 spficklin
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bf802025f2
Added support for paging of chado queries, and adjusted support for genotype templates
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12 vuotta sitten |
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spficklin
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c783298b56
Fixed bug in feature/XXX menu callback
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12 vuotta sitten |
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spficklin
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9964a101c6
Removed preprocess function that accidentally got incorporated but was for a custom site. Also removed api function in organism module that didn't fit
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12 vuotta sitten |
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spficklin
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fb42852fa2
Reorganization of functions into api, includes and theme files to make all modules consistent
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12 vuotta sitten |
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spficklin
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d2b7b59b9e
Fixed issues with the library module
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12 vuotta sitten |
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spficklin
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cf8e652b36
Fixed GFF loader for deleting entries in a GFF file. It was broken
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12 vuotta sitten |
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spficklin
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b6444c78ad
Debugging Tripal CV module and created API function for feature relationships
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12 vuotta sitten |
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spficklin
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d7e679c118
Removed match_part from parent/child variables in the alignment preprocess function
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12 vuotta sitten |
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spficklin
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4560a2dce9
Made some additional bug fixes and improvements to the GFF loader
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12 vuotta sitten |
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spficklin
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8924d71248
Added support to the GFF loader for specifying target species and tyeps
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12 vuotta sitten |
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spficklin
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48631d702c
Fixed a bug when registering a new analysis module. If the module already existed in the table it threw an error. Now it checks first. Also fixed bug with chado_query to not add a 'chado.' prefix in the 'substring' psql function. Also updated the tripal_core_chado_update module to return the primary key if a single record is updated and if the return_record option is given.
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12 vuotta sitten |
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spficklin
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0b674f6e64
Removed old relationship aggregator table and code. We don't use it.
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12 vuotta sitten |
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spficklin
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403d2803cf
Fixed issue #1661530
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12 vuotta sitten |
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spficklin
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9bb94c3748
Fixed issue #1699022. Took out all code that tried to distinguish a revision.
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12 vuotta sitten |
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spficklin
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7c95f3d958
Fixed Issue #1809994. The FASTA loader now correctly loads relationships and external DB referneces. Also, removed the requirement that residues have only IUPAC characters. The check incorrectly forgot protein characters, but also sometimes there may be additional characters and we shouldn't limit the field
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12 vuotta sitten |
 ficklin
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96856a97d5
Added template for feature_cvterm recoords
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12 vuotta sitten |
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spficklin
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5fcf1c8645
Oops fixed type
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12 vuotta sitten |
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spficklin
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a81383d8cf
Added functionality similar to GBrowse. Users can access any feature with the following URL http://<your site>/feature/<name>. Tripal will recoginze the URL, search for a feature of that name, uniquename or synonym and redirect to the page. If there are more than one feature that matches, a table with all matches will be shown and the user can select which one they want to see
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12 vuotta sitten |
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spficklin
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cd87d5a56a
Fixed Drupal formatting standards
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12 vuotta sitten |
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spficklin
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d95e608e34
Oops forgot to take out dpm's
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12 vuotta sitten |
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spficklin
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875cddbbcb
Fixed bug where featurelocs weren't showing up if one of the two FK relationships returned NULL
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12 vuotta sitten |
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spficklin
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a52dc176d2
Fixed bug where featurelocs weren't showing up if one of the two FK relationships returned NULL
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12 vuotta sitten |
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spficklin
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2a743acf56
Made transactions optional in GFF loader. Changed all appropriate db_queryt to chado_query in feature module. Added a drush command to sync a single feature (useful for debugging/testing).
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12 vuotta sitten |
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spficklin
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87400a3502
Added hook to display args in job view
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12 vuotta sitten |
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spficklin
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6cfe5c467e
When syncing features repetitive error logs were entered into the Drupal report log for every synced feature stating that a duplicate feature could not be inserted. This was fixed
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12 vuotta sitten |
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spficklin
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2840b98e85
All node types (except stock) have a function to cleanup orphaned nodes but it wasn't complete for some. A new core API function was created that all modules with node types can use to clean up orphaned nodes. Also, the drush trpjob-run command was fixed so that a username must be provided to run the job
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12 vuotta sitten |
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spficklin
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ac7081027a
Removed the feature browser from the library and anslysis pages.
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12 vuotta sitten |
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spficklin
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138637d6eb
Fixed bug in annotated feature display
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12 vuotta sitten |
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spficklin
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91184c553b
Fixed the get sequence function to work with Postgres 8.4 and fixed the annotated feature so that it can properly display overlapping parts and show the sequence in reverse complement if on the reverse strand
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12 vuotta sitten |
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spficklin
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b4ad2e1b5d
combined object and subject relationships into a single template
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12 vuotta sitten |
