Item 6167: integrate ITN changes into core codebase (#66)

* Conditional and integrate ITN specimen request and reporting changes

* New TrialShareExportAction

Author: labkey-jeckels

module.properties

@@ -1,6 +1,7 @@
 ModuleClass: org.labkey.trialshare.TrialShareModule
 Label: Data Finder for ITN
 Description: Provides a web part for exploring the studies and manuscripts available within ITN.
-URL: http://example.com/FIXME
+URL: https://www.itntrialshare.org
 License: Apache 2.0
 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+ModuleDependencies: Study

src/org/labkey/trialshare/DelegatingSpecimenRequestCustomizer.java

@@ -0,0 +1,66 @@
+package org.labkey.trialshare;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
+import org.labkey.api.settings.AdminConsole;
+import org.labkey.api.settings.ExperimentalFeatureService;
+import org.labkey.api.study.SpecimenService;
+import org.labkey.api.util.HtmlString;
+
+/** Decides whether to supply the default behavior or an ITN-specific one based on an experimental feature flag */
+public class DelegatingSpecimenRequestCustomizer implements SpecimenService.SpecimenRequestCustomizer
+{
+    private final SpecimenService.SpecimenRequestCustomizer _default;
+    private final SpecimenService.SpecimenRequestCustomizer _itn = new ITNSpecimenRequestCustomizer();
+    private SpecimenService.SpecimenRequestCustomizer _active;
+
+    private static final String ITN_SPECIMEN_HANDLING_FEATURE_NAME = "ITNSpecimenHandling";
+
+    public DelegatingSpecimenRequestCustomizer(SpecimenService.SpecimenRequestCustomizer defaultCustomizer)
+    {
+        _default = defaultCustomizer;
+
+        _active = ExperimentalFeatureService.get().isFeatureEnabled(ITN_SPECIMEN_HANDLING_FEATURE_NAME) ? _itn : _default;
+
+        AdminConsole.addExperimentalFeatureFlag(ITN_SPECIMEN_HANDLING_FEATURE_NAME, "ITN specimen behavior",
+                "This feature allows empty specimen requests, adds ITN-specific messages, hides some reporting options, and other tweaks", false);
+
+        ExperimentalFeatureService.get().addFeatureListener(ITN_SPECIMEN_HANDLING_FEATURE_NAME, (feature, enabled) -> _active = enabled ? _itn : _default);
+    }
+
+    @Override
+    public boolean allowEmptyRequests()
+    {
+        return _active.allowEmptyRequests();
+    }
+
+    @Override
+    public Integer getDefaultDestinationSiteId()
+    {
+        return _active.getDefaultDestinationSiteId();
+    }
+
+    @Override
+    public boolean omitTypeGroupingsWhenReporting()
+    {
+        return _active.omitTypeGroupingsWhenReporting();
+    }
+
+    @Override
+    public boolean canChangeStatus(User user)
+    {
+        return _active.canChangeStatus(user);
+    }
+
+    @Override
+    public boolean hideRequestWarnings()
+    {
+        return _active.hideRequestWarnings();
+    }
+
+    @Override
+    public HtmlString getSubmittedMessage(Container c, int requestId)
+    {
+        return _active.getSubmittedMessage(c, requestId);
+    }
+}

src/org/labkey/trialshare/ITNSpecimenRequestCustomizer.java

@@ -0,0 +1,68 @@
+package org.labkey.trialshare;
+
+import org.apache.log4j.Logger;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.security.Group;
+import org.labkey.api.security.GroupManager;
+import org.labkey.api.security.User;
+import org.labkey.api.study.SamplesUrls;
+import org.labkey.api.study.SpecimenService;
+import org.labkey.api.util.HtmlString;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.security.xml.GroupEnumType;
+
+import static org.labkey.api.util.PageFlowUtil.link;
+
+public class ITNSpecimenRequestCustomizer implements SpecimenService.SpecimenRequestCustomizer
+{
+    private static final Logger LOG = Logger.getLogger(ITNSpecimenRequestCustomizer.class);
+
+    @Override
+    public boolean allowEmptyRequests()
+    {
+        return true;
+    }
+
+    @Override
+    public Integer getDefaultDestinationSiteId()
+    {
+        return 9999999;
+    }
+
+    @Override
+    public boolean omitTypeGroupingsWhenReporting()
+    {
+        return true;
+    }
+
+    @Override
+    public boolean canChangeStatus(User user)
+    {
+        Group specimenRequestAdmins = GroupManager.getGroup(ContainerManager.getRoot(), "Specimen Request Administrators", GroupEnumType.SITE);
+        if (specimenRequestAdmins != null)
+        {
+            return user.isInSiteAdminGroup() || user.isInGroup(specimenRequestAdmins.getUserId());
+        }
+        LOG.error("Unable to find site group \"Specimen Request Administrators\", allowing user to update specimen request status");
+        return true;
+    }
+
+    @Override
+    public HtmlString getSubmittedMessage(Container c, int requestId)
+    {
+        SamplesUrls samplesUrls = PageFlowUtil.urlProvider(SamplesUrls.class);
+        return HtmlString.unsafe("Thank you for your request. A representative from the ITN will be in touch " +
+                "with you. You can also contact us at " +
+                link("trialsharesupport@immunetolerance.org").href("mailto:trialsharesupport@immunetolerance.org?Body=" + PageFlowUtil.filter(samplesUrls.getRequestDetailsURL(c, requestId).getURIString())).clearClasses() +
+                " to follow up with us regarding this request.<br/>" +
+                "You may also update this request at any calendar to add comments or supporting " +
+                "documents by clicking here " + link("Update Request").href(samplesUrls.getManageRequestStatusURL(c, requestId)));
+    }
+
+    @Override
+    public boolean hideRequestWarnings()
+    {
+        return true;
+    }
+}