django-to-galaxy 0.6.9.4__py3-none-any.whl → 0.6.9.6__py3-none-any.whl

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/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/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/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/models/workflow.py

@@ -15,6 +15,10 @@ 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."""
+    _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:
@@ -27,6 +31,48 @@ class Workflow(GalaxyElement):
         """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.

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.dist-info → django_to_galaxy-0.6.9.6.dist-info}/METADATA

@@ -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.dist-info → django_to_galaxy-0.6.9.6.dist-info}/RECORD

@@ -7,7 +7,7 @@ django_to_galaxy/admin/galaxy_user.py,sha256=A_VBW0LlPoEHfPhPbo21H6YNhWlTgPCyzPx
 django_to_galaxy/admin/history.py,sha256=eVN-ZCAju0_1ygeSnHEie3a7iy7LoW3bOhWQyU20XTw,2562
 django_to_galaxy/admin/invocation.py,sha256=Rgtkyyl2WrDZN-fF_u5lPlicGe341UGwBMbI06nZG78,4821
 django_to_galaxy/admin/tag.py,sha256=jqQ64sLieq4CSRFHesNt33SqTNnA-z3oiQuj7Ncx_jU,315
-django_to_galaxy/admin/workflow.py,sha256=6t9z7JQPv-D7tzyi9WNUxEQXdetGlNCSzNIoX1SCAdM,1360
+django_to_galaxy/admin/workflow.py,sha256=5rnP7NdxhFVKk8pMkpeJdcZWJoNrgQev0LB7wO6nyt4,1616
 django_to_galaxy/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 django_to_galaxy/api/serializers/asymetricslugrelatedfield.py,sha256=BKdbkblCA5PKodsBqgwg6W_gTSrrmoGBElh_CNVd7dY,1079
 django_to_galaxy/api/serializers/galaxy_instance.py,sha256=r_W9seqc2afc3tFrsWTyZ50-CThsHXutO7TwhYFnyXE,257
@@ -38,6 +38,7 @@ django_to_galaxy/migrations/0006_tag_history_tags_workflow_tags.py,sha256=Zv4Fzm
 django_to_galaxy/migrations/0007_format_alter_history_tags_alter_workflow_tags_and_more.py,sha256=_nKYmJmw6EAoAj3oOCcbDKYPeQYY30Fq1SvguU1V7fs,2000
 django_to_galaxy/migrations/0008_workflowinput_label.py,sha256=UisIOkD73J2dgQXB12eU91g8c9nTkQdHEy111nObN7c,481
 django_to_galaxy/migrations/0009_galaxyoutputfile_unique_galaxy_id_per_invocation.py,sha256=a3zgC01TVtUeuTlISOe4vZ-oJj1opIMkN_8UIvFFjvc,500
+django_to_galaxy/migrations/0010_workflow__is_meta_workflow__step_jobs_count.py,sha256=rESj9tXHrhRdN0V-kc11VSvIwL-TN6sVR3B9zYpaX3w,608
 django_to_galaxy/migrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 django_to_galaxy/models/__init__.py,sha256=5e1Fw1G-mWZnj4vUUY_lO_DH6lQL_P9nO6GYkyyS3zk,370
 django_to_galaxy/models/accepted_input.py,sha256=hIR9rlOaVKdUax21PEpaMzdwj9yOceRaFyFsbRO1C6g,889
@@ -45,17 +46,17 @@ django_to_galaxy/models/galaxy_element.py,sha256=55qUtUks-rC4A7O1DFjeUUm-AN0-qNm
 django_to_galaxy/models/galaxy_instance.py,sha256=931iyrqJxK6YCbkaC6FPdqMRI_hhGQ-UokhW5-N7swk,723
 django_to_galaxy/models/galaxy_output_file.py,sha256=oAq7HZBk3svG88NagFpkpiB5TQoncbpGFxCCTFoCzyo,1915
 django_to_galaxy/models/galaxy_user.py,sha256=Cz6wmyD3PvltFi2yKEKr2z7YTsxlmnNV8xwA0Gltu_o,3264
-django_to_galaxy/models/history.py,sha256=RF661ULnSMO6wvEutZ-qVDY-9vxu-JcWiGbN7MwdVvI,2635
-django_to_galaxy/models/invocation.py,sha256=yPx0wLkVz43bGl9Ct19hZaGOM9ka5HU_RpjaYgrZC3g,8720
-django_to_galaxy/models/workflow.py,sha256=1Ok0TSSIM-LJbaY1Vm19YVg_WwDxznbLDcXI71S_IL8,1891
+django_to_galaxy/models/history.py,sha256=-u0DDrwsNprYf-CMAut4q5eu2IzWXXLoKmuBpac7DKs,2647
+django_to_galaxy/models/invocation.py,sha256=huskr6NTonoqPp-GVL-cOjPxFY2MlaOC3MVj8Trs43U,8359
+django_to_galaxy/models/workflow.py,sha256=tWa27SQhZDZVPSg95BJHI_SOKMD9Wyiv5dYqU52Nv1o,4021
 django_to_galaxy/schemas/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 django_to_galaxy/schemas/dataset.py,sha256=yjwLJGb487VJDXoXGg8fG_TW6TJPeyeGtd9vofU-7HI,396
 django_to_galaxy/settings.py,sha256=Jn1gznlxhlu57D_cdbAhBQTTN9jq4GIb31czhQQUtJo,138
 django_to_galaxy/templates/admin/import_workflows.html,sha256=YB101H99EOR8td_DzfNshhJYpXpGD9aJNh8t4mKPgEQ,2389
 django_to_galaxy/urls.py,sha256=ydMl_0qSyz8GSGkWpiSzU3khqj9mPyZacx532JybLHk,106
 django_to_galaxy/utils.py,sha256=gjUzzqfpili66CY7vFyseqHOD9vqWg_2tzWAiTe3pNE,1625
-django_to_galaxy/version.py,sha256=YspVavZCvh-ZZ7Wk2kq7lZ-f16x-8wa-uUPn_gBeCNo,114
-django_to_galaxy-0.6.9.4.dist-info/LICENSE,sha256=Er3Bp2y6Wf31e0s1-Tdu_d6Gd89FtTizmGUJzGQkWvo,34498
-django_to_galaxy-0.6.9.4.dist-info/METADATA,sha256=KNx7KeNPtDFrRkW8mZYGAjLkq7JmDQZhKPBRYnPbmQc,612
-django_to_galaxy-0.6.9.4.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-django_to_galaxy-0.6.9.4.dist-info/RECORD,,
+django_to_galaxy/version.py,sha256=SWpc-6Xmr8gQ3xBhFnZzJC9V1ErahXEoMU_Gq5UjoDg,114
+django_to_galaxy-0.6.9.6.dist-info/LICENSE,sha256=Er3Bp2y6Wf31e0s1-Tdu_d6Gd89FtTizmGUJzGQkWvo,34498
+django_to_galaxy-0.6.9.6.dist-info/METADATA,sha256=yIFRA2hXY993G0MFhEIBl-3FB4fWi5ja8Uu88NQbRBM,612
+django_to_galaxy-0.6.9.6.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+django_to_galaxy-0.6.9.6.dist-info/RECORD,,

{django_to_galaxy-0.6.9.4.dist-info → django_to_galaxy-0.6.9.6.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.0.1
 Root-Is-Purelib: true
 Tag: py3-none-any