django-to-galaxy 0.6.9.4__tar.gz → 0.6.9.6__tar.gz

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: django-to-galaxy
-Version: 0.6.9.4
+Version: 0.6.9.6
 Summary: Django extension that eases communication with Galaxy instance to execute workflows.
 Author: Kenzo-Hugo Hillion
 Author-email: hillion.kenzo@posteo.net

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/django_to_galaxy/admin/workflow.py

@@ -13,6 +13,8 @@ class WorkflowAdmin(GalaxyElementAdmin):
         "name",
         "annotation",
         "galaxy_id",
+        "get_is_meta",
+        "get_step_jobs_count",
         "published",
         "galaxy_owner",
         "get_tags",
@@ -22,11 +24,19 @@ class WorkflowAdmin(GalaxyElementAdmin):
         "name",
         "annotation",
         "galaxy_id",
+        "get_is_meta",
+        "get_step_jobs_count",
         "published",
         "galaxy_owner",
         "get_tags",
     )
 
+    def get_is_meta(self, obj):
+        return obj.get_is_meta()
+
+    def get_step_jobs_count(self, obj):
+        return obj.get_step_jobs_count()
+
     def get_tags(self, obj):
         return ", ".join([p.label for p in obj.tags.all()])
 

django_to_galaxy-0.6.9.6/django_to_galaxy/migrations/0010_workflow__is_meta_workflow__step_jobs_count.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1 on 2025-02-12 13:28
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0009_galaxyoutputfile_unique_galaxy_id_per_invocation"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="workflow",
+            name="_is_meta",
+            field=models.BooleanField(default=None, null=True),
+        ),
+        migrations.AddField(
+            model_name="workflow",
+            name="_step_jobs_count",
+            field=models.PositiveIntegerField(default=0),
+        ),
+    ]

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/django_to_galaxy/models/history.py

@@ -46,7 +46,7 @@ class History(GalaxyElement):
 
     def delete(self, **kwargs):
         """Overloaded method to also delete history on Galaxy side."""
-        self.galaxy_owner.obj_gi.histories.delete(id_=self.galaxy_id)
+        self.galaxy_owner.obj_gi.histories.delete(id_=self.galaxy_id, purge=True)
         return super().delete(**kwargs)
 
     def synchronize(self):

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/django_to_galaxy/models/invocation.py

@@ -12,7 +12,6 @@ from django_to_galaxy.utils import enabled_cache
 
 from django.core.exceptions import ObjectDoesNotExist
 
-READY = "ready"
 RUNNING = "running"
 DONE = "done"
 ERROR = "error"
@@ -75,19 +74,17 @@ 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, subworkflow_invocation_state):
+    def complet_jobs_summary(self, step):
         subinv = self.galaxy_invocation.gi.invocations.get(
             step.wrapped["subworkflow_invocation_id"]
         )
-        if subinv.state != READY or not subinv.steps:
-            subworkflow_invocation_state = subinv.state
         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, subworkflow_invocation_state)
+                    self.complet_jobs_summary(sub)
 
     @property
     def percentage_done(self) -> float:
@@ -96,23 +93,22 @@ class Invocation(models.Model):
             return 100.0
         self.step_jobs_summary = self.step_jobs_summary()
 
-        subworkflow_invocation_state = None
-        if self.galaxy_invocation.state != READY:
-            subworkflow_invocation_state = PAUSED
         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, subworkflow_invocation_state)
+                    self.complet_jobs_summary(step)
 
         count_states = defaultdict(int)
         for step in self.step_jobs_summary:
             for key in step["states"].keys():
                 count_states[key] += 1
         try:
-            percentage_done = count_states.get("ok", 0) / len(self.step_jobs_summary)
+            percentage_done = (
+                count_states.get("ok", 0) / self.workflow.get_step_jobs_count()
+            )
         except ZeroDivisionError:
             percentage_done = 0
-        if percentage_done == 1 and subworkflow_invocation_state is None:
+        if percentage_done == 1:
             self.status = DONE
             self.save()
         if "error" in count_states.keys():

django_to_galaxy-0.6.9.6/django_to_galaxy/models/workflow.py

@@ -0,0 +1,104 @@
+from bioblend.galaxy.objects import wrappers
+from django.db import models
+
+from .history import History
+from .invocation import Invocation
+from .galaxy_element import GalaxyElement
+
+from django_to_galaxy.utils import load_galaxy_invocation_time_to_datetime
+
+
+class Workflow(GalaxyElement):
+    """Table for Galaxy workflows."""
+
+    galaxy_owner = models.ForeignKey(
+        "GalaxyUser", null=False, on_delete=models.CASCADE, related_name="workflows"
+    )
+    """Galaxy user that owns the workflow."""
+    _step_jobs_count = models.PositiveIntegerField(default=0)
+    """Number of step jobs of the workflow."""
+    _is_meta = models.BooleanField(null=True, default=None, blank=True)
+    """Indicates whether the workflow is a meta (i.e., has sub-workflows) or not."""
+
+    @property
+    def galaxy_workflow(self) -> wrappers.Workflow:
+        """Galaxy object using bioblend."""
+        if getattr(self, "_galaxy_workflow", None) is None:
+            self._galaxy_workflow = self._get_galaxy_workflow()
+        return self._galaxy_workflow
+
+    def _get_galaxy_workflow(self) -> wrappers.Workflow:
+        """Get galaxy object using bioblend."""
+        return self.galaxy_owner.obj_gi.workflows.get(self.galaxy_id)
+
+    def get_is_meta(self):
+        """Sets / returns _is_meta value."""
+        if self._is_meta is None:
+            self._is_meta = False
+            for key, step_dict in self.galaxy_workflow.steps.items():
+                w = step_dict.wrapped
+                if "workflow_id" in w:
+                    self._is_meta = True
+                    break
+            self.save(update_fields=["_is_meta"])
+        return self._is_meta
+
+    def get_step_jobs_count(self):
+        """Sets / returns _step_jobs_count value."""
+        if self._step_jobs_count == 0:
+            galaxy_wf = self.galaxy_workflow
+            step_jobs_count = 0
+            if self.get_is_meta():
+                # Total step jobs count for a meta wf
+                galaxy_client = self.galaxy_owner.obj_gi.gi
+                for key, step_dict in galaxy_wf.steps.items():
+                    w = step_dict.wrapped
+                    if "workflow_id" in w:
+                        sub_wf = galaxy_client.make_get_request(
+                            galaxy_client.base_url
+                            + f"/api/workflows/{w['workflow_id']}",
+                            params={"instance": "true"},
+                        ).json()
+                        for j in range(len(sub_wf["steps"])):
+                            step = sub_wf["steps"][str(j)]
+                            if "input" not in step["type"]:
+                                step_jobs_count += 1
+            else:
+                # Total step jobs count for a simple wf
+                for key, step_dict in galaxy_wf.steps.items():
+                    w = step_dict.wrapped
+                    if "input" not in w["type"]:
+                        step_jobs_count += 1
+            self._step_jobs_count = step_jobs_count
+            self.save(update_fields=["_step_jobs_count"])
+        return self._step_jobs_count
+
+    def invoke(self, datamap: dict, history: History) -> wrappers.Invocation:
+        """
+        Invoke workflow using bioblend.
+
+        Args:
+            datamap: dictionnary to link dataset to workflow inputs
+            history: history obj the dataset(s) come from
+
+        Returns:
+            Invocation object from bioblend
+        """
+        galaxy_inv = self.galaxy_workflow.invoke(
+            datamap, history=history.galaxy_history
+        )
+        # Create invocations
+        invocation = Invocation(
+            galaxy_id=galaxy_inv.id,
+            galaxy_state=galaxy_inv.state,
+            workflow=self,
+            history=history,
+            create_time=load_galaxy_invocation_time_to_datetime(galaxy_inv),
+        )
+        invocation.save()
+        # Create output files
+        invocation.create_output_files()
+        return invocation
+
+    def __repr__(self):
+        return f"Workflow: {super().__str__()}"

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/django_to_galaxy/version.py

@@ -1,3 +1,3 @@
 """Handle library versioning."""
-version_info = (0, 6, 9, 4)
+version_info = (0, 6, 9, 6)
 __version__ = ".".join(str(c) for c in version_info)

{django_to_galaxy-0.6.9.4 → django_to_galaxy-0.6.9.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "django-to-galaxy"
-version = "0.6.9.4"
+version = "0.6.9.6"
 description = "Django extension that eases communication with Galaxy instance to execute workflows."
 authors = ["Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>"]
 

django_to_galaxy-0.6.9.4/django_to_galaxy/models/workflow.py

@@ -1,58 +0,0 @@
-from bioblend.galaxy.objects import wrappers
-from django.db import models
-
-from .history import History
-from .invocation import Invocation
-from .galaxy_element import GalaxyElement
-
-from django_to_galaxy.utils import load_galaxy_invocation_time_to_datetime
-
-
-class Workflow(GalaxyElement):
-    """Table for Galaxy workflows."""
-
-    galaxy_owner = models.ForeignKey(
-        "GalaxyUser", null=False, on_delete=models.CASCADE, related_name="workflows"
-    )
-    """Galaxy user that owns the workflow."""
-
-    @property
-    def galaxy_workflow(self) -> wrappers.Workflow:
-        """Galaxy object using bioblend."""
-        if getattr(self, "_galaxy_workflow", None) is None:
-            self._galaxy_workflow = self._get_galaxy_workflow()
-        return self._galaxy_workflow
-
-    def _get_galaxy_workflow(self) -> wrappers.Workflow:
-        """Get galaxy object using bioblend."""
-        return self.galaxy_owner.obj_gi.workflows.get(self.galaxy_id)
-
-    def invoke(self, datamap: dict, history: History) -> wrappers.Invocation:
-        """
-        Invoke workflow using bioblend.
-
-        Args:
-            datamap: dictionnary to link dataset to workflow inputs
-            history: history obj the dataset(s) come from
-
-        Returns:
-            Invocation object from bioblend
-        """
-        galaxy_inv = self.galaxy_workflow.invoke(
-            datamap, history=history.galaxy_history
-        )
-        # Create invocations
-        invocation = Invocation(
-            galaxy_id=galaxy_inv.id,
-            galaxy_state=galaxy_inv.state,
-            workflow=self,
-            history=history,
-            create_time=load_galaxy_invocation_time_to_datetime(galaxy_inv),
-        )
-        invocation.save()
-        # Create output files
-        invocation.create_output_files()
-        return invocation
-
-    def __repr__(self):
-        return f"Workflow: {super().__str__()}"