Initialize schema to manage studies/cohorts/timepoints

Studies/api-src/org/labkey/api/studies/StudiesService.java

@@ -4,9 +4,11 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.resource.Resource;
 import org.labkey.api.security.User;
+import org.labkey.api.studies.study.EventProvider;
 import org.labkey.api.util.Path;
 
 import java.io.IOException;
+import java.util.List;
 
 /**
  * Created by bimber on 11/3/2016.
@@ -28,4 +30,8 @@ static public void setInstance(StudiesService instance)
     abstract public void importFolderDefinition(Container container, User user, Module m, Path sourceFolderDirPath) throws IOException;
 
     abstract public void loadTsv(Resource tsv, String schemaName, User u, Container c);
+
+    abstract public void registerEventProvider(EventProvider ep);
+
+    abstract public List<EventProvider> getEventProviders(Container c);
 }

Studies/api-src/org/labkey/api/studies/study/AbstractEventProvider.java

@@ -0,0 +1,88 @@
+package org.labkey.api.studies.study;
+
+import org.jetbrains.annotations.Nullable;
+import org.labkey.api.data.Container;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.module.Module;
+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 java.util.Collection;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+public abstract class AbstractEventProvider implements EventProvider
+{
+    private final String _name;
+    private final String _label;
+    private final String _description;
+    private final Module _owner;
+
+    public AbstractEventProvider(String name, String label, String description, Module owner)
+    {
+        _name = name;
+        _label = label;
+        _description = description;
+        _owner = owner;
+    }
+
+    @Override
+    public String getDescription()
+    {
+        return _description;
+    }
+
+    @Override
+    public String getLabel()
+    {
+        return _label;
+    }
+
+    @Override
+    public String getName()
+    {
+        return _name;
+    }
+
+    @Override
+    public boolean isAvailable(Container c)
+    {
+        return c.getActiveModules().contains(_owner);
+    }
+
+    @Override
+    public final Map<String, Date> inferDates(Collection<String> subjectList, Container c, User u)
+    {
+        Map<String, Date> result = new HashMap<>(inferDatesRaw(subjectList, c, u));
+        subjectList.forEach(x -> {
+            if (!result.containsKey(x))
+            {
+                result.put(x, null);
+            }
+        });
+
+        return result;
+    }
+
+    abstract protected Map<String, Date> inferDatesRaw(Collection<String> subjectList, Container c, User u);
+
+    protected @Nullable TableInfo getTable(Container c, User u, String schema, String table)
+    {
+        UserSchema us = QueryService.get().getUserSchema(u, c, schema);
+        if (us == null)
+        {
+            return null;
+        }
+
+        TableInfo ti = us.getTable("assignment");
+        if (ti == null || !ti.hasPermission(u, ReadPermission.class))
+        {
+            return null;
+        }
+
+        return ti;
+    }
+}

Studies/api-src/org/labkey/api/studies/study/EventProvider.java

@@ -0,0 +1,26 @@
+package org.labkey.api.studies.study;
+
+import org.labkey.api.data.Container;
+import org.labkey.api.security.User;
+
+import java.util.Collection;
+import java.util.Date;
+import java.util.Map;
+
+/**
+ * Each study will have a handful of important dates, which are used to define relative dates for each subject/participant.
+ * The EventProvider classes provide a code-based way to establish the handful of critical dates. This code is executed to populate
+ * the KeyEvents table, which maps subject/event to date.
+ */
+public interface EventProvider
+{
+    boolean isAvailable(Container c);
+
+    String getName();
+
+    String getLabel();
+
+    String getDescription();
+
+    Map<String, Date> inferDates(Collection<String> subjectList, Container c, User u);
+}

Studies/resources/schemas/dbscripts/postgresql/studies-23.001-23.002.sql

@@ -0,0 +1,90 @@
+CREATE TABLE studies.studies (
+    rowid serial,
+    studyName varchar(1000),
+    label varchar(1000),
+    category varchar(1000),
+    description varchar(4000),
+
+    lsid entityid,
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_studies PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.studyCohorts (
+    rowid serial,
+    studyId int,
+    cohortName varchar(4000),
+    label varchar(4000),
+    category varchar(4000),
+    description varchar(4000),
+    isControlGroup bool default false,
+    sortOrder int,
+
+    lsid entityid,
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_studyCohorts PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.anchorEvents (
+    rowid serial,
+    studyId int,
+    label varchar(4000),
+    description varchar(4000),
+    eventProviderName varchar(1000),
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_anchorEvents PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.expectedTimepoints (
+    rowid serial,
+    studyId int,
+    cohortId int,
+    label varchar(4000),
+    labelShort varchar(100),
+    description varchar(4000),
+    numericLabel int,
+    anchorEvent int,
+    rangeMin int,
+    rangeMax int,
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_expectedTimepoints PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.timepointToDate (
+    rowid serial,
+    subjectId varchar(4000),
+    timepointId int,
+    dateMin timestamp,
+    dateMax timestamp,
+    isManualOverride bool default false,
+
+    container entityid,
+    created timestamp,
+    createdby int,
+    modified timestamp,
+    modifiedby int,
+
+    CONSTRAINT PK_timepointToDate PRIMARY KEY (rowid)
+);

Studies/resources/schemas/dbscripts/sqlserver/studies-23.001-23.002.sql

@@ -0,0 +1,90 @@
+CREATE TABLE studies.studies (
+    rowid int identity(1,1),
+    studyName varchar(1000),
+    label varchar(1000),
+    category varchar(1000),
+    description varchar(4000),
+
+    lsid entityid,
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_studies PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.studyCohorts (
+    rowid int identity(1,1),
+    studyId int,
+    cohortName varchar(4000),
+    label varchar(4000),
+    category varchar(4000),
+    description varchar(4000),
+    isControlGroup bit default 0,
+    sortOrder int,
+
+    lsid entityid,
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_studyCohorts PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.anchorEvents (
+    rowid int identity(1,1),
+    studyId int,
+    label varchar(4000),
+    description varchar(4000),
+    eventProviderName varchar(1000),
+
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_anchorEvents PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.expectedTimepoints (
+    rowid int identity(1,1),
+    studyId int,
+    cohortId int,
+    label varchar(4000),
+    labelShort varchar(100),
+    description varchar(4000),
+    numericLabel int,
+    anchorEvent int,
+    rangeMin int,
+    rangeMax int,
+
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_expectedTimepoints PRIMARY KEY (rowid)
+);
+
+CREATE TABLE studies.timepointToDate (
+    rowid int identity(1,1),
+    subjectId varchar(4000),
+    timepointId int,
+    dateMin datetime,
+    dateMax datetime,
+    isManualOverride bit default 0,
+
+    container entityid,
+    created datetime,
+    createdby int,
+    modified datetime,
+    modifiedby int,
+
+    CONSTRAINT PK_timepointToDate PRIMARY KEY (rowid)
+);