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update user dataset meta info #55

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d75d494
update user dataset meta info
steve-fischer-200 Apr 28, 2025
8447015
accessibility
steve-fischer-200 Apr 28, 2025
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129 changes: 94 additions & 35 deletions Model/lib/wdk/model/records/datasetRecords.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,11 @@
</linkAttribute>
</attributeQueryRef>
-->
<attributeQueryRef ref="DatasetAttributes.UserDatasetAccessibility">
<columnAttribute name="accessibility" displayName="Accessibility"/>
<columnAttribute name="days_for_approval" displayName="Days for approval"/>
</attributeQueryRef>

<attributeQueryRef ref="DatasetAttributes.ClinepiStudyAttributes" includeProjects="MicrobiomeDB,ClinEpiDB">
<columnAttribute name="project_availability" internal="true"/>
<columnAttribute name="is_public" internal="true"/>
Expand Down Expand Up @@ -285,7 +290,7 @@ while in protected and private studies there will be human intervention in the d

<attributeQueryRef ref="DatasetAttributes.OwnerVisibility" excludeProjects="MicrobiomeDB,ClinEpiDB">
<columnAttribute name="owner" displayName="Owner" />
<columnAttribute name="community" displayName="Community"/>
<columnAttribute name="accessibility" displayName="Community"/>
</attributeQueryRef>


Expand Down Expand Up @@ -429,7 +434,22 @@ OR if the linkName and or URL require access to other attributes....also how to
<columnAttribute name="affiliation" displayName="Affiliation"/>
</table>

<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- User Dataset Properties Table -->
<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->

<table name="UserDatasetPropertiesTable" includeProjects="ClinEpiDB"
displayName="Study Properties"
queryRef="DatasetTables.UserDatasetProperties">
<columnAttribute name="dataset_id" inReportMaker="false" internal="true"/>
<!-- <columnAttribute name="dataset_name" inReportMaker="false" internal="true"/> -->
<columnAttribute name="study_design" displayName="Study design" sortable="false"/>
<columnAttribute name="disease" displayName="Disease" sortable="false"/>
<columnAttribute name="country" displayName="Country" sortable="false"/>
<columnAttribute name="years" displayName="Years" sortable="false"/>
<columnAttribute name="ages" displayName="Ages" sortable="false"/>
<columnAttribute name="sample_type" displayName="Sample type" sortable="false"/>
</table>

<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Study Characteristic -->
Expand Down Expand Up @@ -1082,6 +1102,19 @@ Based on evolutionarily informed expectations of gene content of near-universal
</sql>
</sqlQuery>

<sqlQuery name="UserDatasetAccessibility" isCacheable="false" includeProjects="MicrobiomeDB,ClinEpiDB">
<column name="accessibility" columnType="string"/>
<column name="days_for_approval"/>
<sql>
<![CDATA[
SELECT DISTINCT
CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
d.accessibility, d.days_for_approval
FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets d
]]>
</sql>
</sqlQuery>

<sqlQuery name="ClinepiStudyAttributes" isCacheable="false" includeProjects="MicrobiomeDB,ClinEpiDB">
<column name="dataset_id" columnType="string"/>
<column name="is_public" columnType="string"/>
Expand Down Expand Up @@ -1335,8 +1368,6 @@ where mystudies.dataset_id = dp.dataset_presenter_id
</sqlQuery>




<sqlQuery name="StudyCharacteristic" isCacheable="false" includeProjects="ClinEpiDB">
<column name="dataset_id" columnType="string"/>
<column name="disease" columnType="string"/>
Expand Down Expand Up @@ -1633,7 +1664,7 @@ where mystudies.dataset_id = dp.dataset_presenter_id
where dsp.dataset_presenter_id = dp.dataset_presenter_id(+)
UNION
select CONCAT('EDAUD_', d.user_dataset_id) as dataset_id,
case when is_public = 1 then 'yes' else 'no' end as is_public
case when accessibility != 'private' then 'yes' else 'no' end as is_public
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
]]>
</sql>
Expand Down Expand Up @@ -1940,7 +1971,7 @@ select dsp.dataset_presenter_id as dataset_id,
<![CDATA[
select dsp.dataset_presenter_id as dataset_id,
null as owner,
null as community
null as accessibility
from apidbTuning.DatasetPresenter dsp
]]>
</sql>
Expand All @@ -1949,12 +1980,12 @@ select dsp.dataset_presenter_id as dataset_id,
<![CDATA[
select dsp.dataset_presenter_id as dataset_id,
null as owner,
null as community
null as accessibility
from apidbTuning.DatasetPresenter dsp
UNION
SELECT CONCAT('EDAUD_', dataset_id) as dataset_id,
owner,
is_public as community
accessibility
from @VDI_CONTROL_SCHEMA@.dataset
]]>
</sql>
Expand Down Expand Up @@ -2012,20 +2043,14 @@ select dsp.dataset_presenter_id as dataset_id,
where dsp.dataset_presenter_id = dsc.dataset_presenter_id (+)
and dsc.is_primary_contact = 1
UNION
-- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
-- , dc.name as contact
-- , affiliation as institution
-- , email
-- , short_attribution
-- from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
-- where dc.is_primary = 1
-- and dc.dataset_id = d.user_dataset_id
SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
, null as contact
, null as institution
, null as email
, null as short_attribution
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
, dc.name as contact
, affiliation as institution
, email
, short_attribution
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
where dc.is_primary = 1
and dc.dataset_id = d.user_dataset_id
]]>
</sql>

Expand Down Expand Up @@ -2061,20 +2086,14 @@ select dsp.dataset_presenter_id as dataset_id,
where dsp.dataset_presenter_id = dsc.dataset_presenter_id (+)
and dsc.is_primary_contact = 1
UNION
-- SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
-- , dc.name as contact
-- , affiliation as institution
-- , email
-- , short_attribution
-- from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
-- where dc.is_primary = 1
-- and dc.dataset_id = d.user_dataset_id
SELECT CONCAT('EDAUD_', d.user_dataset_id) as dataset_id
, null as contact
, null as institution
, null as email
, null as short_attribution
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
, dc.name as contact
, affiliation as institution
, email
, short_attribution
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d, @VDI_CONTROL_SCHEMA@.dataset_contact dc
where dc.is_primary = 1
and dc.dataset_id = d.user_dataset_id
]]>
</sql>

Expand Down Expand Up @@ -2170,8 +2189,25 @@ from apidbtuning.datasetnametaxon dsnt
)
group by dataset_id
UNION
select CONCAT('EDAUD_', d.user_dataset_id) as dataset_id, null as organism_prefix
from @VDI_CONTROL_SCHEMA@.availableuserdatasets d
SELECT dataset_id,
REGEXP_REPLACE(
SUBSTR(
LISTAGG(org, '<br>') WITHIN GROUP (ORDER BY org), 1, 4000
),
'<br>[A-Za-z\. <>&]+$', '<br>...'
) AS organism_prefix
FROM (
SELECT DISTINCT 'EDAUD_' || aud.user_dataset_id AS dataset_id,
CASE
WHEN oa.organism_name IS NULL THEN NULL
ELSE REGEXP_REPLACE(oa.organism_name, '^(\w*)\s(\w*)\s(\.*)', '<I>\1 \2</I>') || '</i>'
END AS org
FROM @VDI_CONTROL_SCHEMA@.availableuserdatasets aud
LEFT JOIN @VDI_CONTROL_SCHEMA@.dataset_organism dd ON aud.user_dataset_id = dd.dataset_id
LEFT JOIN apidbtuning.organismattributes oa ON dd.organism_abbrev = oa.internal_abbrev
) t
GROUP BY dataset_id;

]]>
</sql>
<sql includeProjects="EuPathDB">
Expand Down Expand Up @@ -2246,6 +2282,29 @@ from apidbtuning.datasetnametaxon dsnt
<querySet name="DatasetTables" queryType="table"
isCacheable='false'>

<sqlQuery name="UserDatasetProperties" isCacheable="false" includeProjects="ClinEpiDB">
<column name="study_design" columnType="string"/>
<column name="disease" columnType="string"/>
<column name="country" columnType="string"/>
<column name="years" columnType="string"/>
<column name="ages" columnType="string"/>
<column name="sample_type" columnType="string"/>
<sql>
<![CDATA[
SELECT DISTINCT
CONCAT('EDAUD_', dc.dataset_id) as dataset_id,
JSON_value(json, '$.studyDesign' ) AS study_design,
JSON_value(json, '$.disease' ) AS disease,
JSON_value(json, '$.country' ) AS country,
JSON_value(json, '$.years' ) AS years,
JSON_value(json, '$.ages' ) AS ages,
JSON_value(json, '$.sample_type' ) AS sample_type,
FROM @VDI_CONTROL_SCHEMA@.dataset_properties dp, @VDI_CONTROL_SCHEMA@.AvailableUserDatasets aud
where dp.dataset_id = aud.user_dataset_id
]]>
</sql>
</sqlQuery>

<sqlQuery name="RNASeqSamplesInternal" isCacheable='false'>
<column name="dataset_id"/>
<column name="study_name"/>
Expand Down