django-to-galaxy 0.6.4__tar.gz → 0.6.7__tar.gz

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: django-to-galaxy
-Version: 0.6.4
+Version: 0.6.7
 Summary: Django extension that eases communication with Galaxy instance to execute workflows.
 Author: Kenzo-Hugo Hillion
 Author-email: hillion.kenzo@posteo.net
@@ -9,6 +9,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: Django (>=4.0.3,<5.0.0)
 Requires-Dist: Markdown (>=3.3.6,<4.0.0)
 Requires-Dist: bioblend (>=0.16.0,<0.17.0)

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/django_to_galaxy/admin/invocation.py

@@ -36,13 +36,22 @@ class InvocationAdmin(GalaxyElementAdmin):
 
     @admin.display(description="Percentage Done")
     def display_percentage_done(self, obj):
-        return format_html(
-            """
-            <progress value="{0}" max="100"></progress>
-            <span style="font-weight:bold">{0}%</span>
-            """,
-            obj.percentage_done,
-        )
+        try:
+            return format_html(
+                """
+                <progress value="{0}" max="100"></progress>
+                <span style="font-weight:bold">{0}%</span>
+                """,
+                obj.percentage_done,
+            )
+        except ZeroDivisionError:
+            return format_html(
+                """
+                <progress value="{0}" max="100"></progress>
+                <span style="font-weight:bold">{0}%</span>
+                """,
+                0,
+            )
 
     def _get_message_invocation(
         self,

django_to_galaxy-0.6.7/django_to_galaxy/migrations/0009_galaxyoutputfile_unique_galaxy_id_per_invocation.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.1 on 2023-10-27 11:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0008_workflowinput_label"),
+    ]
+
+    operations = [
+        migrations.AddConstraint(
+            model_name="galaxyoutputfile",
+            constraint=models.UniqueConstraint(
+                fields=("galaxy_id", "invocation"),
+                name="unique_galaxy_id_per_invocation",
+            ),
+        ),
+    ]

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/django_to_galaxy/models/galaxy_output_file.py

@@ -40,3 +40,14 @@ class GalaxyOutputFile(models.Model):
 
     def __str__(self):
         return f"{self.history_name} (from {self.invocation.galaxy_id})"
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=(
+                    "galaxy_id",
+                    "invocation",
+                ),
+                name="unique_galaxy_id_per_invocation",
+            )
+        ]

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/django_to_galaxy/models/invocation.py

@@ -10,6 +10,7 @@ from .galaxy_output_file import GalaxyOutputFile
 
 from django_to_galaxy.utils import enabled_cache
 
+from django.core.exceptions import ObjectDoesNotExist
 
 RUNNING = "running"
 DONE = "done"
@@ -58,17 +59,35 @@ class Invocation(models.Model):
         """Get galaxy object using bioblend."""
         return self.workflow.galaxy_owner.obj_gi.invocations.get(self.galaxy_id)
 
+    def complet_jobs_summary(self, step):
+        subinv = self.galaxy_invocation.gi.invocations.get(
+            step.wrapped["subworkflow_invocation_id"]
+        )
+        sub_jobs_summary = subinv.step_jobs_summary()
+        for job in sub_jobs_summary:
+            self.step_jobs_summary.append(job)
+        for sub in subinv.steps:
+            if "subworkflow_invocation_id" in sub.wrapped:
+                if sub.wrapped["subworkflow_invocation_id"]:
+                    self.complet_jobs_summary(sub)
+
     @property
     def percentage_done(self) -> float:
         """Retrieve percentage of jobs done for the invocation."""
         if self.status == DONE:
             return 100.0
-        step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+        self.step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+
+        for step in self.galaxy_invocation.steps:
+            if "subworkflow_invocation_id" in step.wrapped:
+                if step.wrapped["subworkflow_invocation_id"]:
+                    self.complet_jobs_summary(step)
+
         count_states = defaultdict(int)
-        for step in step_jobs_summary:
+        for step in self.step_jobs_summary:
             for key in step["states"].keys():
                 count_states[key] += 1
-        percentage_done = count_states.get("ok", 0) / len(step_jobs_summary)
+        percentage_done = count_states.get("ok", 0) / len(self.step_jobs_summary)
         if percentage_done == 1:
             self.status = DONE
             self.save()
@@ -133,13 +152,19 @@ class Invocation(models.Model):
             number_of_try += 1
         if galaxy_inv_wrapped.get("outputs", {}):
             for output_name, output_content in galaxy_inv_wrapped["outputs"].items():
-                output_file = GalaxyOutputFile(
-                    galaxy_id=output_content["id"],
-                    workflow_name=output_name,
-                    src=output_content["src"],
-                    invocation=self,
-                )
-                output_file.save()
+                try:
+                    output_file = GalaxyOutputFile.objects.get(
+                        galaxy_id=output_content["id"],
+                        invocation=self,
+                    )
+                except ObjectDoesNotExist:
+                    output_file = GalaxyOutputFile(
+                        galaxy_id=output_content["id"],
+                        workflow_name=output_name,
+                        src=output_content["src"],
+                        invocation=self,
+                    )
+                    output_file.save()
                 output_file.synchronize()
         else:
             logger.warning(
@@ -151,13 +176,12 @@ class Invocation(models.Model):
         galaxy_inv_wrapped = self._get_galaxy_invocation().wrapped
         if galaxy_inv_wrapped.get("outputs", {}):
             for output_name, output_content in galaxy_inv_wrapped["outputs"].items():
-                if GalaxyOutputFile.objects.filter(
-                    galaxy_id=output_content["id"]
-                ).exists():
+                try:
                     output_file = GalaxyOutputFile.objects.get(
-                        galaxy_id=output_content["id"]
+                        galaxy_id=output_content["id"],
+                        invocation=self,
                     )
-                else:
+                except ObjectDoesNotExist:
                     output_file = GalaxyOutputFile(
                         galaxy_id=output_content["id"],
                         workflow_name=output_name,

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/django_to_galaxy/version.py

@@ -1,3 +1,3 @@
 """Handle library versioning."""
-version_info = (0, 6, 4)
+version_info = (0, 6, 5)
 __version__ = ".".join(str(c) for c in version_info)

{django_to_galaxy-0.6.4 → django_to_galaxy-0.6.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "django-to-galaxy"
-version = "0.6.4"
+version = "0.6.7"
 description = "Django extension that eases communication with Galaxy instance to execute workflows."
 authors = ["Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>"]