Changeset 22712

Timestamp:

03/09/10 16:23:47 (17 months ago)

Author:

julie

Message:

updated skeleton with new model

Location:

trunk/bio/skeletons/mine/dbmodel

Files:

• project.properties (modified) (2 diffs)
• resources/genomic_keyDefs.properties (modified) (3 diffs)
• resources/genomic_precompute.properties (modified) (2 diffs)

trunk/bio/skeletons/mine/dbmodel/project.properties

@@ -1 @@
-compile.dependencies = intermine/integrate/main
+compile.dependencies = intermine/integrate/main, bio/core/main
 
 objectstore.name = os.production
@@ -5 +5 @@
 
 core.model.path = bio/core
-extra.model.paths.start = build/model/so_additions.xml bio/core/genomic_additions.xml
+extra.model.paths.start = ${mine-dir}/dbmodel/build/model/so_additions.xml bio/core/genomic_additions.xml
 extra.model.paths.end = bio/core/shortcuts.xml
 

trunk/bio/skeletons/mine/dbmodel/resources/genomic_keyDefs.properties

@@ -10 +10 @@
 Protein.key_md5checksum_taxonid=md5checksum, organism
 Sequence.key_md5checksum=md5checksum
-Region.key_primaryidentifier_org=primaryIdentifier, organism
-Synonym.key_synonym = subject, value, type
+Synonym.key_synonym = subject, value
 Organism.key_taxonid=taxonId
 LocatedSequenceFeature.key_primaryidentifier=primaryIdentifier
@@ -19 +18 @@
 DataSource.key_name = name
 Author.key_name = name
-Location.key_all = subject, object, end, start, strand
-OntologyTerm.key_identifier=identifier
-OntologyTerm.key_name_ontology=name, ontology
-OntologyRelation.key=parentTerm, childTerm, relationship
-OntologyTermSynonym.key=name, type
-Ontology.key_title=name
+Location.key_all = locatedOn, locatedFeature, end, start, strand
 Comment.key_comment = text, type, source
 ProteinDomain.key_identifier = primaryIdentifier
@@ -31 +25 @@
 Chromosome.key_primaryidentifier = primaryIdentifier
 
-# IntAct and BioGRID
-InteractionTerm.key_name=name
-InteractionTerm.key_identifier=identifier
-InteractionExperiment.key_name_pub = name, publication
-InteractionRegion.key_region = location, interaction, gene
-Interaction.key_interaction = shortName, gene, experiment
-Interaction.key_name_role = experiment, name, role

trunk/bio/skeletons/mine/dbmodel/resources/genomic_precompute.properties

@@ -1 +1 @@
 # Bag upload queries
-precompute.query.1 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true)
+precompute.query.1 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE a1_.synonyms CONTAINS a2_ 
 
-precompute.query.2 = SELECT a1_.id as a3_, a2_.value as a4_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false)
-
-precompute.query.3 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = true AND a1_.organism CONTAINS a5_)
-
-precompute.query.4 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a2_.isPrimary = false AND a1_.organism CONTAINS a5_)
+precompute.query.3 = SELECT a1_.id AS a3_, a2_.value AS a4_, a5_.shortName as a6_ FROM org.intermine.model.bio.BioEntity AS a1_, org.intermine.model.bio.Synonym AS a2_, org.intermine.model.bio.Organism AS a5_ WHERE (a1_.synonyms CONTAINS a2_ AND a1_.organism CONTAINS a5_)
 
 # gene/protein --> organism [used by some widgets]
@@ -14 +10 @@
 
 # chromosome distribution widget
-precompute.query.7 = SELECT a2_.id as a4_, a1_.primaryIdentifier AS a5_, a2_.primaryIdentifier AS a6_,  a3_.name as a7_ FROM org.intermine.model.bio.Chromosome AS a1_, org.intermine.model.bio.LocatedSequenceFeature AS a2_, org.intermine.model.bio.Organism AS a3_ WHERE (a2_.chromosome CONTAINS a1_ AND a2_.organism CONTAINS a3_)
+precompute.query.7 = SELECT a2_.id as a4_, a1_.primaryIdentifier AS a5_, a2_.primaryIdentifier AS a6_,  a3_.name as a7_ FROM org.intermine.model.bio.Chromosome AS a1_, org.intermine.model.bio.SequenceFeature AS a2_, org.intermine.model.bio.Organism AS a3_ WHERE (a2_.chromosome CONTAINS a1_ AND a2_.organism CONTAINS a3_)