 spficklin
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bf802025f2
Added support for paging of chado queries, and adjusted support for genotype templates
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před 12 roky |
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spficklin
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c783298b56
Fixed bug in feature/XXX menu callback
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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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spficklin
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d2b7b59b9e
Fixed issues with the library module
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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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spficklin
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403d2803cf
Fixed issue #1661530
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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
 ficklin
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96856a97d5
Added template for feature_cvterm recoords
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před 12 roky |
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spficklin
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5fcf1c8645
Oops fixed type
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před 12 roky |
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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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před 12 roky |
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spficklin
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cd87d5a56a
Fixed Drupal formatting standards
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před 12 roky |
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spficklin
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d95e608e34
Oops forgot to take out dpm's
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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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spficklin
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87400a3502
Added hook to display args in job view
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před 12 roky |
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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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před 12 roky |
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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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před 12 roky |
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spficklin
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ac7081027a
Removed the feature browser from the library and anslysis pages.
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před 12 roky |
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spficklin
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138637d6eb
Fixed bug in annotated feature display
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před 12 roky |
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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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před 12 roky |
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spficklin
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b4ad2e1b5d
combined object and subject relationships into a single template
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před 12 roky |
