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beta develop #29

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9bfce3d
do translation for sample fields too
schristley Jun 17, 2026
ca1f584
add cellranger
schristley Jun 24, 2026
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26 changes: 22 additions & 4 deletions app/scripts/config/AnalysisConfig.js
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Original file line number Diff line number Diff line change
Expand Up @@ -202,13 +202,31 @@ var AnalysisConfig = {
}
},
"cellranger": {
"vdjserver:name":"Cellranger",
"vdjserver:name":"Cell Ranger",
"activity": {
"cellranger-ls6-0.1": {
"cellranger-ls6-10.0.0": {
"vdjserver:app:name": "cellranger-ls6",
"vdjserver:app:version": "0.1"
"vdjserver:app:version": "10.0.0",
"vdjserver:app:default": true
}
}
},
"vdjserver:activity:uses": {
"ForwardPairedFiles": ['sequence_forward_paired_reads'],
"ReversePairedFiles": ['sequence_reverse_paired_reads']
},
"vdjserver:activity:generates": [
"AIRR TSV",
"AIRR JSON",
"vdj_sequence_annotation"
],
"vdjserver:schedule": [
{ "inputSize": 2e8, "time": 120 },
{ "inputSize": 1e9, "time": 480, "node": 4 },
{ "inputSize": 5e9, "time": 960, "node": 4 },
{ "inputSize": 1e10, "time": 960, "node": 8 },
{ "inputSize": 2e10, "time": 1440, "node": 8 },
{ "inputSize": 4e10, "time": 2880, "node": 8 }
]
},
"tcrmatch": {
"vdjserver:name":"TCRMatch",
Expand Down
195 changes: 122 additions & 73 deletions app/scripts/controllers/projectController.js
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Original file line number Diff line number Diff line change
Expand Up @@ -2021,6 +2021,127 @@ ProjectController.importTable = async function(request, response) {
return hasData;
}

// manually convert text to ontology for some fields
var manualTranslation = function(field, value) {
if (value == '') return value;
if (value == null) return null;
if (value == undefined) return null;
switch (field) {
case 'species':
case 'cell_species':
switch (value.toLowerCase()) {
case 'human':
case 'h':
case 'homo':
case 'homo sapiens':
return 'NCBITAXON:9606';
case 'mouse':
case 'm':
case 'mice':
case 'mus':
case 'mus musculus':
return 'NCBITAXON:10088';
case 'monkey':
case 'macaque':
case 'macaca mulatta':
return 'NCBITAXON:9544';
case 'vicugna pacos huacaya':
return 'NCBITAXON:273913';
default:
return value.toUpperCase();
}
case 'age_unit':
case 'collection_time_point_relative_unit':
switch(value.toLowerCase()) {
case 'h':
case 'hr':
case 'hrs':
case 'hour':
case 'hours':
case 'hour(s)':
return 'UO:0000032';
case 'd':
case 'day':
case 'days':
case 'day(s)':
case 'dy':
return 'UO:0000033';
case 'w':
case 'week':
case 'weeks':
case 'week(s)':
case 'wk':
return 'UO:0000034';
case 'm':
case 'mth':
case 'mths':
case 'mnth':
case 'month':
case 'months':
case 'month(s)':
return 'UO:0000035';
case 'y':
case 'yr':
case 'yrs':
case 'year':
case 'years':
case 'year(s)':
return 'UO:0000036';
default:
return value;
}
case 'template_amount_unit':
switch(value.toLowerCase()) {
case 'p':
case 'pg':
case 'picogram':
case 'picograms':
case 'picogram(s)':
return 'UO:0000025';
case 'n':
case 'ng':
case 'nanogram':
case 'nanograms':
case 'nanogram(s)':
return 'UO:0000024';
case 'mcg':
case 'ug':
case 'microgram':
case 'micrograms':
case 'microgram(s)':
return 'UO:0000023';
case 'mg':
case 'milligram':
case 'milligrams':
case 'milligram(s)':
return 'UO:0000022';
case 'g':
case 'gram':
case 'grams':
case 'gram(s)':
return 'UO:0000021';
case 'kg':
case 'kilogram':
case 'kilograms':
case 'kilogram(s)':
return 'UO:0000009';
default:
return value;
}
case 'sex':
switch(value.toLowerCase()) {
case 'm':
return 'male';
case 'f':
return 'female';
default:
return value.toLowerCase();
}
}
return value;
}


var validation_errors = [];
var ontology_errors = [];
var curie_cache = {};
Expand All @@ -2040,78 +2161,6 @@ ProjectController.importTable = async function(request, response) {

// TODO: no support for custom fields beyond the schema

var manualTranslation = function(field, value) {
if (value == '') return value;
if (value == null) return null;
if (value == undefined) return null;
switch (field) {
case 'species':
switch (value.toLowerCase()) {
case 'human':
case 'h':
case 'homo':
case 'homo sapiens':
return 'NCBITAXON:9606';
case 'mouse':
case 'm':
case 'mice':
case 'mus':
case 'mus musculus':
return 'NCBITAXON:10088';
case 'monkey':
case 'macaque':
case 'macaca mulatta':
return 'NCBITAXON:9544';
default:
return value;
}
case 'age_unit':
switch(value.toLowerCase()) {
case 'h':
case 'hr':
case 'hrs':
case 'hour':
case 'hours':
return 'UO:0000032';
case 'd':
case 'day':
case 'days':
case 'dy':
return 'UO:0000033';
case 'w':
case 'week':
case 'weeks':
case 'wk':
return 'UO:0000034';
case 'm':
case 'mth':
case 'mths':
case 'mnth':
case 'month':
case 'months':
return 'UO:0000035';
case 'y':
case 'yr':
case 'yrs':
case 'year':
case 'years':
return 'UO:0000036';
default:
return value;
}
case 'sex':
switch(value.toLowerCase()) {
case 'm':
return 'male';
case 'f':
return 'female';
default:
return value.toLowerCase();
}
}
return value;
}

// simple fields
let subject_columns = [];
let airr_schema = new airr.SchemaDefinition('Subject');
Expand Down Expand Up @@ -2457,7 +2506,7 @@ ProjectController.importTable = async function(request, response) {
// take values from import row and stick into appropriate fields in given sample object
var assign_sample_values = async function(i, dataRow, sample) {
for (let j in sample_columns) {
let data_value = dataRow[sample_columns[j]];
let data_value = manualTranslation(sample_columns[j], dataRow[sample_columns[j]]);
if (schema.is_ontology(sample_columns[j])) {
if (data_value != '') {
if (curie_cache[data_value]) sample[sample_columns[j]] = curie_cache[data_value];
Expand Down
2 changes: 1 addition & 1 deletion app/vdjserver-schema
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Submodule vdjserver-schema updated 1 files
+46 −0 vdjserver-schema.yaml