From 52090510cab5e1d297dde8967ee97630b9454437 Mon Sep 17 00:00:00 2001 From: isaherbauts <isabelle.herbauts@univie.ac.at> Date: Thu, 5 Mar 2020 14:51:37 +0100 Subject: [PATCH] lisecnses, warnings, display assay --- src/App.vue | 36 ++++---- .../display/pharma_display/PhDJsonld.vue | 19 +++- src/components/input/PhSubmit.vue | 69 ++------------ .../input/pharma-input-fields/PhFiles.vue | 91 +++++++++++-------- .../input/pharma-input-fields/PhInputForm.vue | 1 - src/utils/fields.js | 60 ++++++------ src/utils/json-ld.js | 8 +- 7 files changed, 125 insertions(+), 159 deletions(-) diff --git a/src/App.vue b/src/App.vue index a43c972..88c7f4e 100644 --- a/src/App.vue +++ b/src/App.vue @@ -737,17 +737,17 @@ export default { var isoform_assayTarget = fields.getField("1-Isoform"); isoform_assayTarget.label = "Assay Target Isoform"; - isoform_assayTarget.type = "pharmaWien:isoform_protein_assayTarget"; + isoform_assayTarget.type = "pharmaWien:assayTarget_isoform_protein"; isoform_assayTarget.category = ["assayTarget"]; var seqAlt_assayTarget = fields.getField("1-Protein-sequence-alteration"); seqAlt_assayTarget.label = "Assay Target Protein sequence alteration"; - seqAlt_assayTarget.type = "pharmaWien:seqAlt_protein_assayTarget"; + seqAlt_assayTarget.type = "pharmaWien:assayTarget_seqAlt_protein"; seqAlt_assayTarget.category = ["assayTarget"]; var protMod_assayTarget = fields.getField("1-Protein-modification"); protMod_assayTarget.label = "Assay Target Protein Modification"; - protMod_assayTarget.type = "pharmaWien:protMod_protein_assayTarget"; + protMod_assayTarget.type = "pharmaWien:assayTarget_protMod_protein"; protMod_assayTarget.category = ["assayTarget"]; this.form.sections[2].categories[2].fields.push(uniprot_assayTarget); this.form.sections[2].categories[2].fields.push(isoform_assayTarget); @@ -757,12 +757,12 @@ export default { var gene_assayTarget = fields.getField("1-Entrez-gene-ID"); gene_assayTarget.label = "Assay Target Entrez Gene ID"; - gene_assayTarget.type = "pharmaWien:geneId_gene_assayTarget"; + gene_assayTarget.type = "pharmaWien:assayTarget_geneId"; gene_assayTarget.category = ["assayTarget"]; var geneMod_assayTarget = fields.getField("1-Gene-modification"); geneMod_assayTarget.label = "Assay Target Gene Modification"; - geneMod_assayTarget.type = "pharmaWien:geneMod_gene_assaytarget"; + geneMod_assayTarget.type = "pharmaWien:assayTarget_geneMod"; geneMod_assayTarget.category = ["assayTarget"]; this.form.sections[2].categories[2].fields.push(gene_assayTarget); this.form.sections[2].categories[2].fields.push(geneMod_assayTarget); @@ -770,13 +770,13 @@ export default { var nacid_assayTarget = fields.getField("1-Nucleic-acid-type"); nacid_assayTarget.label = "Assay Target Nucleic Acid Type"; - nacid_assayTarget.type = "pharmaWien:type_nucleicAcid_assayTarget"; + nacid_assayTarget.type = "pharmaWien:assayTarget_type_nucleicAcid"; nacid_assayTarget.category = ["assayTarget"]; nacid_assayTarget.description = "Nucleic Acid"; var refSeq_assayTarget = fields.getField("1-RefSeq-accession"); refSeq_assayTarget.label = "Assay Target RefSeq accession:"; - refSeq_assayTarget.type = "pharmaWien:refSeq_nucleicAcid_assayTarget"; + refSeq_assayTarget.type = "pharmaWien:assayTarget_refSeq_nucleicAcid"; refSeq_assayTarget.category = ["assayTarget"]; refSeq_assayTarget.description = "Nucleic Acid"; this.form.sections[2].categories[2].fields.push(nacid_assayTarget); @@ -784,7 +784,7 @@ export default { var PFAM_assayTarget = fields.getField("1-PFAM-accession"); PFAM_assayTarget.label = "Assay Target PFAM accession number"; - PFAM_assayTarget.type = "pharmaWien:PFAM_assayTarget"; + PFAM_assayTarget.type = "pharmaWien:assayTarget_PFAM"; PFAM_assayTarget.category = ["assayTarget"]; this.form.sections[2].categories[2].fields.push(PFAM_assayTarget); @@ -792,13 +792,13 @@ export default { uniprotsub_assayTarget.label = "Assay Target Protein Subunit Uniprot record"; - uniprotsub_assayTarget.type = "pharmaWien:uniprot_protSub_assayTarget"; + uniprotsub_assayTarget.type = "pharmaWien:assayTarget_uniprot_protSub"; uniprotsub_assayTarget.category = ["assayTarget"]; uniprotsub_assayTarget.description = "Protein Subunit"; var isoformsub_assayTarget = fields.getField("1-Isoform"); isoformsub_assayTarget.label = "Assay Target Protein Subunit Isoform"; - isoformsub_assayTarget.type = "pharmaWien:isoform_protSub_assayTarget"; + isoformsub_assayTarget.type = "pharmaWien:assayTarget_isoform_protSub"; isoformsub_assayTarget.category = ["assayTarget"]; isoformsub_assayTarget.description = "Protein Subunit"; var seqAltsub_assayTarget = fields.getField( @@ -806,13 +806,13 @@ export default { ); seqAltsub_assayTarget.label = "Assay Target Protein Subunit sequence alteration"; - seqAltsub_assayTarget.type = "pharmaWien:seqAlt_protSub_assayTarget"; + seqAltsub_assayTarget.type = "pharmaWien:assayTarget_seqAlt_protSub"; seqAltsub_assayTarget.category = ["assayTarget"]; seqAltsub_assayTarget.description = "Protein Subunit"; var protModsub_assayTarget = fields.getField("1-Protein-modification"); protModsub_assayTarget.label = "Assay Target Protein Subunit modification"; - protModsub_assayTarget.type = "pharmaWien:protMod_protSub_assayTarget"; + protModsub_assayTarget.type = "pharmaWien:assayTarget_protMod_protSub"; protModsub_assayTarget.category = ["assayTarget"]; protModsub_assayTarget.description = "Protein Subunit"; this.form.sections[2].categories[2].fields.push(uniprotsub_assayTarget); @@ -825,7 +825,7 @@ export default { protcomplex_assayTarget.label = "Assay Target Protein Complex-Portal Accession"; protcomplex_assayTarget.type = - "pharmaWien:portalAcc_protComplex_assayTarget"; + "pharmaWien:assayTarget_portalAcc_protComplex"; protcomplex_assayTarget.category = ["assayTarget"]; this.form.sections[2].categories[2].fields.push(protcomplex_assayTarget); this.form.sections[2].categories[2].fields.push( @@ -833,7 +833,7 @@ export default { ); var lipid_assayTarget = fields.getField("1-Lipid"); lipid_assayTarget.label = "Assay Target Lipid"; - lipid_assayTarget.type = "pharmaWien:lipid_assayTarget"; + lipid_assayTarget.type = "pharmaWien:assayTarget_lipid"; lipid_assayTarget.category = ["assayTarget"]; @@ -850,7 +850,7 @@ export default { //cell_organism_assayTarget.description = ["Cellular organism", "Organism"]; cell_organism_assayTarget.label = "Assay Target Cellular Organism"; cell_organism_assayTarget.type = - "pharmaWien:cellular_organism_assayTarget"; + "pharmaWien:assayTarget_cellular_organism"; cell_organism_assayTarget.category = ["organismAssayTarget"]; // cell_organism_assayTarget.topcategory = "assayTarget"; cell_organism_assayTarget.visible = false; @@ -861,7 +861,7 @@ export default { //viruses_organism_assayTarget.description = ["Viruses", "Organism"]; viruses_organism_assayTarget.label = "Assay Target Viruses"; viruses_organism_assayTarget.type = - "pharmaWien:viruses_organism_assayTarget"; + "pharmaWien:assayTarget_viruses_organism"; // cell_organism_assayTarget.topcategory = "assayTarget"; viruses_organism_assayTarget.category = ["organismAssayTarget"]; @@ -873,7 +873,7 @@ export default { //viroids_organism_assayTarget.description = ["Viroids", "Organism"]; viroids_organism_assayTarget.label = "Assay Target Viroids"; viroids_organism_assayTarget.subjectType = - "pharmaWien:viroids_organism_assayTarget"; + "pharmaWien:assayTarget_viroids_organism"; viroids_organism_assayTarget.category = ["organismAssayTarget"]; // cell_organism_assayTarget.topcategory = "assayTarget"; viroids_organism_assayTarget.visible = false; @@ -882,7 +882,7 @@ export default { ); var cell_line_assayTarget = fields.getField("0-cell-line"); cell_line_assayTarget.label = "Assay Target Cell line (cellosaurus)"; - cell_line_assayTarget.type = "pharmaWien:cellosaurus_assayTarget"; + cell_line_assayTarget.type = "pharmaWien:assayTarget_cellosaurus"; cell_line_assayTarget.visible = false; cell_line_assayTarget.category = ["assayTarget"]; diff --git a/src/components/display/pharma_display/PhDJsonld.vue b/src/components/display/pharma_display/PhDJsonld.vue index 5c42bad..72082eb 100644 --- a/src/components/display/pharma_display/PhDJsonld.vue +++ b/src/components/display/pharma_display/PhDJsonld.vue @@ -317,8 +317,10 @@ <v-toolbar-title class="font-weight-light">{{sec.title}}</v-toolbar-title> </v-layout> </v-toolbar> + <template v-if="sec.selections"> <v-card v-for="s in sec.selections" :key="s.label+'t'"> + s {{s}} {{sec.type}} {{s.label}} <v-layout v-if="getSelectionElem(sec.type,s.label).length>0"> <v-flex xs1 class="subheading"> <a :href="s.id" target="_blank">{{s.label}}</a> @@ -441,6 +443,7 @@ export default { var subcat = subjects[i]["@type"]; // thuis should be unique to each entry field, comes from "subjectType" in jsonld var categ = this.getCategory(subcat); + n_subjects[i] = {}; if (categ) { n_subjects[i].category = categ; @@ -508,7 +511,10 @@ export default { }, { type: "assay", - selections: fields.getFieldsLabelsbyCateg("assay"), + selections: [ + ...fields.getFieldsLabelsbyCateg("assay"), + ...fields.getFieldsLabelsbyCateg("assayOrganism") + ], title: "Bioassay Content" }, { @@ -523,10 +529,15 @@ export default { title: "Relation to anatomical entity" }, { - type: "Matching Gene Ontology Terms", - title: "Matching Gene Ontology Terms" + type: "goTerm", + title: "Matching Gene Ontology Terms", + selections: fields.getFieldsLabelsbyCateg("goTerm") + }, + { + type: "chebi", + title: "Associated CHEBI-terms", + selections: fields.getFieldsLabelsbyCateg("chebi") }, - { type: "", title: "Associated CHEBI-terms", id: this.getinfoRef("") }, { type: "technique", title: "Used techniques", diff --git a/src/components/input/PhSubmit.vue b/src/components/input/PhSubmit.vue index 919eb6e..93d0e93 100644 --- a/src/components/input/PhSubmit.vue +++ b/src/components/input/PhSubmit.vue @@ -23,63 +23,6 @@ :targetpid="targetpid" v-on:submit="checkWarnings()" ></ph-input-form> - - <v-layout align-center justify-end row class="ma-3"> - <v-dialog v-if="templating" v-model="templatedialog" width="500"> - <v-btn - class="mr-3" - slot="activator" - dark - raised - :loading="loading" - :disabled="loading" - color="grey" - >Save as template</v-btn> - <v-card> - <v-card-title class="headline grey lighten-2" primary-title> - <span v-t="'Save as template'"></span> - </v-card-title> - <v-card-text> - <v-text-field v-model="templatename" :label="$t('Template name')"></v-text-field> - </v-card-text> - <v-card-actions> - <v-spacer></v-spacer> - <v-btn - :loading="loading" - :disabled="loading" - color="grey" - dark - @click="templatedialog= false" - > - <span v-t="'Cancel'"></span> - </v-btn> - <v-btn :loading="loading" :disabled="loading" color="primary"> - <span v-t="'Save'"></span> - </v-btn> - </v-card-actions> - </v-card> - </v-dialog> - <v-btn - v-if="targetpid" - raised - :loading="loading" - :disabled="loading" - color="primary" - @click="save()" - > - <span v-t="'Save'"></span> - </v-btn> - <v-btn - v-else - raised - :loading="loading" - :disabled="loading" - color="primary" - @click="checkWarnings()" - > - <span v-t="'Submit'"></span> - </v-btn> - </v-layout> </v-tab-item> <!--second tab--> <v-tab-item class="ma-4"> @@ -228,7 +171,7 @@ export default { }, getMetadata: function() { let jsonlds; - console.log("this.form", this.form); + //console.log("this.form", this.form); if (!this.targetpid && this.submittype === "container") { jsonlds = jsonLd.containerForm2json(this.form); } else { @@ -423,15 +366,15 @@ export default { console.log("in check warning", this.s); var self = this; let missingF = []; - this.submit(); - /* for (var section in self.s) { + //this.submit(); + var w = false; + for (var section in self.s) { let fields = self.s[section].fields; for (var f in fields) { - var w = false; - if (fields[f].warning === true) { w = true; + console.log("warning", fields[f].label); missingF.push(fields[f].label); } } @@ -448,7 +391,7 @@ export default { self.loading = false; self.$store.commit("setAlerts", []); this.submit(); - }*/ + } } }, mounted: function() { diff --git a/src/components/input/pharma-input-fields/PhFiles.vue b/src/components/input/pharma-input-fields/PhFiles.vue index c6b1a5a..7493483 100644 --- a/src/components/input/pharma-input-fields/PhFiles.vue +++ b/src/components/input/pharma-input-fields/PhFiles.vue @@ -211,6 +211,41 @@ export default { if (i === 0) return bytes + " " + sizes[i]; return (bytes / Math.pow(1024, i)).toFixed(2) + " " + sizes[i]; }, + initialiseFileItems: function(i) { + if (this.itemsExt[i] == null) { + this.itemsExt[i] = this.items[i].type; + } + if (this.FileExtFreefield[i] == null) { + this.FileExtFreefield[i] = false; + } + if (this.itemsType[i] == null) { + this.itemsType[i] = ""; + } + if (this.itemsDesc[i] == null) { + this.itemsDesc[i] = ""; + } + if (this.itemsLicense[i] == null) { + this.itemsLicense[i] = ""; + } + }, + commitFileItems: function() { + this.$emit("input-file", this.items); + if (this.items.length > 0) { + this.$emit("validation", false); + } else { + this.$emit("validation", true); + } + //this.$store.commit("setFiles", this.itemsNames); + + this.$emit("input-name", this.itemsNames); + this.$emit("input-extension", this.itemsExt); + this.$emit("input-license", this.itemsLicense); + this.$emit("input-warning", this.itemsWarning); + + this.$emit("input-type", this.itemsType); + this.$emit("input-description", this.itemsDesc); + }, + setFilename(e) { this.loaderVisible = false; @@ -246,36 +281,16 @@ export default { var fileSizes = 0; for (var i = 0; i < this.items.length; i++) { this.itemsNames[i] = this.items[i].name; - //only push the extension type if no value was selected before - if (this.itemsExt[i] == null) { - this.itemsExt[i] = this.items[i].type; - } - if (this.FileExtFreefield[i] == null) { - this.FileExtFreefield[i] = false; - } - //this.itemsType[i] = ; - //this.itemsDesc[i] = ""; - //this.itemsLicense[i] = ""; + this.initialiseFileItems(i); + this.$emit("input-numberFiles", this.items.length); this.itemsWarning[i] = true; this.itemsSizes[i] = this.bytesToSize(this.items[i].size); fileSizes += this.items[i].size; } this.itemsTotalSize = this.bytesToSize(fileSizes); this.itemsAdded = this.items.length; - - this.$emit("input-file", this.items); - if (this.items.length > 0) { - this.$emit("validation", false); - } else { - this.$emit("validation", true); - } - //this.$store.commit("setFiles", this.itemsNames); - this.$emit("input-numberFiles", this.items.length); - this.$emit("input-name", this.itemsNames); - this.$emit("input-extension", this.itemsExt); - this.$emit("input-license", this.itemsLicense); - this.$emit("input-warning", this.itemsWarning); + this.commitFileItems(); }, removeItems() { this.items = []; @@ -290,20 +305,16 @@ export default { this.FileExtFreefield = []; this.itemsTotalSize = ""; this.loaderVisible = true; - if (this.items.length > 0) { + /* if (this.items.length > 0) { this.$emit("validation", false); } else { this.$emit("validation", true); - } + }*/ //this.$store.commit("setFiles", this.itemsNames); + this.$emit("input-numberFiles", 0); - this.$emit("input-file", this.items); - this.$emit("input-name", this.itemsNames); - this.$emit("input-extension", this.itemsExt); - this.$emit("input-type", this.itemsType); - this.$emit("input-description", this.itemsDesc); - this.$emit("input-license", this.itemsLicense); - this.$emit("input-warning", this.itemsWarning); + + this.commitFileItems(); //this.dragging = false }, removeOneItem(i) { @@ -331,16 +342,16 @@ export default { this.loaderVisible = true; } this.itemsTotalSize = this.bytesToSize(fileSizes); - - this.$emit("input-file", this.items); + this.commitFileItems(); + // this.$emit("input-file", this.items); this.$emit("input-numberFiles", this.items.length); //this.$store.commit("setFiles", this.itemsNames); - this.$emit("input-name", this.itemsNames); - this.$emit("input-extension", this.itemsExt); - this.$emit("input-type", this.itemsType); - this.$emit("input-description", this.itemsDesc); - this.$emit("input-license", this.itemsLicense); - this.$emit("input-warning", this.itemsWarning); + //this.$emit("input-name", this.itemsNames); + //this.$emit("input-extension", this.itemsExt); + //this.$emit("input-type", this.itemsType); + //this.$emit("input-description", this.itemsDesc); + //this.$emit("input-license", this.itemsLicense); + //this.$emit("input-warning", this.itemsWarning); //this.dragging = false; } } diff --git a/src/components/input/pharma-input-fields/PhInputForm.vue b/src/components/input/pharma-input-fields/PhInputForm.vue index 02bf453..aaa0045 100644 --- a/src/components/input/pharma-input-fields/PhInputForm.vue +++ b/src/components/input/pharma-input-fields/PhInputForm.vue @@ -107,7 +107,6 @@ <v-flex v-else-if="n== 'file'"> <v-card-text> <v-layout v-for="(f) in s[index].fields" :key="f.id" row wrap> - <v-flex xs12>f.fileLicense {{f.fileLicense}} f.licenseWarning {{f.licenseWarning}}</v-flex> <v-flex v-if="f.component == 'files'"> <ph-files v-bind.sync="f" diff --git a/src/utils/fields.js b/src/utils/fields.js index f4faae0..a19219b 100644 --- a/src/utils/fields.js +++ b/src/utils/fields.js @@ -51,7 +51,7 @@ const fields = [ { id: "contributors", header: "Contributors", - label: "Contributions", + label: "Contributors", type: "schema:Person", predicate: "role", firstname: "", @@ -124,7 +124,7 @@ const fields = [ value: "", definition: "File input." },*/ - /* { + { id: "license", fieldname: "License", predicate: "edm:rights", @@ -132,11 +132,11 @@ const fields = [ vocabulary: "licenses", label: "License", value: "", - warning: true, + warning: false, "skos:prefLabel": [], definition: "The value will indicate the copyright, usage and access rights that apply to this digital representation." - },*/ + }, { id: "file", label: "Files", @@ -857,7 +857,7 @@ const fields = [ { id: "5-Molecular-function", predicate: "dcterms:subject", - type: "pharmaWien:goBioProcess", + type: "pharmaWien:goMolFunct", subjectType: "goMolFunct", visible: true, label: "GO Molecular Function:", @@ -870,6 +870,7 @@ const fields = [ ontology: "go", ontClass: "GO_0003674", topId: "GO_0003674", + category: ["goTerm"], freefield: true, description: "GO Molecular Function:", info: @@ -891,6 +892,7 @@ const fields = [ ontology: "go", ontClass: "GO_0008150", topId: "GO_0008150", + category: ["goTerm"], description: "GO Biological Process:", freefield: true, infoRef: "", @@ -913,6 +915,7 @@ const fields = [ ontology: "go", ontClass: "GO_0005575", topId: "GO_0005575", + category: ["goTerm"], freefield: true, description: "GO Cellular Component:", info: @@ -935,6 +938,7 @@ const fields = [ infoRef: "http://purl.obolibrary.org/obo/CHEBI_24431", freefield: true, inchi: true, + category: ["chebi"], info: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. ", description: "Chemical entity" @@ -997,11 +1001,12 @@ const fields = [ infoRef: "http://purl.obolibrary.org/obo/CHEBI_50906", info: "A role is particular behaviour which a material entity may exhibit.", freefield: true, + category: ["chebi"], description: "Role" }, { id: "6-Subatomic-particle", - predicate: "pharmaWien:dcterms:subject", + predicate: "dcterms:subject", type: "pharmaWien:chebiSubPart", //subjectType: "chebiSubPart", label: "Subatomic particle:", @@ -1014,6 +1019,7 @@ const fields = [ ontology: "chebi", ontClass: "CHEBI_36342", topId: "CHEBI_36342", + category: ["chebi"], freefield: true, infoRef: "http://purl.obolibrary.org/obo/CHEBI_36342", info: "A particle smaller than an atom.", @@ -1117,7 +1123,7 @@ const fields = [ { id: "0-Bioassay-type", predicate: "dcterms:subject", - type: "skos:Concept", + type: "pharmaWien:BioassayType", //subjectType: "Bioassay_type", label: "Bioassay type:", visible: true, @@ -1126,10 +1132,12 @@ const fields = [ component: "selection", commit: true, visible: true, - //category: ["assay"], + category: ["assay"], vocabulary: "bioassay_type", stateVoc: "bioassay_type", - info: "" + info: "", + description: "Bioassay type:", + infoRef: "" }, { id: "0-Bioassay-category", @@ -1144,7 +1152,7 @@ const fields = [ component: "ext-service", ontology: "bao", ontClass: "BAO_0000015", - //category: ["assay"], + category: ["assay"], topId: "BAO_0000015", description: "Bioassay category:", info: @@ -1166,7 +1174,7 @@ const fields = [ ontClass: "BAO_0000019", topId: "BAO_0000019", description: "Assay format:", - //category: ["assay"], + category: ["assay"], info: "Assay format is a conceptualization of assays based on the biological and / or chemical features of the experimental system. For example assay formats include biochemical assays - referring to assays with purified protein, cell-based - referring to assays in whole cells, or organism-based - referring to assays performed in an organism.", infoRef: "http://www.bioassayontology.org/bao#BAO_0000019" @@ -1175,7 +1183,7 @@ const fields = [ id: "0-Assay-design-method", predicate: "dcterms:subject", type: "pharmaWien:assayDesignMethod", - //subjectType: "Assay design method", + subjectType: "Assay design method", label: "Assay design method", visible: true, required: false, @@ -1204,7 +1212,7 @@ const fields = [ value: "", freefield: true, component: "ext-service", - //category: ["assay"], + category: ["assay"], ontology: "bao", //baseurl: "http://www.bioassayontology.org/bao#", ontClass: "BAO_0002094", @@ -1238,7 +1246,7 @@ const fields = [ { id: "0-Organism", predicate: "dcterms:subject", - type: "skos:Concept", + type: "pharmaWien:assayOrganism", //subjectType: "AssayOrganism:", label: "Organism", description: "selection", @@ -1258,7 +1266,7 @@ const fields = [ { id: "0-Organism-assayTarget", predicate: "dcterms:subject", - type: "skos:Concept", + type: "pharmaWien:assayTarget_organism", //subjectType: "AssayOrganism:", label: "Assay Target Organism", description: "Organism", @@ -1279,7 +1287,7 @@ const fields = [ { id: "0-Cellular-organism", predicate: "dcterms:subject", - type: "pharmaWien:assayCellularOrganism", + type: "pharmaWien:assayOrganism_CellularOrganism", //subjectType: "AssayCellularOrganism", label: "Cellular organism", value: "", @@ -1297,7 +1305,7 @@ const fields = [ { id: "0-Viruses", predicate: "dcterms:subject", - type: "pharmaWien:assayViruses", + type: "pharmaWien:assayOrganism_Viruses", //subjectType: "AssayViruses", label: "Viruses", value: "", @@ -1315,7 +1323,7 @@ const fields = [ { id: "0-Viroids", predicate: "dcterms:subject", - type: "pharmaWien:assayViroids", + type: "pharmaWien:assayOrganism_Viroids", //subjectType: "AssayViroids", label: "Viroids", value: "", @@ -1351,7 +1359,7 @@ const fields = [ { id: "0-Assay-target", predicate: "dcterms:subject", - type: "skos:Concept", + type: "pharmaWien:assayTarget", //subjectType: "Assay_target", label: "Assay target ", description: "selection", @@ -1372,7 +1380,7 @@ const fields = [ { id: "0-Small-molecule", predicate: "dcterms:subject", - type: "pharmaWien:smallMol_assayTarget", + type: "pharmaWien:assayTarget_smallMol", //subjectType: "assay target small molecule", label: "Small molecule name:", value: "", @@ -1390,7 +1398,7 @@ const fields = [ { id: "0-cellular-anatomical-entity", predicate: "dcterms:subject", - type: "pharmaWien:cellularAnatomicalEntity", + type: "pharmaWien:assayTarget_cellularAnatomicalEntity", //subjectType: "cellular-anatomical-entity_assayTarget", label: "Assay Target Cellular anatomical entity", value: "", @@ -1410,7 +1418,7 @@ const fields = [ { id: "0-tissue", predicate: "dcterms:subject", - type: "pharmaWien:tissue_assayTarget", + type: "pharmaWien:assayTarget_tissue", //subjectType: "tissue_assayTarget", label: "Assay Target Tissue name:", value: "", @@ -1431,7 +1439,7 @@ const fields = [ { id: "0-carbohydrate", predicate: "dcterms:subject", - type: "harmaWien:carbohydrate_assayTarget", + type: "pharmaWien:assayTarget_carbohydrate", //subjectType: "assay target carbohydrate", label: "Assay Target Carbohydrate:", value: "", @@ -1452,7 +1460,7 @@ const fields = [ { id: "0-detection", predicate: "dcterms:subject", - type: "skos:Concept", + type: "pharmaWien:assay_detection", //subjectType: "assay_detection", label: "Detection method:", description: "selection", @@ -1475,7 +1483,7 @@ const fields = [ { id: "0-detection_method", predicate: "dcterms:subject", - type: "pharmaWien:physicalDetectionMethod", + type: "pharmaWien:assay_physicalDetectionMethod", //subjectType: "physical_detection_method", label: "Physical detection method:", value: "", @@ -1495,7 +1503,7 @@ const fields = [ { id: "0-detection_instrument", predicate: "dcterms:subject", - type: "pharmaWien:physicalDetectionInstrument", + type: "pharmaWien:assay_physicalDetectionInstrument", //subjectType: "detection_instrument", label: "Detection instrument:", value: "", diff --git a/src/utils/json-ld.js b/src/utils/json-ld.js index 676b8de..60d5e1c 100644 --- a/src/utils/json-ld.js +++ b/src/utils/json-ld.js @@ -1713,7 +1713,7 @@ export default { jsonldid = "member_" + k; jsonlds[jsonldid] = {}; - console.log("nfile i", jsonldid, k, s); + this.fields2jsonFile(jsonlds[jsonldid], k, s); } } else { @@ -2064,12 +2064,6 @@ export default { this.push_literal(jsonld, f.predicate, f.fileName[i - 1]); } if (f.fileDescription[i - 1]) { - //console.log( - // "predicate", - // f.fileDescription[i - 1], - // "now", - // this.get_json_general_description(f.fileDescription[i - 1], "eng") - //); this.push_object( jsonld, "bf:note", -- GitLab