diff --git a/backend/analysis/api.py b/backend/analysis/api.py
index 0b5ad353c8ee2a5e1517008b70c343c33e72059a..2bbe6634f5a508b9958262d3376ef448138085da 100644
--- a/backend/analysis/api.py
+++ b/backend/analysis/api.py
@@ -2,7 +2,7 @@ import os
from tempfile import mkstemp
from django.conf import settings
-from ninja import Router, File
+from ninja import Router, File, Form
from ninja.files import UploadedFile
from django_to_galaxy.models import GalaxyInstance
@@ -23,6 +23,7 @@ from django.http import JsonResponse, FileResponse
from analysis.model_schemas import (
AnalysisOutSchema,
AnalysisInSchema,
+ AnalysisPayload,
Error,
GeneOutSchema,
HmmerOutSchema,
@@ -63,11 +64,13 @@ def login(request):
@router.post("add", response={200: AnalysisOutSchema, 503: Error})
def add(
request,
+ payload: AnalysisPayload = Form(...),
genomefile: UploadedFile = File(...),
):
fd, genome_path = mkstemp(
prefix="defense-finder-", suffix="-sequences-input.fasta", dir="/uploaded-files"
)
+
with open(genome_path, "wb+") as f:
for chunk in genomefile.chunks():
f.write(chunk)
@@ -91,7 +94,8 @@ def add(
input_files = [
genome_path,
]
- params = {}
+
+ params = {"1": payload.dict()}
analysis = aw.invoke(session, input_files, params, f"{genomefile.name}")
return analysis
@@ -100,6 +104,7 @@ def add(
@router.post("add-example", response={200: AnalysisOutSchema, 503: Error})
def add_example(
request,
+ payload: AnalysisPayload,
):
request.session.set_expiry(session_expiry)
if request.session.session_key:
@@ -117,12 +122,12 @@ def add_example(
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 = {}
+ params = {"1": payload.dict()}
+
analysis = aw.invoke(session, input_files, params, "GCF_000005845.faa")
return analysis
diff --git a/backend/analysis/model_schemas.py b/backend/analysis/model_schemas.py
index 7df65d0ca7459690aacffb89c290dca4c2b22083..ecfe7c1dd56e6f9e7ae1de3eb594b74ed6b523f3 100644
--- a/backend/analysis/model_schemas.py
+++ b/backend/analysis/model_schemas.py
@@ -62,6 +62,10 @@ class Error(Schema):
message: str
+class AnalysisPayload(Schema):
+ antidefensefinder: bool
+
+
class GeneOutSchema(ModelSchema):
genes: List[GeneEntry]
diff --git a/backend/analysis/models.py b/backend/analysis/models.py
index a3c831b6a38b304c271aa0b13d56fccbdca04692..6c0ed6c29f5948f654d1458c359bab341d73960b 100644
--- a/backend/analysis/models.py
+++ b/backend/analysis/models.py
@@ -75,6 +75,7 @@ class AnalysisWorkflow(Workflow):
history, datamap, params = self.prepare_invocation(
session, input_files, params, history_name
)
+ print(params)
galaxy_inv = self.galaxy_workflow.invoke(
datamap, history=history.galaxy_history, params=params
)
diff --git a/backend/analysis/schemas.py b/backend/analysis/schemas.py
index db4ce9d154ca611f9164b28810a6b0c32f60ab01..85c1b9fe67804a236051bbb1cf7192c4ec94ca65 100644
--- a/backend/analysis/schemas.py
+++ b/backend/analysis/schemas.py
@@ -4,6 +4,7 @@ from ninja import Schema
class GeneEntry(Schema):
replicon: str
+ activity: Optional[str]
hit_id: str
gene_name: str
hit_pos: int
@@ -30,6 +31,7 @@ class GeneEntry(Schema):
class SystemEntry(Schema):
sys_id: str
type: str
+ activity: Optional[str]
subtype: str
sys_beg: str
sys_end: str
diff --git a/backend/poetry.lock b/backend/poetry.lock
index cadcff4180946868fdc6f8cbb36ec8361a40db33..5f8d3b9d632558d6bdd1a23a4d2ff2837cef3b0e 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
[[package]]
name = "appdirs"
@@ -359,13 +359,13 @@ test = ["black", "django-stubs", "flake8", "isort", "mypy (==0.931)", "psycopg2-
[[package]]
name = "django-to-galaxy"
-version = "0.6.4"
+version = "0.6.9"
description = "Django extension that eases communication with Galaxy instance to execute workflows."
optional = false
-python-versions = ">=3.9,<4.0"
+python-versions = "<4.0,>=3.9"
files = [
- {file = "django_to_galaxy-0.6.4-py3-none-any.whl", hash = "sha256:5e813d45eba6cbb5dab4737c2d5b464f46f33119e2828148860b842a4a272ef8"},
- {file = "django_to_galaxy-0.6.4.tar.gz", hash = "sha256:27e7026b276c8b18fb84715b3a8a6b6f06d63d9994b6d00bc118ca7d53127722"},
+ {file = "django_to_galaxy-0.6.9-py3-none-any.whl", hash = "sha256:12fde5b9067ae967bbdf412f177f5e67e6b25a1f995639b3ed31170f77282826"},
+ {file = "django_to_galaxy-0.6.9.tar.gz", hash = "sha256:2f9506905069a093fb76adea8b5de57bc64a12f438dbce88179918997e0f7f0e"},
]
[package.dependencies]
@@ -979,4 +979,4 @@ zstd = ["zstandard (>=0.18.0)"]
[metadata]
lock-version = "2.0"
python-versions = "^3.10"
-content-hash = "0178257066e14753b45a43635af1b8fb9ab5f4773148e50f2ae63573f08e98b7"
+content-hash = "096a9a4ca3a3446ca43aa8ac13a60c8f9856b9395e379397167f50e66d7c6587"
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index 684756c6a271798c4c052f1fac5f97f9a05bf089..5ade0929ad784a8886f5e6da09bcaef8769e32af 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -9,7 +9,7 @@ readme = "README.md"
python = "^3.10"
django-ninja = "^0.22.2"
psycopg = {extras = ["binary"], version = "^3.1.9"}
-django-to-galaxy = "^0.6.4"
+django-to-galaxy = "^0.6.9"
django-environ = "^0.10.0"
gunicorn = "^21.2.0"
biopython = "^1.83"
diff --git a/frontend/components/AnalysisResultDataTable.vue b/frontend/components/AnalysisResultDataTable.vue
index 423921ae0602bd1dd304fd077ffec303b3277dc2..4a1f5f8163b012db6bd4f94e2d99c9a5eaab7112 100644
--- a/frontend/components/AnalysisResultDataTable.vue
+++ b/frontend/components/AnalysisResultDataTable.vue
@@ -64,7 +64,11 @@ const dataTableProps = computed(() => {
<v-card-text>
<v-data-table v-model:items-per-page="itemsPerPage" v-bind="dataTableProps">
<template #[`item.type`]="{ item }">
- <v-chip :href="item?.href ? item.href : undefined" target="_blank">
+ <v-chip v-if="item.activity === 'Defense'" :href="item?.href ? item.href : undefined"
+ target="_blank">
+ {{ item.type }}
+ </v-chip>
+ <v-chip v-else>
{{ item.type }}
</v-chip>
</template>
diff --git a/frontend/components/SubmitAnalysis.vue b/frontend/components/SubmitAnalysis.vue
index b284b9490a58e590fa634aed01abc8338beb7c80..6df871ca152cfb98d73b650a315070aefdadc63a 100644
--- a/frontend/components/SubmitAnalysis.vue
+++ b/frontend/components/SubmitAnalysis.vue
@@ -6,6 +6,7 @@ const uppyComponentRef = ref(null)
const tab = ref<"local" | "paste">("null")
const maxSequenceLength = ref(10000)
const { csrfToken } = await useCsrfToken()
+const antiDefenseSystem = ref(false)
const { handleSubmit } = useForm({
validationSchema: {
// files(value) {
@@ -32,6 +33,9 @@ async function addExample() {
try {
await $fetch('/dfapi/analysis/add-example', {
method: 'POST',
+ body: {
+ antidefensefinder: toValue(antiDefenseSystem)
+ },
headers: { "X-CSRFToken": csrfToken.value }
})
await navigateTo("/analyses/")
@@ -44,10 +48,12 @@ async function addExample() {
}
const submit = handleSubmit(async (values) => {
+ console.log("dans le submit")
loading.value = true
const formData = new FormData();
const blob = new Blob([toValue(sequence)], { type: 'text/plain' })
formData.append('genomefile', blob, 'pasted-sequence.fasta')
+ formData.append('antidefensefinder', toValue(antiDefenseSystem).toString())
try {
await $fetch('/dfapi/analysis/add', {
method: 'POST',
@@ -80,18 +86,27 @@ const submit = handleSubmit(async (values) => {
<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-card flat>
+ <v-card-text>
+ <v-form @submit.prevent="submit">
+ <v-switch v-model="antiDefenseSystem" color="primary" label="anti defense system"
+ hide-details="auto" class="mx-0"></v-switch>
+ <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-card-text>
+ </v-card>
</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-text>
+ <v-switch v-model="antiDefenseSystem" color="primary" label="anti defense system"
+ hide-details="auto"></v-switch>
</v-card-text>
<v-card-actions>
<v-btn variant="elevated" density="default" size="default" :slim="false" rounded="xl"
diff --git a/frontend/components/UppyGenomeUpload.vue b/frontend/components/UppyGenomeUpload.vue
index 848b5b9176efb069be658d09a96e4d62fe86c999..70138677663673d41152dfca4a9afce3870e0eb2 100644
--- a/frontend/components/UppyGenomeUpload.vue
+++ b/frontend/components/UppyGenomeUpload.vue
@@ -28,11 +28,13 @@ const router = useRouter();
const { width } = useDisplay();
const emit = defineEmits(['update:modelValue'])
const { csrfToken } = await useCsrfToken()
-
+const antiDefenseSystem = ref(false)
+const hasAddFiles = ref(false)
+const uploading = ref(false)
const uppyCovar = new Uppy({
- autoProceed: true,
+ autoProceed: false,
restrictions: { maxFileSize: 10000000 },
- // meta: { name: props.analysisName }
+ meta: { antidefensefinder: toValue(antiDefenseSystem) }
})
// .use(DragDrop, { target: '#drag-drop' })
.use(XHR, {
@@ -48,21 +50,43 @@ const uppyCovar = new Uppy({
// router.push()
}
})
+ .on('file-added', (file) => {
+ const files = uppyCovar.getFiles()
+ if (files.length > 0) hasAddFiles.value = true
+ if (files.length === 0) hasAddFiles.value = false
+ })
+ .on("upload", () => {
+ uploading.value = true
+ })
+ // complete
+ .on("complete", () => {
+ uploading.value = false
+ })
+ .on('error', (error) => {
+ uploading.value = false
+ })
.on("file-removed", (file, reason) => {
const files = uppyCovar.getFiles()
const emitObject = (files.length === 0) ? undefined : files
+ if (emitObject === undefined) hasAddFiles.value = false
emit('update:modelValue', emitObject)
})
- // .on("error", (error) => {
- // console.log(error)
- // throw createError("uppy error")
- // });
+
const themeUppy = computed(() => {
return theme.global.current.value.dark ? 'dark' : "light"
})
+watch(antiDefenseSystem, () => {
+ uppyCovar.setMeta({ antidefensefinder: toValue(antiDefenseSystem) })
+})
+
+async function runAnalysis() {
+ console.log('run analsysis')
+ await uppyCovar.upload()
+
+}
defineExpose({
uppyCovar,
@@ -71,17 +95,27 @@ defineExpose({
</script>
<template>
<v-card flat>
- <Dashboard :uppy="uppyCovar" :props="{
- inline: true,
- hideUploadButton: false,
- theme: themeUppy,
- width,
- height: 300,
- metaFields: [{
- id: 'uppy-genome-upload',
- name: 'genome',
- placeholder: 'Genomes'
- }],
- }" />
+ <v-card-text>
+ <v-form @submit.prevent="runAnalysis">
+
+ <v-switch v-model="antiDefenseSystem" color="primary" label="anti defense system"
+ hide-details="auto" class="ml-1"></v-switch>
+
+ <Dashboard :uppy="uppyCovar" :props="{
+ inline: true,
+ hideUploadButton: true,
+ theme: themeUppy,
+ width,
+ height: 300,
+ metaFields: [{
+ id: 'uppy-genome-upload',
+ name: 'genome',
+ placeholder: 'Genomes'
+ }],
+ }" />
+
+ <v-btn type="submit" :disabled="!hasAddFiles" :loading="uploading">Submit</v-btn>
+ </v-form>
+ </v-card-text>
</v-card>
</template>
\ No newline at end of file
diff --git a/frontend/components/tableResults/GenesTable.vue b/frontend/components/tableResults/GenesTable.vue
index 4c3ea83a5522bbc1b24e4f8069e5b83308876d01..4ac05986955c3a7a303126ad5f708459107ca801 100644
--- a/frontend/components/tableResults/GenesTable.vue
+++ b/frontend/components/tableResults/GenesTable.vue
@@ -28,6 +28,7 @@ const headers = ref([
{ title: "Replicon", align: "end", key: "replicon" },
{ title: "Position", align: "end", key: "hit_pos" },
{ title: "Model fqn", align: "end", key: "model_fqn" },
+ { title: "Activity", align: "end", key: "activity"},
{ title: "System id", align: "end", key: "sys_id" },
{ title: "System loci", align: "end", key: "sys_loci" },
{ title: "locus_num", align: "end", key: "locus_num" },
diff --git a/frontend/components/tableResults/SystemsTable.vue b/frontend/components/tableResults/SystemsTable.vue
index 1a8ed3dfe7bd63dfd7bb32d731011496c44d6e56..621a40418691be29cf432d6f87af28d080151af1 100644
--- a/frontend/components/tableResults/SystemsTable.vue
+++ b/frontend/components/tableResults/SystemsTable.vue
@@ -31,6 +31,7 @@ const groupBy = ref([
])
const headers = ref([
{ title: "System id", align: "end", key: "sys_id", fixed: true, },
+ { title: "Activity", align: "end", key: "activity"},
{ title: "type", align: "end", key: "type", },
{ title: "subtype", align: "end", key: "subtype" },
{ title: "sys_beg", align: "end", key: "sys_beg" },