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Begin NCBI_SRA exports
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-1081
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5 files changed

+1140
-1081
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‎web/templates/wastewater/export.js

+61-1
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,62 @@
11
// A dictionary of possible export formats
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export default {};
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export default {
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NCBI_SRA: {
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fileType: 'xls',
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status: 'published',
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method: function(dh) {
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const exportHeaders = new Map([
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["sample_name", []],
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["library_ID", []],
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["title", []],
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["library_strategy", []],
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["library_source", []],
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["library_selection", []],
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["library_layout", []],
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["platform (click for details)", []],
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["instrument_model", []],
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["design_description", []],
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["filetype", []],
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["filename", []],
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["filename2", []],
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["filename3", []],
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["filename4", []],
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["assembly", []],
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["fasta_file", []],
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["enrichment_kit", []],
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["amplicon_PCR_primer_scheme", []],
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["library_preparation_kit", []],
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["amplicon_size", []],
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["quality_control_method", []],
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["quality_control_method_version", []],
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["quality_control_determination", []],
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["quality_control_issues", []],
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["quality_control_details", []],
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["dehosting_method", []],
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["sequence_submitter_contact_email", []],
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["raw_sequence_data_processing_method", []],
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]);
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const outputMatrix = [[...exportHeaders.keys()]];
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const sourceFields = dh.getFields(dh.table);
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const sourceFieldNameMap = dh.getFieldNameMap(sourceFields);
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dh.getHeaderMap(exportHeaders, sourceFields, 'NCBI_SRA');
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for (const inputRow of dh.getTrimmedData(dh.hot)) {
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const outputRow = [];
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let value;
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for (const [headerName, sources] of exportHeaders) {
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value = dh.getMappedField(
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headerName,
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inputRow,
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sources,
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sourceFields,
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sourceFieldNameMap,
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':',
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'NCBI_SRA'
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);
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outputRow.push(value);
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}
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outputMatrix.push(outputRow);
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}
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return outputMatrix;
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},
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},
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};

‎web/templates/wastewater/schema.json

+11-11
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@@ -8666,7 +8666,7 @@
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"description": "The date the sample was sequenced.",
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"title": "sequencing date",
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"todos": [
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">={sample_collection_date}",
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">={sample_collection_start_date}",
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"<={today}"
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],
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"comments": [
@@ -8790,7 +8790,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_strategy",
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"NCBI_SRA:%20library_source"
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"NCBI_SRA:library_source"
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],
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"slot_uri": "GENEPIO:0100997",
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"domain_of": [
@@ -8892,7 +8892,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_selection",
8895-
"NCBI_SRA:%20design_description"
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"NCBI_SRA:design_description"
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],
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"slot_uri": "GENEPIO:0100966",
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"domain_of": [
@@ -15981,7 +15981,7 @@
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"description": "The date the sample was sequenced.",
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"title": "sequencing date",
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"todos": [
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">={sample_collection_date}",
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">={sample_collection_start_date}",
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"<={today}"
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],
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"comments": [
@@ -16121,7 +16121,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_strategy",
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"NCBI_SRA:%20library_source"
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"NCBI_SRA:library_source"
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],
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"rank": 152,
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"slot_uri": "GENEPIO:0100997",
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"description": "The date the sample was sequenced.",
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"title": "sequencing date",
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"todos": [
23217-
">={sample_collection_date}",
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">={sample_collection_start_date}",
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"<={today}"
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],
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"comments": [
@@ -23354,7 +23354,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_strategy",
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"NCBI_SRA:%20library_source"
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"NCBI_SRA:library_source"
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],
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"rank": 153,
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"slot_uri": "GENEPIO:0100997",
@@ -23472,7 +23472,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_selection",
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"NCBI_SRA:%20design_description"
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"NCBI_SRA:design_description"
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],
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"rank": 157,
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"slot_uri": "GENEPIO:0100966",
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"description": "The date the sample was sequenced.",
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"title": "sequencing date",
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"todos": [
30922-
">={sample_collection_date}",
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">={sample_collection_start_date}",
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"<={today}"
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],
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"comments": [
@@ -31059,7 +31059,7 @@
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_strategy",
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"NCBI_SRA:%20library_source"
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"NCBI_SRA:library_source"
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],
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"rank": 167,
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"slot_uri": "GENEPIO:0100997",
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"from_schema": "https://example.com/GRDI",
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"exact_mappings": [
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"NCBI_SRA:library_selection",
31180-
"NCBI_SRA:%20design_description"
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"NCBI_SRA:design_description"
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],
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"rank": 171,
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"slot_uri": "GENEPIO:0100966",

‎web/templates/wastewater/schema.yaml

+3-3
Original file line numberDiff line numberDiff line change
@@ -4730,7 +4730,7 @@ slots:
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slot_uri: GENEPIO:0001447
47314731
range: date
47324732
todos:
4733-
- '>={sample_collection_date}'
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- '>={sample_collection_start_date}'
47344734
- <={today}
47354735
examples:
47364736
- value: '2020-06-22'
@@ -4795,7 +4795,7 @@ slots:
47954795
- value: whole genome sequencing assay
47964796
exact_mappings:
47974797
- NCBI_SRA:library_strategy
4798-
- NCBI_SRA:%20library_source
4798+
- NCBI_SRA:library_source
47994799
library_preparation_kit:
48004800
name: library_preparation_kit
48014801
title: library preparation kit
@@ -4847,7 +4847,7 @@ slots:
48474847
- value: hybrid selection method
48484848
exact_mappings:
48494849
- NCBI_SRA:library_selection
4850-
- NCBI_SRA:%20design_description
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- NCBI_SRA:design_description
48514851
genomic_target_enrichment_method_details:
48524852
name: genomic_target_enrichment_method_details
48534853
title: genomic target enrichment method details

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