django-to-galaxy 0.6.9.6__tar.gz → 0.6.9.8__tar.gz

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: django-to-galaxy
-Version: 0.6.9.6
+Version: 0.6.9.8
 Summary: Django extension that eases communication with Galaxy instance to execute workflows.
 Author: Kenzo-Hugo Hillion
 Author-email: hillion.kenzo@posteo.net
@@ -11,5 +11,6 @@ Requires-Dist: Django (>=5.1.1,<6.0.0)
 Requires-Dist: Markdown (>=3.3.6,<4.0.0)
 Requires-Dist: bioblend (>=0.16.0,<0.17.0)
 Requires-Dist: djangorestframework (>=3.13.1,<4.0.0)
-Requires-Dist: pydantic (>=1.9.1,<2.0.0)
+Requires-Dist: pydantic (>=2.11.0,<3.0.0)
+Requires-Dist: pydantic-settings (>=2.9.0,<3.0.0)
 Requires-Dist: requests-cache (>=0.9.5,<0.10.0)

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/django_to_galaxy/admin/workflow.py

@@ -14,7 +14,7 @@ class WorkflowAdmin(GalaxyElementAdmin):
         "annotation",
         "galaxy_id",
         "get_is_meta",
-        "get_step_jobs_count",
+        "get_step_count",
         "published",
         "galaxy_owner",
         "get_tags",
@@ -25,7 +25,7 @@ class WorkflowAdmin(GalaxyElementAdmin):
         "annotation",
         "galaxy_id",
         "get_is_meta",
-        "get_step_jobs_count",
+        "get_step_count",
         "published",
         "galaxy_owner",
         "get_tags",
@@ -34,8 +34,8 @@ class WorkflowAdmin(GalaxyElementAdmin):
     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_step_count(self, obj):
+        return obj.get_step_count()
 
     def get_tags(self, obj):
         return ", ".join([p.label for p in obj.tags.all()])

django_to_galaxy-0.6.9.8/django_to_galaxy/migrations/0011_rename__step_jobs_count_workflow__step_count_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.2.3 on 2025-07-18 14:07
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0010_workflow__is_meta_workflow__step_jobs_count"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="workflow",
+            old_name="_step_jobs_count",
+            new_name="_step_count",
+        ),
+        migrations.AlterField(
+            model_name="workflow",
+            name="_is_meta",
+            field=models.BooleanField(blank=True, default=None, null=True),
+        ),
+    ]

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/django_to_galaxy/models/invocation.py

@@ -57,7 +57,7 @@ class Invocation(models.Model):
                 step_job_summary["states"] = {}
                 step_job_summary["id"] = step_job.job_id
                 step_job_summary["states"][
-                    self.workflow.galaxy_owner.obj_gi.jobs.get(step_job.job_id).state
+                    self.galaxy_invocation.gi.jobs.get(step_job.job_id).state
                 ] = 1
                 step_jobs_summary.append(step_job_summary)
 
@@ -88,37 +88,66 @@ class Invocation(models.Model):
 
     @property
     def percentage_done(self) -> float:
-        """Retrieve percentage of jobs done for the invocation."""
+        """Retrieve percentage of steps done for the invocation."""
         if self.status == DONE:
             return 100.0
         self.step_jobs_summary = self.step_jobs_summary()
 
-        for step in self.galaxy_invocation.steps:
+        inv_steps = self.galaxy_invocation.steps
+        for step in inv_steps:
             if "subworkflow_invocation_id" in step.wrapped:
                 if step.wrapped["subworkflow_invocation_id"]:
                     self.complet_jobs_summary(step)
 
-        count_states = defaultdict(int)
+        count_job_states = defaultdict(int)
         for step in self.step_jobs_summary:
             for key in step["states"].keys():
-                count_states[key] += 1
+                count_job_states[key] += 1
+        count_scheduled_steps = sum(step.state == "scheduled" for step in inv_steps)
+        wf_step_count = self.workflow._step_count
         try:
-            percentage_done = (
-                count_states.get("ok", 0) / self.workflow.get_step_jobs_count()
-            )
+            percentage_done = count_scheduled_steps / wf_step_count
         except ZeroDivisionError:
             percentage_done = 0
         if percentage_done == 1:
-            self.status = DONE
-            self.save()
-        if "error" in count_states.keys():
+            last_job = inv_steps[wf_step_count - 1]
+            if self.check_if_last_job_is_ok(last_job):
+                self.status = DONE
+                self.save()
+            else:
+                try:
+                    percentage_done = (count_scheduled_steps - 1) / wf_step_count
+                except ZeroDivisionError:
+                    percentage_done = 0
+        if "error" in count_job_states.keys():
             self.status = ERROR
             self.save()
-        elif "paused" in count_states.keys():
+        elif "paused" in count_job_states.keys():
             self.status = PAUSED
             self.save()
         return percentage_done * 100
 
+    def check_if_last_job_is_ok(self, last_job):
+        """Checks if the very last job is done"""
+        if last_job.job_id:
+            return self.galaxy_invocation.gi.jobs.get(last_job.job_id).state == "ok"
+        if (
+            "subworkflow_invocation_id" in last_job.wrapped
+            and last_job.wrapped["subworkflow_invocation_id"]
+            and len(
+                self.galaxy_invocation.gi.invocations.get(
+                    last_job.wrapped["subworkflow_invocation_id"]
+                ).steps
+            )
+            > 0
+        ):
+            return self.check_if_last_job_is_ok(
+                self.galaxy_invocation.gi.invocations.get(
+                    last_job.wrapped["subworkflow_invocation_id"]
+                ).steps[-1]
+            )
+        return False
+
     @property
     def job_id_to_tools(self) -> Dict[str, dict]:
         """Dict of job_id to wrapped tool."""

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/django_to_galaxy/models/workflow.py

@@ -15,8 +15,8 @@ class Workflow(GalaxyElement):
         "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."""
+    _step_count = models.PositiveIntegerField(default=0)
+    """Number of steps in 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."""
 
@@ -43,35 +43,12 @@ class Workflow(GalaxyElement):
             self.save(update_fields=["_is_meta"])
         return self._is_meta
 
-    def get_step_jobs_count(self):
+    def get_step_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
+        if self._step_count == 0:
+            self._step_count = len(self.galaxy_workflow.steps)
+            self.save(update_fields=["_step_count"])
+        return self._step_count
 
     def invoke(self, datamap: dict, history: History) -> wrappers.Invocation:
         """

django_to_galaxy-0.6.9.8/django_to_galaxy/settings.py

@@ -0,0 +1,8 @@
+from pydantic_settings import BaseSettings
+
+
+class Settings(BaseSettings):
+    GALAXY_TIME_FORMAT: str = "%Y-%m-%dT%H:%M:%S.%f"
+
+
+settings = Settings()

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/django_to_galaxy/version.py

@@ -1,3 +1,3 @@
 """Handle library versioning."""
-version_info = (0, 6, 9, 6)
+version_info = (0, 6, 9, 8)
 __version__ = ".".join(str(c) for c in version_info)

{django_to_galaxy-0.6.9.6 → django_to_galaxy-0.6.9.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "django-to-galaxy"
-version = "0.6.9.6"
+version = "0.6.9.8"
 description = "Django extension that eases communication with Galaxy instance to execute workflows."
 authors = ["Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>"]
 
@@ -10,7 +10,8 @@ Django = "^5.1.1"
 bioblend = "^0.16.0"
 djangorestframework = "^3.13.1"
 Markdown = "^3.3.6"
-pydantic = "^1.9.1"
+pydantic = "^2.11.0"
+pydantic-settings = "^2.9.0"
 requests-cache = "^0.9.5"
 
 [tool.poetry.dev-dependencies]

django_to_galaxy-0.6.9.6/django_to_galaxy/settings.py

@@ -1,8 +0,0 @@
-from pydantic import BaseSettings
-
-
-class Settings(BaseSettings):
-    GALAXY_TIME_FORMAT = "%Y-%m-%dT%H:%M:%S.%f"
-
-
-settings = Settings()