Merge branch 'operon-struct-type' into operon-struct-type-article

components/content/ArticleStructure.vue

@@ -45,11 +45,21 @@ onMounted(() => {
     fetchStructures()
 })
 
+function extractGeneName(name: string) {
+    if (name.includes("__")) {
+        return name.split("__")[1]
+    }
+    if (name.includes("_")) {
+        return name.split("_")[1]
+    }
+    return undefined
+}
+
 function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
     if (file === null) {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
+        return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it) }))
     } else {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1], href: `/wiki/${systemDir}/${file}` }))
+        return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it), href: `/wiki/${systemDir}/${file}` }))
     }
 }
 function pdbNameToCif(pdbPath: string) {

components/content/PdockqMatrix.vue

@@ -65,22 +65,30 @@ const computedSystem = computed(() => {
     return toValPage?.system ?? toValPage?.title ?? undefined
 })
 
-
+function extractGeneName(name: string) {
+    if (name.includes("__")) {
+        return name.split("__")[1]
+    }
+    if (name.includes("_")) {
+        return name.split("_")[1]
+    }
+    return undefined
+}
 
 const groupedPdocks = computed(() => {
     const toValData = toValue(data)
-    const getSeqName = (d) => {
-        if (d.includes("__")) {
-            return d.split("__")[1]
-        } else {
-            return d
-        }
-    }
+    // const getSeqName = (d) => {
+    //     if (d.includes("__")) {
+    //         return d.split("__")[1]
+    //     } else {
+    //         return d
+    //     }
+    // }
     if (toValData?.hits) {
         return d3.groups(toValData.hits.flatMap(({ system, pDockQ, pdb, nb_sys, proteins_in_the_prediction, system_genes }) => {
             if (proteins_in_the_prediction.length === 2) {
-                const sanitizedSystemGenes = system_genes.map(getSeqName)
-                const sanitizedProteins = proteins_in_the_prediction.map(getSeqName)
+                const sanitizedSystemGenes = system_genes.map(extractGeneName)
+                const sanitizedProteins = proteins_in_the_prediction.map(extractGeneName)
                 const setProteins = new Set(sanitizedProteins)
                 const key = system_genes.sort().join(" / ")
                 if (setProteins.size === 2) {

components/content/StructureDb.vue

@@ -137,12 +137,21 @@ function toFolseekUrl(item: Item) {
     return toValue(refinedUrl)
 }
 
+function extractGeneName(name: string) {
+    if (name.includes("__")) {
+        return name.split("__")[1]
+    }
+    if (name.includes("_")) {
+        return name.split("_")[1]
+    }
+    return undefined
+}
 
 function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
     if (file === null) {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
+        return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it) }))
     } else {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1], href: `/wiki/${systemDir}/${file}` }))
+        return names.filter((it) => it !== "").map(it => ({ title: extractGeneName(it), href: `/wiki/${systemDir}/${file}` }))
     }
 }
 

components/content/SystemOperonStructure.vue

@@ -34,29 +34,37 @@ const monomerStructures = computed(() => {
                 structImg: `${struct.pdb.split(".pdb")[0]}.png`,
                 structPath: struct.pdb,
                 proteins_in_the_prediction: struct.proteins_in_the_prediction.map(prot => {
-                    return prot.split("__")[1]
+                    return extractGeneName(prot)
                 })
             }
         })
     }
 })
 
+
+function extractGeneName(name: string) {
+    if (name.includes("__")) {
+        return name.split("__")[1]
+    }
+    if (name.includes("_")) {
+        return name.split("_")[1]
+    }
+    return undefined
+}
+
 const sanitizedHits = computed<StructureOperonGeneWithImg[]>(() => {
     const toValMsResponse = toValue(msResponse)
     if (toValMsResponse && toValMsResponse?.hits?.length > 0) {
         return toValMsResponse.hits.map(hit => {
             // get structure information for this prot
             const monomerStructuresVal = toValue(monomerStructures)
-            const sanitizedGene = hit.gene.split("__")[1]
-            const sanitizedExangeableGenes = hit.exchangeables.map(g => g.split("__")[1])
+            const sanitizedGene = extractGeneName(hit.gene)
+            const sanitizedExangeableGenes = hit.exchangeables.map(extractGeneName)
             const genesAndSynonymous = new Set([sanitizedGene, ...sanitizedExangeableGenes])
             if (monomerStructuresVal) {
                 const struct = monomerStructuresVal.find((struct) => {
                     return genesAndSynonymous.has(struct.proteins_in_the_prediction[0])
                 })
-                if (struct === undefined) {
-                    console.log(hit)
-                }
                 const rawImgUrl = joinURL(`/${system.toLowerCase()}`, struct?.structImg ?? '')
                 const rawStructUrl = joinURL(`/${system.toLowerCase()}`, struct?.structPath ?? '')
                 const { refinedUrl: structImgHref } = useRefinedUrl(rawImgUrl)