From 314808cb42c72cc52d386aa5152df39c2caf7351 Mon Sep 17 00:00:00 2001
From: Emilio Righi <righiemilio@gmail.com>
Date: Tue, 15 Oct 2024 14:42:50 +0200
Subject: [PATCH] generate chr_aliases on the fly

---
 .../components/genome-browser/Jbrowse2.vue    |  14 +-
 .../components/ChromosomesTable.vue           |   2 +-
 .../cms/annotation/components/FileForm.vue    | 234 ++++++++++--------
 server/parsers/chromosome.py                  |   1 -
 server/rest/assembly/assemblies_service.py    |   7 +-
 5 files changed, 140 insertions(+), 118 deletions(-)

diff --git a/biogenome-client/src/components/genome-browser/Jbrowse2.vue b/biogenome-client/src/components/genome-browser/Jbrowse2.vue
index 945483ea..18aa64e9 100644
--- a/biogenome-client/src/components/genome-browser/Jbrowse2.vue
+++ b/biogenome-client/src/components/genome-browser/Jbrowse2.vue
@@ -53,14 +53,12 @@ function parseAssembly(assembly: Assembly, chromosomes: ChromosomeInterface[]) {
       },
     },
   }
-  if (assembly.has_chromosomes_aliases) {
-    assemblyAdapter.refNameAliases = {
-      adapter: {
-        type: "RefNameAliasAdapter",
-        location: {
-          uri: `${baseURL}/assemblies/${assembly.accession}/chr_aliases`,
-          locationType: "UriLocation"
-        }
+  assemblyAdapter.refNameAliases = {
+    adapter: {
+      type: "RefNameAliasAdapter",
+      location: {
+        uri: `${baseURL}/assemblies/${assembly.accession}/chr_aliases`,
+        locationType: "UriLocation"
       }
     }
   }
diff --git a/biogenome-client/src/pages/assemblies/components/ChromosomesTable.vue b/biogenome-client/src/pages/assemblies/components/ChromosomesTable.vue
index 17575f66..e391c1d1 100644
--- a/biogenome-client/src/pages/assemblies/components/ChromosomesTable.vue
+++ b/biogenome-client/src/pages/assemblies/components/ChromosomesTable.vue
@@ -29,7 +29,7 @@ import { useI18n } from 'vue-i18n'
 const { t } = useI18n()
 
 const props = defineProps<{
-    items: Record<string, any>
+    items: Record<string, any>[]
 }>()
 
 </script>
\ No newline at end of file
diff --git a/biogenome-client/src/pages/cms/annotation/components/FileForm.vue b/biogenome-client/src/pages/cms/annotation/components/FileForm.vue
index 15a0939e..6c5e58a5 100644
--- a/biogenome-client/src/pages/cms/annotation/components/FileForm.vue
+++ b/biogenome-client/src/pages/cms/annotation/components/FileForm.vue
@@ -1,60 +1,65 @@
 <template>
-    <va-form tag="form" @submit.prevent="handleSubmit">
-        <div class="row justify-center">
-            <div class="flex">
-                <va-button-toggle v-model="uploadMode" preset="secondary" border-color="primary"
-                    :options="uploadModes" />
-            </div>
+    <!-- Toggle Upload Mode -->
+    <div class="row justify-center">
+        <div class="flex">
+            <va-button-toggle v-model="uploadMode" preset="secondary" border-color="primary" :options="uploadModes" />
         </div>
-        <div class="row" v-if="uploadMode === 'links'">
-            <va-input class="flex lg12 md12 xs12 sm12" :disabled="annotationStore.annotationForm.gzipAnnotation"
-                v-model="annotationStore.annotationForm.gff_gz_location" label="gzipped gff3 url"
-                :messages="['URL of the gzipped gff file']" />
-            <va-input class="flex lg12 md12 xs12 sm12" :disabled="annotationStore.annotationForm.tabixAnnotation"
-                v-model="annotationStore.annotationForm.tab_index_location" label="tabindexed gff3 url"
-                :messages="['URL of the tabindexed gzipped gff file']" />
+    </div>
+
+    <!-- Upload Mode: Links -->
+    <div class="row" v-if="uploadMode === 'links'">
+        <va-input class="flex lg12 md12 xs12 sm12" :disabled="annotationStore.annotationForm.gzipAnnotation"
+            v-model="annotationStore.annotationForm.gff_gz_location" label="gzipped gff3 url"
+            :messages="['URL of the gzipped gff file']" />
+        <va-input class="flex lg12 md12 xs12 sm12" :disabled="annotationStore.annotationForm.tabixAnnotation"
+            v-model="annotationStore.annotationForm.tab_index_location" label="tabindexed gff3 url"
+            :messages="['URL of the tabindexed gzipped gff file']" />
+    </div>
+
+    <!-- Upload Mode: Files -->
+    <div class="row" v-else>
+        <div v-if="isLocal" class="flex lg12 md12 sm12 xs12">
+            <p>
+                Update of uploaded files is not supported. If you need to change the file, it is necessary to delete
+                this
+                annotation and create a new one.
+            </p>
+        </div>
+        <div v-else class="flex lg12 md12 sm12 xs12">
+            <va-file-upload :disabled="isInputDisabled(annotationStore.annotationForm.gff_gz_location)" type="single"
+                v-model="annotationStore.annotationForm.gzipAnnotation" dropzone
+                drop-zone-text="Upload a gzipped GFF file" file-types=".gz" />
+            <va-file-upload :disabled="isInputDisabled(annotationStore.annotationForm.tab_index_location)" type="single"
+                v-model="annotationStore.annotationForm.tabixAnnotation" dropzone
+                drop-zone-text="Upload the GFF tabix index file" file-types=".tbi" />
         </div>
-        <div class="row" v-else>
-            <div v-if="isLocalAssembly" class="flex lg12 md12 sm12 xs12">
-                <p>
-                    Update of uploaded files is not supported. If you need to change the file, it is necessary to delete
-                    this
-                    assembly
-                    and create a new one
-                </p>
-            </div>
-            <div v-else class="flex lg12 md12 sm12 xs12">
-                <va-file-upload :disabled="isValid(annotationStore.annotationForm.gff_gz_location)" type="single"
-                    v-model="annotationStore.annotationForm.gzipAnnotation" dropzone
-                    drop-zone-text="Upload a gff gzipped file" file-types=".gz" />
-                <va-file-upload :disabled="isValid(annotationStore.annotationForm.tab_index_location)" type="single"
-                    v-model="annotationStore.annotationForm.tabixAnnotation" dropzone
-                    drop-zone-text="Upload your GFF evidences" file-types=".tbi" />
-            </div>
+    </div>
 
+    <!-- Extra Attributes Section -->
+    <va-divider>Extra Attributes</va-divider>
+    <div v-for="(mt, index) in metadataList" :key="index" class="row align-center justify-between">
+        <div class="flex lg8 md8 sm8 xs8">
+            <va-input v-model="mt.key" label="Attribute name" class="mt-3" :error="isDuplicateAttribute(mt.key)"
+                :error-messages="[`Attribute name '${mt.key}' is already present`]" />
+            <va-input v-model="mt.value" label="Attribute value" class="mt-3" type="textarea" />
         </div>
-        <va-divider>Extra Attributes</va-divider>
-        <div v-for="(mt, index) in metadataList" :key="index" class="row align-center justify-between">
-            <div class="flex lg8 md8 sm8 xs8">
-                <va-input v-model="mt.key" label="attribute name" class="mt-3"
-                    :error="metadataList.filter((m) => m.key === mt.key).length > 1"
-                    :error-messages="[`Attribute name ${mt.key} is already present`]" />
-                <va-input v-model="mt.value" label="attribute value" class="mt-3" type="textarea" />
-            </div>
-            <div class="flex">
-                <va-button icon="delete" color="danger" @click="metadataList.splice(index, 1)">
-                    Delete Attribute
-                </va-button>
-            </div>
+        <div class="flex">
+            <va-button icon="delete" color="danger" @click="removeAttribute(index)">
+                Delete Attribute
+            </va-button>
         </div>
-        <va-button class="mt-3" icon="add" @click="metadataList.push({ key: '', value: '' })">Add new
-            attribute</va-button>
-        <va-card-actions align="between">
-            <va-button type="reset" color="danger" @click="resetForm">Reset</va-button>
-            <va-button type="submit">Submit</va-button>
-        </va-card-actions>
-    </va-form>
+    </div>
+
+    <!-- Add New Attribute Button -->
+    <va-button class="mt-3" icon="add" @click="addNewAttribute">Add new attribute</va-button>
+
+    <!-- Form Actions -->
+    <va-card-actions align="between">
+        <va-button color="danger" @click="resetForm">Reset</va-button>
+        <va-button @click="handleSubmit">Submit</va-button>
+    </va-card-actions>
 </template>
+
 <script setup lang="ts">
 import { onMounted, ref, watch } from 'vue'
 import { useToast } from 'vuestic-ui'
@@ -66,25 +71,28 @@ import { useRouter } from 'vue-router'
 
 const { init } = useToast()
 const annotationStore = useAnnotationStore()
-const uploadMode = ref('files')
+const uploadMode = ref<'files' | 'links'>('files')
 const uploadModes = [
     { label: 'Upload files', value: 'files' },
     { label: 'Insert links', value: 'links' },
 ]
-const props = defineProps<{
-    name?: string
-}>()
-
 const router = useRouter()
 const emits = defineEmits(['onLoading'])
 
-watch(() => props.name, (v) => {
+const isLocal = ref(false)
+const metadataList = ref<{ key: string, value: any }[]>([])
+
+const props = defineProps<{ name?: string }>()
+
+watch(() => props.name, async (name) => {
     resetForm()
-    if (props.name) {
+    if (name) {
         uploadMode.value = 'links'
+        await retrieveAnnotation(name)
     }
 })
 
+// Initialize the component when mounted
 onMounted(async () => {
     if (props.name) {
         await retrieveAnnotation(props.name)
@@ -92,88 +100,102 @@ onMounted(async () => {
     }
 })
 
-
-const isLocalAssembly = ref(false)
-
-const metadataList = ref<Record<string, string>[]>([])
-
+// Reset form and metadata list
 function resetForm() {
     annotationStore.resetForm()
     metadataList.value = []
-    isLocalAssembly.value = false
+    isLocal.value = false
 }
 
+// Retrieve annotation data for the form
 async function retrieveAnnotation(name: string) {
-
     try {
         const { data } = await AnnotationService.getAnnotation(name)
-        isLocalAssembly.value = Boolean(data.external)
-        Object.keys(data)
-            .filter((k: string) => Object.keys(annotationStore.annotationForm).includes(k))
-            .forEach((k) => {
-                annotationStore.annotationForm[k] = data[k]
-            })
-        //parse metadata
-        const parsedMetadata = Object.keys(data.metadata).map((k) => {
-            return {
-                key: k,
-                value: data[k],
+        isLocal.value = Boolean(data.external)
+
+        Object.entries(data).forEach(([key, value]) => {
+            if (key in annotationStore.annotationForm) {
+                annotationStore.annotationForm[key] = value
             }
         })
-        if (parsedMetadata.length) {
-            metadataList.value.push(...parsedMetadata)
-        }
+
+        // Parse metadata
+        metadataList.value = Object.entries(data.metadata || {}).map(([key, value]) => ({ key, value }))
     } catch {
-        init({ message: "Something happened, unable to retrieve annotation", color: 'danger' })
+        init({ message: "Unable to retrieve annotation data.", color: 'danger' })
     }
 }
+
+// Handle form submission
 async function handleSubmit() {
     if (!annotationStore.annotationForm.assembly_accession) {
-        init({ message: "Select an assembly", color: 'danger' })
+        init({ message: "Please select an assembly.", color: 'danger' })
         return
     }
-    //parse form data
+
     const requestData = parseRequestData()
+
     try {
         emits('onLoading', true)
-        const { data } = props.name ? await AuthService.updateAnnotation(props.name, requestData) : await AuthService.createAnnotation(requestData)
-        init({ message: data  + ' saved!', color: 'success' })
-        router.push({name:'cms-assemblies'})
+        const { data } = props.name
+            ? await AuthService.updateAnnotation(props.name, requestData)
+            : await AuthService.createAnnotation(requestData)
+
+        init({ message: `${data} saved successfully!`, color: 'success' })
+        router.push({ name: 'cms-assemblies' })
     } catch (error) {
-        const axiosError = error as AxiosError
-        if (axiosError.response && axiosError.response.data) {
-            init({ message: axiosError.response.data as string, color: 'danger' })
-        } else {
-            init({ message: "Something happened", color: 'danger' })
-        }
+        handleError(error)
     } finally {
         emits('onLoading', false)
     }
 }
-function isValid(value: any) {
-    if (value === undefined || value === null || (typeof value === 'string' && value.trim() === '')) {
-        // Value is considered empty, continue checking the rest of the object
-        return false
-    }
-    // If a non-empty primitive value is found, return false
-    return true;
-
-}
 
+// Parse form data to be sent
 function parseRequestData() {
-    const metadata = Object.fromEntries(metadataList.value.filter((m) => m.key && m.value)
-        .map(m => [m.key, m.value]))
+    const metadata = Object.fromEntries(
+        metadataList.value.filter(m => m.key && m.value).map(m => [m.key, m.value])
+    )
+
     const request = new FormData()
+
     for (const [key, value] of Object.entries(annotationStore.annotationForm)) {
         if (value) {
-            request.append(key, value);
-        }
-        for (const [k, v] of Object.entries(metadata)) {
-            const keyName = `metadata.${k}`
-            request.append(keyName, v)
+            request.append(key, value)
         }
     }
+
+    Object.entries(metadata).forEach(([key, value]) => {
+        request.append(`metadata.${key}`, value)
+    })
+
     return request
 }
 
+// Error handling for Axios responses
+function handleError(error: unknown) {
+    const axiosError = error as AxiosError
+    const errorMessage = axiosError.response?.data as string || "Something went wrong."
+    init({ message: errorMessage, color: 'danger' })
+}
+
+// Add a new attribute
+function addNewAttribute() {
+    metadataList.value.push({ key: '', value: '' })
+}
+
+// Remove an attribute
+function removeAttribute(index: number) {
+    metadataList.value.splice(index, 1)
+}
+
+// Check if an attribute name is duplicate
+function isDuplicateAttribute(key: string): boolean {
+    return metadataList.value.filter(m => m.key === key).length > 1
+}
+
+// Validate input disabling logic
+function isInputDisabled(value: any) {
+    return !!value
+}
+
 </script>
\ No newline at end of file
diff --git a/server/parsers/chromosome.py b/server/parsers/chromosome.py
index 3c1d0c12..51d4ce1b 100644
--- a/server/parsers/chromosome.py
+++ b/server/parsers/chromosome.py
@@ -1,7 +1,6 @@
 from db.models import Chromosome
 
 def parse_chromosomes_from_ncbi_datasets(sequences):
-    ##filter out scaffolds
     chromosomes_to_save=[]
     for sequence in sequences:
         if sequence.get('role') == 'assembled-molecule':
diff --git a/server/rest/assembly/assemblies_service.py b/server/rest/assembly/assemblies_service.py
index c800f876..050f0f34 100644
--- a/server/rest/assembly/assemblies_service.py
+++ b/server/rest/assembly/assemblies_service.py
@@ -99,9 +99,12 @@ def get_chr_aliases_file(accession):
     
     # Assuming chromosomes is a list of dictionaries with fields 'name' and 'accession_version'
     for chromosome in chromosomes:
-        chr_name = chromosome.get('metadata', {}).get('name')
+        print(chromosome)
+        name = chromosome.get('metadata', {}).get('chr_name')
+        if not name:
+            name = chromosome.get('metadata', {}).get('name')
         accession_version = chromosome.get('accession_version')
-        tsv_data.write(f"{chr_name}\t{accession_version}\n")
+        tsv_data.write(f"{name}\t{accession_version}\n")
     
     tsv_data.seek(0)  # Go back to the start of the StringIO object