django-to-galaxy 0.7.0.0__py3-none-any.whl

django_to_galaxy/migrations/0007_format_alter_history_tags_alter_workflow_tags_and_more.py

@@ -0,0 +1,63 @@
+# Generated by Django 4.1 on 2023-03-02 10:28
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0006_tag_history_tags_workflow_tags"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Format",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("format", models.CharField(max_length=200, unique=True)),
+            ],
+        ),
+        migrations.AlterField(
+            model_name="history",
+            name="tags",
+            field=models.ManyToManyField(blank=True, to="django_to_galaxy.tag"),
+        ),
+        migrations.AlterField(
+            model_name="workflow",
+            name="tags",
+            field=models.ManyToManyField(blank=True, to="django_to_galaxy.tag"),
+        ),
+        migrations.CreateModel(
+            name="WorkflowInput",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("galaxy_step_id", models.IntegerField()),
+                ("optional", models.BooleanField(default=False)),
+                ("formats", models.ManyToManyField(to="django_to_galaxy.format")),
+                (
+                    "workflow",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        to="django_to_galaxy.workflow",
+                    ),
+                ),
+            ],
+        ),
+    ]

django_to_galaxy/migrations/0008_workflowinput_label.py

@@ -0,0 +1,21 @@
+# Generated by Django 4.1 on 2023-03-08 17:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "django_to_galaxy",
+            "0007_format_alter_history_tags_alter_workflow_tags_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="workflowinput",
+            name="label",
+            field=models.CharField(blank=True, max_length=100),
+        ),
+    ]

django_to_galaxy/migrations/0009_galaxyoutputfile_unique_galaxy_id_per_invocation.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.1 on 2023-10-27 11:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0008_workflowinput_label"),
+    ]
+
+    operations = [
+        migrations.AddConstraint(
+            model_name="galaxyoutputfile",
+            constraint=models.UniqueConstraint(
+                fields=("galaxy_id", "invocation"),
+                name="unique_galaxy_id_per_invocation",
+            ),
+        ),
+    ]

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/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/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

@@ -0,0 +1,8 @@
+from .galaxy_instance import GalaxyInstance  # noqa
+from .galaxy_user import GalaxyUser  # noqa
+from .galaxy_output_file import GalaxyOutputFile  # noqa
+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, WorkflowInputTextOption  # noqa

django_to_galaxy/models/accepted_input.py

@@ -0,0 +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 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}"
+
+    def __repr__(self):
+        return f"Input: {self!s}"

django_to_galaxy/models/galaxy_element.py

@@ -0,0 +1,52 @@
+from abc import abstractmethod
+
+from django.db import models
+
+
+class Tag(models.Model):
+    label = models.CharField(null=False, max_length=200, unique=True)
+
+    def __str__(self):
+        return f"{self.label}"
+
+    def __repr__(self):
+        return f"Tag: {self!s}"
+
+
+class GalaxyElement(models.Model):
+    """Base class for all Galaxy elements with galaxy id that are likely to evolve or change."""
+
+    galaxy_id = models.CharField(null=False, max_length=50)
+    """Invocation id used on the galaxy side."""
+    name = models.CharField(null=False, max_length=200)
+    """Name used on the galaxy side."""
+    annotation = models.CharField(max_length=200)
+    """Annotation on the galaxy side."""
+    tags = models.ManyToManyField("Tag", blank=True)
+    """tags on the galaxy side."""
+    published = models.BooleanField(null=False)
+    """Whether it is published or not on the galaxy side."""
+    galaxy_owner = models.ForeignKey("GalaxyUser", null=False, on_delete=models.CASCADE)
+    """Galaxy user that owns this element."""
+
+    @abstractmethod
+    def synchronize(self):
+        """
+        @TODO
+        method to synchronize entry in django from galaxy based on galaxy_id.
+        """
+        raise NotImplementedError
+
+    @abstractmethod
+    def is_valid(self):
+        """
+        @TODO
+        method to check if galaxy_id is still pointing to a valid element.
+        """
+        raise NotImplementedError
+
+    def __str__(self):
+        return f"{self.name} ({self.galaxy_id})"
+
+    class Meta:
+        abstract = True

django_to_galaxy/models/galaxy_instance.py

@@ -0,0 +1,29 @@
+import requests
+
+from django.db import models
+
+
+class GalaxyInstance(models.Model):
+    """Table for Galaxy instances."""
+
+    url = models.URLField(max_length=100)
+    """url of the Galaxy instance."""
+    name = models.CharField(max_length=100, unique=True)
+    """Name of the Galaxy Instance."""
+
+    def __str__(self):
+        return f"{self.name} [{self.url}]"
+
+    def is_online(self) -> bool:
+        """
+        Check the status of the instance.
+
+        Returns:
+            Whether the instance is available or not.
+        """
+        try:
+            response = requests.head(self.url, timeout=30)
+            response.raise_for_status()
+            return True
+        except Exception:
+            return False

django_to_galaxy/models/galaxy_output_file.py

@@ -0,0 +1,53 @@
+from bioblend.galaxy.objects import wrappers
+from django.db import models
+
+
+class GalaxyOutputFile(models.Model):
+    """Handle output files."""
+
+    galaxy_id = models.CharField(null=False, max_length=50)
+    """Dataset id used on the galaxy side."""
+    workflow_name = models.CharField(null=False, max_length=200)
+    """Name used in the workflow on the galaxy side."""
+    galaxy_state = models.CharField(max_length=100, null=True)
+    """State on the galaxy side."""
+    history_name = models.CharField(null=True, max_length=200)
+    """Name used in the history on the galaxy side."""
+    src = models.CharField(null=False, max_length=50)
+    """Src type on the galaxy side."""
+    invocation = models.ForeignKey(
+        "Invocation", null=False, on_delete=models.CASCADE, related_name="output_files"
+    )
+    """Invocation that generated the output."""
+
+    @property
+    def galaxy_dataset(self) -> wrappers.Invocation:
+        """Galaxy object using bioblend."""
+        if getattr(self, "_galaxy_dataset", None) is None:
+            self._galaxy_dataset = self._get_galaxy_dataset()
+        return self._galaxy_dataset
+
+    def _get_galaxy_dataset(self) -> wrappers.Invocation:
+        """Get galaxy object using bioblend."""
+        return self.invocation.history.galaxy_history.get_dataset(self.galaxy_id)
+
+    def synchronize(self):
+        """Synchronize state from Galaxy instance."""
+        dataset = self._get_galaxy_dataset()
+        self.galaxy_state = dataset.state
+        self.history_name = dataset.name
+        self.save()
+
+    def __str__(self):
+        return f"{self.history_name} (from {self.invocation.galaxy_id})"
+
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=(
+                    "galaxy_id",
+                    "invocation",
+                ),
+                name="unique_galaxy_id_per_invocation",
+            )
+        ]

django_to_galaxy/models/galaxy_user.py

@@ -0,0 +1,94 @@
+from datetime import datetime
+from typing import List
+
+from bioblend.galaxy.objects import GalaxyInstance as BioblendGalaxyInstance
+from django.db import models
+
+from django_to_galaxy.apps import DjangoToGalaxyConfig
+from django_to_galaxy.utils import load_galaxy_history_time_to_datetime
+from .history import History
+from .workflow import Workflow
+
+
+class GalaxyUser(models.Model):
+    """Table for Galaxy users."""
+
+    email = models.EmailField(null=False)
+    """Email used for the Galaxy account."""
+    api_key = models.CharField(null=False, max_length=50)
+    """API key of the user."""
+    galaxy_instance = models.ForeignKey(
+        "GalaxyInstance", null=False, on_delete=models.CASCADE, related_name="users"
+    )
+    """Galaxy instance the user comes from."""
+
+    @property
+    def obj_gi(self):
+        """Bioblend object to interact with Galaxy instance."""
+        if getattr(self, "_obj_gi", None) is None:
+            self._obj_gi = self.get_bioblend_obj_gi()
+        return self._obj_gi
+
+    @obj_gi.setter
+    def obj_gi(self, val):
+        self._obj_gi = val
+
+    def get_bioblend_obj_gi(self):
+        """Retrieve bioblend object to interact with Galaxy instance."""
+        return BioblendGalaxyInstance(self.galaxy_instance.url, self.api_key)
+
+    @property
+    def available_workflows(self) -> List[Workflow]:
+        """Available workflows for the user."""
+        if getattr(self, "_available_workflows", None) is None:
+            self._available_workflows = self.get_available_workflows()
+        return self._available_workflows
+
+    def get_available_workflows(self) -> List[Workflow]:
+        """List all available workflows for the user."""
+        bioblend_wfs = self.obj_gi.workflows.list()
+        wfs_tag = []
+        for wf in bioblend_wfs:
+            wfs_tag.append(
+                (
+                    Workflow(
+                        galaxy_owner=self,
+                        galaxy_id=wf.id,
+                        name=wf.name,
+                        published=wf.published,
+                        annotation=wf.wrapped["annotation"],
+                    ),
+                    wf.wrapped["tags"],
+                )
+            )
+        return wfs_tag
+
+    def _generate_history_name(self) -> str:
+        """
+        Generate history name using current date.
+
+        Returns:
+            Generated history name.
+        """
+        current_time = datetime.now()
+        str_date = current_time.strftime("%Y%m%d-%f")
+        suffix = f"created_by_{DjangoToGalaxyConfig.name}"
+        return f"{str_date}_{suffix}"
+
+    def create_history(self, name=None):
+        """Create history on the Galaxy instance."""
+        name = self._generate_history_name() if name is None else name
+        galaxy_history = self.obj_gi.histories.create(name=name)
+        local_history = History(
+            galaxy_id=galaxy_history.id,
+            name=galaxy_history.name,
+            published=galaxy_history.published,
+            galaxy_state=galaxy_history.state,
+            create_time=load_galaxy_history_time_to_datetime(galaxy_history),
+            galaxy_owner=self,
+        )
+        local_history.save()
+        return local_history
+
+    def __str__(self):
+        return f"{self.email} at {self.galaxy_instance}"