modifications to add date and column type changes

svn path=/; revision=302

diff --git a/Personnel/athreyab/interactions/interactionPathsFromSif.pl b/Personnel/athreyab/interactions/interactionPathsFromSif.pl
index eb93e75735b78809c2066f7ea415e25a5479620d..cbf4df7584a63ac68f51500ab0845d7f11e991c2 100644 (file)
--- a/Personnel/athreyab/interactions/interactionPathsFromSif.pl
+++ b/Personnel/athreyab/interactions/interactionPathsFromSif.pl
@@ -4,6 +4,7 @@
 use Switch;
 use DBI;
 use Config::IniFiles;
+use POSIX qw/strftime/;
 
 require "interactionPath.pl";
 
@@ -200,8 +201,8 @@ sub importSifData
                                #but in the future, we may allow people other than the devs to upload the data themselves.
                $interactionId = getInteractionId($accession_left_id,$interaction_type_id,$accession_right_id,$curatorId);
                if(isEmpty($interactionId)){
-                       $query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`curator_id`)
-                        VALUES('$accession_left_id','$accession_right_id','$interaction_type_id','$curatorId')";
+                       $query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`curator_id`,`date`)
+                        VALUES('$accession_left_id','$accession_right_id','$interaction_type_id','$curatorId', '".strftime("%Y-%m-%d", localtime)."')";
                         executeDbQuery($query);                                        
                }
        }

diff --git a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl
index bf0b1740db31a316dab59bd07df3e38ef6ce9157..950f0aa762b39d20d2b2dd66eb99015c3180ce99 100644 (file)
--- a/Personnel/athreyab/interactions/interactionPathsFromTsv.pl
+++ b/Personnel/athreyab/interactions/interactionPathsFromTsv.pl
@@ -76,9 +76,9 @@ sub importSeedInteractionData(){
        #if not, insert data into to the database
        if(isEmpty($interaction_id)){
        $query = "INSERT INTO Interaction(`object_id_left`,`object_id_right`,`interaction_type_id`,`mode_of_action_id`,
-       `interactor_type_id_left`,`interactor_type_id_right`,`evidence_id`,`evidence_code_id`,`experiment_id`,`comments`,`curator_id`) 
+       `interactor_type_id_left`,`interactor_type_id_right`,`evidence_id`,`evidence_code_id`,`experiment_id`,`comments`,`curator_id`,`date`) 
        VALUES ('$obj_id_left','$obj_id_right','$interaction_type_id','$mode_of_action_id','$int_type_id_left','$int_type_id_right'
-       ,'$evidence_id','$evidence_code_id','$experiment_id','$comments','$curator_id')";      
+       ,'$evidence_id','$evidence_code_id','$experiment_id','$comments','$curator_id', '".strftime("%Y-%m-%d", localtime)."')";      
        executeDbQuery($query);
       }                                
        }

diff --git a/Personnel/athreyab/interactions/interactionTables.sql b/Personnel/athreyab/interactions/interactionTables.sql
index 26b5b8ac20d3a0810a86849f659b7b321e048eed..ad87626d1b15dd6683d773d1bcb375a23ae340f8 100644 (file)
--- a/Personnel/athreyab/interactions/interactionTables.sql
+++ b/Personnel/athreyab/interactions/interactionTables.sql
@@ -15,6 +15,7 @@ CREATE  TABLE IF NOT EXISTS `interaction`.`Species` (
   `species_id` INT NOT NULL AUTO_INCREMENT ,
   `species` VARCHAR(45) NOT NULL ,
   `NCBI_taxonomy_id` VARCHAR(45) NULL ,
+  `accession_info_url` VARCHAR(45) NULL ,
   PRIMARY KEY (`species_id`) ,
   UNIQUE INDEX `species_UNIQUE` (`species` ASC) )
 ENGINE = InnoDB;
@@ -171,7 +172,7 @@ CREATE  TABLE IF NOT EXISTS `interaction`.`Interaction` (
   `experiment_id` INT NULL ,
   `comments` VARCHAR(255) NULL ,
   `curator_id` INT NULL ,
-  `date` DATE NULL ,
+  `date` VARCHAR(10) NULL ,
   PRIMARY KEY (`interaction_id`) ,
   INDEX `fk_Interactions_1` (`object_id_left` ASC) ,
   INDEX `fk_Interactions_2` (`object_id_right` ASC) ,
@@ -418,53 +419,53 @@ INSERT INTO `Mode_of_action`(`mode_of_action`) VALUE('down regulates');
 -- -----------------------------------------------------
 -- Populate `interaction`.`Species` with known values
 -- -----------------------------------------------------
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('59689','Arabidopsis lyrata');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3702','Arabidopsis thaliana');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('15368','Brachypodium distachyon');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('6239','Caenorhabditis elegans');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3649','Carica papaya');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3055','Chlamydomonas reinhardtii');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('85681','Citrus clementina');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('2711','Citrus sinensis');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3659','Cucumis sativus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('7955','Danio rerio');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('7227','Drosophila melanogaster');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('2880','Ectocarpus siliculosus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('562','Escherichia coli');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('71139','Eucalyptus grandis');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('57918','Fragaria vesca');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('5507','Fusarium oxysporum');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3847','Glycine max');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('9606','Homo sapiens');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('180498','Jatropha curcas');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('29883','Laccaria bicolor');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3983','Manihot esculenta');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3880','Medicago truncatula');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4155','Mimulus guttatus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('10090','Mus musculus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('140110','Nectria haematococca');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('5141','Neurospora crassa');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('272131','Nostoc punctiforme');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4530','Oryza sativa');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('121225','Pediculus humanus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('42345','Phoenix dactylifera');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3218','Physcomitrella patens');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3694','Populus trichocarpa');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3760','Prunus persica');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('10116','Rattus norvegicus');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('64495','Rhizopus oryzae');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3988','Ricinus communis');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4932','Saccharomyces cerevisiae');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4896','Schizosaccharomyces pombe');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('88036','Selaginella moellendorffii');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4113','Solanum tuberosum');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4558','Sorghum bicolor');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('3641','Theobroma cacao');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('29910','Tolypocladium inflatum');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('63577','Trichoderma atroviride');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('1206','Trichodesmium erythraeum');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('29760','Vitis vinifera');
-INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`)  VALUES('4577','Zea mays');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('59689','Arabidopsis lyrata','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3702','Arabidopsis thaliana','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('15368','Brachypodium distachyon','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('6239','Caenorhabditis elegans','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3649','Carica papaya','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3055','Chlamydomonas reinhardtii','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('85681','Citrus clementina','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('2711','Citrus sinensis','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3659','Cucumis sativus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('7955','Danio rerio','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('7227','Drosophila melanogaster','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('2880','Ectocarpus siliculosus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('562','Escherichia coli','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('71139','Eucalyptus grandis','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('57918','Fragaria vesca','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('5507','Fusarium oxysporum','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3847','Glycine max','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('9606','Homo sapiens','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('180498','Jatropha curcas','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('29883','Laccaria bicolor','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3983','Manihot esculenta','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3880','Medicago truncatula','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4155','Mimulus guttatus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('10090','Mus musculus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('140110','Nectria haematococca','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('5141','Neurospora crassa','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('272131','Nostoc punctiforme','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4530','Oryza sativa','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('121225','Pediculus humanus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('42345','Phoenix dactylifera','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3218','Physcomitrella patens','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3694','Populus trichocarpa','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3760','Prunus persica','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('10116','Rattus norvegicus','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('64495','Rhizopus oryzae','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3988','Ricinus communis','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4932','Saccharomyces cerevisiae','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4896','Schizosaccharomyces pombe','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('88036','Selaginella moellendorffii','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4113','Solanum tuberosum','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4558','Sorghum bicolor','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('3641','Theobroma cacao','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('29910','Tolypocladium inflatum','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('63577','Trichoderma atroviride','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('1206','Trichodesmium erythraeum','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('29760','Vitis vinifera','gramene');
+INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`,`accession_info_url`)  VALUES('4577','Zea mays','gramene');
 
 SET SQL_MODE=@OLD_SQL_MODE;
 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;