django-to-galaxy 0.6.9.7__py3-none-any.whl → 0.6.9.9__py3-none-any.whl

django_to_galaxy/migrations/0012_workflowinput_collection_type_and_more.py

@@ -0,0 +1,136 @@
+# Generated by Django 5.2.3 on 2025-09-09 13:15
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "django_to_galaxy",
+            "0011_rename__step_jobs_count_workflow__step_count_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="workflowinput",
+            name="collection_type",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("record", "Record"),
+                    ("paired", "Dataset Pair"),
+                    ("list", "List of Datasets"),
+                    ("list:record", "List of Records"),
+                    ("list:paired", "List of Dataset Pairs"),
+                    (
+                        "list:paired_or_unpaired",
+                        "Mixed List of Paired and Unpaired Datasets",
+                    ),
+                ],
+                default=None,
+                max_length=25,
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="workflowinput",
+            name="default_value",
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AddField(
+            model_name="workflowinput",
+            name="input_type",
+            field=models.CharField(
+                choices=[
+                    ("data_input", "data_input"),
+                    ("data_collection_input", "data_collection_input"),
+                    ("parameter_input", "parameter_input"),
+                ],
+                default="data_input",
+                max_length=25,
+            ),
+        ),
+        migrations.AddField(
+            model_name="workflowinput",
+            name="multiple",
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name="workflowinput",
+            name="parameter_type",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("text", "text"),
+                    ("integer", "integer"),
+                    ("float", "float"),
+                    ("boolean", "boolean"),
+                    ("color", "color"),
+                    ("directory_uri", "directory_uri"),
+                ],
+                default=None,
+                max_length=15,
+                null=True,
+            ),
+        ),
+        migrations.CreateModel(
+            name="WorkflowInputTextOption",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("text_option", models.CharField(max_length=255)),
+                (
+                    "workflow_input",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="django_to_galaxy.workflowinput",
+                    ),
+                ),
+            ],
+        ),
+        migrations.AddField(
+            model_name="workflowinput",
+            name="restrict_text_values",
+            field=models.ManyToManyField(to="django_to_galaxy.workflowinputtextoption"),
+        ),
+        migrations.AddConstraint(
+            model_name="workflowinput",
+            constraint=models.CheckConstraint(
+                condition=models.Q(
+                    models.Q(
+                        ("input_type", "parameter_input"),
+                        ("parameter_type__isnull", False),
+                        ("collection_type__isnull", True),
+                    ),
+                    models.Q(
+                        ("input_type", "data_input"),
+                        ("parameter_type__isnull", True),
+                        ("collection_type__isnull", True),
+                    ),
+                    models.Q(
+                        ("input_type", "data_collection_input"),
+                        ("parameter_type__isnull", True),
+                        ("collection_type__isnull", False),
+                    ),
+                    _connector="OR",
+                ),
+                name="workflowinputs_types_congruant",
+            ),
+        ),
+        migrations.AddConstraint(
+            model_name="workflowinputtextoption",
+            constraint=models.UniqueConstraint(
+                fields=("workflow_input", "text_option"), name="unique_input_option"
+            ),
+        ),
+    ]

django_to_galaxy/models/__init__.py

@@ -5,4 +5,4 @@ from .history import History  # noqa
 from .invocation import Invocation  # noqa
 from .workflow import Workflow  # noqa
 from .galaxy_element import Tag  # noqa
-from .accepted_input import WorkflowInput, Format  # noqa
+from .accepted_input import WorkflowInput, Format, WorkflowInputTextOption  # noqa

django_to_galaxy/models/accepted_input.py

@@ -1,28 +1,139 @@
 from django.db import models
+from django.db.models import Q
+
+DATA = "data_input"
+COLLECTION = "data_collection_input"
+PARAMETER = "parameter_input"
+INPUT_TYPE_CHOICES = [
+    (DATA, "data_input"),
+    (COLLECTION, "data_collection_input"),
+    (PARAMETER, "parameter_input"),
+]
+
+P_TEXT = "text"
+P_INTEGER = "integer"
+P_FLOAT = "float"
+P_BOOLEAN = "boolean"
+P_COLOR = "color"
+P_DIRECTORY_URI = "directory_uri"
+PARAMETER_TYPE_CHOICES = [
+    (P_TEXT, "text"),
+    (P_INTEGER, "integer"),
+    (P_FLOAT, "float"),
+    (P_BOOLEAN, "boolean"),
+    (P_COLOR, "color"),
+    (P_DIRECTORY_URI, "directory_uri"),
+]
+
+C_RECORD = "record"
+C_PAIRED = "paired"
+C_LIST = "list"
+C_LIST_RECORD = "list:record"
+C_LIST_PAIRED = "list:paired"
+C_LIST_PAIRED_UNPAIRED = "list:paired_or_unpaired"
+COLLECTION_TYPE_CHOICES = [
+    (C_RECORD, "Record"),
+    (C_PAIRED, "Dataset Pair"),
+    (C_LIST, "List of Datasets"),
+    (C_LIST_RECORD, "List of Records"),
+    (C_LIST_PAIRED, "List of Dataset Pairs"),
+    (C_LIST_PAIRED_UNPAIRED, "Mixed List of Paired and Unpaired Datasets"),
+]
 
 
 class Format(models.Model):
-    format = models.CharField(max_length=200, unique=True)
     """Format on the galaxy side."""
 
+    format = models.CharField(max_length=200, unique=True)
+
     def __str__(self):
         return f"{self.format}"
 
 
+class WorkflowInputTextOption(models.Model):
+    """Text option for a workflow input on Galaxy side."""
+
+    workflow_input = models.ForeignKey(
+        "WorkflowInput", null=False, on_delete=models.CASCADE
+    )
+    text_option = models.CharField(max_length=255)
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=["workflow_input", "text_option"], name="unique_input_option"
+            )
+        ]
+
+    def __str__(self):
+        return f"{self.text_option}"
+
+    def __repr__(self):
+        return f"Input: {self!s}"
+
+
 class WorkflowInput(models.Model):
+    """Accepted input for a workflow on Galaxy side."""
+
     galaxy_step_id = models.IntegerField(null=False)
     """Step id on the galaxy side."""
     label = models.CharField(max_length=100, blank=True)
     """Label on the galaxy side."""
     workflow = models.ForeignKey("Workflow", null=False, on_delete=models.CASCADE)
     """Workflow id."""
+    input_type = models.CharField(
+        max_length=25, choices=INPUT_TYPE_CHOICES, default=DATA
+    )
+    """Type of input on the galaxy side."""
     formats = models.ManyToManyField("Format")
     """Accepted input formats on the galaxy side."""
+    parameter_type = models.CharField(
+        max_length=15,
+        choices=PARAMETER_TYPE_CHOICES,
+        default=None,
+        null=True,
+        blank=True,
+    )
+    """Type of input if it is a parameter input."""
+    collection_type = models.CharField(
+        max_length=25,
+        choices=COLLECTION_TYPE_CHOICES,
+        default=None,
+        null=True,
+        blank=True,
+    )
+    """Type of input if it is a parameter input."""
     optional = models.BooleanField(default=False)
     """Workflow input optional information on the galaxy side."""
+    default_value = models.CharField(max_length=255, null=True, blank=True)
+    """Default value of the input (either text, integer, float, boolean)"""
+    multiple = models.BooleanField(default=False)
+    """If the input can get multiple values on the galaxy side."""
+
+    class Meta:
+        constraints = [
+            models.CheckConstraint(
+                check=Q(
+                    Q(input_type=PARAMETER)
+                    & Q(parameter_type__isnull=False)
+                    & Q(collection_type__isnull=True)
+                )
+                | Q(
+                    Q(input_type=DATA)
+                    & Q(parameter_type__isnull=True)
+                    & Q(collection_type__isnull=True)
+                )
+                | Q(
+                    Q(input_type=COLLECTION)
+                    & Q(parameter_type__isnull=True)
+                    & Q(collection_type__isnull=False)
+                ),
+                name="workflowinputs_types_congruant",
+            )
+        ]
 
     def __str__(self):
-        return f"{self.label} of {self.workflow!r}"
+        return f"{self.label}"
 
     def __repr__(self):
         return f"Input: {self!s}"

django_to_galaxy/models/galaxy_instance.py

@@ -22,7 +22,7 @@ class GalaxyInstance(models.Model):
             Whether the instance is available or not.
         """
         try:
-            response = requests.get(self.url, timeout=2)
+            response = requests.head(self.url, timeout=30)
             response.raise_for_status()
             return True
         except Exception:

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."""