diff --git a/.gitignore b/.gitignore
index b1cb1601da8c7ca6231d4eebfe7debe6fe703c51..4e790d3694906c5d11427a1d0a3fa85a4a38c06d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
+# Keeping this deployment specific
+models.txt
+
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 0000000000000000000000000000000000000000..be3f7b28e564e7dd05eaf59d64adba1a4065ac0e
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,661 @@
+ GNU AFFERO GENERAL PUBLIC LICENSE
+ Version 3, 19 November 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
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+ The licenses for most software and other practical works are designed
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+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+ When we speak of free software, we are referring to freedom, not
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+ Developers that use our General Public Licenses protect your rights
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+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for the
+specific requirements.
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<https://www.gnu.org/licenses/>.
diff --git a/README.md b/README.md
index 267662dd3c8c990486809cda21c50b89ea11482e..a5d8aeb053304f429bef85b703914df8898ef8c2 100644
--- a/README.md
+++ b/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
diff --git a/app/__init.py__ b/app/__init.py__
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/app/internal/__init.py__ b/app/internal/__init.py__
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/app/internal/model_factory.py b/app/internal/model_factory.py
new file mode 100644
index 0000000000000000000000000000000000000000..4c8821ab99c1e430b0823ef4b9c1864e40427be2
--- /dev/null
+++ b/app/internal/model_factory.py
@@ -0,0 +1,57 @@
+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())
+
+
diff --git a/app/main.py b/app/main.py
new file mode 100644
index 0000000000000000000000000000000000000000..be6ad2e17a966de494790c06b55e036a81399398
--- /dev/null
+++ b/app/main.py
@@ -0,0 +1,94 @@
+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
diff --git a/models_example.txt b/models_example.txt
new file mode 100644
index 0000000000000000000000000000000000000000..cdab0023bc444e594188f54fd5b869e51a406764
--- /dev/null
+++ b/models_example.txt
@@ -0,0 +1,15 @@
+# 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
diff --git a/postman_tests/VIPSCore-Python tests.postman_collection.json b/postman_tests/VIPSCore-Python tests.postman_collection.json
new file mode 100644
index 0000000000000000000000000000000000000000..24920795216a834d41ef2bb3820b11dd311fb507
--- /dev/null
+++ b/postman_tests/VIPSCore-Python tests.postman_collection.json
@@ -0,0 +1,56 @@
+{
+ "info": {
+ "_postman_id": "c34ce901-f203-42e6-9e68-53e859fc9f2c",
+ "name": "VIPSCore-Python tests",
+ "schema": "https://schema.getpostman.com/json/collection/v2.1.0/collection.json",
+ "_exporter_id": "5789128"
+ },
+ "item": [
+ {
+ "name": "Test REFERENCEM",
+ "event": [
+ {
+ "listen": "test",
+ "script": {
+ "exec": [
+ "pm.test(\"Status code is 200\", function () {",
+ " pm.response.to.have.status(200);",
+ "});",
+ "pm.test(\"First warning status is 2 (No risk)\", function () {",
+ " var jsonData = pm.response.json();",
+ " pm.expect(jsonData[0].warningStatus).to.eql(2);",
+ "});"
+ ],
+ "type": "text/javascript"
+ }
+ }
+ ],
+ "request": {
+ "method": "POST",
+ "header": [],
+ "body": {
+ "mode": "raw",
+ "raw": "{\"model_id\": \"REFERENCEM\", \"config_parameters\": {\"sowingDate\": \"2022-03-01\", \"timeZone\": \"Europe/Oslo\", \"observations\": [{\"timeMeasured\": \"2015-03-01T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"1.41025\"}, {\"timeMeasured\": \"2015-03-02T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"2.87608333333333\"}, {\"timeMeasured\": \"2015-03-03T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"1.00854166666667\"}, {\"timeMeasured\": \"2015-03-04T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"-1.44675\"}, {\"timeMeasured\": \"2015-03-05T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"0.506208333333333\"}, {\"timeMeasured\": \"2015-03-06T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"5.055\"}, {\"timeMeasured\": \"2015-03-07T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"5.29470833333333\"}, {\"timeMeasured\": \"2015-03-08T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"5.78691666666667\"}, {\"timeMeasured\": \"2015-03-09T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"3.44725\"}, {\"timeMeasured\": \"2015-03-10T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"6.848625\"}, {\"timeMeasured\": \"2015-03-11T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"5.59816666666667\"}, {\"timeMeasured\": \"2015-03-12T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"2.78283333333333\"}, {\"timeMeasured\": \"2015-03-13T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", 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\"logIntervalId\": \"2\", \"value\": \"1.34791666666667\"}, {\"timeMeasured\": \"2015-03-28T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"1.19704166666667\"}, {\"timeMeasured\": \"2015-03-29T00:00:00+01:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"3.0285\"}, {\"timeMeasured\": \"2015-03-30T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"2.43166666666667\"}, {\"timeMeasured\": \"2015-03-31T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"1.33133333333333\"}, {\"timeMeasured\": \"2015-04-01T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"2.65516666666667\"}, {\"timeMeasured\": \"2015-04-02T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"4.430875\"}, {\"timeMeasured\": \"2015-04-03T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"3.55983333333333\"}, {\"timeMeasured\": \"2015-04-04T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"2.77170833333333\"}, {\"timeMeasured\": \"2015-04-05T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"1.38383333333333\"}, {\"timeMeasured\": \"2015-04-06T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"3.98670833333333\"}, {\"timeMeasured\": \"2015-04-07T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"9.01775\"}, {\"timeMeasured\": \"2015-04-08T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"8.91166666666667\"}, {\"timeMeasured\": \"2015-04-09T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"7.22270833333333\"}, {\"timeMeasured\": 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{\"timeMeasured\": \"2015-04-17T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"7.18533333333333\"}, {\"timeMeasured\": \"2015-04-18T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"6.27766666666667\"}, {\"timeMeasured\": \"2015-04-19T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"9.67808333333333\"}, {\"timeMeasured\": \"2015-04-20T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"12.619375\"}, {\"timeMeasured\": \"2015-04-21T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"9.36679166666667\"}, {\"timeMeasured\": \"2015-04-22T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", \"value\": \"10.2030416666667\"}, {\"timeMeasured\": \"2015-04-23T00:00:00+02:00\", \"elementMeasurementTypeId\": \"TM\", \"logIntervalId\": \"2\", 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\"15.345\"}]}}",
+ "options": {
+ "raw": {
+ "language": "json"
+ }
+ }
+ },
+ "url": {
+ "raw": "{{vipscore_python_url}}/models/REFERENCEM/run",
+ "host": [
+ "{{vipscore_python_url}}"
+ ],
+ "path": [
+ "models",
+ "REFERENCEM",
+ "run"
+ ]
+ },
+ "description": "Test one of the stockpile models of VIPS"
+ },
+ "response": []
+ }
+ ]
+}
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 9ea7bd6e76b2cf500f108c957516d329a33d47ef..dbc3d72cf9cf9c27c3ba708282856c5aeeb09bbf 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,29 +1,2 @@
-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
diff --git a/safe_pip_freeze.py b/safe_pip_freeze.py
new file mode 100644
index 0000000000000000000000000000000000000000..6ddff3e95a97bf520da7d602791aba43bba77458
--- /dev/null
+++ b/safe_pip_freeze.py
@@ -0,0 +1,6 @@
+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
diff --git a/src/main.py b/src/main.py
deleted file mode 100644
index ee60be1f964d199ffd46e7402dc3ca3fb4585e95..0000000000000000000000000000000000000000
--- a/src/main.py
+++ /dev/null
@@ -1,8 +0,0 @@
-from fastapi import FastAPI
-
-app = FastAPI()
-
-
-@app.get("/")
-async def root():
- return {"message": "Hello World"}