Merge pull request #623 from plantbreeding/data-model-separation

Data model separation

.github/workflows/generate-schema.yml

@@ -0,0 +1,21 @@
+name: Java CI with Gradle
+
+on:
+  push:
+  workflow_dispatch:
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 21
+        uses: actions/setup-java@v4
+        with:
+          java-version: '21'
+          distribution: 'temurin'
+      - name: Change wrapper permissions
+        working-directory: ./generator/
+        run: chmod +x ./gradlew
+      - name: Build with Gradle Wrapper
+        working-directory: ./generator/
+        run: ./gradlew validate

.gitignore

@@ -3,6 +3,8 @@
 .DS_Store
 .settings/
 .idea
+.vscode/
+.idea
 
 /_temp
 brapi_blueprint.apib

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt

Scripts/buildReadMes.py

@@ -95,7 +95,7 @@ def buildTitleStr(path, method, params = [], deprecated = False):
 	uniquePathStr = ' /brapi/v2' + path
 	for param in params:
 		if param['in'] == 'query' :
-		    uniquePathStr += '{?' + param['name'] + '}'
+			uniquePathStr += '{?' + param['name'] + '}'
 
 	if uniquePathStr in uniquePaths:
 		uniquePathStr += '/'

Scripts/oauth_cli.py

@@ -0,0 +1,126 @@
+
+import requests
+import webbrowser
+from threading import Lock
+from fastapi import FastAPI
+import uvicorn
+from pyoauth2.client import OAuth2AuthorizationFlow, FileStorage, OAuth2APIRequest
+import contextlib
+import time
+import threading
+import uvicorn
+
+class Server(uvicorn.Server):
+    def install_signal_handlers(self):
+        pass
+
+    @contextlib.contextmanager
+    def run_in_thread(self):
+        thread = threading.Thread(target=self.run)
+        thread.start()
+        try:
+            while not self.started:
+                time.sleep(1e-3)
+            yield
+        finally:
+            self.should_exit = True
+            thread.join()
+
+class BrAPIRequest(OAuth2APIRequest):
+    def __init__(self, access_token):
+        OAuth2APIRequest.__init__(self, access_token)
+        self.authorization_header = {"Authorization": "Bearer %s" % self.access_token}
+
+code_lock = Lock()
+code_val = {"code": ""}
+
+async def root(code: str):
+    code_val["code"] = code
+    code_lock.release()
+
+async def lifespan_func(app: FastAPI):
+     code_lock.acquire()
+     print("temp server start")
+     yield
+     print("temp server shutdown")
+
+def redirect_function(url):
+    print("hello?")
+    app = FastAPI(lifespan=lifespan_func)
+    app.add_api_route("/login/redirect", root)
+
+    config = uvicorn.Config(app=app, host="127.0.0.1", port=8000, log_level="info")
+    server = Server(config=config)
+    with server.run_in_thread():
+        webbrowser.open_new_tab(url)
+        with code_lock:
+            print(code_val["code"] )
+
+    return code_val["code"] 
+
+
+def retrieve_authorization_code(required_params,
+                                       extra_auth_params,
+                                       extra_token_params, redirect_func=None):
+        """ retrieve authorization code to get access token
+        """
+
+        request_param = {
+            "client_id": required_params['client_id'],
+            "redirect_uri": required_params['redirect_uri'],
+            'scope' : required_params['scope']
+        }
+
+        if extra_auth_params:
+            request_param.update(extra_auth_params)
+
+        r = requests.get(required_params['auth_uri'], params=request_param,
+                         allow_redirects=False)
+        url = r.url
+        return url      
+
+if __name__ == '__main__':
+
+    yt_feed_uri = r"https://test-server.brapi.org/brapi/v2/studies"
+
+    required_params = {
+        'client_id': "exampleClient",
+        'client_secret': "pnosdgBScMmNVc2vpY1cEwBYjsImpAZn",
+        'auth_uri': "https://auth.brapi.org/realms/brapi/protocol/openid-connect/auth",
+        'token_uri': "https://test-server.brapi.org/realms/brapi/protocol/openid-connect/token",
+        'scope': [r'openid profile'],
+        'redirect_uri': "http://localhost:8000/login/redirect"
+        }
+
+    extra_auth_params = {
+        'response_type': "code",
+        'access_type': "offline"
+        }
+
+    extra_token_params = {
+        'grant_type': "authorization_code",
+        }
+
+    # storage = FileStorage('/example_client.dat')
+    # credentials = storage.get()
+    credentials = None
+    input("proceed?")
+    if credentials is None:
+        flow = OAuth2AuthorizationFlow(required_params,
+                                       extra_auth_params,
+                                       extra_token_params,
+                                       False)
+
+
+        code = flow.retrieve_authorization_code(redirect_func=redirect_function)
+        flow.set_authorization_code(code)
+        credentials = flow.retrieve_token()
+        # storage.save(credentials)
+
+    access_token = credentials['access_token']
+
+    req = BrAPIRequest(access_token)
+    data = req.request(yt_feed_uri)
+    print(data)
+
+

Specification/BrAPI-Genotyping/Plates/README.md

@@ -17,6 +17,7 @@ Get a filtered list of `Plates`. Each `Plate` is a collection of `Samples` that
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -92,6 +93,7 @@ Get a filtered list of `Plates`. Each `Plate` is a collection of `Samples` that
                     }
                 ],
                 "plateBarcode": "11223344",
+                "plateDbId": "a106467f",
                 "plateFormat": "PLATE_96",
                 "plateName": "Plate_123_XYZ",
                 "programDbId": "bd748e00",
@@ -149,6 +151,7 @@ Submit new Plate entities to the server
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -235,6 +238,7 @@ Submit new Plate entities to the server
                     }
                 ],
                 "plateBarcode": "11223344",
+                "plateDbId": "a106467f",
                 "plateFormat": "PLATE_96",
                 "plateName": "Plate_123_XYZ",
                 "programDbId": "bd748e00",
@@ -280,6 +284,7 @@ Update the details of existing Plates
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -368,6 +373,7 @@ Update the details of existing Plates
                     }
                 ],
                 "plateBarcode": "11223344",
+                "plateDbId": "a106467f",
                 "plateFormat": "PLATE_96",
                 "plateName": "Plate_123_XYZ",
                 "programDbId": "bd748e00",
@@ -413,6 +419,7 @@ Get the details of a specific `Plate`. Each `Plate` is a collection of `Samples`
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -471,6 +478,7 @@ Get the details of a specific `Plate`. Each `Plate` is a collection of `Samples`
             }
         ],
         "plateBarcode": "11223344",
+        "plateDbId": "a106467f",
         "plateFormat": "PLATE_96",
         "plateName": "Plate_123_XYZ",
         "programDbId": "bd748e00",
@@ -544,6 +552,7 @@ Review the <a target="_blank" href="https://wiki.brapi.org/index.php/Search_Serv
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -688,6 +697,7 @@ Review the <a target="_blank" href="https://wiki.brapi.org/index.php/Search_Serv
                     }
                 ],
                 "plateBarcode": "11223344",
+                "plateDbId": "a106467f",
                 "plateFormat": "PLATE_96",
                 "plateName": "Plate_123_XYZ",
                 "programDbId": "bd748e00",
@@ -760,6 +770,7 @@ Review the <a target="_blank" href="https://wiki.brapi.org/index.php/Search_Serv
 
 <table>
 <tr> <th> Field </th> <th> Type </th> <th> Description </th> </tr> 
+<tr><td><span style="font-weight:bold;">plateDbId</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>The ID which uniquely identifies a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">plateName</span></td><td>string<br><span style="font-size: smaller; color: red;">(Required)</span></td><td>A human readable name for a `Plate`</td></tr>
 <tr><td><span style="font-weight:bold;">additionalInfo</span></td><td>object</td><td>A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.</td></tr>
 <tr><td><span style="font-weight:bold;">externalReferences</span></td><td>array[object]</td><td>An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI.</td></tr>
@@ -822,6 +833,7 @@ Review the <a target="_blank" href="https://wiki.brapi.org/index.php/Search_Serv
                     }
                 ],
                 "plateBarcode": "11223344",
+                "plateDbId": "a106467f",
                 "plateFormat": "PLATE_96",
                 "plateName": "Plate_123_XYZ",
                 "programDbId": "bd748e00",

Specification/BrAPI-Genotyping/Plates/Schemas/Plate.yaml

@@ -14,9 +14,9 @@ components:
           module: BrAPI-Genotyping
           title: Plate
           description: A Plate represents the metadata for a collection of Samples. The physical Plate being represented might be a plastic tray full of Samples, or a group of Samples stored in individual containers ie bags, test tubes, etc. Whatever the container is, the Samples in a Plate should be related by the same physical space, though they may or may not be related as part of the same experiment or analysis. 
-      required:
-      - plateDbId
-      properties:
+        required:
+        - plateDbId
+        properties:
           plateDbId:
             description: The ID which uniquely identifies a `Plate`
             type: string

Wiki/Weekly Meeting Notes.wiki

@@ -730,4 +730,4 @@ For next week,
 http://docs.breeding.apiary.io/, disregarding analysisMethod.  Return two
 keys: total_markers, missing_values, in JSON
 * Lukas will get Rebecca to add us as editors.
-* Meet Thursdays at 4pm EDT.
+* Meet Thursdays at 4pm EDT.

docs/conf.py

@@ -27,9 +27,9 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-import sphinx_rtd_theme
+# import sphinx_rtd_theme
 extensions = [
-    'sphinx_rtd_theme'
+   'sphinx_rtd_theme'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -57,4 +57,4 @@
 # or fully qualified paths (eg. https://...)
 html_css_files = [
     'css/custom.css',
-]
+]

docs/docs/best_practices/Alternative_Standards.rst

@@ -30,7 +30,7 @@ In BrAPI V2.1, the `/events` endpoint was made compatible with the International
 MCPD
 ----
 
-Multi-Crop Passport Descriptors (MCPD) "is a widely used international standard to facilitate germplasm passport information exchange" (`bioversityinternational.org <https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/>`__). In BrAPI, the primary way to share Germplasm data is through the "GET /germplasm" endpoint. This endpoint has 24 fields out of the available 41 MCPD fields. The BrAPI specification also defines the endpoint "GET /germplasm/{germplasmDbId}/mcpd". This alternate endpoint allows a user to access all 41 MCPD compliant data points when looking at a specific germplasm entry. 
+Multi-Crop Passport Descriptors (MCPD) "is a widely used international standard to facilitate germplasm passport information exchange" (`BioversityInternational.org <https://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi-crop-passport-descriptors-v21-mcpd-v21/>`__). In BrAPI, the primary way to share Germplasm data is through the "GET /germplasm" endpoint. This endpoint has 24 fields out of the available 41 MCPD fields. The BrAPI specification also defines the endpoint "GET /germplasm/{germplasmDbId}/mcpd". This alternate endpoint allows a user to access all 41 MCPD compliant data points when looking at a specific germplasm entry. 
 
 GeoJSON
 -------