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[dataquery] Add instrument flags to instruments query engine (#9529)
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This adds instrument flags to the data that is bulk loaded by
bulkLoadInstanceData and uses that to address the low hanging fruit of
#9372 of including administration flags in the data query tool.

It does not address the DDE and conflict related fields that are in the
CouchDB import script because we should investigate if those make sense
in the instruments query engine or if it's possible to have those
provided by the conflict resolver module rather than the instruments
module, as they are more related to that module.
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@driusan
driusan authored Jan 24, 2025
1 parent 9f9efc0 commit d908264
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Showing 2 changed files with 143 additions and 29 deletions.
72 changes: 64 additions & 8 deletions modules/instruments/php/instrumentqueryengine.class.inc
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
<?php declare(strict_types=1);

namespace LORIS\instruments;
use \LORIS\Data\Scope;
use \LORIS\Data\Cardinality;

use \LORIS\Data\Types\Enumeration;

/**
* InstrumentQueryEngine implements a LORIS QueryEngine for querying
Expand Down Expand Up @@ -41,19 +45,57 @@ class InstrumentQueryEngine implements \LORIS\Data\Query\QueryEngine
$rows = $DB->pselectCol("SELECT Test_name FROM test_names", []);

$dict = [];

// Use the same option enums for all instruments
$adminoptions = new Enumeration('None', 'Partial', 'All');
$dataentryoptions = new Enumeration('In Progress', 'Complete');
$validityoptions = new Enumeration('Questionable', 'Invalid', 'Valid');

$cardinality = new Cardinality(Cardinality::SINGLE);
$scope = new Scope(Scope::SESSION);

foreach ($rows as $testname) {
try {
$inst = \NDB_BVL_Instrument::factory(
$inst = \NDB_BVL_Instrument::factory(
$this->loris,
$testname,
"",
"",
);
$cat = new \LORIS\Data\Dictionary\Category(
$cat = new \LORIS\Data\Dictionary\Category(
$testname,
$inst->getFullName()
);
$fields = $inst->getDataDictionary();

$fields = [
new DictionaryItem(
$inst->testName.'_Administration',
'Administration flag for ' . $inst->getFullName(),
$scope,
$adminoptions,
$cardinality,
'Administration',
),
new DictionaryItem(
$inst->testName.'_Data_entry',
'Data entry status for ' . $inst->getFullName(),
$scope,
$dataentryoptions,
$cardinality,
'Data_entry',
),
];
if ($inst->ValidityEnabled) {
$fields[] = new DictionaryItem(
$inst->testName.'_Validity',
'Test validity for ' . $inst->getFullName(),
$scope,
$validityoptions,
$cardinality,
'Validity',
);
}
$fields = array_merge($fields, $inst->getDataDictionary());
$dict[] = $cat->withItems($fields);
} catch (\LorisException $e) {
error_log($e);
Expand Down Expand Up @@ -329,11 +371,25 @@ class InstrumentQueryEngine implements \LORIS\Data\Query\QueryEngine
$candData[$dict->getName()] = [];
}
$sid = $loadedInstrument->getSessionID();
$candData[$dict->getName()][$sid->__toString()] = [
'VisitLabel' => $loadedInstrument->getVisitLabel(),
'SessionID' => $sid->__toString(),
'value' => $loadedInstrument->getDictionaryValue($dict),
];
switch ($dict->fieldname) {
case 'Administration':
case 'Data_entry':
case 'Validity':
$flags = $loadedInstrument->getFlags()->toArray();
$candData[$dict->getName()][$sid->__toString()] = [
'VisitLabel' => $loadedInstrument->getVisitLabel(),
'SessionID' => $sid->__toString(),
'value' => $flags[$dict->fieldname],
];
break;
default:
$candData[$dict->getName()][$sid->__toString()] = [
'VisitLabel' => $loadedInstrument->getVisitLabel(),
'SessionID' => $sid->__toString(),
'value' => $loadedInstrument
->getDictionaryValue($dict),
];
}
}
}
yield "$iCandID" => $candData;
Expand Down
100 changes: 79 additions & 21 deletions php/libraries/NDB_BVL_Instrument.class.inc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2275,26 +2275,52 @@ abstract class NDB_BVL_Instrument extends NDB_Page
(SELECT CommentID FROM load_comment_ids)";
}
if ($condition !== null) {
$conditions[] = 'JSON_VALUE(Data, "$.'
. substr(
$fname = substr(
$condition->dictionary->getName(),
strlen($this->testName)+1
)
. '") '
. \LORIS\Data\Query\SQLQueryEngine::sqlOperator($condition->criteria)
. ' '
. \LORIS\Data\Query\SQLQueryEngine::sqlValue(
$condition->dictionary,
$condition->criteria,
$params
)
. ' ';
);
if ($fname == 'Administration'
|| $fname == 'Validity'
|| $fname == 'Data_entry'
) {
$conditions[] = "flag.$fname"
. \LORIS\Data\Query\SQLQueryEngine::sqlOperator(
$condition->criteria
)
. \LORIS\Data\Query\SQLQueryEngine::sqlValue(
$condition->dictionary,
$condition->criteria,
$params
)
. ' ';
} else {

$conditions[] = 'JSON_VALUE(Data, "$.'
. substr(
$condition->dictionary->getName(),
strlen($this->testName)+1
)
. '")'
. \LORIS\Data\Query\SQLQueryEngine::sqlOperator(
$condition->criteria
)
. \LORIS\Data\Query\SQLQueryEngine::sqlValue(
$condition->dictionary,
$condition->criteria,
$params
)
. ' ';
}
$conditions[] ="t.CommentID NOT LIKE 'DDE_%'";
}
$where = 'WHERE ' . join(' AND ', $conditions);
$query = "SELECT CandID,
SessionID,
CommentID,
session.Visit_Label as VisitLabel,
flag.Administration,
flag.Data_entry as DataEntry,
flag.Validity,
Data
FROM flag
JOIN session ON (session.ID=flag.SessionID)
Expand All @@ -2306,12 +2332,18 @@ abstract class NDB_BVL_Instrument extends NDB_Page
foreach ($jsondata as $row) {
$newinst = clone $this;

$newinst->candID = new CandID(strval($row['CandID']));
$newinst->commentID = $row['CommentID'];
$newinst->visitLabel = $row['VisitLabel'];
$newinst->sessionID = new SessionID(
strval($row['SessionID'])
$newinst->candID = new CandID(strval($row['CandID']));
$newinst->commentID = $row['CommentID'];
$newinst->visitLabel = $row['VisitLabel'];
$newinst->sessionID = new SessionID(
strval($row['SessionID'])
);
$newinst->flags = new \InstrumentFlags(
$row['Data_entry'],
$row['Administration'],
$row['Validity']
);
unset($row['Data_entry'], $row['Administration'], $row['Validity']);
$newinst->instanceData = json_decode(
$row['Data'] ?? '{}',
true,
Expand All @@ -2327,11 +2359,21 @@ abstract class NDB_BVL_Instrument extends NDB_Page
(SELECT CommentID FROM load_comment_ids)";
}
if ($condition !== null) {
$conditions[] = 't.'
. substr(
$fname = substr(
$condition->dictionary->getName(),
strlen($this->testName)+1
)
);
if ($fname == 'Administration'
|| $fname == 'Validity'
|| $fname == 'Data_entry'
) {
$tname = 'f.';
} else {
$tname = 't.';
}

$conditions[] = $tname
. $fname
. ' '
. \LORIS\Data\Query\SQLQueryEngine::sqlOperator(
$condition->criteria
Expand All @@ -2343,12 +2385,16 @@ abstract class NDB_BVL_Instrument extends NDB_Page
$params
)
. ' ';
$conditions[] ="t.CommentID NOT LIKE 'DDE_%'";
}
$where = 'WHERE ' . join(' AND ', $conditions);
$query = "SELECT
session.CandID as CandID,
t.CommentID as CommentID,
session.Visit_Label as VisitLabel,
f.Administration,
f.Data_entry,
f.Validity,
session.ID as SessionID, t.*
FROM $this->table t
JOIN flag f ON (t.CommentID=f.CommentID)
Expand All @@ -2365,6 +2411,13 @@ abstract class NDB_BVL_Instrument extends NDB_Page
$newinst->sessionID = new SessionID(strval($row['SessionID']));
unset($row['CommentID'], $row['VisitLabel'], $row['SessionID']);

$newinst->flags = new \InstrumentFlags(
$row['Data_entry'],
$row['Administration'],
$row['Validity']
);
unset($row['Data_entry'], $row['Administration'], $row['Validity']);

$newinst->instanceData = $row;

yield $newinst;
Expand Down Expand Up @@ -3071,13 +3124,17 @@ abstract class NDB_BVL_Instrument extends NDB_Page
return $this->determineDataEntryAllowed();
}

private ?\InstrumentFlags $flags = null;
/**
* Gets the flags of that instrument
*
* @return \InstrumentFlags
*/
public function getFlags(): \InstrumentFlags
{
if ($this->flags !== null) {
return $this->flags;
}
$row = \NDB_Factory::singleton()->database()->pselectRow(
'SELECT
Data_entry as dataentry,
Expand All @@ -3093,11 +3150,12 @@ abstract class NDB_BVL_Instrument extends NDB_Page
$administration = $row['administration'] ?? null;
$validity = $row['validity'] ?? null;

return new \InstrumentFlags(
$this->flags = new \InstrumentFlags(
$dataentry,
$administration,
$validity
);
return $this->flags;
}

/**
Expand Down

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