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",
-- 
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