From 48aac0125ea2ba13ded96225a23be27e2a27b560 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Tue, 26 May 2020 12:27:21 +0200
Subject: [PATCH] add an admin task to update Compound cross-links
---
ippisite/ippidb/tasks.py | 58 +++++++++++++++++++++++++++--
ippisite/ippisite/admin.py | 13 +++++++
ippisite/templates/admin/index.html | 7 +++-
3 files changed, 74 insertions(+), 4 deletions(-)
diff --git a/ippisite/ippidb/tasks.py b/ippisite/ippidb/tasks.py
index 2fe4374d..6a836e42 100644
--- a/ippisite/ippidb/tasks.py
+++ b/ippisite/ippidb/tasks.py
@@ -424,6 +424,24 @@ def generate_pca_plot():
print("Successfully generated PCA biplot data")
+def set_compound_links(compound_ids: List[int]) -> List[int]:
+ """
+ set/update links with external databases:
+ DrugBank, ChEMBL, PubChem
+ for each compound of a queryset
+
+ :param qs: queryset over the compounds to be processed
+ :type qs: QuerySet
+ """
+ qs = Compound.objects.filter(id__in=compound_ids)
+ for c in qs:
+ c.set_drugbank_link()
+ c.set_chembl_link()
+ c.set_pubchem_link()
+ c.save()
+ return [c.id for c in qs]
+
+
@task(base=MonitorTask, bind=True)
def run_compute_compound_properties(self: MonitorTask, compound_id: int) -> int:
"""
@@ -506,9 +524,30 @@ def run_compute_drugbank_similarity(
@task(base=MonitorTask, bind=True)
-def run_validate(
- self: MonitorTask, compound_ids: List[int] = None
-) -> List[int]:
+def run_set_compound_links(self: MonitorTask, compound_id: int) -> int:
+ """
+ task to set/update the DB cross-links for a compound
+
+ :param self: the task the function is binded to as a method
+ :type self: MonitorTask
+ :param compound_id: the ID of the compound
+ :type compound_id: int
+ :return: the ID of the compound
+ :rtype: int
+ """
+ self.update_state(state=states.STARTED)
+ cj = CompoundJob()
+ cj.compound = Compound.objects.get(id=compound_id)
+ cj.job = Job.objects.get(task_result__task_id=self.task_id)
+ cj.save()
+ self.write(std_out=f"Starting setting external cross-links for {compound_id}")
+ result_compound_ids = set_compound_links([compound_id])
+ self.write(std_out=f"Finished setting external cross-links for {compound_id}")
+ return result_compound_ids[0]
+
+
+@task(base=MonitorTask, bind=True)
+def run_validate(self: MonitorTask, compound_ids: List[int] = None) -> List[int]:
"""
task "run method" to validate a list of compounds
@@ -598,3 +637,16 @@ def launch_plots_computing():
"""
workflow = chain(run_le_lle_plot.si(), run_pca_plot.si())
workflow.delay()
+
+
+def launch_set_compound_links():
+ """
+ Launch the tasks to set/update compound links
+ """
+ link_jobs_group = group(
+ [
+ run_set_compound_links.si(compound.id)
+ for compound in Compound.objects.validated()
+ ]
+ )
+ link_jobs_group.delay()
diff --git a/ippisite/ippisite/admin.py b/ippisite/ippisite/admin.py
index 08b377b4..cab9f769 100644
--- a/ippisite/ippisite/admin.py
+++ b/ippisite/ippisite/admin.py
@@ -6,6 +6,7 @@ from ippidb.tasks import (
launch_update_compound_cached_properties,
run_compute_drugbank_similarity,
launch_plots_computing,
+ launch_set_compound_links,
)
from django.shortcuts import render
from ippidb.models import Job
@@ -36,6 +37,10 @@ class IppidbAdmin(admin.AdminSite):
"launch_plots_computing/",
self.admin_view(self.launch_plots_computing_view),
),
+ path(
+ "launch_set_compound_links/",
+ self.admin_view(self.launch_set_compound_links_view),
+ ),
path("tasklog/", self.admin_view(self.tasklog), name="tasklog"),
]
return my_urls + urls
@@ -90,3 +95,11 @@ class IppidbAdmin(admin.AdminSite):
launch_plots_computing()
messages.add_message(request, messages.INFO, "Plots computing launched")
return redirect("/admin/ippidb/job")
+
+ def launch_set_compound_links_view(self, request):
+ """
+ This view launches the task to set/update compound DB cross-links.
+ """
+ launch_set_compound_links()
+ messages.add_message(request, messages.INFO, "DB links update launched")
+ return redirect("/admin/ippidb/job")
\ No newline at end of file
diff --git a/ippisite/templates/admin/index.html b/ippisite/templates/admin/index.html
index 7db55abf..4da111df 100644
--- a/ippisite/templates/admin/index.html
+++ b/ippisite/templates/admin/index.html
@@ -58,7 +58,12 @@
style="display:block">{% csrf_token %}
<input type="submit" value="Plots generation" name="_save"/>
</form>
- <hr/>
+ <hr/>
+ <form method="POST" action="/admin/launch_set_compound_links/"
+ style="display:block">{% csrf_token %}
+ <input type="submit" value="DB links update" name="_save"/>
+ </form>
+ <hr/>
</div>
--
GitLab