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Merged
spamhurts merged 4 commits into from
Feb 4, 2019
Merged

Fb animal groups #4

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6ff2cb0
Merge pull request #1 from LabKey/fb_snprc_scheduler_dev_server
labkey-martyp Jan 28, 2019
53d1777
Merge pull request #2 from LabKey/fb_snprc_scheduler_dev_server
spamhurts Jan 28, 2019
bba9ae3
snprc - bug fixes and code cleanup
spamhurts Feb 1, 2019
b8fc6f1
Merge branch 'fb_animal_groups' of https://github.com/LabKey/snprcEHR…
spamhurts Feb 1, 2019
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3 changes: 1 addition & 2 deletions snprc_ehr/src/org/labkey/snprc_ehr/controllers/AnimalGroupsController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -641,8 +641,7 @@ public ApiResponse execute(GroupMember groupMember, BindException errors)
props.put("success", true);

}
catch (InvalidKeyException | BatchValidationException | QueryUpdateServiceException |
DuplicateKeyException | NullPointerException | SQLException | ValidationException e)
catch (ValidationException e)
{
props.put("success", false);
props.put("message", e.getMessage());
Expand Down
136 changes: 45 additions & 91 deletions snprc_ehr/src/org/labkey/snprc_ehr/services/AnimalsGroupAssignor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@

import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
Expand All @@ -55,10 +56,9 @@
public class AnimalsGroupAssignor
{
ViewContext viewContext;
private AnimalGroup group = null;
private AnimalGroupCategory category = null;
private List<GroupMember> groupMembers = new ArrayList<GroupMember>();
private List<GroupMember> categoryMembers = new ArrayList<GroupMember>();
private AnimalGroup group;
private AnimalGroupCategory category;



public AnimalsGroupAssignor(ViewContext viewContext, int group)
Expand All @@ -70,60 +70,7 @@ public AnimalsGroupAssignor(ViewContext viewContext, int group)
this.group = new TableSelector(SNPRC_EHRSchema.getInstance().getTableInfoAnimalGroups(), filter, null).getObject(AnimalGroup.class);
this.category = new TableSelector(SNPRC_EHRSchema.getInstance().getTableInfoAnimalGroupCategories(), new SimpleFilter(FieldKey.fromString("category_code"), this.group.getCategoryCode(), CompareType.EQUAL), null).getObject(AnimalGroupCategory.class);

this.groupMembers = this.getGroupAssignees();
if (this.category.getEnforceExclusivity().equalsIgnoreCase("Y"))
{
this.categoryMembers = this.getCategoryAssignees();
}

}

/**
* @return all animals that are already assigned and which assignment is still active
*/
private List<GroupMember> getGroupAssignees()
{

Date today = new Date();

UserSchema schema = QueryService.get().getUserSchema(this.viewContext.getUser(), this.viewContext.getContainer(), "study");
TableInfo table = schema.getTable("animal_group_members");
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromString("groupid"), this.group.getCode(), CompareType.EQUAL);

filter.addClause(new SimpleFilter.OrClause(
new CompareType.CompareClause(FieldKey.fromString("enddate"), CompareType.ISBLANK, null),
new CompareType.CompareClause(FieldKey.fromString("enddate"), CompareType.DATE_GTE, today)
));

TableSelector tableSelector = new TableSelector(table, filter, null);
List<GroupMember> members = tableSelector.getArrayList(GroupMember.class);

return members;
}


/**
* @return all animals that are already assigned to the category, needed to enforce assignment exclusivity at the category level
*/
private List<GroupMember> getCategoryAssignees()
{
Date today = new Date();

UserSchema schema = QueryService.get().getUserSchema(this.viewContext.getUser(), this.viewContext.getContainer(), "study");
TableInfo table = schema.getTable("animal_group_members");
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromString("groupid"), this.getCategoryGroups(), CompareType.IN);

filter.addClause(new SimpleFilter.OrClause(
new CompareType.CompareClause(FieldKey.fromString("enddate"), CompareType.ISBLANK, null),
new CompareType.CompareClause(FieldKey.fromString("enddate"), CompareType.DATE_GT, today)
));

TableSelector tableSelector = new TableSelector(table, filter, null);
List<GroupMember> members = tableSelector.getArrayList(GroupMember.class);

return members;
}

private List<Integer> getCategoryGroups()
Expand Down Expand Up @@ -161,17 +108,16 @@ private String getCategoryGroupsString()

/**
* @param groupMembers: Animals to be assigned (animalId, start date, and end date)
* @return - Nothing - Animals are either assigned or an exception is thrown
* returns - Nothing - Animals are either assigned or an exception is thrown
*/
public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, BatchValidationException, QueryUpdateServiceException,
DuplicateKeyException, NullPointerException, SQLException, ValidationException
public void assign(List<GroupMember> groupMembers) throws ValidationException

{
List<Map<String, Object>> rows = new ArrayList<>();
ObjectMapper oMapper = new ObjectMapper();

//Load Demographics Records
List<String> animalIds = new ArrayList<String>();
List<String> animalIds = new ArrayList<>();
for (GroupMember m : groupMembers)
{
animalIds.add(m.getParticipantid());
Expand All @@ -189,9 +135,9 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B
SimpleFilter filter = new SimpleFilter();
filter.addCondition(FieldKey.fromString("id"), animalIds, CompareType.IN);
Map<String, Map<String, Object>> demographicsMap = new HashMap<>();
for (Map a : new TableSelector(demographicsTable, filter, null).getMapCollection())
for (Map<String, Object> a : new TableSelector(demographicsTable, filter, null).getMapCollection())
{
Map oneAnimalDemographicsMap = new HashMap();
Map <String, Object> oneAnimalDemographicsMap = new HashMap<>();
oneAnimalDemographicsMap.put("gender", a.get("gender"));
oneAnimalDemographicsMap.put("species", a.get("species"));
oneAnimalDemographicsMap.put("death", a.get("death"));
Expand All @@ -213,7 +159,14 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B
Date dod = (Date) rowMap.get("death");
Date startDate = groupMember.getDate();
// set endDate to current date if it is null
Date endDate = groupMember.getEnddate() == null ? new Date() : groupMember.getEnddate();


Date now = new Date();
Calendar c = Calendar.getInstance();
c.setTime(now);
c.add(Calendar.YEAR, 10);

Date endDate = groupMember.getEnddate() == null ? c.getTime() : groupMember.getEnddate();


if ((dod != null) && (dod.compareTo(startDate) < 0))
Expand All @@ -227,32 +180,29 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B
throw new ValidationException(AssignmentFailureReason.END_DATE_AFTER_DEATH.toString());
}

sql = new SQLFragment("SELECT\n");
sql.append("agm.participantid as id\n");
sql.append("FROM ");
sql.append(animalGroupMembers, "agm");
sql.append("\n");
sql.append("inner join ehr_lookups.calendar as c on c.targetDate between agm.date and COALESCE(agm.enddate, getDate())\n");
sql.append("where agm.participantid = ? and agm.groupId = ?\n");
sql.append(" and c.targetDate between ? and ?\n");
sql.append("group by agm.participantid");

sql.add(groupMember.getParticipantid());
sql.add(groupMember.getGroupid());
sql.add(groupMember.getDate());
sql.add(endDate);

selector = new SqlSelector(dbStudySchema, sql);
//ignore if record is being updated
if (groupMember.getObjectid() == null )
{
sql = new SQLFragment("SELECT\n");
sql.append("agm.participantid as id\n");
sql.append("FROM ");
sql.append(animalGroupMembers, "agm");
sql.append("\n");
sql.append("inner join ehr_lookups.calendar as c on c.targetDate between agm.date and COALESCE(agm.enddate, getDate())\n");
sql.append("where agm.participantid = ? and agm.groupId = ?\n");
sql.append(" and c.targetDate between ? and ?\n");
sql.append("group by agm.participantid");

// List<String> animalList = new ArrayList<>();
// selector.forEachMap(row -> {
// animalList.add((String) row.get("id"));
// }
// );
sql.add(groupMember.getParticipantid());
sql.add(groupMember.getGroupid());
sql.add(groupMember.getDate());
sql.add(endDate);

if (selector.exists())
throw new ValidationException(AssignmentFailureReason.ALREADY_IN_GROUP.toString() + ": " + groupMember.getParticipantid());
selector = new SqlSelector(dbStudySchema, sql);

if (selector.exists())
throw new ValidationException(AssignmentFailureReason.ALREADY_IN_GROUP.toString() + ": " + groupMember.getParticipantid());
}

// if category groups are mutually exclusive, then we need to make sure animal
// hasn't already been assigned to another category
Expand All @@ -266,15 +216,19 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B
sql.append("FROM ");
sql.append(animalGroupMembers, "agm");
sql.append("\n");
sql.append("inner join ehr_lookups.calendar as c on c.targetDate between agm.date and COALESCE(agm.enddate, getDate())\n");
sql.append("inner join ehr_lookups.calendar as c\n "); //;
sql.append ("on c.targetDate between agm.date and COALESCE(agm.enddate, DATEADD(YEAR, 10, getDate()))\n");
sql.append("where agm.participantid = ? \n");
sql.append(" and agm.groupId in " + getCategoryGroupsString() + "\n");
sql.append(" and c.targetDate between ? and ?\n");
sql.append("group by agm.participantid");
if (groupMember.getObjectid() != null )
sql.append(" and agm.objectId <> ?"); // ignore the record being updated

sql.add(groupMember.getParticipantid());
sql.add(groupMember.getDate());
sql.add(endDate);
if (groupMember.getObjectid() != null )
sql.add(groupMember.getObjectid());

selector = new SqlSelector(dbStudySchema, sql);
if (selector.exists())
Expand Down Expand Up @@ -362,7 +316,7 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B

}

Map groupMemberAsMap = oMapper.convertValue(groupMember, CaseInsensitiveHashMap.class);
Map<String, Object> groupMemberAsMap = oMapper.convertValue(groupMember, CaseInsensitiveHashMap.class);

groupMemberAsMap.remove("Id");
rows.add(groupMemberAsMap);
Expand Down Expand Up @@ -396,7 +350,7 @@ public void assign(List<GroupMember> groupMembers) throws InvalidKeyException, B
catch (InvalidKeyException | BatchValidationException | QueryUpdateServiceException |
DuplicateKeyException | NullPointerException | SQLException e)
{
throw e;
throw new ValidationException(e.getMessage());
}
}
}
Expand Down