diff --git a/server/api/migrations/0002_alter_galaxyworkflowinvocation_status.py b/server/api/migrations/0002_alter_galaxyworkflowinvocation_status.py
new file mode 100644
index 0000000000000000000000000000000000000000..0d9e4d91f016115c406e729b0f1f794802134617
--- /dev/null
+++ b/server/api/migrations/0002_alter_galaxyworkflowinvocation_status.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.20 on 2023-07-19 08:34
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('api', '0001_initial'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='galaxyworkflowinvocation',
+ name='status',
+ field=models.CharField(choices=[('scheduled', 'Scheduled'), ('running', 'Running'), ('paused', 'Paused'), ('error', 'Error'), ('done', 'Done')], default='scheduled', max_length=10),
+ ),
+ ]
diff --git a/server/api/models/galaxy.py b/server/api/models/galaxy.py
index 41f9f311f1e4f1b9f84c5c88926f1dd244dd4ae0..99e375f42b438b8d30d4e9115a307c364b5d7fe6 100644
--- a/server/api/models/galaxy.py
+++ b/server/api/models/galaxy.py
@@ -353,7 +353,8 @@ class GalaxyWorkflow(models.Model):
class GalaxyWorkflowInvocation(models.Model):
class WorkflowInvocationStatus(models.TextChoices):
- RUNNING = ("running", "RUNNING")
+ SCHEDULED = ("scheduled", "Scheduled")
+ RUNNING = ("running", "Running")
PAUSED = ("paused", "Paused")
ERROR = ("error", "Error")
DONE = ("done", "Done")
@@ -367,7 +368,7 @@ class GalaxyWorkflowInvocation(models.Model):
status = models.CharField(
max_length=10,
choices=WorkflowInvocationStatus.choices,
- default=WorkflowInvocationStatus.RUNNING,
+ default=WorkflowInvocationStatus.SCHEDULED,
)
class Meta:
@@ -387,8 +388,11 @@ class GalaxyWorkflowInvocation(models.Model):
workflow_id=self.galaxy_workflow.get_encoded_id(),
history_id=self.galaxy_history.get_encoded_id(),
)
+ print(invocations)
if len(invocations) == 1:
return invocations[0]["id"]
+ elif len(invocations) == 0:
+ return None
else:
raise Exception(f"Multiple wf invocations for {self.galaxy_workflow}")
@@ -401,19 +405,34 @@ class GalaxyWorkflowInvocation(models.Model):
def _get_galaxy_invocation(self):
"""Get galaxy object using bioblend."""
- return self.galaxy_workflow.galaxy_user.bioblend_gi.workflows.show_invocation(
- workflow_id=self.galaxy_workflow.get_encoded_id(),
- invocation_id=self.get_encoded_id(),
- )
+ workflow_invocation_id = self.get_encoded_id()
+
+ if workflow_invocation_id is None:
+ return None
+ else:
+ return (
+ self.galaxy_workflow.galaxy_user.bioblend_gi.workflows.show_invocation(
+ workflow_id=self.galaxy_workflow.get_encoded_id(),
+ invocation_id=workflow_invocation_id,
+ )
+ )
@property
def percentage_done(self) -> float:
"""Retrieve percentage of jobs done for the invocation."""
if self.status == self.WorkflowInvocationStatus.DONE:
return 100.0
- step_jobs_summary = self.galaxy_workflow.galaxy_user.bioblend_gi.invocations.get_invocation_step_jobs_summary(
- self.get_encoded_id()
- )
+
+ workflow_invocation_id = self.get_encoded_id()
+ if workflow_invocation_id:
+ step_jobs_summary = self.galaxy_workflow.galaxy_user.bioblend_gi.invocations.get_invocation_step_jobs_summary(
+ workflow_invocation_id
+ )
+ else:
+ self.status = self.WorkflowInvocationStatus.SCHEDULED
+ self.save()
+ return 0
+
count_states = defaultdict(int)
if len(step_jobs_summary) >= 1:
for step in step_jobs_summary:
@@ -429,8 +448,13 @@ class GalaxyWorkflowInvocation(models.Model):
elif "paused" in count_states.keys():
self.status = self.WorkflowInvocationStatus.PAUSED
self.save()
+ else:
+ self.status = self.WorkflowInvocationStatus.RUNNING
+ self.save()
return percentage_done * 100
else:
+ self.status = self.WorkflowInvocationStatus.SCHEDULED
+ self.save()
return 0
def synchronize(self):
@@ -442,17 +466,14 @@ class GalaxyWorkflowInvocation(models.Model):
}:
return
- galaxy_invocation = self._get_galaxy_invocation()
- self.galaxy_state = galaxy_invocation["state"]
- self.save()
+ if self.galaxy_invocation is not None:
+ self.galaxy_state = self.galaxy_invocation["state"]
+ self.save()
def get_galaxy_invocation(self):
galaxy_user = self.galaxy_workflow.galaxy_user
gi = galaxy_user.bioblend_gi
- invocation = gi.workflows.show_invocation(
- workflow_id=self.galaxy_workflow.get_encoded_id(),
- invocation_id=self.get_encoded_id(),
- )
+ invocation = self.galaxy_invocation
def job_detail(steps):
param_keys_to_remove = {
@@ -460,48 +481,56 @@ class GalaxyWorkflowInvocation(models.Model):
"chromInfo",
"dbkey",
}
- for step in invocation["steps"]:
- if step["job_id"] is not None:
- job = gi.jobs.show_job(step["job_id"], full_details=True)
- tool = gi.tools.show_tool(job["tool_id"], io_details=True)
- metrics = job["job_metrics"] if "job_metrics" in job else []
- yield (
- {
- "order_index": step["order_index"],
- "job_id": step["job_id"],
- "step_id": step["order_index"],
- "tool": tool,
- "job": {
- "create_time": job["create_time"],
- "update_time": job["update_time"],
- "metrics": metrics,
- "state": job["state"],
- "params": dict(
- [
- (key, json.loads(param))
- for (key, param) in job["params"].items()
- if key not in param_keys_to_remove
- ]
- ),
- },
- }
- )
-
- return {
- "invocation": invocation,
- "steps": list(job_detail(invocation["steps"])),
- }
+ if invocation is not None:
+ for step in invocation["steps"]:
+ if step["job_id"] is not None:
+ job = gi.jobs.show_job(step["job_id"], full_details=True)
+ tool = gi.tools.show_tool(job["tool_id"], io_details=True)
+ metrics = job["job_metrics"] if "job_metrics" in job else []
+ yield (
+ {
+ "order_index": step["order_index"],
+ "job_id": step["job_id"],
+ "step_id": step["order_index"],
+ "tool": tool,
+ "job": {
+ "create_time": job["create_time"],
+ "update_time": job["update_time"],
+ "metrics": metrics,
+ "state": job["state"],
+ "params": dict(
+ [
+ (key, json.loads(param))
+ for (key, param) in job["params"].items()
+ if key not in param_keys_to_remove
+ ]
+ ),
+ },
+ }
+ )
+
+ if invocation is not None:
+ return {
+ "invocation": invocation,
+ "steps": list(job_detail(invocation["steps"])),
+ }
+ else:
+ return None
def get_workflow_job_parameters(self):
invocation = self.get_galaxy_invocation()
def job_detail(steps):
- for step in invocation["steps"]:
- if step["job"]["params"] is not None:
- # job = gi.jobs.show_job(step["job_id"])
- yield (step["order_index"], step["job"]["params"])
-
- return dict(job_detail(invocation["steps"]))
+ if invocation is not None:
+ for step in invocation["steps"]:
+ if step["job"]["params"] is not None:
+ # job = gi.jobs.show_job(step["job_id"])
+ yield (step["order_index"], step["job"]["params"])
+
+ if invocation is not None:
+ return dict(job_detail(invocation["steps"]))
+ else:
+ return None
class GalaxyDataset(models.Model):