Skip to content

PIXI-247 and Version upgrade to 1.5.1 #57

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
mohana-xw wants to merge 1 commit into from
Closed

PIXI-247 and Version upgrade to 1.5.1 #57

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion build.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ plugins {
}

group "org.nrg.xnatx.plugins"
version "1.5.0"
version "1.5.1"
description "PIXI Plugin for XNAT."

repositories {
Expand Down
2 changes: 1 addition & 1 deletion gradle/wrapper/gradle-wrapper.properties
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
8 changes: 7 additions & 1 deletion ...a/org/nrg/xnatx/plugins/pixi/xenografts/services/impl/HibernateCellLineEntityService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,16 @@ public boolean hasSubjectReferences(final String sourceId) {

@Override
protected CellLine toDTO(CellLineEntity cellLineEntity) {
return CellLine.builder()
CellLine cell = CellLine.builder()
.sourceId(cellLineEntity.getSourceId())
.source(cellLineEntity.getSource())
.sourceURL(cellLineEntity.getSourceURL())
.createdBy(cellLineEntity.getCreatedBy())
.build();
cell.setPrimarySite(cellLineEntity.getPrimarySite());
cell.setTumorType(cellLineEntity.getTumorType());
return cell;

}

@Override
Expand All @@ -50,5 +54,7 @@ protected void updateEntity(CellLineEntity cellLineEntity, CellLine cellLine) {
cellLineEntity.setSource(cellLine.getSource());
cellLineEntity.setSourceURL(cellLine.getSourceURL());
cellLineEntity.setCreatedBy(cellLine.getCreatedBy());
cellLineEntity.setTumorType(cellLine.getTumorType());
cellLineEntity.setPrimarySite(cellLine.getPrimarySite());
}
}
20 changes: 18 additions & 2 deletions src/main/resources/META-INF/resources/scripts/xnat/plugin/pixi/pixi-xenograft.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,18 @@ XNAT.plugin.pixi.pdxs = getObject(XNAT.plugin.pixi.pdxs || {});
label: self.xenograftType + ' URL',
id: 'sourceURL',
description: 'Optional: A link to this ' + self.xenograftType + ' at the data source provider (if available).'
}).element,
XNAT.ui.panel.input.text({
name: 'tumorType',
label: self.xenograftType + ' Tumor Type',
id: 'tumorType',
description: 'Optional: Tumor type'
}).element,
XNAT.ui.panel.input.text({
name: 'primarySite',
label: self.xenograftType + ' Primary Site',
id: 'primarySite',
description: 'Optional: Primary Site'
}).element
];
}
Expand Down Expand Up @@ -148,6 +160,8 @@ XNAT.plugin.pixi.pdxs = getObject(XNAT.plugin.pixi.pdxs || {});
const sourceIdEl = document.getElementById("sourceId");
const sourceEl = document.getElementById("source");
const sourceURLEl = document.getElementById("sourceURL");
const tumorTypeEl = document.getElementById("tumorType");
const primarySiteEl = document.getElementById("primarySite");

// validator for sourceId (i.e. PDX ID and Cell Line ID)
let validateSourceId = XNAT.validate(sourceIdEl).reset().chain();
Expand Down Expand Up @@ -182,10 +196,12 @@ XNAT.plugin.pixi.pdxs = getObject(XNAT.plugin.pixi.pdxs || {});
let xenograftToSubmit = {
sourceId: sourceIdEl.value,
source: sourceEl.value,
sourceURL: sourceURLEl.value
sourceURL: sourceURLEl.value,
tumorType: tumorTypeEl.value,
primarySite: primarySiteEl.value
};

if (self.xenograftType === "PDX") {
if (self.xenograftType === "Patient-Derived Tumor") {
const storageEl = document.getElementById("storage");
xenograftToSubmit['storage'] = storageEl.value;
}
Expand Down
20 changes: 20 additions & 0 deletions src/main/resources/schemas/pixi/display/pixi_cellLineData_display.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,12 @@
<DisplayField header="Projects" id="PROJECTS" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_CELLLINEDATA_PROJECTS" viewColumn="PROJECTS"/>
</DisplayField>
<DisplayField header="Tumor Type" id="TUMOR_TYPE" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_CELLLINEDATA_TUMOR_MODEL" viewColumn="tumor_type"/>
</DisplayField>
<DisplayField header="Primary Site" id="PRIMARY_SITE" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_CELLLINEDATA_TUMOR_MODEL" viewColumn="primary_site"/>
</DisplayField>
<DisplayField header="Label" id="LABEL" data-type="string">
<DisplayFieldElement name="Field1" schema-element="pixi:cellLineData.ID"/>
<DisplayFieldElement name="Field2" schema-element="pixi:cellLineData.label"/>
Expand Down Expand Up @@ -133,6 +139,8 @@
<DisplayFieldRef id="LABEL"/>
<DisplayFieldRef id="SUBJECT_LABEL" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="NUMCELLSINJECTED"/>
Expand All @@ -153,6 +161,8 @@
<DisplayFieldRef id="EXPT_ID"/>
<DisplayFieldRef id="SUBJECT_LABEL" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="NUMCELLSINJECTED"/>
Expand All @@ -161,6 +171,8 @@
<DisplayVersion versionName="detailed" default-order-by="DATE" default-sort-order="DESC"
brief-description="CellLine" dark-color="9999CC" light-color="CCCCFF">
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="NUMCELLSINJECTED"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -170,6 +182,8 @@
<DisplayFieldRef id="PIXI_CELLLINEDATA_PROJECT_IDENTIFIER"/>
<DisplayFieldRef id="SUB_PROJECT_IDENTIFIER" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -180,6 +194,12 @@
<MappingColumn rootElement="pixi:cellLineData" fieldElement="pixi:cellLineData.ID" mapsTo="id"/>
</Mapping>
</ViewLink>
<ViewLink alias="PIXI_CELLLINEDATA_TUMOR_MODEL">
<Mapping TableName="CELLLINE_TUMOR_MODEL">
<MappingColumn rootElement="pixi:celllineData" fieldElement="pixi:celllineData.ID" mapsTo="id"/>
</Mapping>
</ViewLink>
<SQLView name="PIXI_CELLLINEDATA_PROJECTS"
sql="SELECT id, '&lt;' || expt.project || '&gt;' || xs_a_concat(',&lt;' || shared.project || '&gt;') AS projects FROM xnat_experimentData expt LEFT JOIN xnat_experimentData_share shared ON expt.id=shared.sharing_share_xnat_experimentda_id LEFT JOIN xdat_meta_element xme ON expt.extension = xme.xdat_meta_element_id WHERE element_name='pixi:cellLineData' GROUP BY expt.id,expt.project"/>
<SQLView name="CELLLINE_TUMOR_MODEL" sql="select cell.id, cell.sourceid, pdxe.tumor_type, pdxe.primary_site from pixi_celllinedata cell LEFT JOIN xhbm_pdxentity pdxe on cell.sourceid = pdxe.source_id;"/>
</Displays>
22 changes: 22 additions & 0 deletions src/main/resources/schemas/pixi/display/pixi_pdxData_display.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,12 @@
<DisplayField header="Projects" id="PROJECTS" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_PDXDATA_PROJECTS" viewColumn="PROJECTS"/>
</DisplayField>
<DisplayField header="Tumor Type" id="TUMOR_TYPE" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_PDXDATA_TUMOR_MODEL" viewColumn="tumor_type"/>
</DisplayField>
<DisplayField header="Primary Site" id="PRIMARY_SITE" data-type="string">
<DisplayFieldElement name="Field1" viewName="PIXI_PDXDATA_TUMOR_MODEL" viewColumn="primary_site"/>
</DisplayField>
<DisplayField header="Label" id="LABEL" data-type="string">
<DisplayFieldElement name="Field1" schema-element="pixi:pdxData.ID"/>
<DisplayFieldElement name="Field2" schema-element="pixi:pdxData.label"/>
Expand Down Expand Up @@ -137,6 +143,8 @@
<DisplayFieldRef id="LABEL"/>
<DisplayFieldRef id="SUBJECT_LABEL" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -149,6 +157,8 @@
<DisplayFieldRef id="LABEL"/>
<DisplayFieldRef id="SUBJECT_LABEL" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -161,6 +171,8 @@
<DisplayFieldRef id="EXPT_ID"/>
<DisplayFieldRef id="SUBJECT_LABEL" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -171,6 +183,8 @@
<DisplayVersion versionName="detailed" default-order-by="DATE" default-sort-order="DESC" brief-description="PDX"
dark-color="9999CC" light-color="CCCCFF">
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
<DisplayFieldRef id="NUMCELLSINJECTED"/>
Expand All @@ -182,6 +196,8 @@
<DisplayFieldRef id="PIXI_PDXDATA_PROJECT_IDENTIFIER"/>
<DisplayFieldRef id="SUB_PROJECT_IDENTIFIER" element_name="xnat:subjectData"/>
<DisplayFieldRef id="SOURCEID"/>
<DisplayFieldRef id="TUMOR_TYPE"/>
<DisplayFieldRef id="PRIMARY_SITE"/>
<DisplayFieldRef id="DATE"/>
<DisplayFieldRef id="INJECTIONSITE"/>
<DisplayFieldRef id="INJECTIONTYPE"/>
Expand All @@ -194,6 +210,12 @@
<MappingColumn rootElement="pixi:pdxData" fieldElement="pixi:pdxData.ID" mapsTo="id"/>
</Mapping>
</ViewLink>
<ViewLink alias="PIXI_PDXDATA_TUMOR_MODEL">
<Mapping TableName="PDX_TUMOR_MODEL">
<MappingColumn rootElement="pixi:pdxData" fieldElement="pixi:pdxData.ID" mapsTo="id"/>
</Mapping>
</ViewLink>
<SQLView name="PIXI_PDXDATA_PROJECTS"
sql="SELECT id, '&lt;' || expt.project || '&gt;' || xs_a_concat(',&lt;' || shared.project || '&gt;') AS projects FROM xnat_experimentData expt LEFT JOIN xnat_experimentData_share shared ON expt.id=shared.sharing_share_xnat_experimentda_id LEFT JOIN xdat_meta_element xme ON expt.extension = xme.xdat_meta_element_id WHERE element_name='pixi:pdxData' GROUP BY expt.id,expt.project"/>
<SQLView name="PDX_TUMOR_MODEL" sql="select pdx.id, pdx.sourceid, pdxe.tumor_type, pdxe.primary_site from pixi_pdxdata pdx LEFT JOIN xhbm_pdxentity pdxe on pdx.sourceid = pdxe.source_id;"/>
</Displays>
Loading