 spficklin
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5f1f2e560f
Moved the OBO loader to the tripal_cv module
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14 anni fa |
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spficklin
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20eeab6223
Added the beginning stages of an OBO loader. So far, loads CVterms, cvterm_relationships, cvterm_dbxrefs and cvtermprops.
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14 anni fa |
 ccheng
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efeef2c916
fixed a bug for displaying up/down arrow icons when toggling all expandable boxes.
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14 anni fa |
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spficklin
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5e7b3c4b74
Fixed a bug in chado loader
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14 anni fa |
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spficklin
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372e4626ba
Added the first stages of a chado loader. So far, the additions will load chado v1.11 into a 'chado' schema within the same database that Drupal is installed. It also populates the tables with the same data when using the perl scripts.
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14 anni fa |
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spficklin
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87318da4f6
Fixed more bugs
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14 anni fa |
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spficklin
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53420365ff
Fixed a few bugs in tripal_db module
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14 anni fa |
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spficklin
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3a26c1cb26
Fixed a few minor bugs in CV module
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14 anni fa |
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spficklin
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609262cb3d
Theme fixes
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14 anni fa |
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spficklin
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171730108c
Added back in the generic vocabulary browser
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14 anni fa |
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spficklin
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5416d9c6e3
Added a user name column to the jobs table
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14 anni fa |
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spficklin
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cb72de24bb
Added an interface for editing the controlled vocabularies in the tripal_cv module. We still need something to add/edit terms. Also, fixed the interface for updating the cvtermpath table so that a user can select which ontology/vocabulary to update.
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14 anni fa |
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spficklin
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4fb63ec2d8
Changed the database module so that it functions as an AJAX enabled drop-down rather than a large table.
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14 anni fa |
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ccheng
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db70fc1dc6
fixed problems where strcmp() expects a string, not an array.
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14 anni fa |
 mestato
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678799b710
Removed ORF link from html when it is being parsed.:
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14 anni fa |
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mestato
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aa979332af
Fixed called by reference errors.
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14 anni fa |
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mestato
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6698546c6e
When processing the html from an interProScan job, empty tables are removed from the output. Also, empty rows in tables are removed.
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14 anni fa |
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mestato
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e6feb5a9b6
Moved the synchronize functions from the main module to syncFeatures.php. Moved the search indexing functions to indexFeatures.php. This allows each sync or index job to be submitted as a separate system call, thus circumventing a problem with php not releasing memory. Also, syncing and indexing all features may now be done through a command line call instead of only through the web interface.
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14 anni fa |
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mestato
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3d46597777
Removed materialized view unigene_libraries_mview. This mview exited to associate a unigene with all
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14 anni fa |
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mestato
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832463e97e
The syncing method now tries to figure out what type of analysis is being synchronized by checking the cvterm "analysis_type". This cvterm should be added to each analysis by the individual analysis modules or the user if the upload is directly into chado. The value for this cvterm should reflect the name of the module, "tripal_analysis_unigene", "tripal_analysis_blast", etc.
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14 anni fa |
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mestato
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6729e33bcd
Added missing } on line 469.
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14 anni fa |
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mestato
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61a9834df0
Add abililty for analysis module to detect a unigene-type analysis. Previously made unigene type analyses into generic type analyses.
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14 anni fa |
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mestato
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442a75c16a
Fixed typo where interval was missing dollar sign.
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14 anni fa |
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mestato
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14dde24292
The validate function now handles three schenarios:
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14 anni fa |
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mestato
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4e3a64a161
Complete revision fo the cleanup method. Still deletes any orphans between node and chado_analysis in drupal but also checks for orphans without records in chado.
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14 anni fa |
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mestato
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60d7f0e812
Fixed internal script reference to itself from tripal_job_launcher.php to tripal_jobs_launch_multi.php.
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14 anni fa |
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mestato
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1b4bb14abc
Fixed error Parameter 1 to theme_tripal_analysis_analysis_table() expected to be a reference, value given in /local/sites/drupal/sites/dev.citrusgenomedb.org/modules/devel_themer/devel_themer.module on line 418. Also changed tripal_analysis_analysis_table to tripal_analysis_analysis_page to be more clear.
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14 anni fa |
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mestato
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86062c911f
Fixing error: call_user_func_array() expects parameter 2 to be array, string given in /local/sites/drupal/sites/dev.citrusgenomedb.org/modules/tripal_cv/charts.php on line 18.
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14 anni fa |
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mestato
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617b9c6f5a
This script will allow jobs to be launched from a Drupal installation with more than one Tripal site. It takes the site name as well as an admin name for that site.
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14 anni fa |
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mestato
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3fbd9c6159
Changed tripal_organism_table to tripal_organism_page, since it creates a page, not a table.
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14 anni fa |
