From: <no...@us...> - 2012-01-26 22:10:41
|
Revision: 4145 http://obo.svn.sourceforge.net/obo/?rev=4145&view=rev Author: nomi Date: 2012-01-26 22:10:33 +0000 (Thu, 26 Jan 2012) Log Message: ----------- Nicole thinks we can get rid of the worm configs. zfin-web.cfg doesn't work from standalone Phenote, and webstart Phenote is not currently supported. Modified Paths: -------------- phenote/trunk/conf/demo.cfg Removed Paths: ------------- phenote/trunk/conf/worm-go.cfg phenote/trunk/conf/worm-interaction.cfg phenote/trunk/conf/worm-transgene.cfg phenote/trunk/conf/worm.cfg phenote/trunk/conf/wormRef.cfg phenote/trunk/conf/zfin-web.cfg Modified: phenote/trunk/conf/demo.cfg =================================================================== --- phenote/trunk/conf/demo.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/demo.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -3,7 +3,7 @@ <ns:phenote-configuration xmlns:ns="phenote/config/xml" version="1.5" name="Demo Configuration" author="Phenote Developers" - description="This is a configuration for demonstration purposes only. It shows the different types of fields, ontologies, etc. Use of the sample_data.xls can be loaded into this configuration."> + description="This is a configuration for demonstration purposes only. It shows the different types of fields, ontologies, etc. sample_data.xls can be loaded into this configuration."> <!-- *********************** SETTINGS **************************** --> <!-- master-to-local-config allows one to have a master config that Deleted: phenote/trunk/conf/worm-go.cfg =================================================================== --- phenote/trunk/conf/worm-go.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/worm-go.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,84 +0,0 @@ -<phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd"> - - <!-- master-to-local-config mode="UPDATE" when="ALWAYS"/ --> - <master-to-local-config mode="WIPEOUT" when="ALWAYS" - overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm-go.cfg" /> - - <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> - <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" - enable="true"/> - <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/> - <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/> - - <dataadapter name="phenote.dataadapter.worm.WormGoAdapter" is-queryable="true" enable="true"/> - - <log config-file="conf/log4j.xml"/> - - <uvic-graph enable="false"/> - <term-history enable="false"/> - - <auto-update-ontologies enable="true"/> <!--true=update; false=don't update--> - <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds--> - - <group name="default" title="Main" container="tab" interface="default"/> - - <!-- disable tabbing of fields in main panel --> - <field-panel-tabs enable="false"/> - - <field name="Paper" datatag="Paper" enable="true" groups="default"> - <!--<ontology name="Paper" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi?short=5"/>--> - <ontology name="Paper" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/> - </field> - - <field name="Gene" datatag="Gene" enable="true"> - <!--<ontology name="Gene" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>--> - <ontology name="Gene" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/> - </field> - - <field name="Curator" datatag="Curator" enable="true"> - <!--<ontology name="Curator" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator_go.obo"/>--> - <ontology file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi" slim="curator_slim_go"/> - <!-- ontology name="Curator2" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator.obo"/ --> - </field> - - <field name="GO Ontology" datatag="GoOntology" enable="true"> - <ontology name="GoOntology" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/go_ontology.obo"/> - </field> - - <field name="GO Term" datatag="GoTerm" enable="true"> - <ontology name="GO" file="http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo"/> - </field> - - <field name="GO Evidence" enable="true"> - <ontology name="GoEvidence" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/go_inference.obo"/> - </field> - - <field name="with" datatag="with" enable="true" groups="default"/> - - <field name="Qualifier" enable="true"> - <ontology name="Qualifier" - file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/go_qualifier.obo"/> - </field> - - <field name="DB Object Type" enable="true"> - <ontology name="DbObjectType" - file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/go_dbobjecttype.obo"/> - </field> - - <field name="Gene Product" datatag="GeneProduct" enable="true" groups="default"/> - - <field name="PgdbId" enable="true" copy-field="false" type="READ_ONLY" groups="default"/> - - <field name="Person" datatag="Person" enable="true" groups="default" isList="true"> - <!--<ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi?short=5"/>--> - <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/> - </field> - - <field name="Comment" datatag="Comment" enable="true" groups="default"/> - <field name="Last Updated" datatag="LastUpdated" enable="true" groups="default"/> - - - -<!-- <constraint className="phenote.dataadapter.worm.WormConstraint"/>--> - -</phenote-configuration> Deleted: phenote/trunk/conf/worm-interaction.cfg =================================================================== --- phenote/trunk/conf/worm-interaction.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/worm-interaction.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,85 +0,0 @@ -<phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd"> - - <master-to-local-config mode="UPDATE" when="ALWAYS"/> - <!-- ??? overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm-interaction.cfg" / ??? --> - - <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> - <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" - enable="true"/> - <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/> - <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/> - - <dataadapter name="phenote.dataadapter.worm.WormInteractionAdapter" is-queryable="true" enable="true"/> - - <log config-file="conf/log4j.xml"/> - - <uvic-graph enable="false"/> - <term-history enable="false"/> - - <auto-update-ontologies enable="true"/> <!--true=update; false=don't update--> - <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds--> - - <group name="default" title="Main" container="tab" interface="default"/> - - - <field name="PgdbId" enable="true" copy-field="false" type="READ_ONLY" groups="default"/> - <field name="Interaction ID" datatag="Name" warnIfNull="true" enable="true" groups="default"/> -<!-- <field name="Curator" enable="true"> - <ontology name="Curator" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator_interaction.obo"/> - </field>--> - - <field name="Curator" datatag="Curator" enable="true"> - <ontology file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi" slim="curator_slim_interaction"/> - </field> - <field name="Pub" datatag="Pub" enable="true" groups="default"> - <!--<ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi?short=5"/>--> - <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/> - </field> - <field name="Person" datatag="Person" enable="true" groups="default" isList="true"> - <!--<ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi?short=5"/>--> - <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/> - </field> - <field name="WS_current info" datatag="WS_currentinfo" enable="true" groups="default"> - <ontology name="ws_variation" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/ws_current.obo"/> - </field> - - <field name="Effector" datatag="Effector" enable="true" > - <!--<ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>--> - <ontology name="Effector" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/> - </field> - <field name="tor Variation" datatag="torVariation" enable="true" groups="default"/> - <field name="tor Transgene" datatag="torTransgene" enable="true" groups="default"/> - <!--<field name="tor Remark" datatag="torRemark" enable="true" groups="default"/>--> - <field name="Type" datatag="Type" enable="true"> - <ontology name="Type" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/interaction_type.obo"/> - </field> - <!--<field name="NOT A FIELD" datatag="takingupspace" enable="true" type="READ_ONLY" groups="default"/>--> - - - <field name="Effected" datatag="Effected" enable="true" > - <!--<ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi?short=5"/>--> - <ontology name="Effected" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/> - </field> - <field name="ted Variation" datatag="tedVariation" enable="true" groups="default"/> - <field name="ted Transgene" datatag="tedTransgene" enable="true" groups="default"/> - <!--<field name="ted Remark" datatag="tedRemark" enable="true" groups="default"/>--> - - - <field name="Phenotype" datatag="Phenotype" enable="true" isList="true"> - <!--<ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi?short=short"/> --> - <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/> - </field> - <field name="Remark" datatag="Remark" enable="true" groups="default"/> - <field name="Treatment" datatag="Treatment" enable="true" groups="default"/> - - <field name="Other Evidence" datatag="OtherEvidence" enable="true" groups="default"/> - <field name="RNAi" datatag="RNAi" enable="true" groups="default"/> - - <field name="Gene Extra" datatag="GeneExtra" enable="true" isList="true"> - <ontology name="Gene Extra" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/wbgene_obo.cgi"/> - </field> - <field name="Variation Extra" datatag="VariationExtra" enable="true" groups="default"/> - <field name="Transgene Extra" datatag="TransgeneExtra" enable="true" groups="default"/> - <constraint className="phenote.dataadapter.worm.WormInteractionConstraint"/> - -</phenote-configuration> Deleted: phenote/trunk/conf/worm-transgene.cfg =================================================================== --- phenote/trunk/conf/worm-transgene.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/worm-transgene.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,47 +0,0 @@ -<phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd"> - - <master-to-local-config mode="UPDATE" when="ALWAYS"/> - <!-- ??? overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm-transgene.cfg" / ??? --> - - <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> - <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" - enable="true"/> - <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/> - <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/> - - <dataadapter name="phenote.dataadapter.worm.WormTransgeneAdapter" is-queryable="true" enable="true"/> - - <log config-file="conf/log4j.xml"/> - - <uvic-graph enable="false"/> - <term-history enable="false"/> - - <auto-update-ontologies enable="true"/> <!--true=update; false=don't update--> - <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds--> - - <group name="default" title="Main" container="tab" interface="default"/> - - <field name="PgdbId" enable="true" copy-field="false" type="READ_ONLY" groups="default"/> - <field name="Name" datatag="Name" enable="true" groups="default"/> - <field name="Summary" datatag="Summary" enable="true" enableBigTextBox="true"/> - <field name="Driven by Gene" datatag="Driven_by_Gene" enable="true" groups="default"/> - <field name="Reporter Product" enable="true" groups="default" isList="true"><ontology name="Reporter_Product" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/reporter_product.obo"/></field> - <field name="Other Reporter" datatag="Other_Reporter" enable="true" groups="default"/> - <field name="Gene" datatag="Gene" enable="true" groups="default"/> - <field name="Integrated by" enable="true"><ontology name="Integrated_by" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/integrated_by.obo"/></field> - <field name="Strain" datatag="Strain" enable="true" groups="default"/> - <field name="Map" enable="true" isList="true"><ontology name="Map" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/map.obo"/></field> - <field name="Map Paper" datatag="Map_Paper" enable="true" groups="default"/> - <field name="Map Person" datatag="Map_Person" enable="true" groups="default"/> - <field name="Marker for" datatag="Marker_for" enable="true" groups="default"/> - <field name="Marker Paper" datatag="Marker_for_Paper" enable="true" groups="default"/> - <field name="Reference" datatag="Reference" enable="true" enableBigTextBox="true"/> - <field name="Remark" datatag="Remark" enable="true" enableBigTextBox="true"/> - <field name="Species" datatag="Species" enable="true" groups="default"/> - <field name="Synonym" datatag="Synonym" enable="true" groups="default"/> - <field name="Driven by Construct" datatag="Driven_by_Construct" enable="true" groups="default"/> - <field name="Location" datatag="Location" enable="true" groups="default"/> - <field name="Movie" datatag="Movie" enable="true" groups="default"/> - <field name="Picture" datatag="Picture" enable="true" groups="default"/> - -</phenote-configuration> Deleted: phenote/trunk/conf/worm.cfg =================================================================== --- phenote/trunk/conf/worm.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/worm.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,147 +0,0 @@ -<phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd"> - - <!-- <master-to-local-config mode="UPDATE" when="ALWAYS"/> --> - <!-- ??? overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm.cfg" / ??? --> - - <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> - <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" - enable="false"/> - <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/> - - <dataadapter name="phenote.dataadapter.worm.WormAdapter" is-queryable="true" - enable="true"/> - - <log config-file="conf/log4j.xml"/> - - <uvic-graph enable="false"/> - <term-history enable="false"/> - - <auto-update-ontologies enable="true"/> <!--true=update; false=don't update--> - <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds--> - - <group name="default" title="Main" container="tab" interface="default"/> - -<!-- TAB 1 --> - <field name="PgdbId" enable="true" copy-field="false" type="READ_ONLY" groups="default"/> - <field name="Curation Status" datatag="CurationStatus" enable="true" groups="default"> - <!--<ontology name="CurationStatus" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curation_status.obo"/> --> - <ontology name="CurationStatus" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/cur_status_obo.cgi"/> - </field> - <field name="Curator" enable="true"> - <ontology name="Curator" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/curator.obo"/> - </field> - <field name="Object Type" datatag="Type" warnIfNull="true" enable="true" groups="default"> - <ontology name="ObjectType" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/type.obo"/> - </field> - <field name="WS_current info" datatag="WS_currentinfo" enable="true" groups="default"> - <ontology name="ws_variation" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/ws_current.obo"/> - <!--<ontology name="ws_variation" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>--> - </field> - <field name="Object Name" datatag="Name" warnIfNull="true" enable="true" groups="default"/> - - <field name="Pub" datatag="Pub" enable="true" groups="default"> - <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/> - <!--<ontology name="Pub" file="paper_obo.cgi"/>--> - </field> - <field name="Person" datatag="Person" enable="true" groups="default" isList="true"> - <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/> - </field> - <field name="Object Remark" datatag="ObjRem" enable="true" enableBigTextBox="true"/> - <field name="Allele Status" datatag="AlleleStatus" enable="true" groups="default"> - <ontology name="AlleleStatus" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/allele_status.obo"/> - </field> -<!-- <field name="Finished Curating Paper" enable="true"> - <ontology name="FinishedCuratingPaper" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/> - </field>--> -<!-- END TAB 1 --> - - - -<!-- TAB 2 --> - <field name="NOT" enable="true"> <!-- Boolean checkbox --> - <ontology name="NOT" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/> - </field> - - <field name="Phenotype" datatag="Phenotype" enable="true"> - <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/> - </field> - - <field name="Phenotype Remark" datatag="PhenotypeRemark" enable="true" enableBigTextBox="true"/> - - <field name="Anatomy" enable="true" isList="true"> - <ontology name="Worm Anatomy" - file="http://www.berkeleybop.org/ontologies/obo-all/worm_anatomy/worm_anatomy.obo"/> - </field> - - <field name="Life Stage" datatag="LifeStage" enable="true" isList="true"> - <ontology name="Life Stage" file="http://www.berkeleybop.org/ontologies/obo-all/worm_development/worm_development.obo"/> - </field> - - <field name="Entity" datatag="Entity" enable="true"> - <ontology name="Relationship" file="http://www.berkeleybop.org/ontologies/obo-all/rex/rex.obo" is-postcomp-rel="true"/> - <ontology name="CHEBI" file="http://purl.org/obo/obo/CHEBI.obo"/> - <ontology name="Worm" file="worm_anatomy.obo"/>--> - <ontology name="GO" file="gene_ontology.obo"/> - <!-- stage?? --> - </field> - - <field name="Quality" datatag="Quality" enable="true"> - <ontology name="PATO" - file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/> - </field> - <field name="Suggested" datatag="Suggested" enable="true" groups="default"/> - <field name="Suggested Definition" datatag="SuggestedDefinition" enable="true" groups="default" enableBigTextBox="true"/> - <field name="Child Of" datatag="ChildOf" enable="true" isList="true"> - <ontology name="Child Of" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/> - </field> - - <field name="Allele Nature" enable="true"> - <ontology name="Allele Nature" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/nature.obo"/> - </field> - <field name="Functional Change" enable="true"> - <ontology name="Functional Change" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/func.obo"/> - </field> - <field name="Temperature" enable="true"/> - <field name="Treatment" enable="true" enableBigTextBox="true"/> - <field name="Control Isolate" enable="true"/> - <!--<field name="NOT A FIELD" datatag="takingupspace" enable="true" type="READ_ONLY" groups="default"/>--> - <field name="Penetrance" enable="true"> - <ontology name="Penetrance" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/penetrance.obo"/> - </field> - <field name="Penetrance Remark" enable="true" enableBigTextBox="true"/> -<!-- Karen doesn't want Penetrance Range Start or End 2008 09 03 --> -<!-- <field name="Penetrance Range Start" enable="true"/>--> <!-- Integer --> -<!-- <field name="Penetrance Range End" enable="true"/>--> <!-- Integer --> - <!-- <field name="Quantity Remark" enable="true"/> Karen doesn't want these in phenote 2008 01 28 --> - <!-- <field name="Quantity" enable="true"/> Karen doesn't want these in phenote 2008 01 28 --> - - <field name="Other Attributes" enable="true" isList="true"> - <ontology name="OtherAttributes" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/other_attributes.obo"/> - </field> - <field name="Cold Sensitive Degree" enable="true"/> - <field name="Heat Sensitive Degree" enable="true"/> - -<!-- <field name="Heat Sensitive" enable="true"><ontology name="HeatSensitive" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/></field> - <field name="Cold Sensitive" enable="true"><ontology name="ColdSensitive" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/></field> - <field name="Maternal Effect" enable="true"><ontology name="Maternal Effect" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/mat_effect.obo"/></field> - <field name="Paternal Effect" enable="true"><ontology name="PaternalEffect" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/></field> - <field name="Haplo" enable="true"><ontology name="Haplo" file="http://tazendra.caltech.edu/~azurebrd/var/work/phenote/checked.obo"/></field>--> - - <field name="Genotype" datatag="Genotype" enable="true" groups="default"/> - -<!-- Karen doesn't want Host Strain 2008 09 03 --> -<!-- <field name="Host Strain" datatag="HostStrain" enable="true" groups="default"/>--> - - <field name="Genetic Intx Desc" datatag="IntxDesc" enable="true" groups="default" enableBigTextBox="true"/> - <field name="NBP" datatag="PhenotypeTextRemark" enable="true" type="READ_ONLY" groups="default"/> - <field name="NBP Date" datatag="NBPDate" enable="true" groups="default"/> - - <field name="Laboratory Evidence" datatag="LaboratoryEvidence" enable="true" groups="default"/> - - <field name="Paper Remark" datatag="PaperRemark" enable="true" - groups="default" enableBigTextBox="true"/> - <field name="Paper Remark History" datatag="PapRemHist" enable="true" type="READ_ONLY" groups="default"/> - - <constraint className="phenote.dataadapter.worm.WormConstraint"/> - -</phenote-configuration> Deleted: phenote/trunk/conf/wormRef.cfg =================================================================== --- phenote/trunk/conf/wormRef.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/wormRef.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,119 +0,0 @@ -<phenote-configuration xmlns="phenote/config/xml" xmlns:xsi="http://www.w3.org/1999/XMLSchema/instance" schemaLocation="phenote-config.xsd"> - - <master-to-local-config mode="UPDATE" when="ALWAYS"/> - <!-- ??? overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/worm.cfg" / ??? --> - - <dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/> - <dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" - enable="true"/> - <dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="false"/> - <dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="false"/> - - <dataadapter name="phenote.dataadapter.worm.WormAdapter" is-queryable="true" - enable="true"/> - - <log config-file="conf/log4j.xml"/> - - <uvic-graph enable="false"/> - <term-history enable="false"/> - - <auto-update-ontologies enable="true"/> <!--true=update; false=don't update--> - <update-timer timer="0"/><!--set to 0 if you want to bypass the check; time in seconds--> - - <group name="referenceMaker" title="Reference Maker" container="tab" - interface="default" destination_field="Ref" - group_adapter="phenote.dataadapter.worm.WormReferenceGroupAdapter"/> - - <group name="default" title="Main" container="tab" interface="default"/> - - - - <field name="Object Type" enable="true" groups="referenceMaker default"/> - - <field name="Object Name" enable="true" groups="referenceMaker default"/> - - <field name="PgdbBoxId" enable="true" copy-field="false" type="READ_ONLY" groups="referenceMaker"/> - - <field name="PgdbBoxColId" enable="true" copy-field="false" type="READ_ONLY" groups="default"/> - - <field name="Reference" datatag="Ref" type="TERM" groups="default"/> - - <field name="Ref ID" datatag="RefID" enable="true" type="READ_ONLY" groups="referenceMaker"/> - - <field name="Pub" datatag="Pub" enable="true" groups="referenceMaker"> - <!--<ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/> PUT THIS BACK --> - <ontology name="Pub" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/paper_obo.cgi"/> - <!--<ontology name="Pub" file="paper_obo.cgi"/>--> - </field> - - <field name="Person" datatag="Person" enable="true" groups="referenceMaker"> - <ontology name="Person" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/> - </field> - - <field name="NBP" datatag="PhenotypeTextRemark" enable="true" type="READ_ONLY" groups="referenceMaker"/> - - <field name="NBP Date" datatag="NBPDate" enable="true" groups="referenceMaker"/> - - <field name="Paper Remark" datatag="PaperRemark" enable="true" groups="referenceMaker"/> - - <field name="Paper Remark History" datatag="PapRemHist" enable="true" type="READ_ONLY" groups="referenceMaker"/> - - <field name="Genetic Intx Desc" datatag="IntxDesc" enable="true" groups="referenceMaker"/> - - <field name="Curator" datatag="Curator" enable="true"/> - - <field name="NOT" enable="true"/> <!-- Boolean checkbox --> - - <field name="Phenotype" datatag="Phenotype" enable="true"> - <ontology name="Phenotype" file="http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi"/> - </field> - - <field name="Phenotype Remark" datatag="PhenotypeRemark" enable="true"/> - - <field name="Anatomy" enable="true"> - <ontology name="Worm Anatomy" - file="http://www.berkeleybop.org/ontologies/obo-all/worm_anatomy/worm_anatomy.obo"/> - </field> - - <field name="Entity" datatag="Entity" enable="true"> - <ontology name="Relationship" file="http://www.berkeleybop.org/ontologies/obo-all/rex/rex.obo" is-postcomp-rel="true"/> -<!-- <ontology name="GO" file="gene_ontology.obo"/> - <ontology name="CHEBI" file="CHEBI.obo"/> - <ontology name="Worm" file="worm_anatomy.obo"/>--> - <ontology name="GO" file="gene_ontology.obo"/> - <ontology name="Worm" - file="http://www.berkeleybop.org/ontologies/obo-all/worm_anatomy/worm_anatomy.obo"/> - <!-- stage?? --> - </field> - - <field name="Quality" datatag="Quality" enable="true"> - <ontology name="PATO" - file="http://www.berkeleybop.org/ontologies/obo-all/quality/quality.obo"/> - </field> - - <field name="Life Stage" datatag="LifeStage" enable="true"> - <ontology name="Life Stage" file="http://www.berkeleybop.org/ontologies/obo-all/worm_development/worm_development.obo"/> - </field> - - <field name="Allele Nature" enable="true"/> - - <field name="Functional Change" enable="true"/> - <field name="Temperature" enable="true"/> - <field name="Treatment" enable="true"/> - <field name="Penetrance" enable="true"/> - <field name="Penetrance Remark" enable="true"/> - <field name="Penetrance Range Start" enable="true"/> <!-- Integer --> - <field name="Penetrance Range End" enable="true"/> <!-- Integer --> - <field name="Quantity Remark" enable="true"/> - <field name="Quantity" enable="true"/> - <field name="Heat Sensitive" enable="true"/> <!-- Boolean --> - <field name="Heat Sensitive Degree" enable="true"/> - <field name="Cold Sensitive" enable="true"/> <!-- Boolean --> - <field name="Cold Sensitive Degree" enable="true"/> - <field name="Maternal Effect" enable="true"/> - <field name="Paternal Effect" enable="true"/> <!-- BOOLEAN --> - <field name="Genotype" enable="true"/> - <field name="Strain" enable="true"/> - <field name="Object Remark" datatag="ObjRem" enable="true"/> - -</phenote-configuration> Deleted: phenote/trunk/conf/zfin-web.cfg =================================================================== --- phenote/trunk/conf/zfin-web.cfg 2012-01-26 21:36:53 UTC (rev 4144) +++ phenote/trunk/conf/zfin-web.cfg 2012-01-26 22:10:33 UTC (rev 4145) @@ -1,38 +0,0 @@ -<?xml version="1.5" encoding="UTF-8"?> -<ns:phenote-configuration xmlns:ns="phenote/config/xml" version="1.5" - name="Zfin Web Configuration" - author="ZFIN Phenote Developers" - description="This is zfin's configuration file for their web application."> - - <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/> - - <ns:field name="Genotype" datatag="GT" enable="true"/> - <ns:field name="Entity" datatag="E" enable="true"> - <ns:ontology name="Relationship" file="../data_transfer/ro.obo" is-postcomp-rel="true"> - <ns:onTheFlySlimTerm term="OBO_REL:part_of"/> - </ns:ontology> - <ns:ontology name="GO" file="../data_transfer/gene_ontology.obo" /> - <ns:ontology name="CL" file="../data_transfer/cell.obo" /> - <ns:ontology name="ZF" file="../data_transfer/zebrafish_anatomy.obo" namespace="zebrafish_anatomy"/> - </ns:field> - - <ns:field name="Quality" datatag="Q" enable="true"> - <ns:ontology name="PATO" file="../data_transfer/quality.obo" /> - </ns:field> - <ns:field name="Quality" file="../data_transfer/quality.obo"/> - - - <!-- - <ns:field name="Add'l Entity" datatag="E2" enable="true"> - <ns:ontology name="Relationship" file="../data_transfer/ro.obo" is-postcomp-rel="true"> - <ns:onTheFlySlimTerm term="OBO_REL:part_of"/> - </ns:ontology> - <ns:ontology name="GO" file="../data_transfer/gene_ontology.obo" /> - <ns:ontology name="CL" file="../data_transfer/cell.obo" /> - <ns:ontology name="ZF" file="../data_transfer/zebrafish_anatomy.obo" namespace="zebrafish_anatomy"/> - </ns:field> - --> - - <ns:field name="Date Created" enable="true" desc="Date this annotation was created" isVisible="false"/> - -</ns:phenote-configuration> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |