rorchado 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/lib/rails/generators/rorchado/USAGE +16 -0
- data/lib/rails/generators/rorchado/rorchado_generator.rb +259 -0
- data/lib/rails/generators/rorchado/templates/controllers/contact_controller.rb +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/contact_controller.rb~ +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/cv_controller.rb +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/cv_controller.rb~ +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/cvterm_controller.rb +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/cvterm_controller.rb~ +83 -0
- data/lib/rails/generators/rorchado/templates/controllers/stock_controller.rb +83 -0
- data/lib/rails/generators/rorchado/templates/db_schemas/chado_schema.xml +697 -0
- data/lib/rails/generators/rorchado/templates/migrations/generic_migration_create.erb +18 -0
- data/lib/rails/generators/rorchado/templates/models/generic_model.erb +5 -0
- data/lib/rails/generators/rorchado/templates/views/contact/_form.html.erb +29 -0
- data/lib/rails/generators/rorchado/templates/views/contact/edit.html.erb +6 -0
- data/lib/rails/generators/rorchado/templates/views/contact/index.html.erb +27 -0
- data/lib/rails/generators/rorchado/templates/views/contact/new.html.erb +5 -0
- data/lib/rails/generators/rorchado/templates/views/contact/show.html.erb +20 -0
- data/lib/rails/generators/rorchado/templates/views/cv/_form.html.erb +25 -0
- data/lib/rails/generators/rorchado/templates/views/cv/edit.html.erb +6 -0
- data/lib/rails/generators/rorchado/templates/views/cv/index.html.erb +25 -0
- data/lib/rails/generators/rorchado/templates/views/cv/new.html.erb +5 -0
- data/lib/rails/generators/rorchado/templates/views/cv/show.html.erb +15 -0
- data/lib/rails/generators/rorchado/templates/views/cvterm/_form.html.erb +41 -0
- data/lib/rails/generators/rorchado/templates/views/cvterm/edit.html.erb +6 -0
- data/lib/rails/generators/rorchado/templates/views/cvterm/index.html.erb +33 -0
- data/lib/rails/generators/rorchado/templates/views/cvterm/new.html.erb +5 -0
- data/lib/rails/generators/rorchado/templates/views/cvterm/show.html.erb +35 -0
- data/lib/rails/generators/rorchado/templates/views/stock/_form.html.erb +45 -0
- data/lib/rails/generators/rorchado/templates/views/stock/edit.html.erb +6 -0
- data/lib/rails/generators/rorchado/templates/views/stock/index.html.erb +35 -0
- data/lib/rails/generators/rorchado/templates/views/stock/new.html.erb +5 -0
- data/lib/rails/generators/rorchado/templates/views/stock/show.html.erb +40 -0
- metadata +105 -0
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<?xml version="1.0" encoding="UTF-8" ?>
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<schema>
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<chado version="1.23">
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<modules>
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<module id="general" requires="">
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<tables>
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<table id="db" primary_key="db_id">
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<fields>
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<field id="name" type="string" not_null="1" default="" foreign_key=""/>
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<field id="description" type="string" not_null="" default="" foreign_key=""/>
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<field id="urlprefix" type="string" not_null="" default="" foreign_key=""/>
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<field id="url" type="string" not_null="" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="name" unique="1"/>
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</indexes>
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</table>
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<table id="dbxref" primary_key="dbxref_id">
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<fields>
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<field id="db_id" type="integer" not_null="1" default="" foreign_key="db"/>
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<field id="accession" type="string" not_null="1" default="" foreign_key=""/>
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<field id="version" type="string" not_null="1" default="0" foreign_key=""/>
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<field id="description" type="string" not_null="" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="db_id,accession,version" unique="1"/>
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<index columns="db_id" unique=""/>
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<index columns="accession" unique=""/>
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<index columns="version" unique=""/>
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</indexes>
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</table>
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<table id="project" primary_key="project_id">
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<fields>
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<field id="name" type="string" not_null="1" default="" foreign_key=""/>
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<field id="description" type="string" not_null="1" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="name" unique="1"/>
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</indexes>
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</table>
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<table id="tableinfo" primary_key="tableinfo_id">
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<fields>
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<field id="name" type="string" not_null="" default="" foreign_key=""/>
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<field id="primary_key_column" type="string" not_null="" default="" foreign_key=""/>
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<field id="is_view" type="integer" not_null="1" default="" foreign_key=""/>
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<field id="view_on_table_id" type="integer" not_null="" default="" foreign_key=""/>
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<field id="superclass_table_id" type="integer" not_null="" default="" foreign_key=""/>
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<field id="is_updateable" type="integer" not_null="1" default="1" foreign_key=""/>
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<field id="modification_date" type="timestamp" not_null="1" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="name" unique="1"/>
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</indexes>
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</table>
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</tables>
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</module>
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<module id="cv" requires="general">
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<tables>
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<table id="cv" primary_key="cv_id">
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<fields>
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<field id="name" type="string" not_null="1" default="" foreign_key=""/>
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<field id="definition" type="text" not_null="" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="name" unique="1"/>
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</indexes>
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</table>
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<table id="cvterm" primary_key="cvterm_id">
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<fields>
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<field id="name" type="string" not_null="1" default="" foreign_key=""/>
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<field id="definition" type="text" not_null="" default="" foreign_key=""/>
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<field id="is_obsolete" type="integer" not_null="1" default="0" foreign_key=""/>
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<field id="is_relationshiptype" type="integer" not_null="1" default="0" foreign_key=""/>
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<field id="cv_id" type="integer" not_null="1" default="" foreign_key="cv"/>
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<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
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</fields>
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<indexes>
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<index columns="cv_id" unique=""/>
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<index columns="name" unique=""/>
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<index columns="dbxref_id" unique=""/>
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<index columns="cv_id,name,is_obsolete" unique="1"/>
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<index columns="dbxref_id" unique="1"/>
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</indexes>
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</table>
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<table id="cvterm_dbxref" primary_key="cvterm_dbxref_id">
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<fields>
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<field id="cvterm_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
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<field id="is_for_definition" type="integer" not_null="1" default="0" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="cvterm_id" unique=""/>
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<index columns="dbxref_id" unique=""/>
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<index columns="cvterm_id,dbxref_id" unique="1"/>
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</indexes>
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</table>
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<table id="cvterm_relationship" primary_key="cvterm_relationship_id">
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<fields>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="subject_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="object_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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</fields>
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<indexes>
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<index columns="type_id" unique=""/>
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<index columns="subject_id" unique=""/>
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<index columns="object_id" unique=""/>
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<index columns="type_id,subject_id,object_id" unique="1"/>
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</indexes>
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</table>
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<table id="cvtermpath" primary_key="cvtermpath_id">
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<fields>
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<field id="type_id" type="integer" not_null="" default="" foreign_key="cvterm"/>
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<field id="subject_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="object_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="cv_id" type="integer" not_null="1" default="" foreign_key="cv"/>
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<field id="pathdistance" type="integer" not_null="" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="type_id" unique=""/>
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<index columns="subject_id" unique=""/>
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<index columns="object_id" unique=""/>
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<index columns="cv_id" unique=""/>
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<index columns="type_id,subject_id,object_id,pathdistance" unique="1"/>
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</indexes>
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</table>
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<table id="cvtermprop" primary_key="cvtermprop_id">
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<fields>
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<field id="cvterm_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="rank" type="integer" not_null="1" default="0" foreign_key=""/>
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<field id="value" type="text" not_null="1" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="cvterm_id" unique=""/>
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<index columns="type_id" unique=""/>
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<index columns="value" unique=""/>
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<index columns="cvterm_id,type_id,rank,value" unique="1"/>
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</indexes>
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</table>
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<table id="cvtermsynonym" primary_key="cvtermsynonym_id">
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<fields>
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<field id="cvterm_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="synonym" type="text" not_null="1" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="type_id" unique=""/>
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<index columns="type_id,synonym" unique="1"/>
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</indexes>
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</table>
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<table id="dbxrefprop" primary_key="dbxrefprop_id">
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<fields>
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<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
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<field id="value" type="text" not_null="1" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="dbxref_id" unique=""/>
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<index columns="type_id" unique=""/>
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<index columns="value" unique=""/>
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<index columns="dbxref_id,type_id,rank" unique="1"/>
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</indexes>
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</table>
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</tables>
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</module>
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<module id="contact" requires="cv">
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<tables>
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<table id="contact" primary_key="contact_id">
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<fields>
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<field id="type_id" type="integer" not_null="" default="" foreign_key="cvterm"/>
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<field id="name" type="string" not_null="1" default=""/>
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<field id="description" type="string" not_null="" default=""/>
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</fields>
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<indexes>
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<index columns="name" unique="1"/>
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</indexes>
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</table>
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<table id="contact_relationship" primary_key="contact_relationship_id">
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<fields>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="subject_id" type="integer" not_null="1" default="" foreign_key="contact"/>
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<field id="object_id" type="integer" not_null="1" default="" foreign_key="contact"/>
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</fields>
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<indexes>
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<index columns="type_id,subject_id,object_id" unique="1"/>
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<index columns="type_id" unique="0"/>
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<index columns="subject_id" unique="0"/>
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<index columns="object_id" unique="0"/>
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</indexes>
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</table>
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</tables>
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</module>
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<module id="pub" requires="general,cv">
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<tables>
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<table id="pub" primary_key="pub_id">
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<fields>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="title" type="text" not_null="" default="" foreign_key=""/>
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<field id="series_name" type="string" not_null="" default="" foreign_key=""/>
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<field id="volumetitle" type="text" not_null="" default="" foreign_key=""/>
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<field id="volume" type="string" not_null="" default="" foreign_key=""/>
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<field id="issue" type="string" not_null="" default="" foreign_key=""/>
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<field id="pages" type="string" not_null="" default="" foreign_key=""/>
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<field id="pyear" type="string" not_null="" default="" foreign_key=""/>
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<field id="uniquename" type="text" not_null="1" default="" foreign_key=""/>
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<field id="publisher" type="string" not_null="" default="" foreign_key=""/>
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<field id="miniref" type="string" not_null="" default="" foreign_key=""/>
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<field id="is_obsolete" type="boolean" not_null="" default="FALSE" foreign_key=""/>
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<field id="pubplace" type="string" not_null="" default="" foreign_key=""/>
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</fields>
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<indexes>
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<index columns="uniquename" unique="1"/>
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</indexes>
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</table>
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<table id="pub_dbxref" primary_key="pub_dbxref_id">
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<fields>
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<field id="is_current" type="boolean" not_null="" default="TRUE" foreign_key=""/>
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<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
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<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
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</fields>
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<indexes>
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<index columns="pub_id,dbxref_id" unique="1"/>
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<index columns="pub_id" unique=""/>
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<index columns="dbxref_id" unique=""/>
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</indexes>
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</table>
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<table id="pub_relationship" primary_key="pub_relationship_id">
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<fields>
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<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
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<field id="subject_id" type="integer" not_null="1" default="" foreign_key="pub"/>
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<field id="object_id" type="integer" not_null="1" default="" foreign_key="pub"/>
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</fields>
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<indexes>
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<index columns="type_id,subject_id,object_id" unique="1"/>
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<index columns="type_id" unique=""/>
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|
237
|
+
<index columns="subject_id" unique=""/>
|
|
238
|
+
<index columns="object_id" unique=""/>
|
|
239
|
+
</indexes>
|
|
240
|
+
</table>
|
|
241
|
+
<table id="pubauthor" primary_key="pubauthor_id">
|
|
242
|
+
<fields>
|
|
243
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
244
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
245
|
+
<field id="surname" type="string" not_null="1" default="" foreign_key=""/>
|
|
246
|
+
<field id="givennames" type="string" not_null="" default="" foreign_key=""/>
|
|
247
|
+
<field id="suffix" type="string" not_null="" default="" foreign_key=""/>
|
|
248
|
+
<field id="editor" type="boolean" not_null="" default="FALSE" foreign_key=""/>
|
|
249
|
+
</fields>
|
|
250
|
+
<indexes>
|
|
251
|
+
<index columns="pub_id,rank" unique="1"/>
|
|
252
|
+
<index columns="pub_id" unique=""/>
|
|
253
|
+
</indexes>
|
|
254
|
+
</table>
|
|
255
|
+
<table id="pubprop" primary_key="pubprop_id">
|
|
256
|
+
<fields>
|
|
257
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
258
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
259
|
+
<field id="rank" type="integer" not_null="" default="" foreign_key=""/>
|
|
260
|
+
<field id="value" type="text" not_null="1" default="" foreign_key=""/>
|
|
261
|
+
</fields>
|
|
262
|
+
<indexes>
|
|
263
|
+
<index columns="type_id,pub_id,rank" unique="1"/>
|
|
264
|
+
<index columns="type_id" unique=""/>
|
|
265
|
+
<index columns="pub_id" unique=""/>
|
|
266
|
+
</indexes>
|
|
267
|
+
</table>
|
|
268
|
+
</tables>
|
|
269
|
+
</module>
|
|
270
|
+
<module id="stock" requires="general,cv,pub,organism,genotype,contact">
|
|
271
|
+
<tables>
|
|
272
|
+
<table id="stock" primary_key="stock_id">
|
|
273
|
+
<fields>
|
|
274
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
275
|
+
<field id="organism_id" type="integer" not_null="1" default="" foreign_key="organism"/>
|
|
276
|
+
<field id="name" type="string" not_null="" default="" foreign_key=""/>
|
|
277
|
+
<field id="uniquename" type="text" not_null="1" default="" foreign_key=""/>
|
|
278
|
+
<field id="description" type="text" not_null="" default="" foreign_key=""/>
|
|
279
|
+
<field id="is_obsolete" type="boolean" not_null="1" default="FALSE" foreign_key=""/>
|
|
280
|
+
<field id="dbxref_id" type="integer" not_null="" default="" foreign_key="dbxref"/>
|
|
281
|
+
</fields>
|
|
282
|
+
<indexes>
|
|
283
|
+
<index columns="uniquename,type_id,organism_id" unique="1"/>
|
|
284
|
+
<index columns="type_id" unique=""/>
|
|
285
|
+
<index columns="organism_id" unique=""/>
|
|
286
|
+
<index columns="dbxref_id" unique=""/>
|
|
287
|
+
<index columns="uniquename" unique=""/>
|
|
288
|
+
</indexes>
|
|
289
|
+
</table>
|
|
290
|
+
<table id="stock_cvterm" primary_key="stock_cvterm_id">
|
|
291
|
+
<fields>
|
|
292
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
293
|
+
<field id="cvterm_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
294
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
295
|
+
</fields>
|
|
296
|
+
<indexes>
|
|
297
|
+
<index columns="stock_id" unique=""/>
|
|
298
|
+
<index columns="cvterm_id" unique=""/>
|
|
299
|
+
<index columns="pub_id" unique=""/>
|
|
300
|
+
<index columns="stock_id,cvterm_id,pub_id" unique="1"/>
|
|
301
|
+
</indexes>
|
|
302
|
+
</table>
|
|
303
|
+
<table id="stock_dbxref" primary_key="stock_dbxref_id">
|
|
304
|
+
<fields>
|
|
305
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
306
|
+
<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
|
|
307
|
+
<field id="is_current" type="boolean" not_null="1" default="TRUE" foreign_key=""/>
|
|
308
|
+
</fields>
|
|
309
|
+
<indexes>
|
|
310
|
+
<index columns="stock_id" unique=""/>
|
|
311
|
+
<index columns="dbxref_id" unique=""/>
|
|
312
|
+
<index columns="stock_id,dbxref_id" unique="1"/>
|
|
313
|
+
</indexes>
|
|
314
|
+
</table>
|
|
315
|
+
<table id="stock_genotype" primary_key="stock_genotype_id">
|
|
316
|
+
<fields>
|
|
317
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
318
|
+
<field id="genotype_id" type="integer" not_null="1" default="" foreign_key="genotype"/>
|
|
319
|
+
</fields>
|
|
320
|
+
<indexes>
|
|
321
|
+
<index columns="stock_id" unique=""/>
|
|
322
|
+
<index columns="genotype_id" unique=""/>
|
|
323
|
+
<index columns="stock_id,genotype_id" unique="1"/>
|
|
324
|
+
</indexes>
|
|
325
|
+
</table>
|
|
326
|
+
<table id="stock_pub" primary_key="stock_pub_id">
|
|
327
|
+
<fields>
|
|
328
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
329
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
330
|
+
</fields>
|
|
331
|
+
<indexes>
|
|
332
|
+
<index columns="stock_id" unique=""/>
|
|
333
|
+
<index columns="pub_id" unique=""/>
|
|
334
|
+
<index columns="stock_id,pub_id" unique="1"/>
|
|
335
|
+
</indexes>
|
|
336
|
+
</table>
|
|
337
|
+
<table id="stock_relationship" primary_key="stock_relationship_id">
|
|
338
|
+
<fields>
|
|
339
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
340
|
+
<field id="subject_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
341
|
+
<field id="object_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
342
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
343
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
344
|
+
</fields>
|
|
345
|
+
<indexes>
|
|
346
|
+
<index columns="type_id" unique=""/>
|
|
347
|
+
<index columns="subject_id" unique=""/>
|
|
348
|
+
<index columns="object_id" unique=""/>
|
|
349
|
+
<index columns="type_id,subject_id,object_id,rank" unique="1"/>
|
|
350
|
+
</indexes>
|
|
351
|
+
</table>
|
|
352
|
+
<table id="stock_relationship_pub" primary_key="stock_relationship_pub_id">
|
|
353
|
+
<fields>
|
|
354
|
+
<field id="stock_relationship_id" type="integer" not_null="1" default="" foreign_key="stock_relationship"/>
|
|
355
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
356
|
+
</fields>
|
|
357
|
+
<indexes>
|
|
358
|
+
<index columns="stock_relationship_id" unique=""/>
|
|
359
|
+
<index columns="pub_id" unique=""/>
|
|
360
|
+
<index columns="stock_relationship_id,pub_id" unique="1"/>
|
|
361
|
+
</indexes>
|
|
362
|
+
</table>
|
|
363
|
+
<table id="stockcollection" primary_key="stockcollection_id">
|
|
364
|
+
<fields>
|
|
365
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
366
|
+
<field id="name" type="string" not_null="" default="" foreign_key=""/>
|
|
367
|
+
<field id="uniquename" type="text" not_null="1" default="" foreign_key=""/>
|
|
368
|
+
<field id="contact_id" type="integer" not_null="" default="" foreign_key="contact"/>
|
|
369
|
+
</fields>
|
|
370
|
+
<indexes>
|
|
371
|
+
<index columns="type_id" unique=""/>
|
|
372
|
+
<index columns="contact_id" unique=""/>
|
|
373
|
+
<index columns="uniquename" unique=""/>
|
|
374
|
+
<index columns="type_id,uniquename" unique="1"/>
|
|
375
|
+
</indexes>
|
|
376
|
+
</table>
|
|
377
|
+
<table id="stockcollection_stock" primary_key="stockcollection_stock_id">
|
|
378
|
+
<fields>
|
|
379
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
380
|
+
<field id="stockcollection_id" type="integer" not_null="1" default="" foreign_key="stockcollection"/>
|
|
381
|
+
</fields>
|
|
382
|
+
<indexes>
|
|
383
|
+
<index columns="stock_id" unique=""/>
|
|
384
|
+
<index columns="stockcollection_id" unique=""/>
|
|
385
|
+
<index columns="stock_id,stockcollection_id" unique="1"/>
|
|
386
|
+
</indexes>
|
|
387
|
+
</table>
|
|
388
|
+
<table id="stockcollectionprop" primary_key="stockcollectionprop_id">
|
|
389
|
+
<fields>
|
|
390
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
391
|
+
<field id="stockcollection_id" type="integer" not_null="1" default="" foreign_key="stockcollection"/>
|
|
392
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
393
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
394
|
+
</fields>
|
|
395
|
+
<indexes>
|
|
396
|
+
<index columns="type_id" unique=""/>
|
|
397
|
+
<index columns="stockcollection_id" unique=""/>
|
|
398
|
+
<index columns="type_id,stockcollection_id,rank" unique="1"/>
|
|
399
|
+
</indexes>
|
|
400
|
+
</table>
|
|
401
|
+
<table id="stockprop" primary_key="stockprop_id">
|
|
402
|
+
<fields>
|
|
403
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
404
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
405
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
406
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
407
|
+
</fields>
|
|
408
|
+
<indexes>
|
|
409
|
+
<index columns="stock_id" unique=""/>
|
|
410
|
+
<index columns="type_id" unique=""/>
|
|
411
|
+
<index columns="stock_id,type_id,rank" unique="1"/>
|
|
412
|
+
</indexes>
|
|
413
|
+
</table>
|
|
414
|
+
<table id="stockprop_pub" primary_key="stockprop_pub_id">
|
|
415
|
+
<fields>
|
|
416
|
+
<field id="stockprop_pub_id" type="integer" not_null="1" default="" foreign_key="stockprop_pub"/>
|
|
417
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
418
|
+
</fields>
|
|
419
|
+
<indexes>
|
|
420
|
+
<index columns="stockprop_pub_id" unique=""/>
|
|
421
|
+
<index columns="pub_id" unique=""/>
|
|
422
|
+
<index columns="stockprop_pub_id,pub_id" unique="1"/>
|
|
423
|
+
</indexes>
|
|
424
|
+
</table>
|
|
425
|
+
</tables>
|
|
426
|
+
</module>
|
|
427
|
+
<module id="organism" requires="general,cv,pub,organism,genotype,contact">
|
|
428
|
+
<tables>
|
|
429
|
+
<table id="organism" primary_key="organism_id">
|
|
430
|
+
<fields>
|
|
431
|
+
<field id="abbreviation" type="string" not_null="" default="" foreign_key=""/>
|
|
432
|
+
<field id="genus" type="string" not_null="1" default="" foreign_key=""/>
|
|
433
|
+
<field id="species" type="string" not_null="1" default="" foreign_key=""/>
|
|
434
|
+
<field id="common_name" type="string" not_null="" default="" foreign_key=""/>
|
|
435
|
+
<field id="comment" type="text" not_null="" default="" foreign_key=""/>
|
|
436
|
+
</fields>
|
|
437
|
+
<indexes>
|
|
438
|
+
<index columns="genus,species" unique="1"/>
|
|
439
|
+
</indexes>
|
|
440
|
+
</table>
|
|
441
|
+
<table id="organism_dbxref" primary_key="organism_dbxref_id">
|
|
442
|
+
<fields>
|
|
443
|
+
<field id="organism_id" type="integer" not_null="1" default="" foreign_key="organism"/>
|
|
444
|
+
<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
|
|
445
|
+
</fields>
|
|
446
|
+
<indexes>
|
|
447
|
+
<index columns="organism_id" unique=""/>
|
|
448
|
+
<index columns="dbxref_id" unique=""/>
|
|
449
|
+
<index columns="organism_id,dbxref_id" unique="1"/>
|
|
450
|
+
</indexes>
|
|
451
|
+
</table>
|
|
452
|
+
<table id="organismprop" primary_key="organismprop_id">
|
|
453
|
+
<fields>
|
|
454
|
+
<field id="organism_id" type="integer" not_null="1" default="" foreign_key="organism"/>
|
|
455
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
456
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
457
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
458
|
+
</fields>
|
|
459
|
+
<indexes>
|
|
460
|
+
<index columns="organism_id" unique=""/>
|
|
461
|
+
<index columns="type_id" unique=""/>
|
|
462
|
+
<index columns="organism_id,type_id,rank" unique="1"/>
|
|
463
|
+
</indexes>
|
|
464
|
+
</table>
|
|
465
|
+
</tables>
|
|
466
|
+
</module>
|
|
467
|
+
<module id="nd" requires="general,cv,stock,contact,genotype,phenotype">
|
|
468
|
+
<tables>
|
|
469
|
+
<table id="nd_experiment" primary_key="nd_experiment_id">
|
|
470
|
+
<fields>
|
|
471
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
472
|
+
<field id="nd_geolocation_id" type="integer" not_null="1" default="" foreign_key="nd_geolocation"/>
|
|
473
|
+
</fields>
|
|
474
|
+
<indexes>
|
|
475
|
+
<index columns="type_id" unique=""/>
|
|
476
|
+
<index columns="nd_geolocation_id" unique=""/>
|
|
477
|
+
</indexes>
|
|
478
|
+
</table>
|
|
479
|
+
<table id="nd_experiment_contact" primary_key="nd_experiment_contact_id">
|
|
480
|
+
<fields>
|
|
481
|
+
<field id="contact_id" type="integer" not_null="1" default="" foreign_key="contact"/>
|
|
482
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
483
|
+
</fields>
|
|
484
|
+
<indexes>
|
|
485
|
+
<index columns="contact_id" unique=""/>
|
|
486
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
487
|
+
</indexes>
|
|
488
|
+
</table>
|
|
489
|
+
<table id="nd_experiment_dbxref" primary_key="nd_experiment_dbxref_id">
|
|
490
|
+
<fields>
|
|
491
|
+
<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
|
|
492
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
493
|
+
</fields>
|
|
494
|
+
<indexes>
|
|
495
|
+
<index columns="dbxref_id" unique=""/>
|
|
496
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
497
|
+
</indexes>
|
|
498
|
+
</table>
|
|
499
|
+
<table id="nd_experiment_genotype" primary_key="nd_experiment_genotype_id">
|
|
500
|
+
<fields>
|
|
501
|
+
<field id="genotype_id" type="integer" not_null="1" default="" foreign_key="genotype"/>
|
|
502
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
503
|
+
</fields>
|
|
504
|
+
<indexes>
|
|
505
|
+
<index columns="genotype_id" unique=""/>
|
|
506
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
507
|
+
<index columns="genotype_id,nd_experiment_id" unique="1"/>
|
|
508
|
+
</indexes>
|
|
509
|
+
</table>
|
|
510
|
+
<table id="nd_experiment_phenotype" primary_key="nd_experiment_phenotype_id">
|
|
511
|
+
<fields>
|
|
512
|
+
<field id="phenotype_id" type="integer" not_null="1" default="" foreign_key="phenotype"/>
|
|
513
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
514
|
+
</fields>
|
|
515
|
+
<indexes>
|
|
516
|
+
<index columns="phenotype_id" unique=""/>
|
|
517
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
518
|
+
<index columns="phenotype_id,nd_experiment_id" unique="1"/>
|
|
519
|
+
</indexes>
|
|
520
|
+
</table>
|
|
521
|
+
<table id="nd_experiment_project" primary_key="nd_experiment_project_id">
|
|
522
|
+
<fields>
|
|
523
|
+
<field id="project_id" type="integer" not_null="1" default="" foreign_key="project"/>
|
|
524
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
525
|
+
</fields>
|
|
526
|
+
<indexes>
|
|
527
|
+
<index columns="project_id" unique=""/>
|
|
528
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
529
|
+
</indexes>
|
|
530
|
+
</table>
|
|
531
|
+
<table id="nd_experiment_protocol" primary_key="nd_experiment_protocol_id">
|
|
532
|
+
<fields>
|
|
533
|
+
<field id="protocol_id" type="integer" not_null="1" default="" foreign_key="protocol"/>
|
|
534
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
535
|
+
</fields>
|
|
536
|
+
<indexes>
|
|
537
|
+
<index columns="protocol_id" unique=""/>
|
|
538
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
539
|
+
</indexes>
|
|
540
|
+
</table>
|
|
541
|
+
<table id="nd_experiment_pub" primary_key="nd_experiment_pub_id">
|
|
542
|
+
<fields>
|
|
543
|
+
<field id="pub_id" type="integer" not_null="1" default="" foreign_key="pub"/>
|
|
544
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
545
|
+
</fields>
|
|
546
|
+
<indexes>
|
|
547
|
+
<index columns="pub_id" unique=""/>
|
|
548
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
549
|
+
<index columns="pub_id,nd_experiment_id" unique="1"/>
|
|
550
|
+
</indexes>
|
|
551
|
+
</table>
|
|
552
|
+
<table id="nd_experiment_stock" primary_key="nd_experiment_stock_id">
|
|
553
|
+
<fields>
|
|
554
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
555
|
+
<field id="stock_id" type="integer" not_null="1" default="" foreign_key="stock"/>
|
|
556
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
557
|
+
</fields>
|
|
558
|
+
<indexes>
|
|
559
|
+
<index columns="type_id" unique=""/>
|
|
560
|
+
<index columns="stock_id" unique=""/>
|
|
561
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
562
|
+
</indexes>
|
|
563
|
+
</table>
|
|
564
|
+
<table id="nd_experiment_stock_dbxref" primary_key="nd_experiment_stock_dbxref_id">
|
|
565
|
+
<fields>
|
|
566
|
+
<field id="dbxref_id" type="integer" not_null="1" default="" foreign_key="dbxref"/>
|
|
567
|
+
<field id="nd_experiment_stock_id" type="integer" not_null="1" default="" foreign_key="nd_experiment_stock"/>
|
|
568
|
+
</fields>
|
|
569
|
+
<indexes>
|
|
570
|
+
<index columns="dbxref_id" unique=""/>
|
|
571
|
+
<index columns="nd_experiment_stock_id" unique=""/>
|
|
572
|
+
</indexes>
|
|
573
|
+
</table>
|
|
574
|
+
<table id="nd_experiment_stockprop" primary_key="nd_experiment_stockprop_id">
|
|
575
|
+
<fields>
|
|
576
|
+
<field id="nd_experiment_stock_id" type="integer" not_null="1" default="" foreign_key="nd_experiment_stock"/>
|
|
577
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
578
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
579
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
580
|
+
</fields>
|
|
581
|
+
<indexes>
|
|
582
|
+
<index columns="nd_experiment_stock_id" unique=""/>
|
|
583
|
+
<index columns="type_id" unique=""/>
|
|
584
|
+
<index columns="nd_experiment_stock_id,type_id,rank" unique="1"/>
|
|
585
|
+
</indexes>
|
|
586
|
+
</table>
|
|
587
|
+
<table id="nd_experimentprop" primary_key="nd_experimentprop_id">
|
|
588
|
+
<fields>
|
|
589
|
+
<field id="nd_experiment_id" type="integer" not_null="1" default="" foreign_key="nd_experiment"/>
|
|
590
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
591
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
592
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
593
|
+
</fields>
|
|
594
|
+
<indexes>
|
|
595
|
+
<index columns="nd_experiment_id" unique=""/>
|
|
596
|
+
<index columns="type_id" unique=""/>
|
|
597
|
+
<index columns="nd_experiment_id,type_id,rank" unique="1"/>
|
|
598
|
+
</indexes>
|
|
599
|
+
</table>
|
|
600
|
+
<table id="nd_geolocation" primary_key="nd_geolocation_id">
|
|
601
|
+
<fields>
|
|
602
|
+
<field id="description" type="string" not_null="" default="" foreign_key=""/>
|
|
603
|
+
<field id="latitude" type="float" not_null="" default="" foreign_key=""/>
|
|
604
|
+
<field id="longitude" type="float" not_null="" default="" foreign_key=""/>
|
|
605
|
+
<field id="geodetic_datum" type="string" not_null="" default="" foreign_key=""/>
|
|
606
|
+
<field id="altitude" type="float" not_null="" default="" foreign_key=""/>
|
|
607
|
+
</fields>
|
|
608
|
+
<indexes>
|
|
609
|
+
</indexes>
|
|
610
|
+
</table>
|
|
611
|
+
<table id="nd_geolocationprop" primary_key="nd_geolocationprop_id">
|
|
612
|
+
<fields>
|
|
613
|
+
<field id="nd_geolocation_id" type="integer" not_null="1" default="" foreign_key="nd_geolocation"/>
|
|
614
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
615
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
616
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
617
|
+
</fields>
|
|
618
|
+
<indexes>
|
|
619
|
+
<index columns="nd_geolocation_id" unique=""/>
|
|
620
|
+
<index columns="type_id" unique=""/>
|
|
621
|
+
<index columns="nd_geolocation_id,type_id,rank" unique="1"/>
|
|
622
|
+
</indexes>
|
|
623
|
+
</table>
|
|
624
|
+
<table id="nd_protocol" primary_key="nd_protocol_id">
|
|
625
|
+
<fields>
|
|
626
|
+
<field id="name" type="string" not_null="1" default="" foreign_key=""/>
|
|
627
|
+
</fields>
|
|
628
|
+
<indexes>
|
|
629
|
+
<index columns="name" unique="1"/>
|
|
630
|
+
</indexes>
|
|
631
|
+
</table>
|
|
632
|
+
<table id="nd_protocol_reagent" primary_key="nd_protocol_reagent_id">
|
|
633
|
+
<fields>
|
|
634
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
635
|
+
<field id="nd_protocol_id" type="integer" not_null="1" default="" foreign_key="nd_protocol"/>
|
|
636
|
+
<field id="reagent_id" type="integer" not_null="1" default="" foreign_key="reagent"/>
|
|
637
|
+
</fields>
|
|
638
|
+
<indexes>
|
|
639
|
+
<index columns="type_id" unique=""/>
|
|
640
|
+
<index columns="nd_protocol_id" unique=""/>
|
|
641
|
+
<index columns="reagent_id" unique=""/>
|
|
642
|
+
</indexes>
|
|
643
|
+
</table>
|
|
644
|
+
<table id="nd_protocolprop" primary_key="nd_protocolprop_id">
|
|
645
|
+
<fields>
|
|
646
|
+
<field id="nd_protocol_id" type="integer" not_null="1" default="" foreign_key="nd_protocol"/>
|
|
647
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
648
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
649
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
650
|
+
</fields>
|
|
651
|
+
<indexes>
|
|
652
|
+
<index columns="nd_protocol_id" unique=""/>
|
|
653
|
+
<index columns="type_id" unique=""/>
|
|
654
|
+
<index columns="nd_protocol_id,type_id,rank" unique="1"/>
|
|
655
|
+
</indexes>
|
|
656
|
+
</table>
|
|
657
|
+
<table id="nd_reagent" primary_key="nd_reagent_id">
|
|
658
|
+
<fields>
|
|
659
|
+
<field id="name" type="string" not_null="1" default="" foreign_key=""/>
|
|
660
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
661
|
+
<field id="feature_id" type="integer" not_null="" default="" foreign_key=""/>
|
|
662
|
+
</fields>
|
|
663
|
+
<indexes>
|
|
664
|
+
<index columns="type_id" unique=""/>
|
|
665
|
+
<index columns="feature_id" unique=""/>
|
|
666
|
+
</indexes>
|
|
667
|
+
</table>
|
|
668
|
+
<table id="nd_reagent_relationship" primary_key="nd_reagent_relationship_id">
|
|
669
|
+
<fields>
|
|
670
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
671
|
+
<field id="subject_reagent_id" type="integer" not_null="1" default="" foreign_key="nd_reagent"/>
|
|
672
|
+
<field id="object_reagent_id" type="integer" not_null="1" default="" foreign_key="nd_reagent"/>
|
|
673
|
+
</fields>
|
|
674
|
+
<indexes>
|
|
675
|
+
<index columns="type_id" unique=""/>
|
|
676
|
+
<index columns="subject_reagent_id" unique=""/>
|
|
677
|
+
<index columns="object_reagent_id" unique=""/>
|
|
678
|
+
</indexes>
|
|
679
|
+
</table>
|
|
680
|
+
<table id="nd_reagentprop" primary_key="nd_reagentprop_id">
|
|
681
|
+
<fields>
|
|
682
|
+
<field id="nd_reagent_id" type="integer" not_null="1" default="" foreign_key="nd_reagent"/>
|
|
683
|
+
<field id="type_id" type="integer" not_null="1" default="" foreign_key="cvterm"/>
|
|
684
|
+
<field id="rank" type="integer" not_null="1" default="" foreign_key=""/>
|
|
685
|
+
<field id="value" type="text" not_null="" default="" foreign_key=""/>
|
|
686
|
+
</fields>
|
|
687
|
+
<indexes>
|
|
688
|
+
<index columns="nd_reagent_id" unique=""/>
|
|
689
|
+
<index columns="type_id" unique=""/>
|
|
690
|
+
<index columns="nd_reagent_id,type_id,rank" unique="1"/>
|
|
691
|
+
</indexes>
|
|
692
|
+
</table>
|
|
693
|
+
</tables>
|
|
694
|
+
</module>
|
|
695
|
+
</modules>
|
|
696
|
+
</chado>
|
|
697
|
+
</schema>
|