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 22 21:58:50 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.17: +2 -0 lines
Diff to previous 1.17
add non-active support

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 20:31:52 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.16: +4 -4 lines
Diff to previous 1.16
don't check for resource missing, but look for ^LOCUS when downloading to catch different error cases.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 20:19:27 2009 UTC (9 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.15: +50 -2 lines
Diff to previous 1.15
NCBI will return documents containing "The resource is temporarily
unavailable" when a download times out. The transfer is not flagged as
an HTTP error, so the code was treating them as valid downloads.

This rev checks the content to make sure it does not contain that
message, and fails the download attempt if it does. It also checks the
content of the cache files in the event that there is bad cached data.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 4 18:24:36 2009 UTC (10 years ago) by gdpusch
Branch: MAIN
Changes since 1.14: +101 -18 lines
Diff to previous 1.14
Added limited support for WGS accessions.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 23 20:38:04 2009 UTC (10 years ago) by olson
Branch: MAIN
Changes since 1.13: +2 -3 lines
Diff to previous 1.13
some minor fixups

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 23 20:03:45 2009 UTC (10 years ago) by olson
Branch: MAIN
Changes since 1.12: +56 -5 lines
Diff to previous 1.12
Pull out the URL retrieval code into url_get() which will do a limited number of retries
when a specified set of error codes are returned.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 23 18:43:18 2009 UTC (10 years ago) by olson
Branch: MAIN
Changes since 1.11: +95 -8 lines
Diff to previous 1.11
Parse out the source lines, pull the dbxref from either the source that matches
the overall SOURCE for the genbank file, or from the first in the list if none matches exactly.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 20 17:38:06 2009 UTC (10 years ago) by olson
Branch: MAIN
Changes since 1.10: +66 -1 lines
Diff to previous 1.10
updates to rast submission module

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 29 16:20:08 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.9: +1 -1 lines
Diff to previous 1.9
Fix 666666 problem.
Add support for using the test server.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 26 18:19:57 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.8: +13 -4 lines
Diff to previous 1.8
Add SAS comments.
Add real implementation of user_may_access_job and user_owns_job in RAST_submission
so that the batch interface obeys the permissions set up by the RAST server.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 23 18:30:17 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.7: +13 -9 lines
Diff to previous 1.7
Fix support for retreive_RAST_job so it sr

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 22 21:15:13 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.6: +383 -3 lines
Diff to previous 1.6
Lastest code. working submissions, plus kill & delete job.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 21 21:45:03 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.5: +28 -3 lines
Diff to previous 1.5
Add more details to output of get_contigs_from_entrez:

$VAR1 = {
          'length' => '16660',
          'project' => '15760',
          'name' => 'Mycobacterium gilvum PYR-GCK',
          'contents' => '<genbank file>',
          'id' => 'NC_009341',
          'taxonomy_id' => '350054'
        };

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 21 21:27:02 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.4: +28 -1 lines
Diff to previous 1.4
add get_contigs_from_entrez

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 21 20:05:36 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.3: +224 -1 lines
Diff to previous 1.3
Add support for get_contig_ids_in_project_from_entrez

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 21 17:19:31 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.2: +57 -0 lines
Diff to previous 1.2
added retrieve_RAST_job

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 20 20:43:30 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.1: +69 -6 lines
Diff to previous 1.1
fixes for the status checker

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 19 20:12:18 2009 UTC (10 years, 1 month ago) by olson
Branch: MAIN
Rast submission server modules.

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