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Merge pull request #103 from Public-Health-Bioinformatics/damion---CN…
…PHI-export Damion cnphi export
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| /** | ||
| * Download secondary headers and grid data. | ||
| * @param {String} baseName Basename of downloaded file. | ||
| * @param {Object} hot Handonstable grid instance. | ||
| * @param {Object} data See `data.js`. | ||
| * @param {Object} xlsx SheetJS variable. | ||
| */ | ||
| const exportIRIDA = (baseName, hot, data, xlsx) => { | ||
| // Create an export table with template's headers (2nd row) and remaining rows of data | ||
| const matrix = [getFlatHeaders(data)[1], ...getTrimmedData(hot)]; | ||
| runBehindLoadingScreen(exportFile, [matrix, baseName, 'xls', xlsx]); | ||
| }; | ||
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| /** | ||
| * Download grid mapped to GISAID format. | ||
| * @param {String} baseName Basename of downloaded file. | ||
| * @param {Object} hot Handonstable grid instance. | ||
| * @param {Object} data See `data.js`. | ||
| * @param {Object} xlsx SheetJS variable. | ||
| */ | ||
| const exportGISAID = (baseName, hot, data, xlsx) => { | ||
| // TODO: As we add more formats, we should add such headers to 'data.js' | ||
| // ExportHeaders is an array because it can happen, as below with 'Address', | ||
| // that a column name appears two or more times. | ||
| const ExportHeaders = [ | ||
| 'Submitter', | ||
| 'FASTA filename', | ||
| 'Virus name', | ||
| 'Type', | ||
| 'Passage details/history', | ||
| 'Collection date', | ||
| 'Location', | ||
| 'Additional location information', | ||
| 'Host', | ||
| 'Additional host information', | ||
| 'Gender', | ||
| 'Patient age', | ||
| 'Patient status', | ||
| 'Specimen source', | ||
| 'Outbreak', | ||
| 'Last vaccinated', | ||
| 'Treatment', | ||
| 'Sequencing technology', | ||
| 'Assembly method', | ||
| 'Coverage', | ||
| 'Originating lab', | ||
| 'Address', | ||
| 'Sample ID given by the sample provider', | ||
| 'Submitting lab', | ||
| 'Address', | ||
| 'Sample ID given by the submitting laboratory', | ||
| 'Authors' | ||
| ]; | ||
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| // Create a map of Export format headers to template's fields. It is a | ||
| // one-to-many relationship, with indices representing the maps. | ||
| const headerMap = {}; | ||
| for (const [HeaderIndex, _] of ExportHeaders.entries()) { | ||
| headerMap[HeaderIndex] = []; | ||
| } | ||
| const fields = getFields(data); | ||
| for (const [fieldIndex, field] of fields.entries()) { | ||
| if (field.GISAID) { | ||
| let HeaderIndex = ExportHeaders.indexOf(field.GISAID); | ||
| // GISAID has two fields called 'Address' | ||
| if (field.GISAID === 'Address' && field.fieldName === 'sequence submitter contact address') { | ||
| // This locates 2nd occurance of 'Address' field in ExportHeaders | ||
| HeaderIndex = ExportHeaders.indexOf(field.GISAID, HeaderIndex+1); | ||
| } | ||
| headerMap[HeaderIndex].push(fieldIndex); | ||
| } | ||
| } | ||
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| // Create an export table with target format's headers and remaining rows of data | ||
| const matrix = [ExportHeaders]; | ||
| const unmappedMatrix = getTrimmedData(hot); | ||
| for (const unmappedRow of unmappedMatrix) { | ||
| const mappedRow = []; | ||
| for (const [HeaderIndex, HeaderName] of ExportHeaders.entries()) { | ||
| if (HeaderName === 'Type') { | ||
| // Assign constant value and do next field. | ||
| mappedRow.push('betacoronavirus'); | ||
| continue; | ||
| } | ||
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| const mappedCell = []; | ||
| for (const mappedFieldIndex of headerMap[HeaderIndex]) { | ||
| let mappedCellVal = unmappedRow[mappedFieldIndex]; | ||
| if (!mappedCellVal) continue; | ||
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| // Only map specimen processing if it is "virus passage" | ||
| const field = fields[mappedFieldIndex] | ||
| const standardizedCellVal = mappedCellVal.toLowerCase().trim(); | ||
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| if (field.fieldName === 'specimen processing') { | ||
| // Specimen processing is a multi-select field | ||
| const standardizedCellValArr = standardizedCellVal.split(';'); | ||
| if (!standardizedCellValArr.includes('virus passage')) continue; | ||
| // We only want to map "virus passage" | ||
| mappedCellVal = 'Virus passage'; | ||
| } | ||
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| // All null values should be converted to "Unknown" | ||
| if (field.dataStatus) { | ||
| const standardizedDataStatus = | ||
| field.dataStatus.map(val => val.toLowerCase().trim()); | ||
| if (standardizedDataStatus.includes(standardizedCellVal)) { | ||
| // Don't push "Unknown" to fields with multi, concat mapped values | ||
| if (headerMap[HeaderIndex].length > 1) continue; | ||
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| mappedCellVal = 'Unknown'; | ||
| } | ||
| } | ||
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| if (field.fieldName === 'passage number') { | ||
| mappedCellVal = 'passage number ' + mappedCellVal; | ||
| } | ||
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| mappedCell.push(mappedCellVal); | ||
| } | ||
| mappedRow.push(mappedCell.join(';')); | ||
| } | ||
| matrix.push(mappedRow); | ||
| } | ||
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| runBehindLoadingScreen(exportFile, [matrix, baseName, 'xls', xlsx]); | ||
| }; | ||
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| /** | ||
| * Download grid mapped to CNPHI LaSER format. | ||
| * @param {String} baseName Basename of downloaded file. | ||
| * @param {Object} hot Handonstable grid instance. | ||
| * @param {Object} data See `data.js`. | ||
| * @param {Object} xlsx SheetJS variable. | ||
| */ | ||
| const exportLASER = (baseName, hot, data, xlsx) => { | ||
| const ExportHeaders = [ | ||
| 'Primary Specimen Identification Number', | ||
| 'Related Specimen ID|Related Specimen Relationship Type', | ||
| 'BioProject Accession', | ||
| 'BioSample Accession', | ||
| 'SRA Accession', | ||
| 'Patient Sample Collected Date', | ||
| 'Patient Country', | ||
| 'Patient Province', | ||
| 'GISAID Virus Name', | ||
| 'Pathogen', | ||
| 'Reason for Sampling', | ||
| 'Test Requested', | ||
| 'Specimen Type', | ||
| 'Anatomical Material', | ||
| 'Anatomical Site', | ||
| 'Body Product', | ||
| 'Environmental Material', | ||
| 'Environmental Site', | ||
| 'Specimen Collection Matrix', | ||
| 'Collection Method', | ||
| 'Animal Type', | ||
| 'Specimen Source', | ||
| 'Host Health State', | ||
| 'Host Health State Details', | ||
| 'Host Disease', | ||
| 'Patient Age', | ||
| 'Host Age Category', | ||
| 'Patient Sex', | ||
| 'Symptoms Onset Date', | ||
| 'Symptoms', | ||
| 'Patient Symptomatic', | ||
| 'Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date', | ||
| 'Patient Travelled', | ||
| 'Exposure Event', | ||
| 'Sequencing protocol name', | ||
| 'Gene Target #1', | ||
| 'Gene Target #1 CT Value', | ||
| 'Gene Target #2', | ||
| 'Gene Target #2 CT Value' | ||
| ]; | ||
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| // Create a map of Export format headers to template's fields. It is a | ||
| // one-to-many relationship, with indices representing the maps. | ||
| const headerMap = {}; | ||
| const fieldMap = {}; | ||
| for (const [HeaderIndex, _] of ExportHeaders.entries()) { | ||
| headerMap[HeaderIndex] = []; | ||
| } | ||
| const fields = getFields(data); | ||
| for (const [fieldIndex, field] of fields.entries()) { | ||
| fieldMap[field.fieldName] = fieldIndex; | ||
| if (field.CNPHI) { | ||
| const HeaderIndex = ExportHeaders.indexOf(field.CNPHI); | ||
| if (HeaderIndex > -1) | ||
| headerMap[HeaderIndex].push(fieldIndex); | ||
| else { | ||
| const msg = 'A template CNPHI field was not found in CNPHI export header list:' + field.CNPHI; | ||
| console.log (msg); | ||
| $('#export-to-err-msg').text(msg); | ||
| } | ||
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| } | ||
| } | ||
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| // Create an export table with target format's headers and remaining rows of data | ||
| const matrix = [ExportHeaders]; | ||
| const symptoms_index = ExportHeaders.indexOf('Symptoms'); | ||
| const travel_index = ExportHeaders.indexOf('Country of Travel|Province of Travel|City of Travel|Travel start date|Travel End Date'); | ||
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| for (const unmappedRow of getTrimmedData(hot)) { | ||
| const mappedRow = []; | ||
| for (const [HeaderIndex, HeaderName] of ExportHeaders.entries()) { | ||
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| if (HeaderName === 'Test Requested') { | ||
| // Assign constant value. | ||
| mappedRow.push('CanCOGeN Next Generation Sequencing (NGS)'); | ||
| continue; | ||
| } | ||
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| if (HeaderName === 'Pathogen') { | ||
| // Assign constant value. | ||
| mappedRow.push('SARS-CoV-2'); | ||
| continue; | ||
| } | ||
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| // yes/no calculated field | ||
| if (HeaderName === 'Patient Symptomatic') { | ||
| // Note: if this field eventually gets null values, then must do | ||
| // field.dataStatus check. | ||
| mappedRow.push( mappedRow[symptoms_index] ? 'yes' : 'no' ); | ||
| continue; | ||
| } | ||
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| // yes/no calculated field | ||
| if (HeaderName === 'Patient Travelled') { | ||
| // as above for field.dataStatus check. | ||
| mappedRow.push( mappedRow[travel_index].replace(/\|/g,'').length > 0 ? 'yes' : 'no' ); | ||
| continue; | ||
| } | ||
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| // A complicated rule about what is stored in 'Specimen Source' | ||
| if (HeaderName === 'Specimen Source') { | ||
| var cellValue = ''; | ||
| for (const FieldName of [ | ||
| 'host (scientific name)', | ||
| 'host (common name)', | ||
| 'environmental material', | ||
| 'environmental site'] | ||
| ) { | ||
| const field = fields[fieldMap[FieldName]]; | ||
| const value = unmappedRow[fieldMap[FieldName]]; | ||
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| // Ignore all null value types | ||
| if (!value || field.dataStatus.indexOf(value) >= 0) { | ||
| continue; | ||
| } | ||
| if (FieldName === 'host (scientific name)' || FieldName === 'host (common name)') { | ||
| if (value === 'Homo sapiens' || value === 'Human') | ||
| cellValue = 'Human' | ||
| else | ||
| cellValue = 'Animal' | ||
| break; | ||
| } | ||
| if (FieldName === 'environmental material' || FieldName === 'environmental site') { | ||
| cellValue = 'Environmental' | ||
| break; | ||
| } | ||
| } | ||
| mappedRow.push(cellValue); | ||
| continue; | ||
| } | ||
| // Loop through all template fields that this field is mapped to, and | ||
| // create a bar-separated list of values. EMPTY VALUES MUST STILL have | ||
| // bar placeholder. | ||
| const mappedCell = []; | ||
| for (const mappedFieldIndex of headerMap[HeaderIndex]) { | ||
| let mappedCellVal = unmappedRow[mappedFieldIndex]; | ||
|
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| if (!mappedCellVal) | ||
| mappedCellVal = ''; | ||
|
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| mappedCell.push(mappedCellVal); | ||
| } | ||
| mappedRow.push(mappedCell.join('|')); | ||
| } | ||
| matrix.push(mappedRow); | ||
| } | ||
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| runBehindLoadingScreen(exportFile, [matrix, baseName, 'xls', xlsx]); | ||
| }; | ||
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