diff --git a/ippisite/ippidb/admin.py b/ippisite/ippidb/admin.py
index 45385a302e94dc4d7baa6b881daa52ed54d19646..35003c29988314df1a34ffbfda74cc1f741124d6 100644
--- a/ippisite/ippidb/admin.py
+++ b/ippisite/ippidb/admin.py
@@ -27,8 +27,10 @@ from .models import (
Ppi,
ProteinDomainComplex,
Contribution,
+ Job,
)
from .tasks import launch_validate_contributions
+from django.urls import reverse
class ViewOnSiteModelAdmin(admin.ModelAdmin):
@@ -60,6 +62,68 @@ class ViewOnSiteModelAdmin(admin.ModelAdmin):
)
+@admin.register(Job)
+class JobModelAdmin(admin.ModelAdmin):
+ date_hierarchy = "task_result__date_done"
+ list_display = (
+ "task_result_task_name",
+ "task_result_task_id",
+ "task_result_status",
+ "task_result_date_created",
+ "task_result_date_done",
+ )
+ list_filter = (
+ "task_result__status",
+ "task_result__date_done",
+ "task_result__task_name",
+ )
+ readonly_fields = (
+ "task_result_task_name",
+ "task_result_task_id",
+ "task_result_status",
+ "task_result_date_created",
+ "task_result_date_done",
+ )
+ search_fields = (
+ "task_result__task_name",
+ "task_result__task_id",
+ "task_result__status",
+ )
+ fields = (
+ ("task_result_task_name", "task_result_task_id"),
+ "task_result_status",
+ ("task_result_date_created", "task_result_date_done"),
+ ("std_out", "std_err"),
+ )
+
+ def task_result_task_id(self, x):
+ return x.task_result.task_id
+
+ def task_result_task_name(self, x):
+ return x.task_result.task_name
+
+ def task_result_date_done(self, x):
+ return x.task_result.date_done
+
+ def task_result_status(self, x):
+ return x.task_result.status
+
+ def task_result_date_created(self, x):
+ return x.task_result.date_created
+
+ # def task_link(self, x):
+ # href = reverse("admin:task-results", args=[x.task_result.id])
+ # print(href)
+ # return '<a href="/admin/django_celery_results/taskresult/{}/change/">{}</a>'.format(x.task_result.id, x.task_result.task_id)
+
+ # task_link.allow_tags = True
+ task_result_task_id.short_description = "task_id"
+ task_result_task_name.short_description = "task_name"
+ task_result_date_done.short_description = "date_done"
+ task_result_status.short_description = "status"
+ task_result_date_created.short_description = "date_created"
+
+
@admin.register(Bibliography)
class BibliographyModelAdmin(ViewOnSiteModelAdmin):
list_display = ("authors_list", "title", "journal_name", "biblio_year", "id_source")
diff --git a/ippisite/ippidb/migrations/0041_job.py b/ippisite/ippidb/migrations/0041_job.py
new file mode 100644
index 0000000000000000000000000000000000000000..58db99c1390c1eec38a2cedaa8a2a532b0a2534e
--- /dev/null
+++ b/ippisite/ippidb/migrations/0041_job.py
@@ -0,0 +1,23 @@
+# Generated by Django 2.2.1 on 2020-03-18 23:11
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0040_compound_families'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='Job',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(help_text='task name', max_length=125)),
+ ('status', models.CharField(choices=[('INIT', 'init'), ('RUNNING', 'running'), ('SUCCESS', 'success'), ('ERROR', 'error')], db_index=True, default='INIT', help_text='The status of this job.', max_length=30, verbose_name='job status')),
+ ('std_out', models.TextField(blank=True, help_text='task standard output', null=True)),
+ ('std_err', models.TextField(blank=True, help_text='task error output', null=True)),
+ ],
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0042_auto_20200319_1032.py b/ippisite/ippidb/migrations/0042_auto_20200319_1032.py
new file mode 100644
index 0000000000000000000000000000000000000000..da4735659484fcba18ef7b2906a5fa3d19065cdc
--- /dev/null
+++ b/ippisite/ippidb/migrations/0042_auto_20200319_1032.py
@@ -0,0 +1,23 @@
+# Generated by Django 2.2.1 on 2020-03-19 10:32
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0041_job'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='job',
+ name='std_err',
+ field=models.TextField(blank=True, default='', help_text='task error output', null=True),
+ ),
+ migrations.AlterField(
+ model_name='job',
+ name='std_out',
+ field=models.TextField(blank=True, default='', help_text='task standard output', null=True),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0043_job_task_id.py b/ippisite/ippidb/migrations/0043_job_task_id.py
new file mode 100644
index 0000000000000000000000000000000000000000..1c5ccd79f1f6656197e846ba42e3e228e6506b9f
--- /dev/null
+++ b/ippisite/ippidb/migrations/0043_job_task_id.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.1 on 2020-03-20 17:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0042_auto_20200319_1032'),
+ ]
+
+ operations = [
+ migrations.AddField(
+ model_name='job',
+ name='task_id',
+ field=models.CharField(blank=True, help_text='task id', max_length=50, null=True),
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0044_auto_20200323_1110.py b/ippisite/ippidb/migrations/0044_auto_20200323_1110.py
new file mode 100644
index 0000000000000000000000000000000000000000..09d458a4c876f69cfb6c924b899bbb8535800765
--- /dev/null
+++ b/ippisite/ippidb/migrations/0044_auto_20200323_1110.py
@@ -0,0 +1,34 @@
+# Generated by Django 2.2.1 on 2020-03-23 11:10
+
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('django_celery_results', '0007_remove_taskresult_hidden'),
+ ('ippidb', '0043_job_task_id'),
+ ]
+
+ operations = [
+ migrations.RemoveField(
+ model_name='job',
+ name='name',
+ ),
+ migrations.RemoveField(
+ model_name='job',
+ name='status',
+ ),
+ migrations.RemoveField(
+ model_name='job',
+ name='task_id',
+ ),
+ migrations.AddField(
+ model_name='job',
+ name='task_result',
+ field=models.OneToOneField(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='django_celery_results.TaskResult'),
+ preserve_default=False,
+ ),
+ ]
diff --git a/ippisite/ippidb/migrations/0045_auto_20200323_1235.py b/ippisite/ippidb/migrations/0045_auto_20200323_1235.py
new file mode 100644
index 0000000000000000000000000000000000000000..48fe4e5376c4fb923297bc57cd72de0681f1ddbd
--- /dev/null
+++ b/ippisite/ippidb/migrations/0045_auto_20200323_1235.py
@@ -0,0 +1,19 @@
+# Generated by Django 2.2.1 on 2020-03-23 12:35
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0044_auto_20200323_1110'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='job',
+ name='task_result',
+ field=models.OneToOneField(default=None, on_delete=django.db.models.deletion.CASCADE, to='django_celery_results.TaskResult'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index ddf55fdbf85643a96037f666acb241ca99989ac4..edb2786d57ebcd3fe7f7b0482360cbbc58b23a1a 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -6,6 +6,7 @@ from __future__ import unicode_literals
import operator
import re
+import sys
from django.conf import settings
from django.contrib.auth import get_user_model
@@ -16,6 +17,9 @@ from django.db.models import Max, Count, F, Q, Case, When, Subquery, OuterRef
from django.db.models.functions import Cast
from django.urls import reverse
from django.utils.translation import ugettext_lazy as _
+from django_celery_results.models import TaskResult
+from django.dispatch import receiver
+from django.db.models.signals import post_save
from .utils import FingerPrinter, smi2inchi, smi2inchikey
from .ws import (
@@ -1691,3 +1695,33 @@ def update_compound_cached_properties(compounds_queryset=None):
.values("_lipinsky")[:1]
)
)
+
+
+class Job(models.Model):
+ task_result = models.OneToOneField(
+ TaskResult, on_delete=models.CASCADE, default=None
+ )
+ std_out = models.TextField(
+ null=True, default="", blank=True, help_text="task standard output"
+ )
+ std_err = models.TextField(
+ null=True, default="", blank=True, help_text="task error output"
+ )
+
+ def write(self, message, output="std_out"):
+ if output == "std_out":
+ print(message, file=sys.stdout)
+ self.std_out += "\n{}".format(message)
+ self.save()
+ elif output == "std_err":
+ print(message, file=sys.stderr)
+ self.std_err += "\n{}".format(message)
+ self.save()
+ else:
+ raise Exception("output doesn't exist")
+
+
+@receiver(post_save, sender=TaskResult)
+def post_save_taskresult(sender, instance, created, *args, **kwargs):
+ if created:
+ Job.objects.create(task_result=instance)
diff --git a/ippisite/ippidb/tasks.py b/ippisite/ippidb/tasks.py
index becdf53d629f528b16f3b222823eb255bb781e48..aa28e3ef86d35c116c4ae4adc45727f2e06eb119 100644
--- a/ippisite/ippidb/tasks.py
+++ b/ippisite/ippidb/tasks.py
@@ -6,9 +6,12 @@ import base64
import itertools
-from celery import shared_task
-import seaborn as sns
+from celery import shared_task, task, states
+from ippisite.decorator import IppidbTask
import matplotlib.pyplot as plt
+
+plt.switch_backend("Agg")
+import seaborn as sns
import numpy as np
import pandas as pd
from sklearn.decomposition import PCA
@@ -23,6 +26,7 @@ from .models import (
update_compound_cached_properties,
LeLleBiplotData,
PcaBiplotData,
+ Job,
)
from .utils import smi2sdf
from .gx import GalaxyCompoundPropertiesRunner
@@ -311,6 +315,20 @@ def validate_compounds(compound_ids):
generate_pca_plot()
+@task(base=IppidbTask, bind=True)
+def launch_test_command_caching(self):
+ import time
+ import random
+
+ self.update_job(std_out="Before first sleep, state={}".format(self.state))
+ time.sleep(30)
+ self.update_state(state=states.STARTED)
+ self.update_job(std_out="After first sleep, state={}".format(self.state))
+ num = random.random()
+ if num > 0.5:
+ raise Exception("ERROR: {} is greater than 0.5".format(num))
+
+
@shared_task
def launch_validate_contributions(contribution_ids):
"""
diff --git a/ippisite/ippisite/admin.py b/ippisite/ippisite/admin.py
index 0cc216a8a5d375264d1a95b49c0f9da338ab7948..77f66d97b3c8e505113e7bc1e170631b27bf405e 100644
--- a/ippisite/ippisite/admin.py
+++ b/ippisite/ippisite/admin.py
@@ -2,11 +2,11 @@ from django.contrib import admin
from django.urls import path
from django.shortcuts import redirect
from django.contrib import messages
-
from ippidb.tasks import (
launch_compound_properties_caching,
launch_drugbank_similarity_computing,
launch_plots_computing,
+ launch_test_command_caching,
)
@@ -35,9 +35,19 @@ class IppidbAdmin(admin.AdminSite):
"launch_plots_computing/",
self.admin_view(self.launch_plots_computing_view),
),
+ path("launch_test_command/", self.admin_view(self.launch_test_command),),
]
return my_urls + urls
+ def launch_test_command(self, request):
+ """
+ This view launches the task to test jobs
+ """
+ task = launch_test_command_caching.delay()
+ print(task.state)
+ messages.add_message(request, messages.INFO, "Test job launched")
+ return redirect("/admin/")
+
def launch_compound_properties_caching_view(self, request):
"""
This view launches the task to perform, for all already validated compounds,
diff --git a/ippisite/ippisite/decorator.py b/ippisite/ippisite/decorator.py
new file mode 100644
index 0000000000000000000000000000000000000000..ea9968f6851dbefae935c1253d9a53fcf623c213
--- /dev/null
+++ b/ippisite/ippisite/decorator.py
@@ -0,0 +1,57 @@
+from ippidb.models import Job
+from celery import Task, states
+from django_celery_results.models import TaskResult
+
+
+class AlreadyExistError(Exception):
+ pass
+
+
+class IppidbTask(Task):
+ """
+ Ippidb custom task
+ """
+
+ def __call__(self, *args, **kwargs):
+ """In celery task this function call the run method, here you can
+ set some environment variable before the run of the task"""
+
+ tasks = TaskResult.objects.filter(
+ task_name=self.request.task,
+ status__in=[states.STARTED, states.PENDING, states.RETRY, states.RECEIVED],
+ )
+ count_tasks = tasks.count()
+ if not count_tasks:
+ self.update_state(state=states.PENDING)
+ return self.run(*args, **kwargs)
+ else:
+ message_exc = "Job {} in state {} already exist".format(
+ tasks[0].task_name, tasks[0].status
+ )
+ raise AlreadyExistError(message_exc)
+
+ def update_job(self, std_out=None, std_err=None):
+ job = Job.objects.get(task_result__task_id=self.task_id)
+ if std_out:
+ job.write(std_out, output="std_out")
+ elif std_err:
+ job.write(std_err, output="std_err")
+
+ def on_success(self, retval, task_id, args, kwargs):
+ self.update_job(std_out="SUCCESS")
+ super(IppidbTask, self).on_success(retval, task_id, args, kwargs)
+
+ def on_failure(self, exc, task_id, args, kwargs, einfo):
+ self.update_job(std_err=exc)
+ super(IppidbTask, self).on_failure(exc, task_id, args, kwargs, einfo)
+
+ def update_state(self, task_id=None, state=None, meta=None, **kwargs):
+ self.state = state
+ if task_id is None:
+ self.task_id = self.request.id
+ else:
+ self.task_id = task_id
+ super(IppidbTask, self).update_state(
+ task_id=task_id, state=state, meta=meta, **kwargs
+ )
+
diff --git a/ippisite/ippisite/settings.py b/ippisite/ippisite/settings.py
index e6d355db3a13129f94d7edf4fcf63256031ac491..0d92a88a396028dde8c9cd3303eddb9976b2ee4f 100644
--- a/ippisite/ippisite/settings.py
+++ b/ippisite/ippisite/settings.py
@@ -43,6 +43,7 @@ INSTALLED_APPS = [
"django.contrib.messages",
"django.contrib.staticfiles",
"django_extensions",
+ "django_celery_results",
"crispy_forms",
"live_settings",
"ippidb",
@@ -182,3 +183,6 @@ MARVINJS_APIKEY = None
GALAXY_BASE_URL = None
GALAXY_APIKEY = None
GALAXY_COMPOUNDPROPERTIES_WORKFLOWID = None
+
+# celery setting.
+CELERY_RESULT_BACKEND = 'django-db'
diff --git a/ippisite/ippisite/settings.template.py b/ippisite/ippisite/settings.template.py
index b96e3bde7238b8f9593c22f25dc7904dea7f7b5d..f971d198766ae090eaa5165b86ed3cbde0808f02 100644
--- a/ippisite/ippisite/settings.template.py
+++ b/ippisite/ippisite/settings.template.py
@@ -45,6 +45,7 @@ INSTALLED_APPS = [
"django.contrib.messages",
"django.contrib.staticfiles",
"django_extensions",
+ "django_celery_results",
"crispy_forms",
"live_settings",
"ippidb",
@@ -161,3 +162,6 @@ LOGOUT_REDIRECT_URL = "/"
# django-crispy-forms
################################################################################
CRISPY_TEMPLATE_PACK = "bootstrap4"
+
+# celery setting.
+CELERY_RESULT_BACKEND = 'django-db'
diff --git a/ippisite/templates/admin/index.html b/ippisite/templates/admin/index.html
index 212e9632b58eaaa9a3c089fa4615f9d2924ba30e..d147b65995fe69eebececa685c1c9d0e2edd2adc 100644
--- a/ippisite/templates/admin/index.html
+++ b/ippisite/templates/admin/index.html
@@ -59,6 +59,12 @@
<input type="submit" value="Plots generation" name="_save"/>
</form>
<hr/>
+ <form method="POST" action="/admin/launch_test_command/"
+ style="display:block">{% csrf_token %}
+ <input type="submit" value="test command" name="_save"/>
+ </form>
+ <hr/>
+
</div>