Copy paste sequence

backend/analysis/api.py

@@ -97,6 +97,37 @@ def add(
     return analysis
 
 
+@router.post("add-example", response={200: AnalysisOutSchema, 503: Error})
+def add_example(
+    request,
+):
+    request.session.set_expiry(session_expiry)
+    if request.session.session_key:
+        session_key = request.session.session_key
+    else:
+        request.session.create()
+        request.session.set_expiry(session_expiry)
+        session_key = request.session.session_key
+    session = Session.objects.get(session_key=session_key)
+
+    aw = AnalysisWorkflow.objects.get(galaxy_id=settings.GALAXY_WORKFLOW_ID)
+
+    # check if Galaxy online
+
+    is_galaxy_online = aw.analysis_owner.galaxy_instance.is_online()
+    if not is_galaxy_online:
+        return 503, {"message": "The Galaxy instance is offline"}
+    print(settings.BASE_DIR)
+
+    input_files = [
+        f"{settings.BASE_DIR}/analysis/data/GCF_000005845.faa",
+    ]
+    params = {}
+    analysis = aw.invoke(session, input_files, params, "GCF_000005845.faa")
+
+    return analysis
+
+
 @router.get("/", response={200: list[AnalysisOutSchema], 503: Error})
 def list(request):
     session_key = request.session.session_key

frontend/components/SubmitAnalysis.vue

 <script setup lang="ts">
-import { ref } from "vue";
-import { useField, useForm } from "vee-validate";
-const router = useRouter();
-const uppyComponentRef = ref(null)
+import { useField, useForm } from 'vee-validate'
+import { useCsrfToken } from "@/composables/useCsrfToken"
 
-const { meta, handleSubmit } = useForm({
+const uppyComponentRef = ref(null)
+const tab = ref<"local" | "paste">("null")
+const maxSequenceLength = ref(10000)
+const { csrfToken } = await useCsrfToken()
+const { handleSubmit } = useForm({
   validationSchema: {
-    files(value) {
-      if (value?.length > 0) return true
+    // files(value) {
+    //   if (value?.length > 0) return true
+    //   return "You need to pass at least one file"
+    // },
+    sequence(value: string) {
+      const seqLength = value?.length
+      if (seqLength <= maxSequenceLength.value) return true
+      return `Sequences needs to be less than ${maxSequenceLength.value} characters.`
     }
   }
 });
-const files = useField("files");
+const files = useField("files")
+const { value: sequence, errorMessage: sequenceErrorMessage } = useField("sequence");
+const { data } = await useAPI<{ is_online: boolean }>("/analysis/is-galaxy-online")
 
+if (data.value !== null && !data.value.is_online) {
+  throw createError("The galaxy instance is offline")
+}
+const loading = ref(false)
+async function addExample() {
+  loading.value = true
+  try {
+    await $fetch('/dfapi/analysis/add-example', {
+      method: 'POST',
+      headers: { "X-CSRFToken": csrfToken.value }
+    })
+    await navigateTo("/analyses/")
+  } catch (error) {
+    throw createError("Cannot upload the pasted sequence")
+  } finally {
+    loading.value = false
 
-const { data, error } = await useAPI<{ is_online: boolean }>("/analysis/is-galaxy-online", {
-  onRequest({ request }) {
   }
-})
 
-if (data.value !== null && !data.value.is_online) {
-  throw createError("The galaxy instance is offline")
 }
+const submit = handleSubmit(async (values) => {
+  loading.value = true
+  const formData = new FormData();
+  const blob = new Blob([toValue(sequence)], { type: 'text/plain' })
+  formData.append('genomefile', blob, 'pasted-sequence.fasta')
+  try {
+    await $fetch('/dfapi/analysis/add', {
+      method: 'POST',
+      body: formData,
+      headers: { "X-CSRFToken": csrfToken.value }
+    })
+    await navigateTo("/analyses/")
+  } catch (error) {
+    throw createError("Cannot upload the pasted sequence")
+  } finally {
+    loading.value = false
+
+  }
 
+})
 </script>
 <template>
   <v-card flat color="transparent">
     <v-form id="form-upload-genome">
       <v-card-text>
-        <UppyGenomeUpload v-model="files.value.value" ref="uppyComponentRef" class="mb-2" />
+        <v-card>
+          <v-tabs v-model="tab" align-tabs="start">
+            <v-tab value="local" :rounded="false">Local fasta files</v-tab>
+            <v-tab value="paste" :rounded="false">Paste fasta sequences</v-tab>
+            <v-tab value="example" :rounded="false">Example</v-tab>
+          </v-tabs>
+          <v-card-text>
+            <v-window v-model="tab">
+              <v-window-item value="local">
+                <UppyGenomeUpload v-model="files.value.value" ref="uppyComponentRef" class="mb-2" />
+              </v-window-item>
+              <v-window-item value="paste">
+                <v-form @submit.prevent="submit">
+                  <v-textarea v-model="sequence" :error-messages="sequenceErrorMessage" :count="maxSequenceLength"
+                    label="Fasta sequences" variant="filled" auto-grow></v-textarea>
+                  <v-btn type="submit" :loading="loading">Submit</v-btn>
+                </v-form>
+              </v-window-item>
+              <v-window-item value="example">
+                <v-card flat color="transparent">
+                  <v-card-text>
+                    You can try an example with Escherichia coli str. K-12 substr. MG1655 proteins (<a target="_blank"
+                      href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2">GCF_000005845.2</a>)
+
+                  </v-card-text>
+                  <v-card-actions>
+                    <v-btn variant="elevated" density="default" size="default" :slim="false" rounded="xl"
+                      :loading="loading" @click="addExample()">Run
+                      analysis for GCF_000005845.2</v-btn>
+                  </v-card-actions>
+                </v-card>
+              </v-window-item>
+            </v-window>
+          </v-card-text>
+        </v-card>
       </v-card-text>
     </v-form>
   </v-card>

frontend/package.json

@@ -37,6 +37,6 @@
     "@vue-flow/minimap": "^1.1.1",
     "@vueuse/core": "^10.7.2",
     "d3": "^7.8.5",
-    "vee-validate": "^4.12.4"
+    "vee-validate": "^4.12.6"
   }
 }

frontend/pages/index.vue

@@ -78,6 +78,12 @@ function resetError(error) {
                       title="MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes"
                       subtitle="Néron, B; Denise, R; Coluzzi, C; Touchon, M; Rocha, E.P.C.; Abby, S.S., Peer Community Journal, 2023">
                     </v-list-item>
+                    <v-list-item href="https://doi.org/10.1101/2024.01.25.577194" target="_blank"
+                      title="A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases"
+                      subtitle="Tesson, F., Planel, R., Egorov, A., Georjon, H., Vaysset, H., Brancotte, B., Néron, B., Mordret, E., Bernheim, A., Atkinson, G., & Cury, J., Preprint, 2024
+
+">
+                    </v-list-item>
                   </v-list>
                 </v-card>
               </v-col></v-row>