diff --git a/backend/analysis/api.py b/backend/analysis/api.py
index ce4129ea5a67338cba95ac54298a93b72f0c25b3..ca66b6195943b77b05303d931901e8c9234ecc3e 100644
--- a/backend/analysis/api.py
+++ b/backend/analysis/api.py
@@ -1,13 +1,11 @@
import os
-import tarfile
from tempfile import mkstemp
from django.conf import settings
-from ninja import Router, File, Form
+from ninja import Router, File
from ninja.files import UploadedFile
from analysis.models import (
Analysis,
- AnalysisHistory,
AnalysisWorkflow,
Gene,
Hmmer,
@@ -101,7 +99,9 @@ def get_analysis(request, analysis_id: int):
analysis = Analysis.objects.get(
pk=analysis_id, analysis_history__session=session
)
+
analysis.synchronize()
+ analysis.set_stderr()
analysis.load_genes()
analysis.load_systems()
analysis.load_hmmers()
diff --git a/backend/analysis/migrations/0008_analysis_stderr.py b/backend/analysis/migrations/0008_analysis_stderr.py
new file mode 100644
index 0000000000000000000000000000000000000000..ee93bb9b9d71f2e381f38075bd47a682e89baeb1
--- /dev/null
+++ b/backend/analysis/migrations/0008_analysis_stderr.py
@@ -0,0 +1,18 @@
+# Generated by Django 4.2.3 on 2024-03-05 13:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('analysis', '0007_protein'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='analysis',
+ name='stderr',
+ field=models.TextField(blank=True),
+ ),
+ ]
diff --git a/backend/analysis/model_schemas.py b/backend/analysis/model_schemas.py
index 1b63c716a4145fbf480537cf20e1f9eb8f140ede..7df65d0ca7459690aacffb89c290dca4c2b22083 100644
--- a/backend/analysis/model_schemas.py
+++ b/backend/analysis/model_schemas.py
@@ -51,6 +51,7 @@ class AnalysisOutSchema(ModelSchema):
analysis_workflow: AnalysisWorkflowSchema
history: AnalysisHistorySchema
percentage_done: float = 0.0
+ stderr: str
class Config:
model = Analysis
@@ -90,4 +91,4 @@ class ProteinOutSchema(ModelSchema):
class Config:
model = Protein
- model_fields = ["analysis", "proteins"]
\ No newline at end of file
+ model_fields = ["analysis", "proteins"]
diff --git a/backend/analysis/models.py b/backend/analysis/models.py
index 65db950209fa1c38c8f789af5daabb5399e50f7d..3d42eb62957479fe821df4d14fc2a69c28f8a6c4 100644
--- a/backend/analysis/models.py
+++ b/backend/analysis/models.py
@@ -2,11 +2,16 @@ import csv
import tarfile
from typing import Any
from django.db import models
+from django_to_galaxy.utils import enabled_cache
from django.contrib.sessions.models import Session
from tempfile import mkstemp
from django.conf import settings
from Bio import SeqIO
from pathlib import Path
+from rich.console import Console
+from typing import List, Dict
+
+console = Console()
# from galaxy.models import WorkflowInvocation
@@ -16,7 +21,7 @@ from django_to_galaxy.models import (
GalaxyUser,
History as DgHistory,
)
-from django_to_galaxy.models.invocation import DONE
+from django_to_galaxy.models.invocation import DONE, ERROR
from django_to_galaxy.utils import (
load_galaxy_invocation_time_to_datetime,
load_galaxy_history_time_to_datetime,
@@ -124,10 +129,33 @@ class Analysis(Invocation):
analysis_history = models.ForeignKey(AnalysisHistory, on_delete=models.CASCADE)
params = models.JSONField()
datamap = models.JSONField()
+ stderr = models.TextField(blank=True)
class Meta:
ordering = ["-create_time"]
+ def _build_job_id_to_tools(self) -> Dict[str, dict]:
+ step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+ job_id_to_tools = {}
+ for step in step_jobs_summary:
+ job_id = step["id"]
+ job = self.workflow.galaxy_owner.obj_gi.jobs.get(job_id)
+ wrapped_tool = self.workflow.galaxy_owner.obj_gi.tools.get(
+ job.wrapped["tool_id"]
+ ).wrapped
+ job_id_to_tools[job_id] = wrapped_tool
+ return job_id_to_tools
+
+ """Retrive `step_jobs_summary` with details of tool used."""
+ step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+ detailed_jobs_summary = []
+ for step in step_jobs_summary:
+ detailed_step = step
+ job_id = step["id"]
+ detailed_step["tool"] = self.job_id_to_tools_perso.get(job_id, {})
+ detailed_jobs_summary.append(detailed_step)
+ return detailed_jobs_summary
+
def download_results(
self,
):
@@ -243,6 +271,18 @@ class Analysis(Invocation):
prots = Protein(analysis=self, proteins=json_prots)
prots.save()
+ def set_stderr(self):
+
+ if self.status == ERROR and self.stderr == "":
+ steps = self.detailed_step_jobs_summary
+ for step in steps:
+ job_id = step["id"]
+ job = self.analysis_history.analysis_owner.obj_gi.jobs.get(
+ job_id, full_details=True
+ )
+ self.stderr = job.wrapped["tool_stderr"]
+ self.save()
+
def read_fasta_file(self, file_path):
sequences = []
if file_path is not None:
@@ -251,19 +291,16 @@ class Analysis(Invocation):
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
diff --git a/backend/defense_finder_api/settings.py b/backend/defense_finder_api/settings.py
index 878ff3ed4bf38a7154acc01cba7f3e4143b35561..fcfc47007df775718e14b7b5fb89d5484d367327 100644
--- a/backend/defense_finder_api/settings.py
+++ b/backend/defense_finder_api/settings.py
@@ -18,7 +18,7 @@ env = environ.Env(
# set casting, default value
DEBUG=(bool, False),
DF_HOSTNAME=(str, "localhost"),
- STATIC_URL=(str, "/static/")
+ STATIC_URL=(str, "/static/"),
)
environ.Env.read_env()
@@ -52,7 +52,7 @@ INSTALLED_APPS = [
"django.contrib.sessions",
"django.contrib.messages",
"django.contrib.staticfiles",
- "galaxy",
+ # "galaxy",
"analysis",
"django_to_galaxy",
]
@@ -93,12 +93,12 @@ WSGI_APPLICATION = "defense_finder_api.wsgi.application"
DATABASES = {
"default": env.db(),
- # {
+ # "default": {
# "ENGINE": "django.db.backends.postgresql",
- # "NAME": "df-db",
- # "USER": "df",
- # "PASSWORD": "password",
- # "HOST": "postgresql",
+ # "NAME": env("POSTGRES_DB"),
+ # "USER": env("POSTGRES_USER"),
+ # "PASSWORD": env("POSTGRES_PASSWORD"),
+ # "HOST": env("POSTGRES_HOST"),
# "PORT": "5432",
# }
}
diff --git a/backend/galaxy/__init__.py b/backend/galaxy/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/backend/galaxy/admin.py b/backend/galaxy/admin.py
deleted file mode 100644
index 8c38f3f3dad51e4585f3984282c2a4bec5349c1e..0000000000000000000000000000000000000000
--- a/backend/galaxy/admin.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from django.contrib import admin
-
-# Register your models here.
diff --git a/backend/galaxy/apps.py b/backend/galaxy/apps.py
deleted file mode 100644
index 042bab42cd5991225fb3aaa16c3feec1242d09f1..0000000000000000000000000000000000000000
--- a/backend/galaxy/apps.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from django.apps import AppConfig
-
-
-class GalaxyConfig(AppConfig):
- default_auto_field = "django.db.models.BigAutoField"
- name = "galaxy"
diff --git a/backend/galaxy/managers.py b/backend/galaxy/managers.py
deleted file mode 100644
index 2e550c346761450cac8d6226c33ece2bea264113..0000000000000000000000000000000000000000
--- a/backend/galaxy/managers.py
+++ /dev/null
@@ -1,11 +0,0 @@
-from django.db import models
-
-
-class InstanceManager(models.Manager):
- def get_by_natural_key(self, name):
- return self.get(name=name)
-
-
-class UserManager(models.Manager):
- def get_by_natural_key(self, username, instance):
- return self.get(username=username, instance=instance)
diff --git a/backend/galaxy/migrations/0001_initial.py b/backend/galaxy/migrations/0001_initial.py
deleted file mode 100644
index 8e078bb5d6e678c800455c69f9292fc70ec7e275..0000000000000000000000000000000000000000
--- a/backend/galaxy/migrations/0001_initial.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# Generated by Django 4.2.3 on 2023-07-25 11:56
-
-from django.db import migrations, models
-import django.db.models.deletion
-import django.utils.timezone
-
-
-class Migration(migrations.Migration):
- initial = True
-
- dependencies = []
-
- operations = [
- migrations.CreateModel(
- name="Instance",
- fields=[
- (
- "id",
- models.BigAutoField(
- auto_created=True,
- primary_key=True,
- serialize=False,
- verbose_name="ID",
- ),
- ),
- ("name", models.CharField(max_length=200, unique=True)),
- ("url", models.URLField(unique=True)),
- ("description", models.TextField(blank=True)),
- ],
- options={
- "ordering": ["name"],
- },
- ),
- migrations.CreateModel(
- name="WorkflowInvocation",
- fields=[
- (
- "id",
- models.BigAutoField(
- auto_created=True,
- primary_key=True,
- serialize=False,
- verbose_name="ID",
- ),
- ),
- ("name", models.CharField(max_length=20)),
- (
- "creation_date",
- models.DateTimeField(default=django.utils.timezone.now),
- ),
- ],
- ),
- migrations.CreateModel(
- name="User",
- fields=[
- (
- "id",
- models.BigAutoField(
- auto_created=True,
- primary_key=True,
- serialize=False,
- verbose_name="ID",
- ),
- ),
- ("username", models.EmailField(max_length=254)),
- ("api_key", models.CharField(blank=True, max_length=254)),
- (
- "instance",
- models.ForeignKey(
- on_delete=django.db.models.deletion.CASCADE,
- to="galaxy.instance",
- ),
- ),
- ],
- options={
- "ordering": ["username", "instance"],
- "unique_together": {("username", "instance")},
- },
- ),
- ]
diff --git a/backend/galaxy/migrations/__init__.py b/backend/galaxy/migrations/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/backend/galaxy/models.py b/backend/galaxy/models.py
deleted file mode 100644
index 46899499191eaf641beee8a7c615cb559636e4a4..0000000000000000000000000000000000000000
--- a/backend/galaxy/models.py
+++ /dev/null
@@ -1,43 +0,0 @@
-from django.utils import timezone
-from django.db import models
-
-from galaxy.managers import InstanceManager, UserManager
-
-# Create your models here.
-
-
-class Instance(models.Model):
- name = models.CharField(max_length=200, unique=True)
- url = models.URLField(unique=True)
- description = models.TextField(blank=True)
-
- objects = InstanceManager()
-
- class Meta:
- ordering = ["name"]
-
- def natural_key(self):
- return (self.name,)
-
- def __str__(self):
- return self.name
-
-
-class User(models.Model):
- username = models.EmailField(max_length=254)
- api_key = models.CharField(max_length=254, blank=True)
- instance = models.ForeignKey(Instance, on_delete=models.CASCADE)
-
- objects = UserManager()
-
- class Meta:
- ordering = ["username", "instance"]
- unique_together = [["username", "instance"]]
-
- def natural_key(self):
- return (self.username, self.instance)
-
-
-class WorkflowInvocation(models.Model):
- name = models.CharField(max_length=20)
- creation_date = models.DateTimeField(default=timezone.now)
diff --git a/backend/galaxy/tests.py b/backend/galaxy/tests.py
deleted file mode 100644
index 7ce503c2dd97ba78597f6ff6e4393132753573f6..0000000000000000000000000000000000000000
--- a/backend/galaxy/tests.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from django.test import TestCase
-
-# Create your tests here.
diff --git a/backend/galaxy/views.py b/backend/galaxy/views.py
deleted file mode 100644
index 91ea44a218fbd2f408430959283f0419c921093e..0000000000000000000000000000000000000000
--- a/backend/galaxy/views.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from django.shortcuts import render
-
-# Create your views here.
diff --git a/backend/poetry.lock b/backend/poetry.lock
index 3b67d8e5d85f1bcc73026b3e0ab183ed7b309a57..cadcff4180946868fdc6f8cbb36ec8361a40db33 100644
--- a/backend/poetry.lock
+++ b/backend/poetry.lock
@@ -450,6 +450,41 @@ files = [
[package.extras]
testing = ["coverage", "pyyaml"]
+[[package]]
+name = "markdown-it-py"
+version = "3.0.0"
+description = "Python port of markdown-it. Markdown parsing, done right!"
+optional = false
+python-versions = ">=3.8"
+files = [
+ {file = "markdown-it-py-3.0.0.tar.gz", hash = "sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb"},
+ {file = "markdown_it_py-3.0.0-py3-none-any.whl", hash = "sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1"},
+]
+
+[package.dependencies]
+mdurl = ">=0.1,<1.0"
+
+[package.extras]
+benchmarking = ["psutil", "pytest", "pytest-benchmark"]
+code-style = ["pre-commit (>=3.0,<4.0)"]
+compare = ["commonmark (>=0.9,<1.0)", "markdown (>=3.4,<4.0)", "mistletoe (>=1.0,<2.0)", "mistune (>=2.0,<3.0)", "panflute (>=2.3,<3.0)"]
+linkify = ["linkify-it-py (>=1,<3)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["jupyter_sphinx", "mdit-py-plugins", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx_book_theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
+
+[[package]]
+name = "mdurl"
+version = "0.1.2"
+description = "Markdown URL utilities"
+optional = false
+python-versions = ">=3.7"
+files = [
+ {file = "mdurl-0.1.2-py3-none-any.whl", hash = "sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8"},
+ {file = "mdurl-0.1.2.tar.gz", hash = "sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba"},
+]
+
[[package]]
name = "mypy-extensions"
version = "1.0.0"
@@ -682,6 +717,21 @@ typing-extensions = ">=4.2.0"
dotenv = ["python-dotenv (>=0.10.4)"]
email = ["email-validator (>=1.0.3)"]
+[[package]]
+name = "pygments"
+version = "2.17.2"
+description = "Pygments is a syntax highlighting package written in Python."
+optional = false
+python-versions = ">=3.7"
+files = [
+ {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
+ {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
+]
+
+[package.extras]
+plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
+
[[package]]
name = "pytz"
version = "2023.3"
@@ -817,6 +867,24 @@ files = [
[package.dependencies]
requests = ">=2.0.1,<3.0.0"
+[[package]]
+name = "rich"
+version = "13.7.1"
+description = "Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal"
+optional = false
+python-versions = ">=3.7.0"
+files = [
+ {file = "rich-13.7.1-py3-none-any.whl", hash = "sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222"},
+ {file = "rich-13.7.1.tar.gz", hash = "sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432"},
+]
+
+[package.dependencies]
+markdown-it-py = ">=2.2.0"
+pygments = ">=2.13.0,<3.0.0"
+
+[package.extras]
+jupyter = ["ipywidgets (>=7.5.1,<9)"]
+
[[package]]
name = "six"
version = "1.16.0"
@@ -911,4 +979,4 @@ zstd = ["zstandard (>=0.18.0)"]
[metadata]
lock-version = "2.0"
python-versions = "^3.10"
-content-hash = "89a87025d377cb3257ccd2e8e2d4eafab8ac82c7714d350dd7d50f09226ca9d8"
+content-hash = "0178257066e14753b45a43635af1b8fb9ab5f4773148e50f2ae63573f08e98b7"
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index 31d51f3ffe5e3365401639a4051a144a0ec7a4b2..684756c6a271798c4c052f1fac5f97f9a05bf089 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -13,6 +13,7 @@ django-to-galaxy = "^0.6.4"
django-environ = "^0.10.0"
gunicorn = "^21.2.0"
biopython = "^1.83"
+rich = "^13.7.1"
[tool.poetry.group.dev.dependencies]
diff --git a/deploy/charts/djangoninja/templates/deployment.yaml b/deploy/charts/djangoninja/templates/deployment.yaml
index 7eb4b594be90f95b4d14745949f0fbe111fb2756..78458349d5b0c4555d1a3ee06cc522291e0c0e05 100644
--- a/deploy/charts/djangoninja/templates/deployment.yaml
+++ b/deploy/charts/djangoninja/templates/deployment.yaml
@@ -74,18 +74,20 @@ spec:
secretKeyRef:
name: "{{ .Values.postgresql.user }}.{{ .Values.postgresql.teamId }}-postgresql.credentials.postgresql.acid.zalan.do"
key: username
+ - name: POSTGRES_HOST
+ value: "{{ .Values.postgresql.teamId }}-postgresql"
- name: POSTGRES_DB
value: {{ .Values.postgresql.name }}
- name: DATABASE_URL
value: "psql://$(POSTGRES_USER):$(POSTGRES_PASSWORD)@{{ .Values.postgresql.teamId }}-postgresql:5432/$(POSTGRES_DB)"
- # livenessProbe:
- # httpGet:
- # path: /
- # port: 8000
- # readinessProbe:
- # httpGet:
- # path: /
- # port: 8000
+ livenessProbe:
+ httpGet:
+ path: /api/docs
+ port: 8000
+ readinessProbe:
+ httpGet:
+ path: /api/docs
+ port: 8000
resources:
{{- toYaml .Values.resources | nindent 12 }}
volumeMounts:
@@ -93,6 +95,57 @@ spec:
# name: server-static
- mountPath: /uploaded-files
name: uploaded-files
+ - name: "{{ .Chart.Name }}-sidecar"
+ securityContext:
+ {{- toYaml .Values.securityContext | nindent 12 }}
+ image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+ imagePullPolicy: {{ .Values.image.pullPolicy }}
+ command: [ "/bin/bash", "-c", "--" ]
+ args: [ "while true; do python manage.py clear-sessions-history; python manage.py clearsessions; find /uploaded-files -type f -mmin +360 -delete; sleep 3600; done;" ]
+ ports:
+ - name: http
+ containerPort: {{ .Values.service.port }}
+ protocol: TCP
+ envFrom:
+ - configMapRef:
+ name: galaxy-config-map
+ env:
+ - name: DEBUG
+ value: "True"
+ - name: SECRET_KEY
+ value: {{ .Values.django.secret }}
+ - name: GALAXY_API_KEY
+ valueFrom:
+ secretKeyRef:
+ name: galaxy-secret
+ key: galaxy_key
+ - name: DF_HOSTNAME
+ value: {{ .Release.Name }}
+ - name: POSTGRES_PASSWORD
+ valueFrom:
+ secretKeyRef:
+ name: "{{ .Values.postgresql.user }}.{{ .Values.postgresql.teamId }}-postgresql.credentials.postgresql.acid.zalan.do"
+ key: password
+ - name: POSTGRES_USER
+ valueFrom:
+ secretKeyRef:
+ name: "{{ .Values.postgresql.user }}.{{ .Values.postgresql.teamId }}-postgresql.credentials.postgresql.acid.zalan.do"
+ key: username
+ - name: POSTGRES_DB
+ value: {{ .Values.postgresql.name }}
+ - name: POSTGRES_HOST
+ value: "{{ .Values.postgresql.teamId }}-postgresql"
+ - name: DATABASE_URL
+ value: "psql://$(POSTGRES_USER):$(POSTGRES_PASSWORD)@{{ .Values.postgresql.teamId }}-postgresql:5432/$(POSTGRES_DB)"
+ resources:
+ {{- toYaml .Values.resources | nindent 12 }}
+ volumeMounts:
+ # - mountPath: /code/public/static
+ # name: server-static
+ - mountPath: /uploaded-files
+ name: uploaded-files
+
+
{{- with .Values.nodeSelector }}
nodeSelector:
{{- toYaml . | nindent 8 }}
diff --git a/deploy/charts/djangoninja/values.yaml b/deploy/charts/djangoninja/values.yaml
index 858f109edc2dd62afae1342e25ced6ba7204dfdf..8d45c08398dd67a9055d4ed67e1c997c285b102c 100644
--- a/deploy/charts/djangoninja/values.yaml
+++ b/deploy/charts/djangoninja/values.yaml
@@ -38,7 +38,7 @@ securityContext:
# readOnlyRootFilesystem: true
runAsNonRoot: true
runAsUser: 1001
- fsGroup: 1001
+ # fsGroup: 1001
service:
type: ClusterIP
diff --git a/deploy/charts/nuxt/templates/deployment.yaml b/deploy/charts/nuxt/templates/deployment.yaml
index d85e96f17b71ceebde9131e500f8b0f16e631709..257e257959c73710e04b865bf0ec38d27219be06 100644
--- a/deploy/charts/nuxt/templates/deployment.yaml
+++ b/deploy/charts/nuxt/templates/deployment.yaml
@@ -39,14 +39,14 @@ spec:
- name: http
containerPort: {{ .Values.service.port }}
protocol: TCP
- # livenessProbe:
- # httpGet:
- # path: /
- # port: http
- # readinessProbe:
- # httpGet:
- # path: /
- # port: http
+ livenessProbe:
+ httpGet:
+ path: /
+ port: 3000
+ readinessProbe:
+ httpGet:
+ path: /
+ port: 3000
resources:
{{- toYaml .Values.resources | nindent 12 }}
{{- with .Values.nodeSelector }}
diff --git a/deploy/templates/postgres-operator.yaml b/deploy/templates/postgres-operator.yaml
index 7ea69dde834430ca2d3dc9440fe95624bc85aaaf..83e5fab5d8b8e9d027bdf6b1081ae7aa1dba6bc5 100644
--- a/deploy/templates/postgres-operator.yaml
+++ b/deploy/templates/postgres-operator.yaml
@@ -3,7 +3,7 @@ kind: postgresql
metadata:
name: {{ .Values.postgresql.teamId }}-postgresql
spec:
- dockerImage: ghcr.io/zalando/spilo-15:3.0-p1
+ dockerImage: harbor.pasteur.fr/dockerhub/spilo:15.13-latest
teamId: {{ .Values.postgresql.teamId }}
numberOfInstances: 1
users:
diff --git a/deploy/values.development.yaml b/deploy/values.development.yaml
index 1cabaaed1163ba82d3d102211991c01dcdde32e8..dbeea52f0959cd6e6f78cad18f22855dca28b664 100644
--- a/deploy/values.development.yaml
+++ b/deploy/values.development.yaml
@@ -39,6 +39,7 @@ postgresql:
cpu: 1000m
memory: 3Gi
logical_backup: false
+ shared_buffers: "250MB"
django:
secret: "not-secret"
diff --git a/deploy/values.production.yaml b/deploy/values.production.yaml
index 545daaba5f6d3b17a453e2985f932fe81580f6a7..681280676c1547816914fc929ee78178e3d8f317 100644
--- a/deploy/values.production.yaml
+++ b/deploy/values.production.yaml
@@ -76,6 +76,7 @@ postgresql:
memory: "2Gi"
ephemeral-storage: "1Gi"
logical_backup: true
+ shared_buffers: "300MB"
wiki:
diff --git a/frontend/pages/analyses/[analysisId].vue b/frontend/pages/analyses/[analysisId].vue
index a78b0b5b22c3f0b4a6f5620737a6832d4c2ce7a3..cf4510d81836bfa1b2d19aa0221d7f886e087e2c 100644
--- a/frontend/pages/analyses/[analysisId].vue
+++ b/frontend/pages/analyses/[analysisId].vue
@@ -415,6 +415,7 @@ watchEffect(() => {
const selectedResult = ref(null);
</script>
+
<template>
<v-card v-if="analysis" flat color="transparent">
@@ -425,10 +426,11 @@ const selectedResult = ref(null);
<v-card>
<v-toolbar density="compact" class="pr-2">
<v-toolbar-title>{{ analysis.name }}</v-toolbar-title>
- <v-btn color="primary" prepend-icon="mdi-download" :href="`/api/analysis/${analysis.id}/results-archive`">Download
+ <v-btn color="primary" prepend-icon="mdi-download"
+ :href="`/api/analysis/${analysis.id}/results-archive`">Download
all results</v-btn>
<v-chip color="primary" rounded>{{ new Date(analysis.create_time).toLocaleString() }}</v-chip>
- <template v-if="analysis.percentage_done !== 100" #extension>
+ <template v-if="analysis.percentage_done !== 100 && analysis.stderr === ''" #extension>
<v-row>
<v-col cols="12">
<v-card flat color="transparent">
@@ -440,36 +442,48 @@ 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
+
+ <template v-if="analysis.stderr !== ''">
+ <v-card color="error" variant="tonal" class="my-2">
+ <v-card-title>Standard error</v-card-title>
+ <v-card-text>
+ <pre> {{ analysis.stderr }} </pre>
+ </v-card-text>
+ </v-card>
+ </template>
+
+ <template v-else>
+ <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/${analysis.id}/systems`">
-
- Systems
- </v-btn>
- <v-btn value="genes" exact :to="`/analyses/${analysis.id}/genes`">
- Genes
- </v-btn>
- <v-btn value="hmmer" :to="`/analyses/${analysis.id}/hmmer`">
- Hmmer
- </v-btn>
- </v-btn-toggle>
- <!-- <NuxtLink :to="`/analyses/${analysis.id}/genes`">Genes</NuxtLink> -->
- </v-card-text>
+ </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/${analysis.id}/systems`">
+
+ Systems
+ </v-btn>
+ <v-btn value="genes" exact :to="`/analyses/${analysis.id}/genes`">
+ Genes
+ </v-btn>
+ <v-btn value="hmmer" :to="`/analyses/${analysis.id}/hmmer`">
+ Hmmer
+ </v-btn>
+ </v-btn-toggle>
+ <!-- <NuxtLink :to="`/analyses/${analysis.id}/genes`">Genes</NuxtLink> -->
+ </v-card-text>
+ </template>
<NuxtPage />
</v-card>
</v-card>