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bbimberbbimber
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Initialize schema to manage studies/cohorts/timepoints (#335)
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+843
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15 files changed

+843
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lines changed

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

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

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

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

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

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

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

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

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

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

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