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Bump guzzlehttp/psr7 from 2.4.3 to 2.5.0 #296

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Bump guzzlehttp/psr7 from 2.4.3 to 2.5.0 #296

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848fe52
Bump guzzlehttp/psr7 from 2.4.3 to 2.5.0
dependabot[bot] Apr 19, 2023
8c218fd
Apply fixes from StyleCI
StyleCIBot Apr 19, 2023
e651be8
Merge pull request #297 from sfu-ireceptor/analysis-O3RvaJ
jeromejaglale Apr 19, 2023
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2 changes: 0 additions & 2 deletions app/AirrCell.php
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Original file line number Diff line number Diff line change
Expand Up @@ -284,7 +284,6 @@ public static function airrCellResponse($response_list, $response_type, $params)
}

foreach ($cell as $return_key => $return_element) {

//flatten any MongoDB ObjectId types
if (is_a($return_element, "MongoDB\BSON\ObjectId")) {
$return_element = $return_element->__toString();
Expand Down Expand Up @@ -340,7 +339,6 @@ public static function airrCellResponse($response_list, $response_type, $params)

public static function airrCellResponseSingle($cell)
{

//take a single cell from database query and create a response as per
// AIRR API standard
$required_fields = FileMapping::createMappingArray('ir_adc_api_response', 'airr_required', ['ir_class'=>['cell', 'ir_cell', 'Cell', 'IR_Cell']]);
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2 changes: 0 additions & 2 deletions app/AirrClone.php
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Expand Up @@ -292,7 +292,6 @@ public static function airrCloneResponse($response_list, $response_type, $params
}

foreach ($clone as $return_key => $return_element) {

//make all the requested fields null before populating if there are results
if (isset($repository_to_airr[$return_key]) && $repository_to_airr[$return_key] != '') {
$service_name = $db_to_service[$return_key];
Expand Down Expand Up @@ -351,7 +350,6 @@ public static function airrCloneResponse($response_list, $response_type, $params

public static function airrCloneResponseSingle($clone)
{

//take a single clone from database query and create a response as per
// AIRR API standard
$required_fields = FileMapping::createMappingArray('ir_adc_api_response', 'airr_required', ['ir_class'=>['clone', 'ir_clone', 'Clone', 'IR_Clone']]);
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2 changes: 0 additions & 2 deletions app/AirrGeneExpression.php
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Expand Up @@ -284,7 +284,6 @@ public static function airrGeneExpressionResponse($response_list, $response_type
}

foreach ($expression as $return_key => $return_element) {

//flatten any MongoDB ObjectId types
if (is_a($return_element, "MongoDB\BSON\ObjectId")) {
$return_element = $return_element->__toString();
Expand Down Expand Up @@ -341,7 +340,6 @@ public static function airrGeneExpressionResponse($response_list, $response_type

public static function airrGeneExpressionResponseSingle($expression)
{

//take a single gene expression from database query and create a response as per
// AIRR API standard
$required_fields = FileMapping::createMappingArray('ir_adc_api_response', 'airr_required', ['ir_class'=>['geneexpression', 'cellexpression', 'ir_expression', 'GeneExpression', 'CellExpression', 'IR_Expression']]);
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2 changes: 0 additions & 2 deletions app/AirrRearrangement.php
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Expand Up @@ -274,7 +274,6 @@ public static function airrRearrangementResponse($response_list, $response_type,
}

foreach ($rearrangement as $return_key => $return_element) {

//make all the requested fields null before populating if there are results
if (isset($repository_to_airr[$return_key]) && $repository_to_airr[$return_key] != '') {
//skip over
Expand Down Expand Up @@ -388,7 +387,6 @@ public static function airrRearrangementFacetsResponse($response_list)

public static function airrRearrangementResponseSingle($rearrangement)
{

//take a single rearrangement from database query and create a response as per
// AIRR API standard
$required_fields = FileMapping::createMappingArray('ir_adc_api_response', 'airr_required', ['ir_class'=>['rearrangement', 'ir_rearrangement', 'Rearrangement', 'IR_Rearrangement']]);
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208 changes: 103 additions & 105 deletions app/AirrRepertoire.php
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53 changes: 24 additions & 29 deletions app/AirrUtils.php
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Expand Up @@ -258,27 +258,27 @@ public static function processAirrFilter($f, $airr_to_db_array, $airr_types_arra
//bad data type
return;
break;
}
}

//check also that 'in' and 'exlcude' ops have array parameter, and all
// others do not
// 'and' and 'or' can go either ways so ignore them
switch ($f['op']) {
case 'and':
case 'or':
break;
case 'in':
case 'exclude':
if (! (is_array($content['value']))) {
return;
}
break;
default:
if (is_array($content['value'])) {
return;
}
break;
}
case 'and':
case 'or':
break;
case 'in':
case 'exclude':
if (! is_array($content['value'])) {
return;
}
break;
default:
if (is_array($content['value'])) {
return;
}
break;
}
}
switch ($f['op']) {
case '=':
Expand Down Expand Up @@ -429,14 +429,13 @@ public static function queryOptimizable($query)
$airr_names = FileMapping::createMappingArray('service_name', 'ir_adc_api_query', ['ir_class'=>['rearrangement', 'ir_rearrangement', 'Rearrangement', 'IR_Rearrangement']]);
// array of indexed fields - as usual, hard-coded terms are in 'service_name' column of the mapping file
// note that indexed fields on non-AIRR terms can and do exist
$indexed_fields = ([$airr_names['ir_project_sample_id'], $airr_names['junction_aa_length'],
$indexed_fields = [$airr_names['ir_project_sample_id'], $airr_names['junction_aa_length'],
$airr_names['junction_aa'], $airr_names['v_call'], $airr_names['d_call'],
$airr_names['j_call'],
$airr_names['functional'],
$airr_names['vgene_gene'], $airr_names['vgene_family'],
$airr_names['dgene_gene'], $airr_names['dgene_family'],
$airr_names['jgene_gene'], $airr_names['jgene_family'], ]
);
$airr_names['jgene_gene'], $airr_names['jgene_family'], ];
$filters = '';
$facets = '';

Expand Down Expand Up @@ -660,7 +659,6 @@ public static function convertDbToAirr($result_list, $db_to_airr_mapping, $db_to
//given a single repository query result and mapping fields, process it
// into an array suitable for display
foreach ($result_list as $return_key => $return_element) {

//flatten any MongoDB ObjectId types
if (is_a($return_element, "MongoDB\BSON\ObjectId")) {
$return_element = $return_element->__toString();
Expand Down Expand Up @@ -722,13 +720,12 @@ public static function cloneQueryOptimizable($query)
$airr_names = FileMapping::createMappingArray('service_name', 'ir_adc_api_query', ['ir_class'=>['clone', 'ir_clone', 'Clone', 'IR_Clone']]);
// array of indexed fields - as usual, hard-coded terms are in 'service_name' column of the mapping file
// note that indexed fields on non-AIRR terms can and do exist
$indexed_fields = ([$airr_names['repertoire_id'], $airr_names['junction_aa_length'],
$indexed_fields = [$airr_names['repertoire_id'], $airr_names['junction_aa_length'],
$airr_names['junction_aa'], $airr_names['v_call'], $airr_names['d_call'],
$airr_names['j_call'],
$airr_names['vgene_gene'], $airr_names['vgene_family'],
$airr_names['dgene_gene'], $airr_names['dgene_family'],
$airr_names['jgene_gene'], $airr_names['jgene_family'], ]
);
$airr_names['jgene_gene'], $airr_names['jgene_family'], ];
$filters = '';
$facets = '';

Expand Down Expand Up @@ -951,10 +948,9 @@ public static function cellQueryOptimizable($query)
$airr_names = FileMapping::createMappingArray('service_name', 'ir_adc_api_query', ['ir_class'=>['cell', 'ir_cell', 'Cell', 'IR_Cell']]);
// array of indexed fields - as usual, hard-coded terms are in 'service_name' column of the mapping file
// note that indexed fields on non-AIRR terms can and do exist
$indexed_fields = ([$airr_names['repertoire_id'], $airr_names['data_processing_id'],
$indexed_fields = [$airr_names['repertoire_id'], $airr_names['data_processing_id'],
$airr_names['cell_id'], $airr_names['expression_study_method'], $airr_names['virtual_pairing'],
]
);
];
$filters = '';
$facets = '';

Expand Down Expand Up @@ -1145,10 +1141,9 @@ public static function geneExpressionQueryOptimizable($query)
$airr_names = FileMapping::createMappingArray('service_name', 'ir_adc_api_query', ['ir_class'=>['geneexpression', 'cellexpression', 'ir_expression', 'GeneExpression', 'CellExpression', 'IR_Expression']]);
// array of indexed fields - as usual, hard-coded terms are in 'service_name' column of the mapping file
// note that indexed fields on non-AIRR terms can and do exist
$indexed_fields = ([$airr_names['repertoire_id'], $airr_names['data_processing_id'],
$indexed_fields = [$airr_names['repertoire_id'], $airr_names['data_processing_id'],
$airr_names['cell_id'], $airr_names['property_id'], $airr_names['property'], $airr_names['value'],
]
);
];
$filters = '';
$facets = '';

Expand Down
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