diff --git a/backend/analysis/api.py b/backend/analysis/api.py
index 76a9f7047b2062c4105bac9c1c9bcb0cccb63f39..73d559bb9d68cfc542e9406f19300a562e842b74 100644
--- a/backend/analysis/api.py
+++ b/backend/analysis/api.py
@@ -3,7 +3,7 @@ from tempfile import mkstemp
from ninja import Router, File, Form
from ninja.files import UploadedFile
-from analysis.models import Analysis, AnalysisHistory, AnalysisWorkflow, Gene, Hmmer, System
+from analysis.models import Analysis, AnalysisHistory, AnalysisWorkflow, Gene, Hmmer, Protein, System
from django.contrib.sessions.models import Session
from django.middleware.csrf import get_token
from django.views.decorators.csrf import ensure_csrf_cookie
@@ -14,6 +14,7 @@ from analysis.model_schemas import (
Error,
GeneOutSchema,
HmmerOutSchema,
+ ProteinOutSchema,
SystemOutSchema,
)
@@ -42,7 +43,7 @@ def add(
request,
genomefile: UploadedFile = File(...),
):
- fd, genome_path = mkstemp(prefix="defense-finder-genome")
+ fd, genome_path = mkstemp(prefix="defense-finder-", suffix="-sequences-input.fasta")
with open(genome_path, "wb+") as f:
for chunk in genomefile.chunks():
f.write(chunk)
@@ -91,6 +92,7 @@ def get_analysis(request, analysis_id: int):
analysis.load_genes()
analysis.load_systems()
analysis.load_hmmers()
+ analysis.load_proteins()
except Analysis.DoesNotExist:
return 404, {
"message": f"No analysis {analysis_id} found in current session"
@@ -168,6 +170,8 @@ def genes(request, analysis_id: int):
return 404, {"message": "No session"}
+
+
@router.get("/{analysis_id}/systems", response={200: SystemOutSchema, 404: Error})
def systems(request, analysis_id: int):
session_key = request.session.session_key
@@ -220,3 +224,30 @@ def hmmers(request, analysis_id: int):
else:
return 404, {"message": "No session"}
+
+
+@router.get("/{analysis_id}/proteins", response={200: ProteinOutSchema, 404: Error})
+def proteins(request, analysis_id: int):
+ session_key = request.session.session_key
+ if session_key:
+ session = Session.objects.get(session_key=session_key)
+ try:
+ analysis = Analysis.objects.get(
+ pk=analysis_id, analysis_history__session=session
+ )
+ analysis.load_proteins()
+ try:
+ gene_list = Protein.objects.get(analysis=analysis)
+ except Protein.DoesNotExist:
+ return 404, {
+ "message": f"No proteins for analysis {analysis.name} found in current session"
+ }
+ else:
+ return gene_list
+ except Analysis.DoesNotExist:
+ return 404, {
+ "message": f"No analysis '{analysis.name}' found in current session"
+ }
+
+ else:
+ return 404, {"message": "No session"}
diff --git a/backend/analysis/migrations/0007_protein.py b/backend/analysis/migrations/0007_protein.py
new file mode 100644
index 0000000000000000000000000000000000000000..11cdae1870fde2724eff798a3954b0564d6a1234
--- /dev/null
+++ b/backend/analysis/migrations/0007_protein.py
@@ -0,0 +1,22 @@
+# Generated by Django 4.2.3 on 2024-01-18 15:26
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('analysis', '0006_alter_analysis_options'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Protein',
+ fields=[
+ ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('proteins', models.JSONField()),
+ ('analysis', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, to='analysis.analysis')),
+ ],
+ ),
+ ]
diff --git a/backend/analysis/model_schemas.py b/backend/analysis/model_schemas.py
index 6b92f06d31fd94c10e71289f9c4812638e418479..1b63c716a4145fbf480537cf20e1f9eb8f140ede 100644
--- a/backend/analysis/model_schemas.py
+++ b/backend/analysis/model_schemas.py
@@ -7,9 +7,10 @@ from analysis.models import (
AnalysisHistory,
Gene,
Hmmer,
+ Protein,
System,
)
-from analysis.schemas import GeneEntry, HmmerEntry, SystemEntry
+from analysis.schemas import GeneEntry, HmmerEntry, ProteinEntry, SystemEntry
class AnalysisHistorySchema(ModelSchema):
@@ -82,3 +83,11 @@ class HmmerOutSchema(ModelSchema):
class Config:
model = Hmmer
model_fields = ["analysis", "hmmers"]
+
+
+class ProteinOutSchema(ModelSchema):
+ proteins: List[ProteinEntry]
+
+ class Config:
+ model = Protein
+ model_fields = ["analysis", "proteins"]
\ No newline at end of file
diff --git a/backend/analysis/models.py b/backend/analysis/models.py
index de2a887355ced8de992ce4f9678b3b3bb8d9e3e6..40fb607002dbb7ebb7f80ea24967c77477e448e5 100644
--- a/backend/analysis/models.py
+++ b/backend/analysis/models.py
@@ -4,7 +4,7 @@ from django.db import models
from django.contrib.sessions.models import Session
from tempfile import mkstemp
from django.conf import settings
-
+from Bio import SeqIO
# from galaxy.models import WorkflowInvocation
@@ -20,7 +20,7 @@ from django_to_galaxy.utils import (
load_galaxy_history_time_to_datetime,
)
-from .schemas import GeneEntry, HmmerEntry, SystemEntry
+from .schemas import GeneEntry, HmmerEntry, ProteinEntry, SystemEntry
# Create your models here.
@@ -102,11 +102,14 @@ class AnalysisWorkflow(Workflow):
history = self.analysis_owner.create_history(session, history_name)
# upload files
+
datamap = dict()
for i, file_path in enumerate(input_files):
upload_response = history.upload_file(file_path)
datamap[i] = {"id": upload_response.id, "src": "hda"}
-
+ print(history.id)
+ print(upload_response.id)
+ self.analysis_owner.obj_gi.gi.histories.update_dataset(history.galaxy_id, upload_response.id, tags=["sequences"])
return history, datamap, params
@@ -128,9 +131,9 @@ class Analysis(Invocation):
galaxy_id
).content_infos
)
-
+ # print(galaxy_history_datasets)
for dataset in galaxy_history_datasets:
- if dataset.name.endswith(pattern):
+ if pattern in dataset.wrapped["tags"]:
dataset_id = dataset.id
fd, file_path = mkstemp(prefix=f"defense-finder-{type}-{dataset_id}-")
self.analysis_history.galaxy_owner.obj_gi.gi.datasets.download_dataset(
@@ -138,6 +141,9 @@ class Analysis(Invocation):
)
return file_path
return None
+
+
+
def load_genes(self):
queryset = Gene.objects.filter(analysis=self)
@@ -178,7 +184,7 @@ class Analysis(Invocation):
def load_hmmers(self):
queryset = Hmmer.objects.filter(analysis=self)
if self.status == DONE and queryset.count() == 0:
- hmmers_path = self.load_dataset("hmmer", "hmmers")
+ hmmers_path = self.load_dataset("hmmers", "hmmers")
if hmmers_path is not None:
with open(hmmers_path, newline="") as csvfile:
reader = csv.reader(csvfile, delimiter="\t")
@@ -192,6 +198,52 @@ class Analysis(Invocation):
instance = Hmmer(analysis=self, hmmers=entries)
instance.save()
+ def load_proteins(self):
+ queryset = Protein.objects.filter(analysis=self)
+ if self.status == DONE and queryset.count() == 0:
+ file_path = self.load_dataset("proteins", "proteins")
+ proteins = self.read_fasta_file(file_path)
+ if len(proteins) <= 1:
+ file_path = self.load_dataset("sequences", "proteins")
+ proteins = self.read_fasta_file(file_path)
+ # print(proteins)
+ json_prots = [
+ ProteinEntry(**prot).dict()
+ for prot in proteins
+ ]
+
+ prots = Protein(analysis=self, proteins=json_prots)
+ prots.save()
+
+
+ def read_fasta_file(self, file_path):
+ sequences = []
+ if file_path is not None:
+ with open(file_path) as handle:
+
+
+ for record in SeqIO.parse(handle, "fasta"):
+ prot = {"id": record.id, "length": len(record), "strand": None}
+ description_list = record.description.split(' # ')
+ print(description_list)
+ if len(description_list) == 5:
+ start = description_list[1]
+ end = description_list[2]
+ strand = description_list[3]
+ print(strand)
+ if strand == "1" or strand == "-1":
+ prot["strand"] = int(strand)
+ prot["start"] = int(start)
+ prot["end"] = int(end)
+ else:
+ strand = None
+ print(prot)
+ sequences.append(prot)
+ return sequences
+class Protein(models.Model):
+ analysis = models.OneToOneField(Analysis, on_delete=models.CASCADE)
+ proteins = models.JSONField()
+
class Gene(models.Model):
analysis = models.OneToOneField(Analysis, on_delete=models.CASCADE)
@@ -206,3 +258,5 @@ class System(models.Model):
class Hmmer(models.Model):
analysis = models.OneToOneField(Analysis, on_delete=models.CASCADE)
hmmers = models.JSONField()
+
+
diff --git a/backend/analysis/schemas.py b/backend/analysis/schemas.py
index 4f9960256e858aa1a0648b7af96ddc35e58cb260..db4ce9d154ca611f9164b28810a6b0c32f60ab01 100644
--- a/backend/analysis/schemas.py
+++ b/backend/analysis/schemas.py
@@ -1,3 +1,4 @@
+from typing import Optional
from ninja import Schema
@@ -49,3 +50,11 @@ class HmmerEntry(Schema):
hit_seq_cov: float
hit_begin_match: int
hit_end_match: int
+
+
+class ProteinEntry(Schema):
+ id: str
+ length: int
+ strand: Optional[int]
+ start: Optional[int]
+ end: Optional[int]
\ No newline at end of file
diff --git a/backend/poetry.lock b/backend/poetry.lock
index 460e104599c3b5ef906504d3f5d4468bab3303f1..3b67d8e5d85f1bcc73026b3e0ab183ed7b309a57 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -66,6 +66,40 @@ requests-toolbelt = ">=0.5.1,<0.9.0 || >0.9.0"
[package.extras]
testing = ["pytest"]
+[[package]]
+name = "biopython"
+version = "1.83"
+description = "Freely available tools for computational molecular biology."
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "biopython-1.83-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e2cc737906d8de47eedbc4476f711b960c16a65daa8cdd021875398c81999a09"},
+ {file = "biopython-1.83-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:2df408be9816dd98c28fe181ea93fb6e0d375bf1763ad9ed503ac30bb2df5b1a"},
+ {file = "biopython-1.83-cp310-cp310-win32.whl", hash = "sha256:a0c1c70789c7e2a26563db5ba533fb9fea0cc1f2c7bc7ad240146cb223ba44a3"},
+ {file = "biopython-1.83-cp310-cp310-win_amd64.whl", hash = "sha256:56f03f43c183acb88c082bc31e5f047fcc6d0aceb5270fbd29c31ab769795b86"},
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+ {file = "biopython-1.83-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ec82350c24cdcf34a8d4a5f189d0ff7dc025658098a60e6f0e681d24b6a1414e"},
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+ {file = "biopython-1.83-cp39-cp39-win_amd64.whl", hash = "sha256:aae1b156a76907c2abfe9d141776b0aead65695ea914eaecdf12bd1e8991f869"},
+ {file = "biopython-1.83.tar.gz", hash = "sha256:78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7"},
+]
+
+[package.dependencies]
+numpy = "*"
+
[[package]]
name = "black"
version = "23.7.0"
@@ -427,6 +461,51 @@ files = [
{file = "mypy_extensions-1.0.0.tar.gz", hash = "sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782"},
]
+[[package]]
+name = "numpy"
+version = "1.26.3"
+description = "Fundamental package for array computing in Python"
+optional = false
+python-versions = ">=3.9"
+files = [
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+ {file = "numpy-1.26.3-cp39-cp39-win32.whl", hash = "sha256:9bc6d1a7f8cedd519c4b7b1156d98e051b726bf160715b769106661d567b3f03"},
+ {file = "numpy-1.26.3-cp39-cp39-win_amd64.whl", hash = "sha256:867e3644e208c8922a3be26fc6bbf112a035f50f0a86497f98f228c50c607bb2"},
+ {file = "numpy-1.26.3-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:3c67423b3703f8fbd90f5adaa37f85b5794d3366948efe9a5190a5f3a83fc34e"},
+ {file = "numpy-1.26.3-pp39-pypy39_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:46f47ee566d98849323f01b349d58f2557f02167ee301e5e28809a8c0e27a2d0"},
+ {file = "numpy-1.26.3-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:a8474703bffc65ca15853d5fd4d06b18138ae90c17c8d12169968e998e448bb5"},
+ {file = "numpy-1.26.3.tar.gz", hash = "sha256:697df43e2b6310ecc9d95f05d5ef20eacc09c7c4ecc9da3f235d39e71b7da1e4"},
+]
+
[[package]]
name = "packaging"
version = "23.1"
@@ -832,4 +911,4 @@ zstd = ["zstandard (>=0.18.0)"]
[metadata]
lock-version = "2.0"
python-versions = "^3.10"
-content-hash = "f84a622ad4938155eb1684c17f4c9ec84f5627496462308a30c9f6885dccd012"
+content-hash = "89a87025d377cb3257ccd2e8e2d4eafab8ac82c7714d350dd7d50f09226ca9d8"
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index b8a47a1ddc40f1c81ea7b4c8f94fcf7f1d6c733c..31d51f3ffe5e3365401639a4051a144a0ec7a4b2 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -12,6 +12,7 @@ psycopg = {extras = ["binary"], version = "^3.1.9"}
django-to-galaxy = "^0.6.4"
django-environ = "^0.10.0"
gunicorn = "^21.2.0"
+biopython = "^1.83"
[tool.poetry.group.dev.dependencies]
diff --git a/deploy/templates/ingress.yaml b/deploy/templates/ingress.yaml
index defc9e7ef4157d1089e8d585d2d98106a18ad1e2..379ecb7017c62ce31261b258431c1bc3b6aaa2b9 100644
--- a/deploy/templates/ingress.yaml
+++ b/deploy/templates/ingress.yaml
@@ -60,7 +60,7 @@ spec:
service:
name: {{ .Values.wiki.service.name }}
port:
- number: 8080
+ number: 3000
# - path: /msearch(/|$)(.*)
# pathType: Prefix
# backend:
diff --git a/frontend/components/AnalysisList.vue b/frontend/components/AnalysisList.vue
index d790c221b9998b3a6dd9cb7bb0a01beca192d8b9..4bf8eaf8cd44060a5ddca6de497ea7381f40b453 100644
--- a/frontend/components/AnalysisList.vue
+++ b/frontend/components/AnalysisList.vue
@@ -25,10 +25,9 @@ const sanitizedAnalyses = computed(() => {
async function deleteAnalysis(analysisId: number) {
if (csrfToken.value) {
- await useFetch<null>(`/api/analysis/${analysisId}`,
+ await useAPI<null>(`/api/analysis/${analysisId}`,
{
method: "DELETE",
- headers: [["X-CSRFToken", csrfToken.value]]
}
)
refresh()
@@ -42,10 +41,9 @@ function editionMode(analysisId: number, name: string) {
}
async function editAnalysis(analysisId: number) {
if (csrfToken.value) {
- await useFetch<null>(`/api/analysis/${analysisId}`,
+ await useAPI<null>(`/api/analysis/${analysisId}`,
{
method: "PUT",
- headers: [["X-CSRFToken", csrfToken.value]],
body: {
name: newTitle.value
},
diff --git a/frontend/components/AnalysisResultDataTable.vue b/frontend/components/AnalysisResultDataTable.vue
index 85c45f2c8b20c324e2234f1129e58914eb8ccb19..bfab4fd6a288bb3e2ba033fe5456e9d1c6ceb342 100644
--- a/frontend/components/AnalysisResultDataTable.vue
+++ b/frontend/components/AnalysisResultDataTable.vue
@@ -1,5 +1,7 @@
<script setup lang="ts">
import { useWikiUrl } from '~/composables/useWikiUrl';
+import { useSelectedProtein } from '@/composables/useSelectedProtein'
+import CollapsibleChips from './CollapsibleChips.vue';
interface Props {
items: any[]
headers: Object[]
@@ -8,15 +10,13 @@ interface Props {
const props = defineProps<Props>()
const search = ref('')
const itemsPerPage = ref(25);
-
+const { setSelectedProtein } = useSelectedProtein()
const computedItems = computed(() => {
if (props.items?.length > 0) {
return props.items.map((item) => {
if (item?.type) {
- console.log(item.type)
const { wikiUrl } = useWikiUrl(`/defense-systems/${item.type.toLowerCase()}/`)
- console.log(wikiUrl.value)
return {
...item,
href: wikiUrl.value
@@ -26,12 +26,10 @@ const computedItems = computed(() => {
})
} else { return [] }
})
+function namesToCollapsibleChips(names: string[]) {
+ return names.filter((it) => it !== "").map(it => ({ title: it }))
+}
-// function getModelName(modelFqn: string) {
-// console.log(modelFqn)
-// // console.log(modelFqn.split("/").slice(-1).toLowerCase())
-// return modelFqn.split("/").slice(-1)[0].toLowerCase()
-// }
</script>
<template>
@@ -42,12 +40,21 @@ const computedItems = computed(() => {
<v-card-text>
<v-data-table v-model:items-per-page="itemsPerPage" :headers="headers" :items="computedItems" item-value="name"
:search="search">
-
<template #[`item.type`]="{ item }">
<v-chip :href="item?.href ? item.href : undefined" target="_blank" color="info">
{{ item.type }}
</v-chip>
</template>
+ <template #[`item.hit_id`]="{ item }">
+ <v-chip color="info" @click="setSelectedProtein(item)">
+ {{ item.hit_id }}
+ </v-chip>
+ </template>
+
+ <template #[`item.protein_in_syst`]="{ item }">
+ <CollapsibleChips :items="namesToCollapsibleChips(item.protein_in_syst)">
+ </CollapsibleChips>
+ </template>
</v-data-table>
diff --git a/frontend/components/AnalysisState.vue b/frontend/components/AnalysisState.vue
index a5e53e31bb3f60c7bf01c749ef5a59d42ea1eddf..6523693185c7296742fd252f270d292c65c369ca 100644
--- a/frontend/components/AnalysisState.vue
+++ b/frontend/components/AnalysisState.vue
@@ -1,6 +1,5 @@
<script setup lang="ts">
-import type { AnalysisStatus } from "../composables/useFetchAnalysis"
interface Props {
state: AnalysisStatus
diff --git a/frontend/components/CollapsibleChips.vue b/frontend/components/CollapsibleChips.vue
new file mode 100644
index 0000000000000000000000000000000000000000..2f7a08ea757cc5e74d5f59d1f3f060065fdad0d5
--- /dev/null
+++ b/frontend/components/CollapsibleChips.vue
@@ -0,0 +1,57 @@
+<script setup lang="ts">
+
+
+interface item {
+ title: string;
+ href?: string | undefined
+}
+
+export interface Props {
+ items: item[];
+ itemsToDisplay?: number;
+}
+
+const props = withDefaults(defineProps<Props>(), {
+ items: () => [],
+ itemsToDisplay: 1,
+
+});
+
+
+const show = ref(false);
+
+
+</script>
+<template>
+ <!-- class="d-inline-flex justify-start align-center" -->
+
+ <span v-if="show" class="d-flex flex-wrap align-center justify-start">
+ <template v-if="items.length > itemsToDisplay">
+ <template v-for="item in items" :key="item.title">
+ <v-chip :href="item?.href" :target="item?.href === undefined ? item?.href : '_blank'" color="info"
+ class="mr-1 my-1 align-self-center" size="small">
+ {{ item.title }}
+ </v-chip>
+ </template>
+ </template>
+ <v-btn v-if="itemsToDisplay < items.length" variant="text" :icon="'mdi-chevron-up'" @click="show = !show"></v-btn>
+ </span>
+ <span v-else class="d-flex flex-wrap align-center justify-start">
+ <template v-for="(item, index) in items" :key="item.title">
+ <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0 || items.length - itemsToDisplay === 1" :href="item?.href"
+ :target="item?.href === undefined ? item?.href : '_blank'" color="info" class="mr-1 my-1 align-self-center"
+ size="small">
+ {{ item.title }}
+ </v-chip>
+ <template v-if="index === itemsToDisplay && items.length - itemsToDisplay > 1">
+ <v-chip v-if="!show" variant="text" class="text-grey text-caption align-self-center px-1"
+ @click="show = !show">
+ (+{{ items.length - itemsToDisplay }} others)
+ </v-chip>
+ <v-btn v-if="itemsToDisplay < items.length && !show" variant="text" :icon="'mdi-chevron-down'"
+ @click="show = !show"></v-btn>
+ </template>
+ </template>
+
+ </span>
+</template>
\ No newline at end of file
diff --git a/frontend/components/Main.vue b/frontend/components/Main.vue
index 9b518edc1cd826229dad98de3692a7c1f254b2b8..f7571ffe1b18527b7fc15fa7afbfad11cc6fc715 100644
--- a/frontend/components/Main.vue
+++ b/frontend/components/Main.vue
@@ -22,10 +22,7 @@ const computedMinWidth = computed(() => {
watchEffect(async () => {
if (csrfToken.value) {
// init session
- const { data, pending, error } = await useFetch("/api/analysis/init-session", {
- headers: [["X-CSRFToken", csrfToken.value]]
-
- })
+ const { data, pending, error } = await useAPI("/api/analysis/init-session")
sessionExpiryDate.value = data.value?.expire_date ?? "NA"
}
diff --git a/frontend/components/UppyGenomeUpload.vue b/frontend/components/UppyGenomeUpload.vue
index fdafef210f431dc15f8bec7ec04c308f0e93a0e6..d5718afb369538fd38e42e56e2719de308f2a091 100644
--- a/frontend/components/UppyGenomeUpload.vue
+++ b/frontend/components/UppyGenomeUpload.vue
@@ -15,7 +15,6 @@ import XHR from '@uppy/xhr-upload';
// import ProgresBar from '@uppy/progress-bar'
// import StatusBar from '@uppy/status-bar'
-// console.log(Form)
// Don't forget the CSS: core and UI components + plugins you are using
import '@uppy/core/dist/style.css';
import '@uppy/dashboard/dist/style.css';
diff --git a/frontend/composables/useAPI.ts b/frontend/composables/useAPI.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b3f3d633db44fd54f22ce54383ed9309e1f7f30c
--- /dev/null
+++ b/frontend/composables/useAPI.ts
@@ -0,0 +1,12 @@
+import type { UseFetchOptions } from 'nuxt/app';
+
+export function useAPI<T>(
+ url: string | (() => string),
+ options: UseFetchOptions<T> = {}
+) {
+
+ return useFetch(url, {
+ ...options,
+ $fetch: useNuxtApp().$api,
+ })
+}
\ No newline at end of file
diff --git a/frontend/composables/useCsrfToken.ts b/frontend/composables/useCsrfToken.ts
index e7e0872eb2dd9220e458cb20244a7bf664586258..efb768944dcb0cfba9f5177cf2b5182dea848d9d 100644
--- a/frontend/composables/useCsrfToken.ts
+++ b/frontend/composables/useCsrfToken.ts
@@ -1,6 +1,6 @@
export const useCsrfToken = async () => {
const currentCsrfToken = useCookie('csrftoken')
- const csrfToken: Ref<string | null | undefined> = ref(null)
+ const csrfToken: Ref<string | undefined> = ref(undefined)
const pending = ref()
const error = ref()
// if (!currentCsrfToken.value) {
diff --git a/frontend/composables/useFetchAnalyses.ts b/frontend/composables/useFetchAnalyses.ts
index fc304321058a1daa8e6ec1c7bc5125c2e2cb893f..f0f33d04bab4e263f41fc4b565527c88065316b3 100644
--- a/frontend/composables/useFetchAnalyses.ts
+++ b/frontend/composables/useFetchAnalyses.ts
@@ -1,31 +1,4 @@
import { type Fn, useIntervalFn } from "@vueuse/core";
-import { useFetch } from '#imports'
-
-
-export type AnalysisStatus = "running" | "done" | "error" | "paused"
-
-
-export interface Analysis {
- id: number;
- name: string;
- status: AnalysisStatus;
- percentage_done: number;
- create_time: string
-}
-
-export const NON_TERMINAL_STATE = [
- "running",
-] as const
-export type NonTerminalState = typeof NON_TERMINAL_STATE[number]
-
-export const TERMINAL_STATE = ["done", "error", "pause"] as const
-
-export type TerminalJobState = typeof TERMINAL_STATE[number]
-
-export type JobState = NonTerminalState | TerminalJobState
-
-
-
export const useFetchAnalyses = async (interval = 5000, polling = true,) => {
const pause = ref<Fn | null>(null)
@@ -36,7 +9,7 @@ export const useFetchAnalyses = async (interval = 5000, polling = true,) => {
error,
refresh,
pending,
- } = await useFetch<Analysis[]>(
+ } = await useAPI<Analysis[]>(
`/api/analysis/`,
);
@@ -68,7 +41,7 @@ export const useFetchAnalyses = async (interval = 5000, polling = true,) => {
// pause interval if the invocation is in terminal state
// Nothing will change
watchEffect(() => {
- if (data.value?.length > 0) {
+ if (data.value && data.value?.length > 0) {
let canPause = true
for (const analysis of data.value) {
if (nonTerminalState.value.has(analysis.status)) {
diff --git a/frontend/composables/useFetchAnalysis.ts b/frontend/composables/useFetchAnalysis.ts
index 2beeaec5497b83c91ab7d72919581e11a739b7e9..a835ddcf0ea2465f6342a6cc747ad6ae22150155 100644
--- a/frontend/composables/useFetchAnalysis.ts
+++ b/frontend/composables/useFetchAnalysis.ts
@@ -36,7 +36,7 @@ export const useFetchAnalysis = async (analysisId: number, interval = 5000, poll
error,
refresh,
pending,
- } = await useFetch<Analysis>(
+ } = await useAPI<Analysis>(
`/api/analysis/${analysisId}`,
);
diff --git a/frontend/composables/useSelectedProtein.ts b/frontend/composables/useSelectedProtein.ts
new file mode 100644
index 0000000000000000000000000000000000000000..6c5431446a09ffc997311bfd7ddd05f686c340e9
--- /dev/null
+++ b/frontend/composables/useSelectedProtein.ts
@@ -0,0 +1,14 @@
+
+const selectedProtein = ref<Protein | undefined>(undefined)
+
+export function useSelectedProtein() {
+
+
+
+
+ function setSelectedProtein(protein: Protein | undefined) {
+ selectedProtein.value = protein
+ }
+
+ return { selectedProtein, setSelectedProtein }
+}
\ No newline at end of file
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index 86973dbe5ce2612b28101b8a869e757126afe43e..82f96100f5ae12d29d0f04b44cee6c089616f846 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1,9 +1,10 @@
{
- "name": "app",
+ "name": "defense-finder-webservice",
"lockfileVersion": 3,
"requires": true,
"packages": {
"": {
+ "name": "defense-finder-webservice",
"hasInstallScript": true,
"dependencies": {
"@uppy/dashboard": "^3.5.0",
@@ -12,20 +13,21 @@
"@uppy/progress-bar": "^3.0.2",
"@uppy/status-bar": "^3.2.3",
"@uppy/vue": "^1.1.0",
- "@uppy/xhr-upload": "^3.3.1",
+ "@uppy/xhr-upload": "^3.6.0",
"@vue-flow/background": "^1.2.0",
"@vue-flow/controls": "^1.1.0",
"@vue-flow/core": "^1.21.3",
"@vue-flow/minimap": "^1.1.1",
- "@vueuse/core": "^10.2.1",
- "vee-validate": "^4.10.8"
+ "@vueuse/core": "^10.7.2",
+ "d3": "^7.8.5",
+ "vee-validate": "^4.12.4"
},
"devDependencies": {
"@nuxt/devtools": "latest",
- "@types/node": "^18.17.0",
- "nuxt": "^3.8.1",
+ "@types/node": "^20.11.6",
+ "nuxt": "^3.9.3",
"nuxt-security": "^0.14.2",
- "vuetify-nuxt-module": "^0.6.7"
+ "vuetify-nuxt-module": "^0.10.2"
}
},
"node_modules/@ampproject/remapping": {
@@ -42,89 +44,27 @@
}
},
"node_modules/@antfu/utils": {
- "version": "0.7.6",
- "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.6.tgz",
- "integrity": "sha512-pvFiLP2BeOKA/ZOS6jxx4XhKzdVLHDhGlFEaZ2flWWYf2xOqVniqpk38I04DFRyz+L0ASggl7SkItTc+ZLju4w==",
+ "version": "0.7.7",
+ "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.7.tgz",
+ "integrity": "sha512-gFPqTG7otEJ8uP6wrhDv6mqwGWYZKNvAcCq6u9hOj0c+IKCEsY4L1oC9trPq2SaWIzAfHvqfBDxF591JkMf+kg==",
"dev": true,
"funding": {
"url": "https://github.com/sponsors/antfu"
}
},
"node_modules/@babel/code-frame": {
- "version": "7.22.13",
- "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.13.tgz",
- "integrity": "sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w==",
+ "version": "7.23.5",
+ "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.23.5.tgz",
+ "integrity": "sha512-CgH3s1a96LipHCmSUmYFPwY7MNx8C3avkq7i4Wl3cfa662ldtUe4VM1TPXX70pfmrlWTb6jLqTYrZyT2ZTJBgA==",
"dev": true,
"dependencies": {
- "@babel/highlight": "^7.22.13",
+ "@babel/highlight": "^7.23.4",
"chalk": "^2.4.2"
},
"engines": {
"node": ">=6.9.0"
}
},
- "node_modules/@babel/code-frame/node_modules/ansi-styles": {
- "version": "3.2.1",
- "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-3.2.1.tgz",
- "integrity": "sha512-VT0ZI6kZRdTh8YyJw3SMbYm/u+NqfsAxEpWO0Pf9sq8/e94WxxOpPKx9FR1FlyCtOVDNOQ+8ntlqFxiRc+r5qA==",
- "dev": true,
- "dependencies": {
- "color-convert": "^1.9.0"
- },
- "engines": {
- "node": ">=4"
- }
- },
- "node_modules/@babel/code-frame/node_modules/chalk": {
- "version": "2.4.2",
- "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
- "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
- "dev": true,
- "dependencies": {
- "ansi-styles": "^3.2.1",
- "escape-string-regexp": "^1.0.5",
- "supports-color": "^5.3.0"
- },
- "engines": {
- "node": ">=4"
- }
- },
- "node_modules/@babel/code-frame/node_modules/color-convert": {
- "version": "1.9.3",
- "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-1.9.3.tgz",
- "integrity": "sha512-QfAUtd+vFdAtFQcC8CCyYt1fYWxSqAiK2cSD6zDB8N3cpsEBAvRxp9zOGg6G/SHHJYAT88/az/IuDGALsNVbGg==",
- "dev": true,
- "dependencies": {
- "color-name": "1.1.3"
- }
- },
- "node_modules/@babel/code-frame/node_modules/color-name": {
- "version": "1.1.3",
- "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.3.tgz",
- "integrity": "sha512-72fSenhMw2HZMTVHeCA9KCmpEIbzWiQsjN+BHcBbS9vr1mtt+vJjPdksIBNUmKAW8TFUDPJK5SUU3QhE9NEXDw==",
- "dev": true
- },
- "node_modules/@babel/code-frame/node_modules/escape-string-regexp": {
- "version": "1.0.5",
- "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-1.0.5.tgz",
- "integrity": "sha512-vbRorB5FUQWvla16U8R/qgaFIya2qGzwDrNmCZuYKrbdSUMG6I1ZCGQRefkRVhuOkIGVne7BQ35DSfo1qvJqFg==",
- "dev": true,
- "engines": {
- "node": ">=0.8.0"
- }
- },
- "node_modules/@babel/code-frame/node_modules/supports-color": {
- "version": "5.5.0",
- "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-5.5.0.tgz",
- "integrity": "sha512-QjVjwdXIt408MIiAqCX4oUKsgU2EqAGzs2Ppkm4aQYbjm+ZEWEcW4SfFNTr4uMNZma0ey4f5lgLrkB0aX0QMow==",
- "dev": true,
- "dependencies": {
- "has-flag": "^3.0.0"
- },
- "engines": {
- "node": ">=4"
- }
- },
"node_modules/@babel/compat-data": {
"version": "7.23.3",
"resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.23.3.tgz",
@@ -174,12 +114,12 @@
}
},
"node_modules/@babel/generator": {
- "version": "7.23.3",
- "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.3.tgz",
- "integrity": "sha512-keeZWAV4LU3tW0qRi19HRpabC/ilM0HRBBzf9/k8FFiG4KVpiv0FIy4hHfLfFQZNhziCTPTmd59zoyv6DNISzg==",
+ "version": "7.23.6",
+ "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.23.6.tgz",
+ "integrity": "sha512-qrSfCYxYQB5owCmGLbl8XRpX1ytXlpueOb0N0UmQwA073KZxejgQTzAmJezxvpwQD9uGtK2shHdi55QT+MbjIw==",
"dev": true,
"dependencies": {
- "@babel/types": "^7.23.3",
+ "@babel/types": "^7.23.6",
"@jridgewell/gen-mapping": "^0.3.2",
"@jridgewell/trace-mapping": "^0.3.17",
"jsesc": "^2.5.1"
@@ -226,17 +166,17 @@
}
},
"node_modules/@babel/helper-create-class-features-plugin": {
- "version": "7.22.15",
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+ },
+ "funding": {
+ "url": "https://github.com/sponsors/isaacs"
+ }
+ },
+ "node_modules/@npmcli/package-json/node_modules/minimatch": {
+ "version": "9.0.3",
+ "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.3.tgz",
+ "integrity": "sha512-RHiac9mvaRw0x3AYRgDC1CxAP7HTcNrrECeA8YYJeWnpo+2Q5CegtZjaotWTWxDG3UeGA1coE05iH1mPjT/2mg==",
+ "dev": true,
+ "dependencies": {
+ "brace-expansion": "^2.0.1"
+ },
+ "engines": {
+ "node": ">=16 || 14 >=14.17"
+ },
+ "funding": {
+ "url": "https://github.com/sponsors/isaacs"
+ }
+ },
"node_modules/@npmcli/promise-spawn": {
- "version": "7.0.0",
- "resolved": "https://registry.npmjs.org/@npmcli/promise-spawn/-/promise-spawn-7.0.0.tgz",
- "integrity": "sha512-wBqcGsMELZna0jDblGd7UXgOby45TQaMWmbFwWX+SEotk4HV6zG2t6rT9siyLhPk4P6YYqgfL1UO8nMWDBVJXQ==",
+ "version": "7.0.1",
+ "resolved": "https://registry.npmjs.org/@npmcli/promise-spawn/-/promise-spawn-7.0.1.tgz",
+ "integrity": "sha512-P4KkF9jX3y+7yFUxgcUdDtLy+t4OlDGuEBLNs57AZsfSfg+uV6MLndqGpnl4831ggaEdXwR50XFoZP4VFtHolg==",
"dev": true,
"dependencies": {
"which": "^4.0.0"
@@ -1519,15 +1108,15 @@
}
},
"node_modules/@npmcli/run-script": {
- "version": "7.0.2",
- "resolved": "https://registry.npmjs.org/@npmcli/run-script/-/run-script-7.0.2.tgz",
- "integrity": "sha512-Omu0rpA8WXvcGeY6DDzyRoY1i5DkCBkzyJ+m2u7PD6quzb0TvSqdIPOkTn8ZBOj7LbbcbMfZ3c5skwSu6m8y2w==",
+ "version": "7.0.4",
+ "resolved": "https://registry.npmjs.org/@npmcli/run-script/-/run-script-7.0.4.tgz",
+ "integrity": "sha512-9ApYM/3+rBt9V80aYg6tZfzj3UWdiYyCt7gJUD1VJKvWF5nwKDSICXbYIQbspFTq6TOpbsEtIC0LArB8d9PFmg==",
"dev": true,
"dependencies": {
"@npmcli/node-gyp": "^3.0.0",
+ "@npmcli/package-json": "^5.0.0",
"@npmcli/promise-spawn": "^7.0.0",
"node-gyp": "^10.0.0",
- "read-package-json-fast": "^3.0.0",
"which": "^4.0.0"
},
"engines": {
@@ -1565,15 +1154,15 @@
"dev": true
},
"node_modules/@nuxt/devtools": {
- "version": "1.0.2",
- "resolved": "https://registry.npmjs.org/@nuxt/devtools/-/devtools-1.0.2.tgz",
- "integrity": "sha512-nfqvRc36Sh20gDVs3pViHvcyyz3NmaNqgJnWUXgfjSCsT7G/p2wHsoNUXYYTF7kpk3kbNusftaWrIzAiTiXC9A==",
+ "version": "1.0.8",
+ "resolved": "https://registry.npmjs.org/@nuxt/devtools/-/devtools-1.0.8.tgz",
+ "integrity": "sha512-o6aBFEBxc8OgVHV4OPe2g0q9tFIe9HiTxRiJnlTJ+jHvOQsBLS651ArdVtwLChf9UdMouFlpLLJ1HteZqTbtsQ==",
"dev": true,
"dependencies": {
- "@antfu/utils": "^0.7.6",
- "@nuxt/devtools-kit": "1.0.2",
- "@nuxt/devtools-wizard": "1.0.2",
- "@nuxt/kit": "^3.8.1",
+ "@antfu/utils": "^0.7.7",
+ "@nuxt/devtools-kit": "1.0.8",
+ "@nuxt/devtools-wizard": "1.0.8",
+ "@nuxt/kit": "^3.9.1",
"birpc": "^0.2.14",
"consola": "^3.2.3",
"destr": "^2.0.2",
@@ -1581,60 +1170,57 @@
"execa": "^7.2.0",
"fast-glob": "^3.3.2",
"flatted": "^3.2.9",
- "get-port-please": "^3.1.1",
- "h3": "^1.8.2",
+ "get-port-please": "^3.1.2",
"hookable": "^5.5.3",
"image-meta": "^0.2.0",
"is-installed-globally": "^1.0.0",
"launch-editor": "^2.6.1",
"local-pkg": "^0.5.0",
"magicast": "^0.3.2",
- "nitropack": "^2.7.2",
- "nypm": "^0.3.3",
- "ofetch": "^1.3.3",
+ "nypm": "^0.3.4",
"ohash": "^1.1.3",
- "pacote": "^17.0.4",
- "pathe": "^1.1.1",
+ "pacote": "^17.0.5",
+ "pathe": "^1.1.2",
"perfect-debounce": "^1.0.0",
"pkg-types": "^1.0.3",
"rc9": "^2.1.1",
- "scule": "^1.0.0",
+ "scule": "^1.2.0",
"semver": "^7.5.4",
- "simple-git": "^3.20.0",
- "sirv": "^2.0.3",
- "unimport": "^3.5.0",
- "vite-plugin-inspect": "^0.7.42",
- "vite-plugin-vue-inspector": "^4.0.0",
+ "simple-git": "^3.22.0",
+ "sirv": "^2.0.4",
+ "unimport": "^3.7.1",
+ "vite-plugin-inspect": "^0.8.1",
+ "vite-plugin-vue-inspector": "^4.0.2",
"which": "^3.0.1",
- "ws": "^8.14.2"
+ "ws": "^8.16.0"
},
"bin": {
"devtools": "cli.mjs"
},
"peerDependencies": {
- "nuxt": "^3.8.1",
+ "nuxt": "^3.9.0",
"vite": "*"
}
},
"node_modules/@nuxt/devtools-kit": {
- "version": "1.0.2",
- "resolved": "https://registry.npmjs.org/@nuxt/devtools-kit/-/devtools-kit-1.0.2.tgz",
- "integrity": "sha512-iFi54NNCcPsF/jW14HbRlq3aOClOWdfiein0CvKoQ5shobHgn1s3xULh8o9QPKI2oTarcuJL+EFIK43CwfoXyw==",
+ "version": "1.0.8",
+ "resolved": "https://registry.npmjs.org/@nuxt/devtools-kit/-/devtools-kit-1.0.8.tgz",
+ "integrity": "sha512-j7bNZmoAXQ1a8qv6j6zk4c/aekrxYqYVQM21o/Hy4XHCUq4fajSgpoc8mjyWJSTfpkOmuLyEzMexpDWiIVSr6A==",
"dev": true,
"dependencies": {
- "@nuxt/kit": "^3.8.1",
- "@nuxt/schema": "^3.8.1",
+ "@nuxt/kit": "^3.9.1",
+ "@nuxt/schema": "^3.9.1",
"execa": "^7.2.0"
},
"peerDependencies": {
- "nuxt": "^3.8.1",
+ "nuxt": "^3.9.0",
"vite": "*"
}
},
"node_modules/@nuxt/devtools-wizard": {
- "version": "1.0.2",
- "resolved": "https://registry.npmjs.org/@nuxt/devtools-wizard/-/devtools-wizard-1.0.2.tgz",
- "integrity": "sha512-fY9Y0eCJG7eSuUgnjImWVfLZPZymoHxjrVsdhfKs3yRJvB2siaabluxvdy2OTYc+WpIxuey0hjqpv+dVtnYw1A==",
+ "version": "1.0.8",
+ "resolved": "https://registry.npmjs.org/@nuxt/devtools-wizard/-/devtools-wizard-1.0.8.tgz",
+ "integrity": "sha512-RxyOlM7Isk5npwXwDJ/rjm9ekX5sTNG0LS0VOBMdSx+D5nlRPMRr/r9yO+9WQDyzPLClLzHaXRHBWLPlRX3IMw==",
"dev": true,
"dependencies": {
"consola": "^3.2.3",
@@ -1642,7 +1228,7 @@
"execa": "^7.2.0",
"global-directory": "^4.0.1",
"magicast": "^0.3.2",
- "pathe": "^1.1.1",
+ "pathe": "^1.1.2",
"pkg-types": "^1.0.3",
"prompts": "^2.4.2",
"rc9": "^2.1.1",
@@ -1653,28 +1239,28 @@
}
},
"node_modules/@nuxt/kit": {
- "version": "3.8.1",
- "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.8.1.tgz",
- "integrity": "sha512-DrhG1Z85iH68QOTkgfb0HVfM2g7+CfcMWrFWMDwck9ofyM2RXQUZyfmvMedwBnui1AjjpgpLO9078yZM+RqNUg==",
+ "version": "3.9.3",
+ "resolved": "https://registry.npmjs.org/@nuxt/kit/-/kit-3.9.3.tgz",
+ "integrity": "sha512-bHGXpTB6E+YJCC1L9tTwrP7txgLZzyuFes/tgy1ZM4dlfrCsGqLK/K4mddROMdC3D81scnH84u7yQsN0JRgoTg==",
"dev": true,
"dependencies": {
- "@nuxt/schema": "3.8.1",
- "c12": "^1.5.1",
+ "@nuxt/schema": "3.9.3",
+ "c12": "^1.6.1",
"consola": "^3.2.3",
- "defu": "^6.1.3",
- "globby": "^13.2.2",
+ "defu": "^6.1.4",
+ "globby": "^14.0.0",
"hash-sum": "^2.0.0",
- "ignore": "^5.2.4",
+ "ignore": "^5.3.0",
"jiti": "^1.21.0",
"knitwork": "^1.0.0",
- "mlly": "^1.4.2",
- "pathe": "^1.1.1",
+ "mlly": "^1.5.0",
+ "pathe": "^1.1.2",
"pkg-types": "^1.0.3",
- "scule": "^1.0.0",
+ "scule": "^1.2.0",
"semver": "^7.5.4",
- "ufo": "^1.3.1",
+ "ufo": "^1.3.2",
"unctx": "^2.3.1",
- "unimport": "^3.4.0",
+ "unimport": "^3.7.1",
"untyped": "^1.4.0"
},
"engines": {
@@ -1682,20 +1268,21 @@
}
},
"node_modules/@nuxt/schema": {
- "version": "3.8.1",
- "resolved": "https://registry.npmjs.org/@nuxt/schema/-/schema-3.8.1.tgz",
- "integrity": "sha512-fSaWRcI/2mUskfTZTGSnH6Ny0x05CRzylbVn6WFV0d6UEKIVy42Qd6n+h7yoFfp4cq4nji6u16PT4SqS1DEhsw==",
+ "version": "3.9.3",
+ "resolved": "https://registry.npmjs.org/@nuxt/schema/-/schema-3.9.3.tgz",
+ "integrity": "sha512-pchkGBYdEJ9TAOoC5DKnLuAaFPjzgn2k0OUTr31QwbtHdTR3Q2Ua/oKsS1g9CPU7KRzSE5Vkf7ECE8zVydqF5A==",
"dev": true,
"dependencies": {
"@nuxt/ui-templates": "^1.3.1",
"consola": "^3.2.3",
- "defu": "^6.1.3",
+ "defu": "^6.1.4",
"hookable": "^5.5.3",
- "pathe": "^1.1.1",
+ "pathe": "^1.1.2",
"pkg-types": "^1.0.3",
- "std-env": "^3.4.3",
- "ufo": "^1.3.1",
- "unimport": "^3.4.0",
+ "scule": "^1.2.0",
+ "std-env": "^3.7.0",
+ "ufo": "^1.3.2",
+ "unimport": "^3.7.1",
"untyped": "^1.4.0"
},
"engines": {
@@ -1703,48 +1290,33 @@
}
},
"node_modules/@nuxt/telemetry": {
- "version": "2.5.2",
- "resolved": "https://registry.npmjs.org/@nuxt/telemetry/-/telemetry-2.5.2.tgz",
- "integrity": "sha512-kZ+rWq/5MZonMhp8KGFI5zMaR2VsiWpnlkOLJIuIX2WoJl0DkHvtxCtuFq2erAqMVruWLpKU+tgMC+1cno/QmA==",
+ "version": "2.5.3",
+ "resolved": "https://registry.npmjs.org/@nuxt/telemetry/-/telemetry-2.5.3.tgz",
+ "integrity": "sha512-Ghv2MgWbJcUM9G5Dy3oQP0cJkUwEgaiuQxEF61FXJdn0a69Q4StZEP/hLF0MWPM9m6EvAwI7orxkJHM7MrmtVg==",
"dev": true,
"dependencies": {
- "@nuxt/kit": "^3.7.4",
- "ci-info": "^3.8.0",
+ "@nuxt/kit": "^3.8.2",
+ "ci-info": "^4.0.0",
"consola": "^3.2.3",
"create-require": "^1.1.1",
- "defu": "^6.1.2",
- "destr": "^2.0.1",
+ "defu": "^6.1.3",
+ "destr": "^2.0.2",
"dotenv": "^16.3.1",
- "git-url-parse": "^13.1.0",
+ "git-url-parse": "^13.1.1",
"is-docker": "^3.0.0",
- "jiti": "^1.20.0",
+ "jiti": "^1.21.0",
"mri": "^1.2.0",
"nanoid": "^4.0.2",
"ofetch": "^1.3.3",
"parse-git-config": "^3.0.0",
"pathe": "^1.1.1",
"rc9": "^2.1.1",
- "std-env": "^3.4.3"
+ "std-env": "^3.5.0"
},
"bin": {
"nuxt-telemetry": "bin/nuxt-telemetry.mjs"
}
},
- "node_modules/@nuxt/telemetry/node_modules/is-docker": {
- "version": "3.0.0",
- "resolved": "https://registry.npmjs.org/is-docker/-/is-docker-3.0.0.tgz",
- "integrity": "sha512-eljcgEDlEns/7AXFosB5K/2nCM4P7FQPkGc/DWLy5rmFEWvZayGrik1d9/QIY5nJ4f9YsVvBkA6kJpHn9rISdQ==",
- "dev": true,
- "bin": {
- "is-docker": "cli.js"
- },
- "engines": {
- "node": "^12.20.0 || ^14.13.1 || >=16.0.0"
- },
- "funding": {
- "url": "https://github.com/sponsors/sindresorhus"
- }
- },
"node_modules/@nuxt/ui-templates": {
"version": "1.3.1",
"resolved": "https://registry.npmjs.org/@nuxt/ui-templates/-/ui-templates-1.3.1.tgz",
@@ -1752,42 +1324,42 @@
"dev": true
},
"node_modules/@nuxt/vite-builder": {
- "version": "3.8.1",
- "resolved": "https://registry.npmjs.org/@nuxt/vite-builder/-/vite-builder-3.8.1.tgz",
- "integrity": "sha512-Ot/twGONxj22T9U4bxp771ibKVFlZxIiYDHY/e6mZsE4Blc0efKo6MzPPPo0W4/tXQbtKKEq41uINN3dMI3mag==",
+ "version": "3.9.3",
+ "resolved": "https://registry.npmjs.org/@nuxt/vite-builder/-/vite-builder-3.9.3.tgz",
+ "integrity": "sha512-HruOrxn0g6TS31j3jycJvGZ7pt3JNEbcXNByVh7YJwQx6ToFX8kPWRu4LPeMhrLYvZzeUr2w3iELBECFxbDmvw==",
"dev": true,
"dependencies": {
- "@nuxt/kit": "3.8.1",
+ "@nuxt/kit": "3.9.3",
"@rollup/plugin-replace": "^5.0.5",
- "@vitejs/plugin-vue": "^4.4.0",
- "@vitejs/plugin-vue-jsx": "^3.0.2",
+ "@vitejs/plugin-vue": "^5.0.3",
+ "@vitejs/plugin-vue-jsx": "^3.1.0",
"autoprefixer": "^10.4.16",
"clear": "^0.1.0",
"consola": "^3.2.3",
- "cssnano": "^6.0.1",
- "defu": "^6.1.3",
- "esbuild": "^0.19.5",
+ "cssnano": "^6.0.3",
+ "defu": "^6.1.4",
+ "esbuild": "^0.19.11",
"escape-string-regexp": "^5.0.0",
"estree-walker": "^3.0.3",
"externality": "^1.0.2",
- "fs-extra": "^11.1.1",
- "get-port-please": "^3.1.1",
- "h3": "^1.8.2",
+ "fs-extra": "^11.2.0",
+ "get-port-please": "^3.1.2",
+ "h3": "^1.10.0",
"knitwork": "^1.0.0",
"magic-string": "^0.30.5",
- "mlly": "^1.4.2",
+ "mlly": "^1.5.0",
"ohash": "^1.1.3",
- "pathe": "^1.1.1",
+ "pathe": "^1.1.2",
"perfect-debounce": "^1.0.0",
"pkg-types": "^1.0.3",
- "postcss": "^8.4.31",
- "rollup-plugin-visualizer": "^5.9.2",
- "std-env": "^3.4.3",
- "strip-literal": "^1.3.0",
- "ufo": "^1.3.1",
- "unplugin": "^1.5.0",
- "vite": "^4.5.0",
- "vite-node": "^0.33.0",
+ "postcss": "^8.4.33",
+ "rollup-plugin-visualizer": "^5.12.0",
+ "std-env": "^3.7.0",
+ "strip-literal": "^2.0.0",
+ "ufo": "^1.3.2",
+ "unplugin": "^1.6.0",
+ "vite": "5.0.11",
+ "vite-node": "^1.1.1",
"vite-plugin-checker": "^0.6.2",
"vue-bundle-renderer": "^2.0.0"
},
@@ -1798,6 +1370,19 @@
"vue": "^3.3.4"
}
},
+ "node_modules/@nuxt/vite-builder/node_modules/@vitejs/plugin-vue": {
+ "version": "5.0.3",
+ "resolved": "https://registry.npmjs.org/@vitejs/plugin-vue/-/plugin-vue-5.0.3.tgz",
+ "integrity": "sha512-b8S5dVS40rgHdDrw+DQi/xOM9ed+kSRZzfm1T74bMmBDCd8XO87NKlFYInzCtwvtWwXZvo1QxE2OSspTATWrbA==",
+ "dev": true,
+ "engines": {
+ "node": "^18.0.0 || >=20.0.0"
+ },
+ "peerDependencies": {
+ "vite": "^5.0.0",
+ "vue": "^3.2.25"
+ }
+ },
"node_modules/@nuxt/vite-builder/node_modules/estree-walker": {
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/estree-walker/-/estree-walker-3.0.3.tgz",
@@ -1807,6 +1392,61 @@
"@types/estree": "^1.0.0"
}
},
+ "node_modules/@nuxt/vite-builder/node_modules/vite": {
+ "version": "5.0.11",
+ "resolved": "https://registry.npmjs.org/vite/-/vite-5.0.11.tgz",
+ "integrity": "sha512-XBMnDjZcNAw/G1gEiskiM1v6yzM4GE5aMGvhWTlHAYYhxb7S3/V1s3m2LDHa8Vh6yIWYYB0iJwsEaS523c4oYA==",
+ "dev": true,
+ "dependencies": {
+ "esbuild": "^0.19.3",
+ "postcss": "^8.4.32",
+ "rollup": "^4.2.0"
+ },
+ "bin": {
+ "vite": "bin/vite.js"
+ },
+ "engines": {
+ "node": "^18.0.0 || >=20.0.0"
+ },
+ "funding": {
+ "url": "https://github.com/vitejs/vite?sponsor=1"
+ },
+ "optionalDependencies": {
+ "fsevents": "~2.3.3"
+ },
+ "peerDependencies": {
+ "@types/node": "^18.0.0 || >=20.0.0",
+ "less": "*",
+ "lightningcss": "^1.21.0",
+ "sass": "*",
+ "stylus": "*",
+ "sugarss": "*",
+ "terser": "^5.4.0"
+ },
+ "peerDependenciesMeta": {
+ "@types/node": {
+ "optional": true
+ },
+ "less": {
+ "optional": true
+ },
+ "lightningcss": {
+ "optional": true
+ },
+ "sass": {
+ "optional": true
+ },
+ "stylus": {
+ "optional": true
+ },
+ "sugarss": {
+ "optional": true
+ },
+ "terser": {
+ "optional": true
+ }
+ }
+ },
"node_modules/@parcel/watcher": {
"version": "2.3.0",
"resolved": "https://registry.npmjs.org/@parcel/watcher/-/watcher-2.3.0.tgz",
@@ -1841,37 +1481,17 @@
"@parcel/watcher-win32-x64": "2.3.0"
}
},
- "node_modules/@parcel/watcher-android-arm64": {
- "version": "2.3.0",
- "resolved": "https://registry.npmjs.org/@parcel/watcher-android-arm64/-/watcher-android-arm64-2.3.0.tgz",
- "integrity": "sha512-f4o9eA3dgk0XRT3XhB0UWpWpLnKgrh1IwNJKJ7UJek7eTYccQ8LR7XUWFKqw6aEq5KUNlCcGvSzKqSX/vtWVVA==",
- "cpu": [
- "arm64"
- ],
- "dev": true,
- "optional": true,
- "os": [
- "android"
- ],
- "engines": {
- "node": ">= 10.0.0"
- },
- "funding": {
- "type": "opencollective",
- "url": "https://opencollective.com/parcel"
- }
- },
- "node_modules/@parcel/watcher-darwin-arm64": {
+ "node_modules/@parcel/watcher-linux-x64-glibc": {
"version": "2.3.0",
- "resolved": "https://registry.npmjs.org/@parcel/watcher-darwin-arm64/-/watcher-darwin-arm64-2.3.0.tgz",
- "integrity": "sha512-mKY+oijI4ahBMc/GygVGvEdOq0L4DxhYgwQqYAz/7yPzuGi79oXrZG52WdpGA1wLBPrYb0T8uBaGFo7I6rvSKw==",
+ "resolved": "https://registry.npmjs.org/@parcel/watcher-linux-x64-glibc/-/watcher-linux-x64-glibc-2.3.0.tgz",
+ "integrity": "sha512-P7Wo91lKSeSgMTtG7CnBS6WrA5otr1K7shhSjKHNePVmfBHDoAOHYRXgUmhiNfbcGk0uMCHVcdbfxtuiZCHVow==",
"cpu": [
- "arm64"
+ "x64"
],
"dev": true,
"optional": true,
"os": [
- "darwin"
+ "linux"
],
"engines": {
"node": ">= 10.0.0"
@@ -1881,17 +1501,17 @@
"url": "https://opencollective.com/parcel"
}
},
- "node_modules/@parcel/watcher-darwin-x64": {
+ "node_modules/@parcel/watcher-linux-x64-musl": {
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},
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},
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+ "d3-transition": "3",
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@@ -4361,6 +4021,28 @@
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@@ -4381,6 +4063,30 @@
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+ "dsv2json": "bin/dsv2json.js",
+ "json2csv": "bin/json2dsv.js",
+ "json2dsv": "bin/json2dsv.js",
+ "json2tsv": "bin/json2dsv.js",
+ "tsv2csv": "bin/dsv2dsv.js",
+ "tsv2json": "bin/dsv2json.js"
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@@ -6709,6 +6515,27 @@
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+ },
+ "funding": {
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@@ -7357,48 +7184,60 @@
"url": "https://github.com/sponsors/sindresorhus"
}
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+ "resolved": "https://registry.npmjs.org/is-docker/-/is-docker-2.2.1.tgz",
+ "integrity": "sha512-F+i2BKsFrH66iaUFc0woD8sLy8getkwTwtOBjvs56Cx4CgJDeKQeqfz8wAYiSb8JOprWhHH5p77PbmYCvvUuXQ==",
+ "dev": true,
+ "bin": {
+ "is-docker": "cli.js"
+ },
+ "engines": {
+ "node": ">=8"
+ },
+ "funding": {
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+ "resolved": "https://registry.npmjs.org/is-wsl/-/is-wsl-2.2.0.tgz",
+ "integrity": "sha512-fKzAra0rGJUUBwGBgNkHZuToZcn+TtXHpeCgmkMJMMYx1sQDYaCSyjJBSCa2nH1DGm7s3n1oBnohoVTBaN7Lww==",
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- "undici": "^5.27.2",
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+ "node_modules/openapi-typescript/node_modules/supports-color": {
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+ "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-9.4.0.tgz",
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"dev": true,
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"engines": {
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- "dev": true,
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- },
- "engines": {
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+ "url": "https://github.com/chalk/supports-color?sponsor=1"
}
},
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@@ -7432,9 +7271,9 @@
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+ "version": "6.2.0",
+ "resolved": "https://registry.npmjs.org/p-retry/-/p-retry-6.2.0.tgz",
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@@ -7458,19 +7297,10 @@
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+ "resolved": "https://registry.npmjs.org/pacote/-/pacote-17.0.6.tgz",
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@@ -7488,7 +7318,7 @@
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@@ -7545,15 +7375,6 @@
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- "resolved": "https://registry.npmjs.org/webpack-virtual-modules/-/webpack-virtual-modules-0.5.0.tgz",
- "integrity": "sha512-kyDivFZ7ZM0BVOUteVbDFhlRt7Ah/CSPwJdi8hBpkK7QLumUqdLtVfm/PX/hkcnrvr0i77fO5+TjZ94Pe+C9iw==",
+ "version": "0.6.1",
+ "resolved": "https://registry.npmjs.org/webpack-virtual-modules/-/webpack-virtual-modules-0.6.1.tgz",
+ "integrity": "sha512-poXpCylU7ExuvZK8z+On3kX+S8o/2dQ/SVYueKA0D4WEMXROXgY8Ez50/bQEUmvoSMMrWcrJqCHuhAbsiwg7Dg==",
"dev": true
},
"node_modules/whatwg-url": {
@@ -10868,6 +10298,72 @@
"url": "https://github.com/chalk/wrap-ansi?sponsor=1"
}
},
+ "node_modules/wrap-ansi-cjs/node_modules/ansi-styles": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+ "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+ "dev": true,
+ "dependencies": {
+ "color-convert": "^2.0.1"
+ },
+ "engines": {
+ "node": ">=8"
+ },
+ "funding": {
+ "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+ }
+ },
+ "node_modules/wrap-ansi-cjs/node_modules/color-convert": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
+ "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+ "dev": true,
+ "dependencies": {
+ "color-name": "~1.1.4"
+ },
+ "engines": {
+ "node": ">=7.0.0"
+ }
+ },
+ "node_modules/wrap-ansi-cjs/node_modules/color-name": {
+ "version": "1.1.4",
+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+ "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+ "dev": true
+ },
+ "node_modules/wrap-ansi/node_modules/ansi-styles": {
+ "version": "4.3.0",
+ "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz",
+ "integrity": "sha512-zbB9rCJAT1rbjiVDb2hqKFHNYLxgtk8NURxZ3IZwD3F6NtxbXZQCnnSi1Lkx+IDohdPlFp222wVALIheZJQSEg==",
+ "dev": true,
+ "dependencies": {
+ "color-convert": "^2.0.1"
+ },
+ "engines": {
+ "node": ">=8"
+ },
+ "funding": {
+ "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+ }
+ },
+ "node_modules/wrap-ansi/node_modules/color-convert": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
+ "integrity": "sha512-RRECPsj7iu/xb5oKYcsFHSppFNnsj/52OVTRKb4zP5onXwVF3zVmmToNcOfGC+CRDpfK/U584fMg38ZHCaElKQ==",
+ "dev": true,
+ "dependencies": {
+ "color-name": "~1.1.4"
+ },
+ "engines": {
+ "node": ">=7.0.0"
+ }
+ },
+ "node_modules/wrap-ansi/node_modules/color-name": {
+ "version": "1.1.4",
+ "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.4.tgz",
+ "integrity": "sha512-dOy+3AuW3a2wNbZHIuMZpTcgjGuLU/uBL/ubcZF9OXbDo8ff4O8yVp5Bf0efS8uEoYo5q4Fx7dY9OgQGXgAsQA==",
+ "dev": true
+ },
"node_modules/wrappy": {
"version": "1.0.2",
"resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
@@ -10875,9 +10371,9 @@
"dev": true
},
"node_modules/ws": {
- "version": "8.14.2",
- "resolved": "https://registry.npmjs.org/ws/-/ws-8.14.2.tgz",
- "integrity": "sha512-wEBG1ftX4jcglPxgFCMJmZ2PLtSbJ2Peg6TmpJFTbe9GZYOQCDPdMYu/Tm0/bGZkw8paZnJY45J4K2PZrLYq8g==",
+ "version": "8.16.0",
+ "resolved": "https://registry.npmjs.org/ws/-/ws-8.16.0.tgz",
+ "integrity": "sha512-HS0c//TP7Ina87TfiPUz1rQzMhHrl/SG2guqRcTOIUYD2q8uhUdNHZYJUaQ8aTGPzCh+c6oawMKW35nFl1dxyQ==",
"dev": true,
"engines": {
"node": ">=10.0.0"
diff --git a/frontend/package.json b/frontend/package.json
index 9572117b30ce49b147fd580e14f49664c233f9cd..fce9bb014890e2da57343ec1328256967286448c 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -1,4 +1,5 @@
{
+ "name": "defense-finder-webservice",
"private": true,
"scripts": {
"build": "nuxt build",
@@ -9,10 +10,10 @@
},
"devDependencies": {
"@nuxt/devtools": "latest",
- "@types/node": "^18.17.0",
- "nuxt": "^3.8.1",
+ "@types/node": "^20.11.6",
+ "nuxt": "^3.9.3",
"nuxt-security": "^0.14.2",
- "vuetify-nuxt-module": "^0.6.7"
+ "vuetify-nuxt-module": "^0.10.2"
},
"dependencies": {
"@uppy/dashboard": "^3.5.0",
@@ -21,12 +22,13 @@
"@uppy/progress-bar": "^3.0.2",
"@uppy/status-bar": "^3.2.3",
"@uppy/vue": "^1.1.0",
- "@uppy/xhr-upload": "^3.3.1",
+ "@uppy/xhr-upload": "^3.6.0",
"@vue-flow/background": "^1.2.0",
"@vue-flow/controls": "^1.1.0",
"@vue-flow/core": "^1.21.3",
"@vue-flow/minimap": "^1.1.1",
- "@vueuse/core": "^10.2.1",
- "vee-validate": "^4.10.8"
+ "@vueuse/core": "^10.7.2",
+ "d3": "^7.8.5",
+ "vee-validate": "^4.12.4"
}
}
diff --git a/frontend/pages/analyses/[analysisId].vue b/frontend/pages/analyses/[analysisId].vue
index 08ec4b25448385ff1223e992a669dd967dd45360..9d880549199b9817086149ce6aafbce951074ff8 100644
--- a/frontend/pages/analyses/[analysisId].vue
+++ b/frontend/pages/analyses/[analysisId].vue
@@ -1,7 +1,15 @@
<script setup lang="ts">
+import { useThrottleFn } from '@vueuse/core'
import { useFetchAnalysis } from "../../composables/useFetchAnalysis";
+import { useSelectedProtein } from '@/composables/useSelectedProtein'
+
import { useRoute, computed } from "#imports";
+import * as d3 from "d3";
+import { useDisplay } from 'vuetify'
+import { useElementSize } from '@vueuse/core'
+const { width } = useDisplay()
const route = useRoute();
+const { selectedProtein } = useSelectedProtein()
const { data: analysis } = await useFetchAnalysis(
route.params.analysisId,
@@ -9,6 +17,7 @@ const { data: analysis } = await useFetchAnalysis(
true
);
+
useHead({
title: analysis.value?.name ?? 'analysis',
})
@@ -35,6 +44,375 @@ const breadcrumbItems = computed(() => {
})
+const { data: rawProteins, error } = await useFetch<ProteinsOut>(
+ `/api/analysis/${route.params.analysisId}/proteins`
+);
+
+const { data: genes } = await useFetch<GenesOut>(
+ `/api/analysis/${route.params.analysisId}/genes`
+);
+
+const { data: rawHmmer } = await useFetch<HmmersOut>(
+ `/api/analysis/${route.params.analysisId}/hmmers`
+);
+
+
+const genesMap = computed(() => {
+ const mapGenes = new Map<string, Gene>()
+ const toValGenes = toValue(genes)
+ if (toValGenes !== null) {
+ for (const gene of toValGenes.genes) {
+ mapGenes.set(gene.hit_id, { ...gene, hit_gene_ref: gene.hit_gene_ref.split('__')[0].toLowerCase() })
+ }
+ }
+ return mapGenes
+})
+
+const hmmersMap = computed(() => {
+ const hmmMap = new Map<string, Hmmer>()
+ const toValHmmers = toValue(rawHmmer)
+ if (toValHmmers !== null) {
+ for (const hmmer of toValHmmers.hmmers) {
+ if (hmmMap.has(hmmer.hit_id)) {
+ const hmmerInMapScore = hmmMap.get(hmmer.hit_id)?.hit_score ?? -1
+ if (hmmerInMapScore < hmmer.hit_score) {
+ hmmMap.set(hmmer.hit_id, { ...hmmer })
+ }
+ } else {
+ hmmMap.set(hmmer.hit_id, { ...hmmer })
+ }
+ }
+ }
+ return hmmMap
+})
+
+const computedXUnit = computed(() => {
+ if (rawProteins.value?.proteins) {
+ if (rawProteins.value.proteins[0].start === null && rawProteins.value.proteins[0].end === null) {
+ return "aa"
+ }
+ else { return "bp" }
+ }
+})
+
+const sanitizedData = computed(() => {
+ if (rawProteins.value?.proteins) {
+ const toValGenesMap = toValue(genesMap)
+ const toValHmmerMap = toValue(hmmersMap)
+ const prots = rawProteins.value.proteins.map(prot => {
+ const isHmmerHit = toValHmmerMap.has(prot.id)
+ const isDefenseSystem = toValGenesMap.has(prot.id)
+ return {
+
+ ...prot,
+ name: prot.id,
+ gene_name: toValHmmerMap.get(prot.id)?.gene_name,
+ strand: prot.strand,
+ defenseSystem: toValGenesMap.get(prot.id)?.hit_gene_ref,
+ isDefenseSystem,
+ isHmmerHit
+ }
+ })
+ const proteins = []
+ let currentGenomeIndex = 1
+
+ for (const prot of prots) {
+ if (prot?.start !== null && prot?.end !== null) {
+ proteins.push({ ...prot, length: prot.end - prot.start, protLength: prot.length })
+ }
+ else {
+ proteins.push({ ...prot, start: currentGenomeIndex, end: currentGenomeIndex + prot.length - 1, protLength: prot.length })
+ currentGenomeIndex = currentGenomeIndex + prot.length + 20
+ }
+ }
+ return proteins
+ }
+ else { return [] }
+})
+
+const proteinIndex = computed(() => {
+ return new Map(sanitizedData.value.map((d, i, arr) => {
+ let previousStart = 0
+ if (i > 0) {
+ previousStart = arr[i - 1].start - 10
+ }
+ let nextEnd = previousStart + 400
+ if (i < arr.length - 1) {
+ nextEnd = arr[i + 1].end + 10
+ }
+ return [d.id, { ...d, previousStart, nextEnd }]
+ }))
+
+})
+
+
+
+const height = ref(300)
+
+const displayHmmerHits = ref<boolean>(true)
+type ColorScale = (value: string | number) => string
+const color = computed<ColorScale>(() => {
+
+ return d3.scaleOrdinal(["default", undefined, "df", "hmmer"], d3.schemeTableau10)
+})
+
+
+const gbContainer = ref(null)
+const gbContainerWidth = ref(useElementSize(gbContainer, { width: 500, height: 0 }, { box: 'border-box' }).width)
+
+const computedWidth = computed(() => {
+ return gbContainerWidth.value
+})
+
+
+
+
+
+watch(selectedProtein, () => {
+ const toValSearchResults = toValue(selectedProtein)
+ const toValProtIndex = toValue(proteinIndex)
+ if (toValSearchResults && toValProtIndex.size > 0 && toValProtIndex.has(toValSearchResults.hit_id)) {
+
+ const prot = toValProtIndex.get(toValSearchResults.hit_id)
+ domain.value = [prot?.previousStart ?? 0, prot?.nextEnd ?? 400]
+ }
+})
+
+const marginLeftGb = ref(10)
+const marginRightGb = ref(10)
+const marginBottomGb = ref(10)
+
+const innerWidth = computed(() => {
+ return computedWidth.value - marginLeftGb.value - marginRightGb.value
+})
+const innerHeigth = computed(() => {
+ return height.value - marginBottomGb.value
+})
+
+const minRange = ref(0)
+const maxRange = ref(innerWidth.value)
+
+
+const svgRef = ref(null)
+
+const domain = ref([0, 10000])
+// const range = ref()
+const xScale = ref(d3.scaleLinear()
+ .domain(domain.value)
+ .range([minRange.value, maxRange.value])
+);
+const yScale = ref(d3.scaleLinear()
+ .domain([-1, 1])
+ .range([0, innerHeigth.value]));
+
+
+
+
+const computedData = computed(() => {
+ const newData = sanitizedData.value.filter(gene => {
+ const { start, end } = gene
+ const [scaleStart, scaleEnd] = xScale.value.domain()
+
+ return start <= scaleEnd && end >= scaleStart
+
+ }).map(gene => {
+ const width = xScale.value(gene.end) - xScale.value(gene.start)
+ const height = yScale.value(-0.75)
+ const x = xScale.value(gene.start) + marginLeftGb.value
+ const y = yScale.value(-0.75) - marginBottomGb.value
+
+ return {
+ ...gene,
+ width,
+ height,
+ x,
+ y
+ }
+ })
+ return newData
+})
+
+function drawGene({ width, height, strand }) {
+ const context = d3.path()
+ const halfHeight = height / 2
+ const isWidthLonger = halfHeight < width
+ if (strand < 0) {
+ context.moveTo(0, halfHeight)
+ if (isWidthLonger) context.lineTo(halfHeight, 0)
+ context.lineTo(width, 0)
+ context.lineTo(width, height)
+ if (isWidthLonger) context.lineTo(halfHeight, height)
+ context.closePath()
+ } else if (strand > 0) {
+ context.moveTo(0, 0)
+ if (isWidthLonger) context.lineTo(width - halfHeight, 0)
+ context.lineTo(width, halfHeight)
+ if (isWidthLonger) context.lineTo(width - halfHeight, height)
+ context.lineTo(0, height)
+ context.closePath()
+ }
+ else {
+ context.moveTo(0, 0)
+ context.lineTo(width, 0)
+ context.lineTo(width, height)
+ context.lineTo(0, height)
+ context.closePath()
+ }
+ return context
+}
+
+function positionText(selection) {
+ selection.each(function (d) {
+ const textWidth = this.clientWidth
+ if (d.width < 10) {
+ d3.select(this)
+ .text('')
+ }
+ // else {
+
+ const halfW = d.width / 2
+ const halfTw = textWidth / 2
+ const k = d.height / 8
+ const x = d.strand > 0 ? halfW - halfTw - k : halfW - halfTw + k
+ d3.select(this)
+ .attr("transform", `translate(${halfW},45) rotate(45)`)
+ // }
+ })
+}
+
+function proteinText(item) {
+
+ if (item.isHmmerHit) {
+ return `${item.gene_name} / ${item.name}`
+ }
+}
+
+function proteinTitle(item) {
+ let title = `name=${item.name} | length=${item.length}`
+
+ if (item.isHmmerHit && !item.isDefenseSystem) {
+ title = `gene name=${item.gene_name} | ${title}`
+ }
+ if (item.isDefenseSystem) {
+ title = `system=${item.defenseSystem} | ${title}`
+ }
+
+ return title
+}
+
+const maxLabelSize = ref(38)
+
+function proteinTextTrunc(item) {
+ const text = proteinText(item)
+ return (text && text.length > maxLabelSize.value) ? text.slice(0, maxLabelSize.value - 1) + '...' : text;
+}
+
+
+function drawGenes(genesSelection) {
+ genesSelection
+ .selectAll("g.gene") // get all "existing" lines in svg
+ .data(computedData.value) // sync them with our data
+ .join(
+ enter => {
+ const g = enter.append("g")
+ .classed("gene", true);
+ g.append("path").classed("gene", true)
+ g.append("text")
+ // .attr("fill", "white")
+ .classed("gene-label", true)
+ .attr("fill", "currentColor")
+ .attr("dominant-baseline", "middle")
+ g.append("title")
+ },
+ update => {
+ update
+ .attr("transform", d => `translate(${d.x},${d.y})`)
+ update.select("path.gene")
+ .attr("d", d => drawGene(d).toString())
+ .attr("fill", d => {
+
+ if (d.isDefenseSystem) return toValue(color)("df")
+ if (displayHmmerHits.value && d.isHmmerHit) return toValue(color)("hmmer")
+ return toValue(color)("default")
+ })
+ update.select("text.gene-label").text(proteinTextTrunc).call(positionText)
+ update.select("title").text(proteinTitle)
+ },
+ exit => exit.remove()
+ )
+
+}
+
+function draw() {
+
+ const throttledZoomed = useThrottleFn((event) => {
+ zoomed(event)
+ }, 50)
+
+
+ function zoomed(event) {
+ const { transform } = event
+ const zx = transform.rescaleX(xScale.value);
+ domain.value = zx.domain()
+ minRange.value = zx.range()[0]
+ maxRange.value = zx.range()[1]
+ }
+
+
+ const svg = d3.select(svgRef.value);
+ const zoom = d3.zoom()
+ .scaleExtent([0.5, 32])
+ .on("zoom", throttledZoomed);
+ const xAxis = d3.axisBottom(xScale.value)
+ let gx = svg.select("g.xaxis")
+ if (gx.empty()) {
+ gx = svg.append("g").classed("xaxis", true)
+
+ }
+ gx
+ .attr("transform", `translate(${marginLeftGb.value},${height.value - 18})`)
+ .call(xAxis)
+
+ let gxTitle = gx.select("text.x-axis-title")
+ if (gxTitle.empty()) {
+ gxTitle = gx.append("text")
+ .classed("x-axis-title", true)
+ .attr("text-anchor", "end")
+ .attr("fill", "currentColor")
+ .html(() => `${computedXUnit.value} →`)
+ }
+ gxTitle
+ .attr("x", innerWidth.value)
+ .attr("y", - 10)
+
+
+
+
+ let gGenes = svg.select("g.genes")
+ if (gGenes.empty()) {
+ gGenes = svg.append("g").classed("genes", true)
+ }
+ gGenes.call(drawGenes, xScale, yScale)
+ svg.call(zoom).call(zoom.transform, d3.zoomIdentity);
+
+
+
+}
+
+onMounted(() => {
+
+ draw()
+})
+
+watchEffect(() => {
+ xScale.value = d3.scaleLinear()
+ .domain(domain.value) // input values...
+ .range([minRange.value, innerWidth.value])
+ draw()
+})
+
+
+
const selectedResult = ref(null);
</script>
<template>
@@ -62,6 +440,21 @@ const selectedResult = ref(null);
</v-row>
</template>
</v-toolbar>
+ <v-card-text>
+ <div ref="gbContainer">
+ <v-card flat color="transparent">
+ <v-toolbar variant="flat" density="compact" color="transparent">
+ <v-spacer></v-spacer><v-toolbar-items>
+ <v-switch v-model="displayHmmerHits" color="primary" label="Display HMM-only hits
+ " class="mr-2"></v-switch>
+ </v-toolbar-items></v-toolbar>
+
+ <svg ref="svgRef" :width="computedWidth" :height="height">
+ <g class="x-axis" />
+ </svg>
+ </v-card>
+ </div>
+ </v-card-text>
<v-card-text>
<v-btn-toggle v-model="selectedResult" rounded="0" color="primary" group>
<v-btn value="systems" :to="`/analyses/${analysis.id}/systems`">
diff --git a/frontend/pages/analyses/[analysisId]/genes.vue b/frontend/pages/analyses/[analysisId]/genes.vue
index 4fb2bdd7e62c1c4569297eb9be36e4aac88dc6d8..229eb007d681c85dfc76e3ad98a20070a6a92e83 100644
--- a/frontend/pages/analyses/[analysisId]/genes.vue
+++ b/frontend/pages/analyses/[analysisId]/genes.vue
@@ -3,39 +3,6 @@ import { useFetch, useRoute, computed } from "#imports";
const route = useRoute();
-export interface Gene {
- replicon: string,
- hit_id: string,
- gene_name: string,
- hit_pos: number,
- model_fqn: string,
- sys_id: string,
- sys_loci: number,
- locus_num: number,
- sys_wholeness: number,
- sys_score: number,
- sys_occ: number,
- hit_gene_ref: string,
- hit_status: string,
- hit_seq_len: number,
- hit_i_eval: number,
- hit_score: number,
- hit_profile_cov: number,
- hit_seq_cov: number,
- hit_begin_match: number,
- hit_end_match: number,
- counterpart: string,
- used_in: string
-}
-
-export interface GenesOut {
- analysis: number,
- genes: Gene[]
-
-}
-
-
-
const { data: genes, error } = await useFetch<GenesOut>(
`/api/analysis/${route.params.analysisId}/genes`
@@ -45,29 +12,31 @@ const { data: genes, error } = await useFetch<GenesOut>(
const search = ref('')
const groupBy = ref([{ key: 'model_fqn', order: 'asc' }])
const headers = ref([
+ { title: "Hit id", align: "end", key: "hit_id", fixed: true },
{ title: "Replicon", align: "end", key: "replicon" },
- { title: "Hit Id", align: "end", key: "hit_id" },
- { title: "Hit Position", align: "end", key: "hit_pos" },
- { title: "Model Fqn", align: "end", key: "model_fqn" },
- { title: "sys_id", align: "end", key: "sys_id" },
- { title: "sys_loci", align: "end", key: "sys_loci" },
+ { title: "Position", align: "end", key: "hit_pos" },
+ { title: "Model fqn", align: "end", key: "model_fqn" },
+ { title: "System id", align: "end", key: "sys_id" },
+ { title: "System loci", align: "end", key: "sys_loci" },
{ title: "locus_num", align: "end", key: "locus_num" },
- { title: "sys_wholeness", align: "end", key: "sys_wholeness" },
- { title: "sys_score", align: "end", key: "sys_score" },
+ // { title: "sys_wholeness", align: "end", key: "sys_wholeness" },
+ { title: "Score", align: "end", key: "sys_score" },
{ title: "sys_occ", align: "end", key: "sys_occ" },
- { title: "hit_gene_ref", align: "end", key: "hit_gene_ref" },
- { title: "hit_status", align: "end", key: "hit_status" },
- { title: "hit_seq_len", align: "end", key: "hit_seq_len" },
- { title: "hit_i_eval", align: "end", key: "hit_i_eval" },
- { title: "hit_score", align: "end", key: "hit_score" },
- { title: "hit_profile_cov", align: "end", key: "hit_profile_cov" },
- { title: "hit_seq_cov", align: "end", key: "hit_seq_cov" },
+ { title: "Gene ref", align: "end", key: "hit_gene_ref" },
+ { title: "Status", align: "end", key: "hit_status" },
+ { title: "Seq length", align: "end", key: "hit_seq_len" },
+ { title: "i_eval", align: "end", key: "hit_i_eval" },
+ { title: "Score", align: "end", key: "hit_score" },
+ { title: "Profile cov", align: "end", key: "hit_profile_cov" },
+ { title: "Seq cov", align: "end", key: "hit_seq_cov" },
]);
const sanitizedGenes = computed(() => {
if (genes.value?.genes) {
- return genes.value.genes
+ return genes.value.genes.map(gene => {
+ return { ...gene, model_fqn: gene.model_fqn.split("/").slice(-2).join(" - "), sys_id: gene.sys_id.split(gene.replicon)[1].slice(1) }
+ })
}
else { return [] }
})
diff --git a/frontend/pages/analyses/[analysisId]/hmmer.vue b/frontend/pages/analyses/[analysisId]/hmmer.vue
index c2f7ba91e1dba432a02b366d672a481a87a860c1..0c781c03cd9d2703b8da89634b1fcbc5a3c4317b 100644
--- a/frontend/pages/analyses/[analysisId]/hmmer.vue
+++ b/frontend/pages/analyses/[analysisId]/hmmer.vue
@@ -2,46 +2,24 @@
import { useFetch, useRoute } from "#imports";
-export interface Hmmer {
- hit_id: string,
- replicon: string,
- hit_pos: number,
- hit_sequence_length: string,
- gene_name: string,
- i_eval: number,
- hit_score: number,
- hit_profile_cov: number,
- hit_seq_cov: number,
- hit_begin_match: number,
- hit_end_match: number
-}
-
-export interface HmmersOut {
- analysis: number,
- hmmers: Hmmer[]
-
-}
const route = useRoute();
-console.log("testsetests ");
const { data: hmmers, error } = await useFetch<HmmersOut>(
`/api/analysis/${route.params.analysisId}/hmmers`
);
-console.log(hmmers);
-console.log(error);
const headers = ref([
- { title: "hit_id", align: "end", key: "hit_id" },
- { title: "replicon", align: "end", key: "replicon" },
- { title: "hit_pos", align: "end", key: "hit_pos" },
- { title: "hit_sequence_length", align: "end", key: "hit_sequence_length" },
- { title: "gene_name", align: "end", key: "gene_name" },
+ { title: "Hit identifier", align: "end", key: "hit_id", fixed: true },
+ { title: "Replicon", align: "end", key: "replicon" },
+ { title: "Position", align: "end", key: "hit_pos" },
+ { title: "Sequence length", align: "end", key: "hit_sequence_length" },
+ { title: "Gene name", align: "end", key: "gene_name" },
{ title: "i_eval", align: "end", key: "i_eval" },
- { title: "hit_score", align: "end", key: "hit_score" },
- { title: "hit_profile_cov", align: "end", key: "hit_profile_cov" },
- { title: "hit_seq_cov", align: "end", key: "hit_seq_cov" },
- { title: "hit_begin_match", align: "end", key: "hit_begin_match" },
- { title: "hit_end_match", align: "end", key: "hit_end_match" },
+ { title: "Score", align: "end", key: "hit_score" },
+ { title: "Profile cov", align: "end", key: "hit_profile_cov" },
+ { title: "Seq cov", align: "end", key: "hit_seq_cov" },
+ { title: "Begin match", align: "end", key: "hit_begin_match" },
+ { title: "End match", align: "end", key: "hit_end_match" },
]);
@@ -52,6 +30,5 @@ const sanitizedHmmer = computed(() => {
})
</script>
<template>
- <AnalysisResultDataTable v-if="sanitizedHmmer.length > 0" :items="sanitizedHmmer" :headers="headers" />
-
+ <AnalysisResultDataTable v-if="sanitizedHmmer.length > 0" :items="sanitizedHmmer" :headers="headers" />
</template>
diff --git a/frontend/pages/analyses/[analysisId]/systems.vue b/frontend/pages/analyses/[analysisId]/systems.vue
index f6b3a0a1f8e8a686b3a7ea540d440ed4cb4623e6..1b50c42cc2f178bf2d80d357c38a9e0bdde04369 100644
--- a/frontend/pages/analyses/[analysisId]/systems.vue
+++ b/frontend/pages/analyses/[analysisId]/systems.vue
@@ -1,24 +1,6 @@
<script setup lang="ts">
import { useFetch, useRoute } from "#imports";
-export interface System {
-
- sys_id: string,
- type: string,
- subtype: string,
- sys_beg: string,
- sys_end: string,
- protein_in_syst: string,
- genes_count: number,
- name_of_profiles_in_sys: string
-
-}
-
-export interface SystemsOut {
- analysis: number,
- systems: System[]
-
-}
const route = useRoute();
const { data: systems, error } = await useFetch<SystemsOut>(
@@ -26,8 +8,8 @@ const { data: systems, error } = await useFetch<SystemsOut>(
);
const headers = ref([
- { title: "sys_id", align: "end", key: "sys_id" },
- { title: "type", align: "end", key: "type" },
+ { title: "type", align: "end", key: "type", fixed: true, },
+ { title: "System id", align: "end", key: "sys_id" },
{ title: "subtype", align: "end", key: "subtype" },
{ title: "sys_beg", align: "end", key: "sys_beg" },
{ title: "sys_end", align: "end", key: "sys_end" },
@@ -36,7 +18,11 @@ const headers = ref([
const sanitizedSystems = computed(() => {
if (systems.value?.systems) {
- return systems.value.systems
+ return systems.value.systems.map((system) => {
+ let newSystem = { ...system, protein_in_syst: system.protein_in_syst.split(',') }
+ if (system.type === 'CasFinder') return { ...newSystem, type: 'Cas' }
+ return newSystem
+ })
} else { return [] }
})
diff --git a/frontend/plugins/api.ts b/frontend/plugins/api.ts
new file mode 100644
index 0000000000000000000000000000000000000000..887143b409d14e76f0744464b3fe1819972e7796
--- /dev/null
+++ b/frontend/plugins/api.ts
@@ -0,0 +1,29 @@
+export default defineNuxtPlugin(() => {
+ const $api = $fetch.create({
+ baseURL: '/api',
+ async onRequest({ request, options, error }) {
+ const { csrfToken } = await useCsrfToken()
+ const toValToken = toValue(csrfToken)
+ if (toValToken !== undefined) {
+ // Add Authorization header
+ if (Array.isArray(options.headers)) {
+ options.headers = options.headers || []
+ options.headers = [...options.headers, ["X-CSRFToken", toValToken]]
+ }
+ else {
+ options.headers = options.headers || {}
+ options.headers = { ...options.headers, "X-CSRFToken": toValToken }
+ }
+ }
+ },
+ onResponseError({ response }) {
+ console.log(response)
+ }
+ })
+ // Expose to useNuxtApp().$api
+ return {
+ provide: {
+ api: $api
+ }
+ }
+})
diff --git a/frontend/types.d.ts b/frontend/types.d.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0973ed9477b20616a7bbbc52d7cca4e2093fdcb2
--- /dev/null
+++ b/frontend/types.d.ts
@@ -0,0 +1,129 @@
+
+
+
+type AnalysisStatus = "running" | "done" | "error" | "paused"
+
+
+interface Analysis {
+ id: number;
+ name: string;
+ status: AnalysisStatus;
+ percentage_done: number;
+ create_time: string
+}
+
+const NON_TERMINAL_STATE = [
+ "running",
+] as const
+type NonTerminalState = typeof NON_TERMINAL_STATE[number]
+
+const TERMINAL_STATE = ["done", "error", "pause"] as const
+
+type TerminalJobState = typeof TERMINAL_STATE[number]
+
+type JobState = NonTerminalState | TerminalJobState
+
+
+
+
+
+
+
+
+
+
+interface Protein {
+ id: string,
+ length: number
+ protLength: number
+ strand: -1 | 1 | null,
+ start: number | null
+ end: number | null
+ name?: string,
+ defenseSystem?: string | undefined,
+ isDefenseSystem?: boolean,
+ isHmmerHit?: boolean
+
+}
+
+interface ProteinsOut {
+ analysis: number,
+ proteins: Protein[]
+
+}
+
+
+// Genes
+interface Gene {
+ replicon: string,
+ hit_id: string,
+ gene_name: string,
+ hit_pos: number,
+ model_fqn: string,
+ sys_id: string,
+ sys_loci: number,
+ locus_num: number,
+ sys_wholeness: number,
+ sys_score: number,
+ sys_occ: number,
+ hit_gene_ref: string,
+ hit_status: string,
+ hit_seq_len: number,
+ hit_i_eval: number,
+ hit_score: number,
+ hit_profile_cov: number,
+ hit_seq_cov: number,
+ hit_begin_match: number,
+ hit_end_match: number,
+ counterpart: string,
+ used_in: string
+}
+
+interface GenesOut {
+ analysis: number,
+ genes: Gene[]
+
+}
+
+
+// hmmers
+
+interface Hmmer {
+ hit_id: string,
+ replicon: string,
+ hit_pos: number,
+ hit_sequence_length: string,
+ gene_name: string,
+ i_eval: number,
+ hit_score: number,
+ hit_profile_cov: number,
+ hit_seq_cov: number,
+ hit_begin_match: number,
+ hit_end_match: number
+}
+
+interface HmmersOut {
+ analysis: number,
+ hmmers: Hmmer[]
+
+}
+
+
+interface System {
+
+ sys_id: string,
+ type: string,
+ subtype: string,
+ sys_beg: string,
+ sys_end: string,
+ protein_in_syst: string,
+ genes_count: number,
+ name_of_profiles_in_sys: string
+
+}
+
+interface SystemsOut {
+ analysis: number,
+ systems: System[]
+
+}