 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 years ago |
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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 years ago |
 ccheng
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db70fc1dc6
fixed problems where strcmp() expects a string, not an array.
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14 years ago |
 mestato
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678799b710
Removed ORF link from html when it is being parsed.:
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14 years ago |
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mestato
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aa979332af
Fixed called by reference errors.
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14 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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mestato
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6729e33bcd
Added missing } on line 469.
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14 years ago |
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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 years ago |
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mestato
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442a75c16a
Fixed typo where interval was missing dollar sign.
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14 years ago |
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mestato
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14dde24292
The validate function now handles three schenarios:
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14 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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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 years ago |
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mestato
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fa3285fc9f
Add the correct pass by reference ampersand to return theme('tripal_library_library_table', &$libraries), as required by the new version of php.
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14 years ago |
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mestato
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a957c97937
When taxonomy is assigned to a node, all analyses are included, not just one.
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14 years ago |
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mestato
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9e5d97f27f
changed parse_NCBI_Blast_XML_index_version to tripal_analysis_blast_results_index_version, to be consistent with the naming of the methods of for non-index node building
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14 years ago |
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spficklin
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d9d2e156a4
Fixed a bug that added error messages to the administration form for features and did not properly set the defaults for some of the fields
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15 years ago |
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ccheng
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7dd59af10c
Fix a bug for parsing keg files. When there is a single quote ' in the value (e.g. 3'-deoxyribose), the SQL insertion to analysisprop fails. Single quote was replaced by html code (') before executing the SQL statement. Also, tabs in the code are replaced by spaces for proper formatting.
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15 years ago |
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ccheng
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c4baa32f1c
The blast module now loads all xml files in a directory if you input a directory instead of a file name.
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15 years ago |
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ccheng
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309927249d
fixed the loading problem for GO/Kegg on organism page where base_url is not '/'
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15 years ago |
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ccheng
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0e7b4ee987
KEGG links to the features don't work if the base url has been rewritten.
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15 years ago |
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ccheng
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68577d8681
Fixing a bug for interpro results. Interpro box should not display results that do not belong to the cvterm 'analysis_interpro_output_hit'
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15 years ago |
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ccheng
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83d3143980
When uploading a blast xml file, tripal now take the first word of <Iteration_query-def> tag to match the chado feature uniquename, instead of using the whole content of the tag for matching.
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15 years ago |
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ccheng
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254240c41f
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15 years ago |
