Initialize schema to manage studies/cohorts/timepoints

SivStudies/src/org/labkey/sivstudies/SivStudiesModule.java

@@ -21,6 +21,9 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.ldk.ExtendedSimpleModule;
 import org.labkey.api.module.ModuleContext;
+import org.labkey.api.studies.StudiesService;
+import org.labkey.sivstudies.study.ArtInitiationEventProvider;
+import org.labkey.sivstudies.study.SivInfectionEventProvider;
 
 import java.util.Collection;
 import java.util.Collections;
@@ -51,7 +54,8 @@ protected void init()
     @Override
     public void doStartupAfterSpringConfig(ModuleContext moduleContext)
     {
-
+        StudiesService.get().registerEventProvider(new SivInfectionEventProvider());
+        StudiesService.get().registerEventProvider(new ArtInitiationEventProvider());
     }
 
     @Override

SivStudies/src/org/labkey/sivstudies/study/ArtInitiationEventProvider.java

@@ -0,0 +1,58 @@
+package org.labkey.sivstudies.study;
+
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.User;
+import org.labkey.api.studies.study.AbstractEventProvider;
+import org.labkey.api.study.DatasetTable;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.sivstudies.SivStudiesModule;
+
+import java.util.Collection;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ArtInitiationEventProvider extends AbstractEventProvider
+{
+    public ArtInitiationEventProvider()
+    {
+        super("ART_Initiation", "ART Initiation", "This is the first date when the subject was assigned to the study, as defined in the study assignment table", ModuleLoader.getInstance().getModule(SivStudiesModule.class));
+    }
+
+    @Override
+    protected Map<String, Date> inferDatesRaw(Collection<String> subjectList, Container c, User u)
+    {
+        TableInfo ti = getTable(c, u, "study", "treatments");
+        if (ti == null)
+        {
+            return null;
+        }
+
+        if (ti instanceof DatasetTable ds)
+        {
+            Map<String, Date> ret = new HashMap<>();
+            final String subjectCol = ds.getDataset().getStudy().getSubjectColumnName();
+            new TableSelector(ti, PageFlowUtil.set(subjectCol, "date"), new SimpleFilter(FieldKey.fromString(subjectCol), subjectList, CompareType.IN), null).forEachResults(rs -> {
+                String subjectId = rs.getString(FieldKey.fromString(subjectCol));
+                Date date = rs.getDate(FieldKey.fromString("date"));
+
+                if (!ret.containsKey(subjectId) || date.before(ret.get(subjectId)))
+                {
+                    ret.put(subjectId, date);
+                }
+            });
+
+            return ret;
+        }
+        else
+        {
+            throw new IllegalStateException("Expected study.assignment to be a DatasetTable");
+        }
+    }
+}

SivStudies/src/org/labkey/sivstudies/study/SivInfectionEventProvider.java

@@ -0,0 +1,62 @@
+package org.labkey.sivstudies.study;
+
+import org.labkey.api.data.CompareType;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.TableSelector;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryService;
+import org.labkey.api.query.UserSchema;
+import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.ReadPermission;
+import org.labkey.api.studies.study.AbstractEventProvider;
+import org.labkey.api.study.DatasetTable;
+import org.labkey.api.util.PageFlowUtil;
+import org.labkey.sivstudies.SivStudiesModule;
+
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+public class SivInfectionEventProvider extends AbstractEventProvider
+{
+    public SivInfectionEventProvider()
+    {
+        super("SIV_Infection", "SIV Infection", "This is the official date of SIV infection, used to calculate days-post-infection", ModuleLoader.getInstance().getModule(SivStudiesModule.class));
+    }
+
+    @Override
+    protected Map<String, Date> inferDatesRaw(Collection<String> subjectList, Container c, User u)
+    {
+        UserSchema us = QueryService.get().getUserSchema(u, c, "study");
+        if (us == null)
+        {
+            return Collections.emptyMap();
+        }
+
+        TableInfo ti = us.getTable("assignment");
+        if (ti == null || !ti.hasPermission(u, ReadPermission.class))
+        {
+            return Collections.emptyMap();
+        }
+
+        if (ti instanceof DatasetTable ds)
+        {
+            Map<String, Date> ret = new HashMap<>();
+            final String subjectCol = ds.getDataset().getStudy().getSubjectColumnName();
+            new TableSelector(ti, PageFlowUtil.set(subjectCol, "date"), new SimpleFilter(FieldKey.fromString(subjectCol), subjectList, CompareType.IN), null).forEachResults(rs -> {
+                ret.put(rs.getString(FieldKey.fromString(subjectCol)), rs.getDate(FieldKey.fromString("date")));
+            });
+
+            return ret;
+        }
+        else
+        {
+            throw new IllegalStateException("Expected study.assignment to be a DatasetTable");
+        }
+    }
+}