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

django_to_galaxy/api/views/invoke_workflow.py

@@ -0,0 +1,181 @@
+import django.apps
+from django.db.models.fields.files import FieldFile
+from django.core.exceptions import ObjectDoesNotExist
+from drf_yasg.utils import swagger_auto_schema
+from rest_framework.response import Response
+
+from rest_framework.generics import GenericAPIView, RetrieveAPIView
+from rest_framework.status import HTTP_404_NOT_FOUND
+
+from django_to_galaxy.models import History, Workflow, GalaxyUser
+from django_to_galaxy.api.serializers.invoke_workflow import (
+    InvokeWorkflowSerializer,
+    ExecuteWorkflowSerializer,
+    GenericDictSerializer,
+)
+
+
+class InvokeWorkflowView(GenericAPIView):
+    serializer_class = InvokeWorkflowSerializer
+
+    @swagger_auto_schema(
+        operation_description="Invoke workflow using data from a history.",
+        operation_summary="Invoke workflow using data from a history.",
+        tags=["workflows"],
+    )
+    def post(self, request):
+        serializer_class = self.get_serializer_class()
+        serializer = serializer_class(data=request.data, context={"request": request})
+        serializer.is_valid(raise_exception=True)
+        data = serializer.data
+        # Retrieve history
+        try:
+            history = History.objects.get(id=data["history_id"])
+        except ObjectDoesNotExist:
+            return Response(
+                {
+                    "message": (
+                        "Galaxy history with id ",
+                        f"<{data['history_id']}> not found!",
+                    )
+                },
+                status=HTTP_404_NOT_FOUND,
+            )
+        # Retrieve workflow
+        try:
+            workflow = Workflow.objects.get(id=data["workflow_id"])
+        except ObjectDoesNotExist:
+            return Response(
+                {
+                    "message": (
+                        "Galaxy workflow with id ",
+                        f"<{data['history_id']}> not found!",
+                    )
+                },
+                status=HTTP_404_NOT_FOUND,
+            )
+        inv = workflow.invoke(data["datamap"], history=history)
+        data["message"] = "Workflow successfully invoked."
+        data["invocation_id"] = inv.id
+        return Response(data=data)
+
+
+class GetWorkflowDatamapTemplateView(RetrieveAPIView):
+    queryset = Workflow.objects.all()
+    serializer_class = GenericDictSerializer
+
+    @swagger_auto_schema(
+        operation_description="Get workflow datamap to prepare workflow invocation.",
+        operation_summary="Get workflow datamap to prepare workflow invocation.",
+        tags=["workflows"],
+        responses={200: GenericDictSerializer},
+    )
+    def get(self, request, *args, **kwargs):
+        instance = self.get_object()
+        datamap = instance.get_workflow_datamap_template()
+
+        return Response(data=datamap)
+
+
+"""
+class GetWorkflowInputsView(RetrieveAPIView):
+    queryset = Workflow.objects.all()
+
+    @swagger_auto_schema(
+        operation_description="Get workflow inputs information from Galaxy.",
+        operation_summary="Get workflow inputs information from Galaxy.",
+        tags=["workflows"],
+    )
+    def get(self, request, *args, **kwargs):
+        instance = self.get_object()
+        data = instance.get_workflow_inputs()
+
+        return Response(data=data)
+"""
+
+
+class ExecuteWorkflowView(GenericAPIView):
+    serializer_class = ExecuteWorkflowSerializer
+
+    @swagger_auto_schema(
+        operation_description="Execute workflow using data from a model and a Galaxy user.",
+        operation_summary="Execute workflow using data from a model and a Galaxy user.",
+        tags=["workflows"],
+    )
+    def post(self, request):
+        # Get data from POST request
+        serializer_class = self.get_serializer_class()
+        serializer = serializer_class(data=request.data, context={"request": request})
+        serializer.is_valid(raise_exception=True)
+        data = serializer.data
+        # Create History -> @TODO to refactor in function
+        # - First retrieve galaxy user
+        galaxy_user_id = data["galaxy_user_id"]
+        try:
+            galaxy_user = GalaxyUser.objects.get(id=galaxy_user_id)
+        except ObjectDoesNotExist:
+            return Response(
+                {
+                    "message": (
+                        "Galaxy User with id ",
+                        f"<{galaxy_user_id}> not found!",
+                    )
+                },
+                status=HTTP_404_NOT_FOUND,
+            )
+        history = galaxy_user.create_history()
+        # Upload data to history -> @TODO to refactor in function
+        # - Retrieve all models
+        all_models = django.apps.apps.get_models()
+        all_models_dict = {m.__name__.lower(): m for m in all_models}
+        fake_datamap = data["fake_datamap"]
+        # - Upload each data to history
+        datamap = {}
+        for input_id, input_object in fake_datamap.items():
+            try:
+                file = all_models_dict[input_object["model"]].objects.get(
+                    id=input_object["id"]
+                )
+            except ObjectDoesNotExist:
+                return Response(
+                    {"message": f"File with id <{input_object['id']}> not found!"},
+                    status=HTTP_404_NOT_FOUND,
+                )
+            try:
+                file_path = getattr(file, input_object["path_field"])
+            except AttributeError:
+                return Response(
+                    {"message": f"File with id <{input_object['id']}> not found!"},
+                    status=HTTP_404_NOT_FOUND,
+                )
+            if isinstance(file_path, FieldFile):
+                file_path = file_path.path
+            try:
+                file_type = input_object["file_type"]
+            except AttributeError:
+                return Response(
+                    {"message": f"File with id <{input_object['id']}> not found!"},
+                    status=HTTP_404_NOT_FOUND,
+                )
+            history_association = history.upload_file(file_path, file_type=file_type)
+            datamap[input_id] = {"id": history_association.id, "src": "hda"}
+        # Invoke workflow -> @TODO to refactor in function
+        # - Retrieve workflow
+        try:
+            workflow = Workflow.objects.get(id=data["workflow_id"])
+        except ObjectDoesNotExist:
+            return Response(
+                {
+                    "message": (
+                        "Galaxy workflow with id ",
+                        f"<{data['history_id']}> not found!",
+                    )
+                },
+                status=HTTP_404_NOT_FOUND,
+            )
+        # - Invoke workflow
+        inv = workflow.invoke(datamap, history=history)
+        data["message"] = "Workflow successfully invoked."
+        data["invocation_id"] = inv.id
+        data["datamap"] = datamap
+        return Response(data=data)

django_to_galaxy/api/views/upload_to_history.py

@@ -0,0 +1,78 @@
+import django.apps
+from django.core.exceptions import ObjectDoesNotExist
+from drf_yasg.utils import swagger_auto_schema
+from rest_framework.response import Response
+from django.db.models.fields.files import FieldFile
+
+from rest_framework.generics import GenericAPIView
+from rest_framework.status import HTTP_404_NOT_FOUND
+
+from django_to_galaxy.models import History
+from django_to_galaxy.api.serializers.upload_to_history import UploadHistorySerializer
+
+
+class UploadToHistoryView(GenericAPIView):
+    serializer_class = UploadHistorySerializer
+
+    @swagger_auto_schema(
+        operation_description="Upload file from django file system to a Galaxy history.",
+        operation_summary="Upload file from a model with filepath to history.",
+        tags=["histories"],
+    )
+    def post(self, request):
+        serializer_class = self.get_serializer_class()
+        serializer = serializer_class(data=request.data, context={"request": request})
+        serializer.is_valid(raise_exception=True)
+        data = serializer.data
+        # Retrieve history
+        try:
+            history = History.objects.get(id=data["history_id"])
+        except ObjectDoesNotExist:
+            return Response(
+                {
+                    "message": (
+                        "Galaxy history with id ",
+                        f"<{data['history_id']}> not found!",
+                    )
+                },
+                status=HTTP_404_NOT_FOUND,
+            )
+        # Retrieve file & file path
+        all_models = django.apps.apps.get_models()
+        all_models_dict = {m.__name__.lower(): m for m in all_models}
+        try:
+            file = all_models_dict[data["file"]["model"]].objects.get(
+                id=data["file"]["id"]
+            )
+        except ObjectDoesNotExist:
+            return Response(
+                {"message": f"File with id <{data['file']['id']}> not found!"},
+                status=HTTP_404_NOT_FOUND,
+            )
+        try:
+            file_path = getattr(file, data["file"]["path_field"])
+        except AttributeError:
+            return Response(
+                {"message": f"File with id <{data['file']['id']}> not found!"},
+                status=HTTP_404_NOT_FOUND,
+            )
+        if isinstance(file_path, FieldFile):
+            file_path = file_path.path
+        try:
+            file_type = data["file"]["file_type"]
+        except AttributeError:
+            return Response(
+                {"message": f"File with id <{data['file']['id']}> not found!"},
+                status=HTTP_404_NOT_FOUND,
+            )
+        history_association = history.upload_file(file_path, file_type=file_type)
+        message = (
+            f"File <{str(file)}> has been uploaded to Galaxy History <{str(history)}>"
+        )
+        return Response(
+            {
+                "message": message,
+                "file_galaxy_id": history_association.id,
+                "history_id": history.id,
+            }
+        )

django_to_galaxy/api/views/workflow.py

@@ -0,0 +1,14 @@
+from rest_framework import viewsets
+
+from django_to_galaxy.models.workflow import Workflow
+from django_to_galaxy.api.serializers.workflow import WorkflowSerializer
+
+
+class WorkflowViewSet(viewsets.ReadOnlyModelViewSet):
+    """
+    API endpoint that allows workflows to be viewed.
+    """
+
+    queryset = Workflow.objects.all()
+    lookup_field = "galaxy_id"
+    serializer_class = WorkflowSerializer

django_to_galaxy/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class DjangoToGalaxyConfig(AppConfig):
+    name = "django_to_galaxy"
+    verbose_name = "Django to Galaxy"

django_to_galaxy/migrations/0001_new_initial.py

@@ -0,0 +1,171 @@
+# Generated by Django 4.0.3 on 2022-07-19 09:09
+
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    replaces = [
+        ("django_to_galaxy", "0001_initial"),
+        (
+            "django_to_galaxy",
+            "0002_alter_galaxyuser_galaxy_instance_alter_history_owner_and_more",
+        ),
+        ("django_to_galaxy", "0003_remove_history_latest_payload_and_more"),
+        ("django_to_galaxy", "0004_alter_history_unique_together_and_more"),
+        ("django_to_galaxy", "0005_alter_workflow_unique_together_invocation"),
+        ("django_to_galaxy", "0006_rename_owner_history_galaxy_owner_and_more"),
+        ("django_to_galaxy", "0007_history_create_time"),
+    ]
+
+    initial = True
+
+    dependencies = []
+
+    operations = [
+        migrations.CreateModel(
+            name="GalaxyInstance",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("url", models.URLField(max_length=100)),
+                ("name", models.CharField(max_length=100, unique=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name="GalaxyUser",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                (
+                    "email",
+                    models.EmailField(
+                        help_text="Email used for the Galaxy account", max_length=254
+                    ),
+                ),
+                ("api_key", models.CharField(max_length=50)),
+                (
+                    "galaxy_instance",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="users",
+                        to="django_to_galaxy.galaxyinstance",
+                    ),
+                ),
+            ],
+        ),
+        migrations.CreateModel(
+            name="History",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("galaxy_id", models.CharField(max_length=50)),
+                ("name", models.CharField(max_length=200)),
+                ("annotation", models.CharField(max_length=200)),
+                ("published", models.BooleanField()),
+                ("state", models.CharField(max_length=100)),
+                (
+                    "galaxy_owner",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="histories",
+                        to="django_to_galaxy.galaxyuser",
+                    ),
+                ),
+                (
+                    "create_time",
+                    models.DateTimeField(default=django.utils.timezone.now),
+                ),
+            ],
+            options={
+                "abstract": False,
+                "verbose_name_plural": "Histories",
+                "unique_together": {("galaxy_id", "galaxy_owner")},
+            },
+        ),
+        migrations.CreateModel(
+            name="Workflow",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("galaxy_id", models.CharField(max_length=50)),
+                ("name", models.CharField(max_length=200)),
+                ("annotation", models.CharField(max_length=200)),
+                ("published", models.BooleanField()),
+                (
+                    "galaxy_owner",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="workflows",
+                        to="django_to_galaxy.galaxyuser",
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+                "unique_together": set(),
+            },
+        ),
+        migrations.CreateModel(
+            name="Invocation",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("galaxy_id", models.CharField(max_length=50)),
+                ("state", models.CharField(max_length=200)),
+                (
+                    "history",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="histories",
+                        to="django_to_galaxy.history",
+                    ),
+                ),
+                (
+                    "workflow",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="workflows",
+                        to="django_to_galaxy.workflow",
+                    ),
+                ),
+            ],
+        ),
+    ]

django_to_galaxy/migrations/0002_rename_state_history_galaxy_state_and_more.py

@@ -0,0 +1,37 @@
+# Generated by Django 4.0.3 on 2022-07-21 12:37
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0001_new_initial"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="history",
+            old_name="state",
+            new_name="galaxy_state",
+        ),
+        migrations.RenameField(
+            model_name="invocation",
+            old_name="state",
+            new_name="galaxy_state",
+        ),
+        migrations.AddField(
+            model_name="invocation",
+            name="status",
+            field=models.CharField(
+                choices=[("running", "Running"), ("done", "Done")],
+                default="running",
+                max_length=10,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="history",
+            name="create_time",
+            field=models.DateTimeField(),
+        ),
+    ]

django_to_galaxy/migrations/0003_invocation_create_time.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.0.3 on 2022-07-26 09:55
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0002_rename_state_history_galaxy_state_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="invocation",
+            name="create_time",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+            preserve_default=False,
+        ),
+    ]

django_to_galaxy/migrations/0004_alter_galaxyuser_email_galaxyoutputfile.py

@@ -0,0 +1,46 @@
+# Generated by Django 4.0.3 on 2022-08-01 12:47
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0003_invocation_create_time"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="galaxyuser",
+            name="email",
+            field=models.EmailField(max_length=254),
+        ),
+        migrations.CreateModel(
+            name="GalaxyOutputFile",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("galaxy_id", models.CharField(max_length=50)),
+                ("workflow_name", models.CharField(max_length=200)),
+                ("galaxy_state", models.CharField(max_length=100, null=True)),
+                ("history_name", models.CharField(max_length=200, null=True)),
+                ("src", models.CharField(max_length=50)),
+                (
+                    "invocation",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="outputs",
+                        to="django_to_galaxy.invocation",
+                    ),
+                ),
+            ],
+        ),
+    ]

django_to_galaxy/migrations/0005_alter_galaxyoutputfile_invocation_and_more.py

@@ -0,0 +1,37 @@
+# Generated by Django 4.0.3 on 2022-08-03 12:58
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0004_alter_galaxyuser_email_galaxyoutputfile"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="galaxyoutputfile",
+            name="invocation",
+            field=models.ForeignKey(
+                on_delete=django.db.models.deletion.CASCADE,
+                related_name="output_files",
+                to="django_to_galaxy.invocation",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="invocation",
+            name="status",
+            field=models.CharField(
+                choices=[
+                    ("running", "Running"),
+                    ("paused", "Paused"),
+                    ("error", "Error"),
+                    ("done", "Done"),
+                ],
+                default="running",
+                max_length=10,
+            ),
+        ),
+    ]

django_to_galaxy/migrations/0006_tag_history_tags_workflow_tags.py

@@ -0,0 +1,42 @@
+# Generated by Django 4.1 on 2023-03-02 10:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("django_to_galaxy", "0005_alter_galaxyoutputfile_invocation_and_more"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="Tag",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("label", models.CharField(max_length=200, unique=True)),
+            ],
+        ),
+        migrations.AddField(
+            model_name="history",
+            name="tags",
+            field=models.ManyToManyField(
+                blank=True, null=True, to="django_to_galaxy.tag"
+            ),
+        ),
+        migrations.AddField(
+            model_name="workflow",
+            name="tags",
+            field=models.ManyToManyField(
+                blank=True, null=True, to="django_to_galaxy.tag"
+            ),
+        ),
+    ]