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update comm dataset with metadata #39

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124 changes: 116 additions & 8 deletions Model/lib/wdk/Shared/commDatasetQueries.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,12 +50,11 @@

<sqlQuery name="hyperlinks">
<column name="dataset_id"/>
<column name="url"/>
<column name="text"/>
<column name="description"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, url, text, description
select aud.user_dataset_id as dataset_id, text, description
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_hyperlinks dh
where aud.project_id = '@PROJECT_ID@'
Expand All @@ -70,7 +69,8 @@
<column name="organism_name"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, organism_name
select aud.user_dataset_id as dataset_id,
species || ' ' || strain as organism_name
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_organism do, apidbtuning.organismAttributes oa
where aud.project_id = '@PROJECT_ID@'
Expand All @@ -88,17 +88,125 @@
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id,
dc.name as contact_name, affiliation
concat(dc.first_name, ' ', dc.middle_name, ' ', dc.last_name) as contact_name, affiliation
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_contact dc
@VDI_CONTROL_SCHEMA@dataset_contact dc
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dh.dataset_id
and aud.dataset_id = dc.dataset_id
]]>
</sql>
</sqlQuery>



<sqlQuery name="countries">
<column name="dataset_id"/>
<column name="country"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, country
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_country dc
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dc.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="species">
<column name="dataset_id"/>
<column name="species"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, species
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_species ds
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = ds.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="diseases">
<column name="dataset_id"/>
<column name="disease"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, disease
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_disease dd
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dd.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="associatedFactors">
<column name="dataset_id"/>
<column name="factor"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, factor
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_associated_factor daf
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = daf.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="dois">
<column name="dataset_id"/>
<column name="doi"/>
<column name="description"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, doi, description
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_doi dd
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dd.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="bioprojectIds">
<column name="dataset_id"/>
<column name="bioproject_id"/>
<column name="description"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, bioproject_id, description
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_bioproject_id dbi
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dbi.dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="fundingAwards">
<column name="dataset_id"/>
<column name="agency"/>
<column name="award_number"/>
<sql>
<![CDATA[
select aud.user_dataset_id as dataset_id, agency, award_number
from @VDI_CONTROL_SCHEMA@AvailableUserDatasets aud,
@VDI_CONTROL_SCHEMA@dataset_funding_award dfa
where aud.project_id = '@PROJECT_ID@'
and aud.is_public = true and aud.is_owner = 1
and aud.dataset_id = dfa.dataset_id
]]>
</sql>
</sqlQuery>


</querySet>

</wdkModel>
95 changes: 69 additions & 26 deletions Model/lib/wdk/Shared/commDatasetRecord.xml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,5 @@
<wdkModel>

<constant name="datasetRecordName" includeProjects="ClinEpiDB">Study Name</constant>
<constant name="datasetRecordName" excludeProjects="ClinEpiDB">Name</constant>


<recordClassSet name="communityDatasetRecordClasses">

<!-- ################################################################### -->
Expand All @@ -19,16 +15,7 @@
<columnRef>dataset_id</columnRef>
</primaryKey>

<idAttribute name="primary_key" displayName="%%datasetRecordName%%" excludeProjects="ClinEpiDB">
<propertyList name="boost">
<value>100</value>
</propertyList>
<text>
<![CDATA[ $$display_name$$ ]]>
</text>
</idAttribute>

<idAttribute name="primary_key" displayName="Study Name" includeProjects="ClinEpiDB">
<idAttribute name="primary_key" displayName="Dataset Name">
<propertyList name="boost">
<value>100</value>
</propertyList>
Expand All @@ -42,21 +29,20 @@
scopes=""
implementation="org.eupathdb.sitesearch.data.model.report.SolrLoaderReporter"/>

<!-- for ClinEpi and mbio, boost all fields in dataset record, so that Studies generally come out on top of search results -->
<attributeQueryRef ref="CommunityDatasetAttributes.All">
<columnAttribute name="project" displayName="dontcare" internal="true"/> <!-- special field for project filtering -->
<columnAttribute name="hyperlinkName" displayName="dontcare" internal="true"/> <!-- used for display in ss results -->
<columnAttribute name="display_name" internal="true"/>
<columnAttribute name="description" displayName="Description">
<propertyList name="boost" includeProjects="ClinEpiDB, MicrobiomeDB">
<propertyList name="boost">
<value>20</value>
</propertyList>
</columnAttribute>
<columnAttribute name="summary" displayName="Summary">
<propertyList name="isSummary">
<value>true</value>
</propertyList>
<propertyList name="boost" includeProjects="ClinEpiDB, MicrobiomeDB">
<propertyList name="boost">
<value>20</value>
</propertyList>
</columnAttribute>
Expand All @@ -65,7 +51,7 @@
<table name="Contacts"
displayName="Principal Investigator and Collaborators"
queryRef="DatasetTables.Contacts">
<propertyList name="boost" includeProjects="ClinEpiDB, MicrobiomeDB">
<propertyList name="boost">
<value>20</value>
</propertyList>
<columnAttribute name="dataset_id"/>
Expand All @@ -76,12 +62,20 @@
<table name="Publications"
displayName="Associated publications"
queryRef="DatasetTables.Publications">
<propertyList name="boost" includeProjects="ClinEpiDB, MicrobiomeDB">
<propertyList name="boost">
<value>20</value>
</propertyList>
</propertyList>
<columnAttribute name="dataset_id"/>
<columnAttribute name="pmid" displayName="Pubmed ID"/>
<columnAttribute name="citation" displayName="Citation"/>
<columnAttribute name="citation" displayName="Citation"/>
</table>

<table name="Hyperlinks"
displayName="Related links"
queryRef="DatasetTables.Hyperlinks">
<columnAttribute name="dataset_id"/>
<columnAttribute name="text" displayName="Link text"/>
<columnAttribute name="description" displayName="Description"/>
</table>

<table name="Organisms"
Expand All @@ -102,14 +96,63 @@
<value>AmoebaDB</value>
<value>UniDB</value>
</propertyList>
<propertyList name="boost" includeProjects="ClinEpiDB, MicrobiomeDB">
<value>20</value>
</propertyList>
<columnAttribute name="dataset_id"/>
<columnAttribute name="organism_name"/>

</table>


<table name="Countries"
displayName="Countries"
queryRef="DatasetTables.Countries">
<columnAttribute name="dataset_id"/>
<columnAttribute name="country" displayName="Country"/>
</table>

<table name="Species"
displayName="Species"
queryRef="DatasetTables.Species">
<columnAttribute name="dataset_id"/>
<columnAttribute name="species" displayName="Species"/>
</table>

<table name="Diseases"
displayName="Diseases"
queryRef="DatasetTables.Diseases">
<columnAttribute name="dataset_id"/>
<columnAttribute name="disease" displayName="Disease"/>
</table>

<table name="AssociatedFactors"
displayName="Associated factors"
queryRef="DatasetTables.AssociatedFactors">
<columnAttribute name="dataset_id"/>
<columnAttribute name="factor" displayName="Factor"/>
</table>

<table name="DOIs"
displayName="DOIs"
queryRef="DatasetTables.DOIs">
<columnAttribute name="dataset_id"/>
<columnAttribute name="doi" displayName="DOI"/>
<columnAttribute name="description" displayName="Description"/>
</table>

<table name="BioprojectIds"
displayName="Bioproject IDs"
queryRef="DatasetTables.BioprojectIds">
<columnAttribute name="dataset_id"/>
<columnAttribute name="bioproject_id" displayName="Bioproject ID"/>
<columnAttribute name="description" displayName="Description"/>
</table>

<table name="FundingAwards"
displayName="Funding awards"
queryRef="DatasetTables.FundingAwards">
<columnAttribute name="dataset_id"/>
<columnAttribute name="agency" displayName="Agency"/>
<columnAttribute name="award_number" displayName="Award number"/>
</table>


</recordClass>

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