django-to-galaxy 0.6.7__py3-none-any.whl → 0.6.9__py3-none-any.whl

django_to_galaxy/admin/galaxy_user.py

@@ -157,14 +157,15 @@ class GalaxyUserAdmin(admin.ModelAdmin):
                                     label=elem_dict["label"],
                                     workflow=wf,
                                 )
-                                for format in step_dict.tool_inputs["format"]:
-                                    (
-                                        winputformat,
-                                        created,
-                                    ) = Format.objects.get_or_create(
-                                        format=format.strip()
-                                    )
-                                    workflowinput.formats.add(winputformat.id)
+                                if hasattr(step_dict.tool_inputs, "format"):
+                                    for format in step_dict.tool_inputs["format"]:
+                                        (
+                                            winputformat,
+                                            created,
+                                        ) = Format.objects.get_or_create(
+                                            format=format.strip()
+                                        )
+                                        workflowinput.formats.add(winputformat.id)
                                 workflowinput.optional = step_dict.tool_inputs[
                                     "optional"
                                 ]

django_to_galaxy/admin/invocation.py

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

django_to_galaxy/models/invocation.py

@@ -1,7 +1,7 @@
 import logging
 from collections import defaultdict
 from time import sleep
-from typing import List, Dict
+from typing import Any, List, Dict
 
 from bioblend.galaxy.objects import wrappers
 from django.db import models
@@ -48,6 +48,21 @@ class Invocation(models.Model):
     create_time = models.DateTimeField()
     """Time the invocation was created."""
 
+    def step_jobs_summary(self) -> List[Dict[str, Any]]:
+        """Workaround self.galaxy_invocation.step_jobs_summary() due to v24.0 db issue"""
+        step_jobs_summary = []
+        for step_job in self.galaxy_invocation.steps:
+            if step_job.job_id is not None:
+                step_job_summary = {}
+                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
+                ] = 1
+                step_jobs_summary.append(step_job_summary)
+
+        return step_jobs_summary
+
     @property
     def galaxy_invocation(self) -> wrappers.Invocation:
         """Galaxy object using bioblend."""
@@ -76,7 +91,7 @@ class Invocation(models.Model):
         """Retrieve percentage of jobs done for the invocation."""
         if self.status == DONE:
             return 100.0
-        self.step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+        self.step_jobs_summary = self.step_jobs_summary()
 
         for step in self.galaxy_invocation.steps:
             if "subworkflow_invocation_id" in step.wrapped:
@@ -87,7 +102,10 @@ class Invocation(models.Model):
         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(self.step_jobs_summary)
+        try:
+            percentage_done = count_states.get("ok", 0) / len(self.step_jobs_summary)
+        except ZeroDivisionError:
+            percentage_done = 0
         if percentage_done == 1:
             self.status = DONE
             self.save()
@@ -107,7 +125,7 @@ class Invocation(models.Model):
         return self._job_id_to_tools
 
     def _build_job_id_to_tools(self) -> Dict[str, dict]:
-        step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+        step_jobs_summary = self.step_jobs_summary()
         job_id_to_tools = {}
         for step in step_jobs_summary:
             job_id = step["id"]
@@ -122,7 +140,7 @@ class Invocation(models.Model):
     @property
     def detailed_step_jobs_summary(self) -> List[dict]:
         """Retrive `step_jobs_summary` with details of tool used."""
-        step_jobs_summary = self.galaxy_invocation.step_jobs_summary()
+        step_jobs_summary = self.step_jobs_summary()
         detailed_jobs_summary = []
         for step in step_jobs_summary:
             detailed_step = step

{django_to_galaxy-0.6.7.dist-info → django_to_galaxy-0.6.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: django-to-galaxy
-Version: 0.6.7
+Version: 0.6.9
 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-0.6.7.dist-info → django_to_galaxy-0.6.9.dist-info}/RECORD

@@ -3,9 +3,9 @@ django_to_galaxy/admin/__init__.py,sha256=Rf8utzaDbRa3MAFmerhMC8kybejbiUlDFt8mbF
 django_to_galaxy/admin/galaxy_element.py,sha256=pDdFWQO5BHt251kIW8Gawe0M0O8r5z4cI6EJqQsDBqI,159
 django_to_galaxy/admin/galaxy_instance.py,sha256=yVlbA5fVbMQBKyKwaFJM3CRFQ2HDjzYHsni_l8MBndU,834
 django_to_galaxy/admin/galaxy_output_file.py,sha256=bnpwlAH8cQe6nkWIln8iSFDtVyr0kqI5P-QNbISWCfE,2321
-django_to_galaxy/admin/galaxy_user.py,sha256=NO0qzhsk6WVnWwvXuodGPLi0o4CPbg0yTZh4VxYvH0k,7278
+django_to_galaxy/admin/galaxy_user.py,sha256=A_VBW0LlPoEHfPhPbo21H6YNhWlTgPCyzPxQM-3Yv84,7387
 django_to_galaxy/admin/history.py,sha256=eVN-ZCAju0_1ygeSnHEie3a7iy7LoW3bOhWQyU20XTw,2562
-django_to_galaxy/admin/invocation.py,sha256=BsVrgMlnEisGcK3ni5oBbcL__yH0PsXYUkPNkIPpEsQ,5121
+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/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -46,7 +46,7 @@ django_to_galaxy/models/galaxy_instance.py,sha256=931iyrqJxK6YCbkaC6FPdqMRI_hhGQ
 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=VfNeP_yplKlh0Uzx9ZYMOErpX7uH2yVOHvZhN94zN00,7620
+django_to_galaxy/models/invocation.py,sha256=kexyKXY2I5QaPlBUs9cva1jzsN2EczIwcPKElgG6Sng,8319
 django_to_galaxy/models/workflow.py,sha256=1Ok0TSSIM-LJbaY1Vm19YVg_WwDxznbLDcXI71S_IL8,1891
 django_to_galaxy/schemas/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 django_to_galaxy/schemas/dataset.py,sha256=yjwLJGb487VJDXoXGg8fG_TW6TJPeyeGtd9vofU-7HI,396
@@ -55,7 +55,7 @@ django_to_galaxy/templates/admin/import_workflows.html,sha256=YB101H99EOR8td_Dzf
 django_to_galaxy/urls.py,sha256=ydMl_0qSyz8GSGkWpiSzU3khqj9mPyZacx532JybLHk,106
 django_to_galaxy/utils.py,sha256=gjUzzqfpili66CY7vFyseqHOD9vqWg_2tzWAiTe3pNE,1625
 django_to_galaxy/version.py,sha256=O9WfyDkb-iJLGWlnKx2K7kFtcDgFCboBiFm553-3Sjk,111
-django_to_galaxy-0.6.7.dist-info/LICENSE,sha256=Er3Bp2y6Wf31e0s1-Tdu_d6Gd89FtTizmGUJzGQkWvo,34498
-django_to_galaxy-0.6.7.dist-info/METADATA,sha256=wnFfuwrnXc-YA10ZGhBsgac0XRE5I9bojn3IhYwzO08,764
-django_to_galaxy-0.6.7.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-django_to_galaxy-0.6.7.dist-info/RECORD,,
+django_to_galaxy-0.6.9.dist-info/LICENSE,sha256=Er3Bp2y6Wf31e0s1-Tdu_d6Gd89FtTizmGUJzGQkWvo,34498
+django_to_galaxy-0.6.9.dist-info/METADATA,sha256=egbQux6CxINf3spU2jrz2LzRslamR4T6JtvoLnzPm3U,764
+django_to_galaxy-0.6.9.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+django_to_galaxy-0.6.9.dist-info/RECORD,,