Merge branch 'model_factory' into 'main'

Model factory

See merge request !2

.gitignore

+# Keeping this deployment specific
+models.txt
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -32,6 +32,8 @@ Install dependencies from requirements.txt
 
 This was done at start of project, and must be repeated after all dependency changes:
 
+TODO: Decide on whether to use pip freeze or manage requirements.txt manually. Ref e.g. [this blogpost](https://medium.com/@tomagee/pip-freeze-requirements-txt-considered-harmful-f0bce66cf895)
+
 ```sh
 (venv)$ pip install "fastapi[all]" (and others)
 (venv)$ pip freeze > requirements.txt
@@ -44,6 +46,13 @@ $ . venv/bin/activate
 (venv)$ deactivate
 ```
 
+### Install VIPS models
+The VIPS models available will vary between deployments of VIPSCore-Python. They are installed using pip, and specified in `models.txt` - which can be considered a deployment specific addendum to `requirements.txt`. Copy `models_example.txt` to `models.txt` to get started.
+
+```sh
+pip install -r models.txt
+```
+
 ## Development
 
 ### Run application locally

app/internal/model_factory.py

+import importlib
+import pkgutil
+from vipscore_common.vips_model import VIPSModel
+
+_models = None
+_packages = None
+
+def discover_models():
+    """
+    Searches the current Python path for packages that contains "vips" in the package or module name
+    """
+    models = {}
+    global _packages
+    _packages = []
+    for package in pkgutil.walk_packages():
+        # Package or module has to contain "vips",
+        # otherwise it will not be indexed
+        if "vips" in package.name:
+            _packages.append(package)
+            print(package.name)
+            try:
+                importlib.import_module(package.name)
+            except:
+                pass
+    for vipsmodel_subclass in VIPSModel.__subclasses__():
+        # We must have an instance to reach the property
+        vipsmodel_instance = vipsmodel_subclass()
+        if models.get(vipsmodel_instance.model_id) is None:
+            models[vipsmodel_instance.model_id] = vipsmodel_subclass
+        else:
+            possible_duplicate = models.get(vipsmodel_instance.model_id)
+            raise ValueError("ERROR when trying to index VIPS model %s: VIPS model %s has the same ID (%s). Please check your model installations" % (vipsmodel_subclass, possible_duplicate, vipsmodel_instance.model_id))
+
+    return models
+
+def get_model_instance(model_id):
+    return get_vips_models().get(model_id)()
+
+def get_vips_model_packages():
+    global _packages
+    if _packages is None:
+        discover_models()
+    return _packages
+
+def get_vips_models():
+    global _models
+    if _models is None:
+        #print("Indexing models")
+        _models = discover_models()
+    return _models
+
+# USAGE EXAMPLE. REMOVE when U start using the module from elsewhere
+#model = get_model_instance("REFERENCEM")
+#print(model.get_model_name())
+#print(get_vips_model_packages())
+
+

app/main.py

+from fastapi import FastAPI
+from fastapi.responses import PlainTextResponse
+from app.internal.model_factory import *
+from vipscore_common.vips_model import VIPSModel
+from vipscore_common.entities import ModelConfiguration, Result
+
+description = """
+    Python implementation of VIPSCore, to enable models written in Python.
+"""
+
+
+app = FastAPI(
+    title = "VIPSCore-Python",
+    description=description,
+    contact= {
+        "name": "Berit Nordskog",
+        "email": "post@vips.no",
+        "url": "https://nibio.no/en/employees/berit-nordskog",
+    },
+    license_info={
+        "name": "GNU Affero General Public License v3",
+        "url": "https://www.gnu.org/licenses/agpl-3.0.en.html"
+    }
+)
+
+# TODO Create a nice welcome page
+@app.get("/")
+async def root():
+    return {"message": "Hello World"}
+
+#######  Model listing endpoints #######
+
+@app.get("/models/json", name="List all models (Json, default language)")
+async def print_model_list_json_default_language():
+    return _print_model_list_json(VIPSModel.default_language)
+
+@app.get("/models/json/{language}", name="List all models (Json)")
+async def print_model_list_json(language:str):
+    return _print_model_list_json(language)
+
+@app.get("/models", response_class=PlainTextResponse, name="List all models (plain text, default language)")
+async def print_model_list_default_language() -> str:
+    return _print_model_list(VIPSModel.default_language)
+
+@app.get("/models/{language}", response_class=PlainTextResponse, name="List all models (plain text)")
+async def print_model_list(language: str) -> str:
+    return _print_model_list(language)
+
+
+#######  Model running endpoints #######
+@app.post("/models/run/", name="Run a model")
+async def run_model_from_config_only(model_configuration:ModelConfiguration):
+    return _run_model(model_configuration.model_id, model_configuration)
+
+@app.post("/models/{model_id}/run/", name="Run a model")
+async def run_model_from_config_only(model_id, model_configuration:ModelConfiguration):
+    return _run_model(model_id, model_configuration)
+
+
+#######  Helper functions #######
+# Dealing with no method overload in Python :-)
+
+def _run_model(model_id:str, model_configuration:ModelConfiguration):
+    """
+    Run a model, using provided model_id and ModelConfiguration
+    Return a list of Result objects
+    """
+    requested_model = get_model_instance(model_id)
+    requested_model.set_configuration(model_configuration)
+    return requested_model.get_result()
+
+
+def _print_model_list(language:str):
+    """
+    Returns the list of available models in plain text format
+    """
+    model_list = ""
+    vips_models = get_vips_models()
+    for model_id in vips_models:
+        model_list = "%s%s %s\n" %(model_list, model_id, get_model_instance(model_id).get_model_name(language))
+    return model_list
+
+def _print_model_list_json(language:str):
+    """
+    Returns the list of available models in Json format
+    """
+    model_list = []
+    vips_models = get_vips_models()
+    for model_id in vips_models:
+        model_list.append({
+            "modelId" : model_id, 
+            "modelName" : get_model_instance(model_id).get_model_name()
+        }) 
+    return model_list
\ No newline at end of file

models_example.txt

+# All the models that should be available through this instance of VIPSCore-Python must be
+# installed through running pip install -r models.txt
+
+# The file models.txt is ignored by git, so it will be instance specific.
+# To start, copy the models_example.txt file to models.txt and add models from 
+# the preferred sources
+
+# pyPIP example
+# model_name
+
+# Gitlab/github example
+# git+https://gitlab.nibio.no/VIPS/models/python/referencemodel.git@0.1.5
+
+# Local disk example
+# /home/treinar/prosjekter/vips/Sourcecode/models/Python/ReferenceModel
\ No newline at end of file

requirements.txt

-anyio==3.6.2
-certifi==2022.12.7
-click==8.1.3
-dnspython==2.3.0
-email-validator==1.3.0
 fastapi==0.89.1
-h11==0.14.0
-httpcore==0.16.3
-httptools==0.5.0
-httpx==0.23.3
-idna==3.4
-itsdangerous==2.1.2
-Jinja2==3.1.2
-MarkupSafe==2.1.1
-orjson==3.8.5
-pydantic==1.10.4
-python-dotenv==0.21.0
-python-multipart==0.0.5
-PyYAML==6.0
-rfc3986==1.5.0
-six==1.16.0
-sniffio==1.3.0
-starlette==0.22.0
-typing_extensions==4.4.0
-ujson==5.7.0
-uvicorn==0.20.0
-uvloop==0.17.0
-watchfiles==0.18.1
-websockets==10.4
+git+https://gitlab.nibio.no/VIPS/vipscore-python-common.git@0.1.9
\ No newline at end of file

safe_pip_freeze.py

+import sys
+import subprocess
+import src.model_factory
+
+# Intention: Make sure that pip freeze doesn't include VIPS models
+# Only necessary if we decide to stick with using pip freeze
\ No newline at end of file

src/main.py

-from fastapi import FastAPI
-
-app = FastAPI()
-
-
-@app.get("/")
-async def root():
-    return {"message": "Hello World"}