Add MCC fields and new statuses (#103)

bbimber · web-flow · commit 6318a70b1f47 · 2023-04-13T21:43:59.000-07:00
* Add disease focus to MCC and allow widthdrawl of requests
diff --git a/mGAP/resources/etls/prime-seq.xml b/mGAP/resources/etls/prime-seq.xml
@@ -133,7 +133,7 @@
         </transform>
         <transform id="step5" type="RemoteQueryTransformStep">
             <description>Copy to local table</description>
-            <source schemaName="mGAP" queryName="variantList" remoteSource="PRIMESEQ">
+            <source schemaName="mGAP" queryName="variantList" remoteSource="PRIMESEQ" sourceTimeout="0">
                 <sourceColumns>
                     <column>releaseId</column>
                     <column>contig</column>
diff --git a/mcc/package-lock.json b/mcc/package-lock.json
diff --git a/mcc/resources/etls/snprc-datasets.xml b/mcc/resources/etls/snprc-datasets.xml
@@ -7,7 +7,7 @@
     <transforms>
         <transform type="RemoteQueryTransformStep" id="demographics">
             <description>Copy to target</description>
-            <source remoteSource="SNPRC" schemaName="study" queryName="Demographics">
+            <source remoteSource="SNPRC" schemaName="study" queryName="Demographics" sourceTimeout="0">
                 <sourceColumns>
                     <column>AnimalId</column>
                     <column>date</column>
diff --git a/mcc/resources/queries/mcc/animalRequests/Non-Draft.qview.xml b/mcc/resources/queries/mcc/animalRequests/Non-Draft.qview.xml
@@ -1,6 +1,8 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView" canOverride="false">
     <filters>
         <filter column="status" operator="neqornull" value="draft" />
+        <filter column="status" operator="neqornull" value="withdrawn" />
+        <filter column="status" operator="neqornull" value="fulfilled" />
     </filters>
     <sorts>
         <sort column="rowid" descending="true"/>
diff --git a/mcc/resources/queries/mcc/requestScores/Pending Requests.qview.xml b/mcc/resources/queries/mcc/requestScores/Pending Requests.qview.xml
@@ -1,6 +1,7 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView" label="Pending Requests" canOverride="false">
     <filters>
-        <filter column="requestId/status" operator="neqornull" value="Approved"/>
+        <filter column="requestId/status" operator="neqornull" value="Withdrawn"/>
+        <filter column="requestId/status" operator="neqornull" value="Fulfilled"/>
     </filters>
     <sorts>
         <sort column="requestId/rowid" descending="true"/>
diff --git a/mcc/resources/schemas/dbscripts/postgresql/mcc-20.013-20.014.sql b/mcc/resources/schemas/dbscripts/postgresql/mcc-20.013-20.014.sql
@@ -0,0 +1 @@
+ALTER TABLE mcc.animalrequests add diseasefocus varchar(4000);
diff --git a/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.013-20.014.sql b/mcc/resources/schemas/dbscripts/sqlserver/mcc-20.013-20.014.sql
@@ -0,0 +1 @@
+ALTER TABLE mcc.animalrequests add diseasefocus varchar(4000);
diff --git a/mcc/resources/schemas/mcc.xml b/mcc/resources/schemas/mcc.xml
@@ -302,6 +302,9 @@
                 <columnTitle>Neuroscience Relevance</columnTitle>
                 <nullable>true</nullable>
             </column>
+            <column columnName="diseasefocus">
+                <columnTitle>Research/Disease Focus</columnTitle>
+            </column>
             <column columnName="census">
                 <columnTitle>Participate In Census?</columnTitle>
                 <nullable>true</nullable>
diff --git a/mcc/resources/views/mccRequestAdmin.html b/mcc/resources/views/mccRequestAdmin.html
@@ -44,7 +44,7 @@
             frame: 'left-nav',
             schemaName: 'mcc',
             queryName: 'requestScores',
-            //viewName: 'Pending Requests',
+            viewName: 'Pending Requests',
             showRecordSelectors: true,
             showDetailsColumn: true
         }).render(webpart.wrapperDivId + '-webpartPending');
diff --git a/mcc/resources/web/mcc/window/ChangeStatusWindow.js b/mcc/resources/web/mcc/window/ChangeStatusWindow.js
@@ -0,0 +1,68 @@
+/**
+ * @cfg dataRegionName
+ */
+Ext4.define('MCC.window.ChangeStatusWindow', {
+    extend: 'Ext.window.Window',
+
+    fieldName: 'disabled',
+
+    statics: {
+        buttonHandler: function(dataRegionName, requestId, status){
+            Ext4.create('MCC.window.ChangeStatusWindow', {
+                dataRegionName: dataRegionName,
+                requestId: requestId,
+                status: status
+            }).show();
+        },
+    },
+
+    initComponent: function(){
+        Ext4.apply(this, {
+            modal: true,
+            title: 'Change Status',
+            closeAction: 'destroy',
+            width: 380,
+            items: [{
+                bodyStyle: 'padding: 5px;',
+                html: 'This will update request #' + this.requestId + ' to: ' + this.status
+            }],
+            buttons: [{
+                text:'Submit',
+                disabled:false,
+                scope: this,
+                handler: this.onSubmit
+            },{
+                text: 'Close',
+                handler: function(btn){
+                    btn.up('window').close();
+                }
+            }]
+        });
+
+        this.callParent(arguments);
+    },
+
+    onSubmit: function(btn){
+        Ext4.Msg.wait('Loading...');
+        var dataRegion = this.dataRegionName ? LABKEY.DataRegions[this.dataRegionName] : null;
+
+        LABKEY.Query.updateRows({
+            method: 'POST',
+            schemaName: 'mcc',
+            queryName: 'animalRequests',
+            rows: [{
+                rowid: this.requestId,
+                status: this.status
+            }],
+            scope: this,
+            success: function(){
+                this.close();
+                Ext4.Msg.hide();
+                if (dataRegion) {
+                    dataRegion.refresh();
+                }
+            },
+            failure: LDK.Utils.getErrorCallback()
+        });
+    }
+});
diff --git a/mcc/src/client/AnimalRequest/animal-request.tsx b/mcc/src/client/AnimalRequest/animal-request.tsx
@@ -132,6 +132,13 @@ export function AnimalRequest() {
         return "Draft" === requestData.request.status
     }
 
+    function shouldShowWithdraw()
+    {
+        const ctx = getServerContext().getModuleContext('mcc') || {};
+
+        return !!ctx.hasRequestAdminPermission
+    }
+
     function handleSubmitButton(e, isSubmitting) {
         setIsSubmitting(isSubmitting);
 
@@ -273,6 +280,7 @@ export function AnimalRequest() {
                         "title": data.get("project-title"),
                         "narrative": data.get("project-narrative"),
                         "neuroscience": data.get("neuroscience"),
+                        "diseasefocus": data.get("diseasefocus"),
                         "lastname": data.get("investigator-last-name"),
                         "firstname": data.get("investigator-first-name"),
                         "middleinitial": data.get("investigator-middle-initial"),
@@ -453,7 +461,14 @@ export function AnimalRequest() {
                 </ErrorMessageHandler>
             </div>
 
-            <Title text="3. How does the research relate to neuroscience?*"/>
+            <Title text="3. Research/Disease Focus*"/>
+            <div className="tw-w-full tw-px-3 tw-mb-6 md:tw-mb-0">
+                <ErrorMessageHandler isSubmitting={isSubmitting}>
+                    <Input id="diseasefocus" ariaLabel="Research/Disease Focus" isSubmitting={isSubmitting} required={doEnforceRequiredFields()} placeholder="What is the research area or disease focus of this project" defaultValue={requestData.request.diseasefocus}/>
+                </ErrorMessageHandler>
+            </div>
+
+            <Title text="4. How does the research relate to neuroscience?*"/>
             <div className="tw-w-full tw-px-3 tw-mb-6 md:tw-mb-0">
                 <ErrorMessageHandler isSubmitting={isSubmitting}>
                     <TextArea id="neuroscience" ariaLabel="Connection to neuroscience" isSubmitting={isSubmitting} placeholder="How does the research relate to neuroscience" required={doEnforceRequiredFields()} defaultValue={requestData.request.neuroscience}/>
@@ -694,6 +709,11 @@ export function AnimalRequest() {
                 <Button onClick={(e) => {
                     handleSubmitButton(e, true);
                  }} text={getSubmitButtonText()} display={hasEditPermission()}/>
+
+                <Button onClick={(e) => {
+                    requestData.request.status = "withdrawn"
+                    handleSubmitButton(e, false);
+                }} text={"Widthdraw"} display={shouldShowWithdraw()}/>
             </div>
         </form>
 
diff --git a/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx b/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx
@@ -91,6 +91,12 @@ export default function ReadOnlyRequest(props: {requestData: AnimalRequestModel}
                 <Grid item xs={10}>
                     {requestData.request.narrative}
                 </Grid>
+                <Grid item xs={2} className={styles.fieldLabel}>
+                    Research/disease focus:
+                </Grid>
+                <Grid item xs={10}>
+                    {requestData.request.diseasefocus}
+                </Grid>
                 <Grid item xs={2} className={styles.fieldLabel}>
                     Relation to neuroscience:
                 </Grid>
diff --git a/mcc/src/client/components/RequestUtils.tsx b/mcc/src/client/components/RequestUtils.tsx
@@ -14,6 +14,7 @@ export class AnimalRequestProps {
     narrative: string;
     title: string;
     neuroscience: string;
+    diseasefocus: string;
     census: boolean;
     censusreason: string;
     middleinitial: string;
@@ -88,6 +89,7 @@ export async function queryRequestInformation(requestId, handleFailure) {
                 "narrative",
                 "title",
                 "neuroscience",
+                "diseasefocus",
                 "census",
                 "censusreason",
                 "terminalprocedures",
diff --git a/mcc/src/org/labkey/mcc/MccManager.java b/mcc/src/org/labkey/mcc/MccManager.java
@@ -53,7 +53,8 @@ public enum RequestStatus
         Approved(5, "Approved", MccRequestAdminPermission.class),
         Rejected(6, "Rejected", MccRequestAdminPermission.class),
         Processing(7, "Processing", MccRequestAdminPermission.class),
-        Fulfilled(8, "Fulfilled", MccRequestAdminPermission.class);
+        Fulfilled(8, "Fulfilled", MccRequestAdminPermission.class),
+        Withdrawn(9, "Withdrawn", MccRequestorPermission.class);
 
         int sortOrder;
         String label;
diff --git a/mcc/src/org/labkey/mcc/MccModule.java b/mcc/src/org/labkey/mcc/MccModule.java
@@ -59,7 +59,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 20.013;
+        return 20.014;
     }
 
     @Override
diff --git a/mcc/src/org/labkey/mcc/query/MccRequest.java b/mcc/src/org/labkey/mcc/query/MccRequest.java
@@ -13,6 +13,7 @@ public class MccRequest
     private String _title;
     private String _narrative;
     private String _neuroscience;
+    private String _diseasefocus;
     private boolean _census;
     private String _censusReason;
 
diff --git a/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java b/mcc/src/org/labkey/mcc/query/RequestScoreActionsDisplayColumnFactory.java
@@ -5,21 +5,22 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.Container;
-import org.labkey.api.data.DataColumn;
 import org.labkey.api.data.DisplayColumn;
 import org.labkey.api.data.DisplayColumnFactory;
 import org.labkey.api.data.RenderContext;
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
+import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.template.ClientDependency;
 import org.labkey.mcc.MccManager;
 import org.labkey.mcc.security.MccFinalReviewPermission;
 import org.labkey.mcc.security.MccRequestAdminPermission;
 
 import java.io.IOException;
 import java.io.Writer;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
 public class RequestScoreActionsDisplayColumnFactory implements DisplayColumnFactory
@@ -73,6 +74,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
                             {
                                 DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=primaryReview", requestContainer);
                                 out.write("<br><a class=\"labkey-text-link\" href=\"" + url.getActionURL().addReturnURL(ctx.getViewContext().getActionURL()) + "\">Enter MCC Internal Review</a>");
+                                out.write(getWithdrawnLine(ctx, requestRowId));
                             }
                         }
                         else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString("pendingRabReviews"), Integer.class) == 0)
@@ -81,6 +83,7 @@ else if (st == MccManager.RequestStatus.RabReview && ctx.get(FieldKey.fromString
                             {
                                 DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=resourceAvailability", requestContainer);
                                 out.write("<br><a class=\"labkey-text-link\" href=\"" + url.getActionURL().addReturnURL(ctx.getViewContext().getActionURL()) + "\">Enter Resource Availability Assessment</a>");
+                                out.write(getWithdrawnLine(ctx, requestRowId));
                             }
                         }
                         else if (st == MccManager.RequestStatus.PendingDecision)
@@ -89,11 +92,13 @@ else if (st == MccManager.RequestStatus.PendingDecision)
                             {
                                 DetailsURL url = DetailsURL.fromString("/mcc/requestReview.view?requestId=" + requestId + "&mode=finalReview", requestContainer);
                                 out.write("<br><a class=\"labkey-text-link\" href=\"" + url.getActionURL().addReturnURL(ctx.getViewContext().getActionURL()) + "\">Enter Final Review</a>");
+                                out.write(getWithdrawnLine(ctx, requestRowId));
                             }
                         }
                         else if (st == MccManager.RequestStatus.Approved)
                         {
-                            out.write("<br><a class=\"labkey-text-link\" href=\"javascript:alert('This is not enabled yet')\">Update Animal Availability</a>");
+                            out.write("<br><a class=\"labkey-text-link\" onclick=\"MCC.window.ChangeStatusWindow.buttonHandler(" + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + "," + requestRowId + ", 'Fulfilled')\">Mark Fulfilled</a>");
+                            out.write(getWithdrawnLine(ctx, requestRowId));
                         }
                     }
                     catch (IllegalArgumentException e)
@@ -115,6 +120,21 @@ public void addQueryFieldKeys(Set<FieldKey> keys)
                 keys.add(getBoundKey("requestId", "status"));
                 keys.add(getBoundKey("requestId" , "rowid"));
             }
+
+            @Override
+            public @NotNull Set<ClientDependency> getClientDependencies()
+            {
+                Set<ClientDependency> ret = new LinkedHashSet<>(super.getClientDependencies());
+                ret.add(ClientDependency.fromPath("LDK/LDKApi.lib.xml"));
+                ret.add(ClientDependency.fromPath("mcc/window/ChangeStatusWindow.js"));
+
+                return ret;
+            }
         };
     }
+
+    private String getWithdrawnLine(RenderContext ctx, int requestRowId)
+    {
+        return "<br><a class=\"labkey-text-link\" onclick=\"MCC.window.ChangeStatusWindow.buttonHandler(" + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + "," + requestRowId + ", 'Withdrawn')\">Withdraw Request</a>";
+    }
 }
diff --git a/mcc/test/src/org/labkey/test/tests/mcc/MccTest.java b/mcc/test/src/org/labkey/test/tests/mcc/MccTest.java
@@ -362,6 +362,7 @@ else if ("radio".equals(inputType))
             new FormElement("project-narrative", "narrative", "the narrative").inputType("textarea"),
             new FormElement("investigator-last-name", "lastName", "last name"),
             new FormElement("neuroscience", "neuroscience", "neuroscience connection").inputType("textarea"),
+            new FormElement("diseasefocus", "diseasefocus", "my disease focus"),
             new FormElement("investigator-first-name", "firstName", "first name"),
             new FormElement("investigator-middle-initial", "middleinitial", "m"),
             new FormElement("is-early-stage-investigator", "earlystageinvestigator", true).radio(),

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+ALTER TABLE mcc.animalrequests add diseasefocus varchar(4000);`