diff --git a/OntoMaton.gs b/OntoMaton.gs index 1fb3d33..6effe21 100644 --- a/OntoMaton.gs +++ b/OntoMaton.gs @@ -37,6 +37,8 @@ function onOpen() { .addItem('Ontology Search', 'showOntologySearch') .addItem('Ontology Annotator', 'showAnnotator') .addSeparator() + .addItem('PROMA','showPROMA') + .addSeparator() .addItem('Settings', 'showSettings') .addItem('About', 'showAbout') .addToUi(); diff --git a/SDRF-PROMA-Template.html b/SDRF-PROMA-Template.html new file mode 100644 index 0000000..78dc37a --- /dev/null +++ b/SDRF-PROMA-Template.html @@ -0,0 +1,496 @@ + + + + + + + + + + + + +
+ +
+
+
+ +
+ + +
+ +
+ * Select a Template: Selecting the template and applying it will overwrite the first line of the current sheet! + +
+ +
+ +
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+ +
+ +
+ + +
+
+ +
+ + +
+
+ +
+ + * +
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+ +
+ + +
+ +
+
+ + +
+ * Annotation: When the first row is complete, search, click on the cell to determine the range and insert. + +
+ +
+ +
+ +
+ +
+
+ +
+
+ + +
+
+ Powered by OntoMaton + +
+ + + + + + + diff --git a/SDRF-PROMA.gs b/SDRF-PROMA.gs new file mode 100644 index 0000000..cf57ba0 --- /dev/null +++ b/SDRF-PROMA.gs @@ -0,0 +1,153 @@ +function showPROMA() { + var html = HtmlService.createHtmlOutputFromFile('SDRF-PROMA-Template') + .setTitle('PROMA - Ontology Search & SDRF Anotate') + .setWidth(300); + + SpreadsheetApp.getUi() + .showSidebar(html); +} + +function runSearchSDRF(term) { + return searchSDRF(term); +} + + +function searchSDRF(term) { + try { + var restriction = findRestrictionForCurrentColumn("OLS"); + var ontologies = getOLSOntologies(); + var url = OLS_API_BASE_URI + '/search'; + var queryObj = { + q: term, + rows: OLS_PAGINATION_SIZE, + start: 0, + ontology: restriction ? restriction.ontologyId : undefined + }; + var queryString = jsonToQueryString(queryObj); + url += '?' + queryString; + var cacheResult = fetchFromCache(url); + if (cacheResult) { + return JSON.parse(cacheResult); + } + var text = UrlFetchApp.fetch(url).getContentText(), json = JSON.parse(text), ontologyDict = {}; + + var docs = json.response && json.response.docs; + if (!docs || docs.length === 0) { + throw "No Result found."; + } + docs.forEach(function(elem) { + var ontology = ontologies[elem.ontology_name], ontologyLabel = elem.ontology_prefix, record; + if (!ontologyDict[ontologyLabel]) { + ontologyDict[ontologyLabel] = {"ontology-name": elem.ontology_name, "terms": []}; + record = { + label: elem.label, + id: elem.id, + 'ontology-label': elem.ontology_prefix, + 'ontology-name': elem.ontology_name, + 'ontology-obo_id': elem.obo_id, + accession: elem.iri, + ontology: elem.ontology_name, + details: '', + url: elem.iri + }; + + storeInCache(record.id, JSON.stringify(record)); + ontologyDict[ontologyLabel].terms.push(record); + } + }); + storeInCache(url, JSON.stringify(ontologyDict)); + return ontologyDict; + } + catch(e) { + Logger.log(e); + throw(e); + } +} + + +function handleSDRFInsertion(term_id,MT,TA,parameter) { + try { + var Sheet = SpreadsheetApp.getActiveSheet(); + var selectedRange = Sheet.getActiveSelection(); + var selectedRow = selectedRange.getRow(); + var selectedColumn = selectedRange.getColumn(); + var textTerm = fetchFromCache(term_id); + var term = JSON.parse(textTerm); + + var ontologyObject = { + "term": term["label"], + "accession": term_id, + "ontologyId": term["ontology-label"], + "ontologyVersion": term["ontology"], + "ontologyDescription": term["ontology-name"], + "url": term["url"], + "obo_id": term["ontology-obo_id"] + } + + if(parameter == 'modification parameters'){ + if(MT == ''){ + var modification = "NT=" + ontologyObject.term + ';TA=' + TA + ";AC=" + ontologyObject.obo_id; + } + else{ + var modification = "NT=" + ontologyObject.term + ";MT=" + MT + ';TA=' + TA + ";AC=" + ontologyObject.obo_id; + } + for (var row = selectedRow; row <= selectedRange.getLastRow(); row++) { + Sheet.getRange(row,selectedColumn).setValue(modification); + } + } + else if(parameter == 'instrument' || parameter == 'cleavage agent details' || parameter == 'label'){ + var modification = "NT=" + ontologyObject.term + ";AC=" + ontologyObject.obo_id; + for (var row = selectedRow; row <= selectedRange.getLastRow(); row++) { + Sheet.getRange(row,selectedColumn).setValue(modification); + } + } + insertSDRFInRecordSheet(modification,parameter,ontologyObject); + } + catch(err) { + Logger.log(err); + throw err; + } +} + +function handleTemplateInsertion(template){ + var Sheet = SpreadsheetApp.getActiveSheet(); + //var selectedRange = Sheet.getActiveSelection(); + //var selectedRow = selectedRange.getRow(); + var data = Sheet.getDataRange().getValues(); + + for(var i = 0; i < data[0].length; i++){ //Clear the first row. + Sheet.getRange(1, i+1).setValue(''); + } + + SpreadsheetApp.getActiveSpreadsheet().toast("Select a region to insert information; Add or delete columns according to your needs.", + "Template successfully deployed!", -1); + + var cell_line_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[cell type]","characteristics[disease]","characteristics[cell line]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[cleavage agent details]","comment[instrument]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + var default_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[disease]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[cleavage agent details]","comment[instrument]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + var human_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[cell type]","characteristics[ancestry category]","characteristics[age]","characteristics[sex]","characteristics[disease]","characteristics[individual]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[instrument]","comment[cleavage agent details]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + var nonvertebrates_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[disease]","characteristics[cell type]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[instrument]","comment[cleavage agent details]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + var plants_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[cell type]","characteristics[disease]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[instrument]","comment[cleavage agent details]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + var vertebrates_Template = ["source name","characteristics[organism]","characteristics[organism part]","characteristics[cell type]","characteristics[developmental stage]","characteristics[disease]","characteristics[biological replicate]","technology type","assay name","comment[technical replicate]","comment[data file]","comment[fraction identifier]","comment[label]","comment[cleavage agent details]","comment[instrument]","comment[modification parameters]","comment[modification parameters]","factor value[]"]; + + if (template == 'cell-line'){ + var application = cell_line_Template; + } + else if (template == 'default'){ + var application = default_Template; + } + else if (template == 'human'){ + var application = human_Template; + } + else if (template == 'nonvertebrates'){ + var application = nonvertebrates_Template; + } + else if (template == 'plants'){ + var application = plants_Template; + } + else if (template == 'vertebrates'){ + var application = vertebrates_Template; + } + for (var i = 0; i < application.length; i++){ + Sheet.getRange(1, i+1).setValue(application[i]); + } +}