Merge pull request #6 from terraref/call-season-impl

helper function + implementation of different endpoints

.gitignore

@@ -62,3 +62,6 @@ target/
 
 #Ipython Notebook
 .ipynb_checkpoints
+
+# pycharm
+.idea

README.md

@@ -13,7 +13,7 @@ Python 3.5.2+
 To run, first start an intance of the BETY database:
 
 ```
-docker run -h betydb -d -p 5432:5432 terraref/bety-postgis
+docker run --name betydb -d -p 5431:5432 terraref/bety-postgis
 ```
 
 Install the python requirements and start the Flask server:
@@ -30,3 +30,35 @@ http://localhost:8080/brapi/v1/ui/
 
 The only call implemented is the `GET phenotypes-search` with a very very
 preliminary mapping of BETY fields to BRAPI objects.
+
+
+## Mappings from BETY to BRAPI models
+
+| BRAPI      | BETY        | Notes |
+|------------|-------------|-------|
+| /calls     | generated   |       |
+| /locations | sitegroups  | lat/lon computed from sites part of sitegroup |
+| /seasons   | experiments | season = month of start_date, year of start_date |
+| /germplasm  | cultivars.  |       | 
+| /observations | traits | |
+
+
+## How to add an endpoint
+
+Example: see controllers/crops_controller.py and CropsController_impl.py
+
+## Showing data in BETY database
+
+You can use the following command to start a docker container that is connected to the database
+allowing you to browse the database.
+
+```
+docker run -ti --rm -p 8000:8000 --link betydb:postgres pecan/bety
+```
+
+To enable the guest user you can run the following sql query when connected to the database:
+
+```
+INSERT INTO users (login, name, email, crypted_password, salt, city, state_prov, postal_code, country, area, access_level, page_access_level, created_at, updated_at, apikey, remember_token, remember_token_expires_at)
+ VALUES ('guestuser', 'guestuser', '[email protected]', '994363a949b6486fc7ea54bf40335127f5413318', 'bety', 'Urbana', 'IL', '61801', 'USA', '', 4, 4, NOW(), NOW(), NULL, NULL, NULL);
+```

bety_brapi/__main__.py

@@ -12,12 +12,6 @@ def main():
     app = connexion.App(__name__, specification_dir='./swagger/')
     app.app.json_encoder = encoder.JSONEncoder
     app.add_api('swagger.yaml', arguments={'title': 'BrAPI'})
-    app.run(port=8080)
-
-    handler = logging.StreamHandler(sys.stdout)
-    handler.setLevel(logging.DEBUG)
-
-    app.app.logger.addHandler(handler)
     app.app.logger.setLevel(logging.DEBUG)
 
     app.run(port=8080)

bety_brapi/controllers/calls_controller.py

@@ -1,6 +1,6 @@
 import connexion
 import six
-#from bety_brapi.controllers_impl import CallsController_impl
+from bety_brapi.controllers_impl import CallsController_impl
 
 from bety_brapi.models.calls_response import CallsResponse  # noqa: E501
 from bety_brapi import util
@@ -21,6 +21,5 @@ def calls_get(datatype=None, pageSize=None, page=None):  # noqa: E501
     :rtype: CallsResponse
     """
 
-#    return CallsController_impl.calls_get(datatype=None, pageSize=None, page=None)
-    return "Not implemented"
+    return CallsController_impl.calls_get(datatype, pageSize, page)
 

bety_brapi/controllers/crops_controller.py

@@ -1,6 +1,6 @@
 import connexion
 import six
-#from bety_brapi.controllers_impl import CropsController_impl
+from bety_brapi.controllers_impl import CropsController_impl
 
 from bety_brapi.models.common_crop_names_response import CommonCropNamesResponse  # noqa: E501
 from bety_brapi import util
@@ -19,8 +19,7 @@ def common_crop_names_get(pageSize=None, page=None):  # noqa: E501
     :rtype: CommonCropNamesResponse
     """
 
-#    return CropsController_impl.common_crop_names_get(pageSize=None, page=None)
-    return "Not implemented"
+    return CropsController_impl.common_crop_names_get(pageSize, page)
 
 
 def crops_get(pageSize=None, page=None):  # noqa: E501
@@ -36,6 +35,5 @@ def crops_get(pageSize=None, page=None):  # noqa: E501
     :rtype: CommonCropNamesResponse
     """
 
-#    return CropsController_impl.crops_get(pageSize=None, page=None)
-    return "Not implemented"
+    return CropsController_impl.crops_get(pageSize, page)
 

bety_brapi/controllers/germplasm_controller.py

@@ -1,6 +1,6 @@
 import connexion
 import six
-#from bety_brapi.controllers_impl import GermplasmController_impl
+from bety_brapi.controllers_impl import GermplasmController_impl
 
 from bety_brapi.models.breeding_method_response import BreedingMethodResponse  # noqa: E501
 from bety_brapi.models.breeding_methods_response import BreedingMethodsResponse  # noqa: E501
@@ -155,8 +155,7 @@ def germplasm_search_get(germplasmPUI=None, germplasmDbId=None, germplasmName=No
     :rtype: GermplasmResponse
     """
 
-#    return GermplasmController_impl.germplasm_search_get(germplasmPUI=None, germplasmDbId=None, germplasmName=None, commonCropName=None, pageSize=None, page=None)
-    return "Not implemented"
+    return GermplasmController_impl.germplasm_search_get(germplasmPUI, germplasmDbId, germplasmName, commonCropName, pageSize, page)
 
 
 def germplasm_search_post(body=None):  # noqa: E501

bety_brapi/controllers/locations_controller.py

@@ -1,6 +1,6 @@
 import connexion
 import six
-#from bety_brapi.controllers_impl import LocationsController_impl
+from bety_brapi.controllers_impl import LocationsController_impl
 
 from bety_brapi.models.location_response import LocationResponse  # noqa: E501
 from bety_brapi.models.locations_response import LocationsResponse  # noqa: E501
@@ -22,8 +22,7 @@ def locations_get(locationType=None, pageSize=None, page=None):  # noqa: E501
     :rtype: LocationsResponse
     """
 
-#    return LocationsController_impl.locations_get(locationType=None, pageSize=None, page=None)
-    return "Not implemented"
+    return LocationsController_impl.locations_get(locationType, pageSize, page)
 
 
 def locations_location_db_id_get(locationDbId):  # noqa: E501
@@ -37,6 +36,5 @@ def locations_location_db_id_get(locationDbId):  # noqa: E501
     :rtype: LocationResponse
     """
 
-#    return LocationsController_impl.locations_location_db_id_get(locationDbId)
-    return "Not implemented"
+    return LocationsController_impl.locations_location_db_id_get(locationDbId)
 

bety_brapi/controllers/studies_controller.py

@@ -1,6 +1,6 @@
 import connexion
 import six
-#from bety_brapi.controllers_impl import StudiesController_impl
+from bety_brapi.controllers_impl import StudiesController_impl
 
 from bety_brapi.models.germplasm_summary_list_response import GermplasmSummaryListResponse  # noqa: E501
 from bety_brapi.models.new_observation_db_ids_response import NewObservationDbIdsResponse  # noqa: E501
@@ -38,8 +38,7 @@ def seasons_get(year=None, pageSize=None, page=None):  # noqa: E501
     :rtype: SeasonsResponse
     """
 
-#    return StudiesController_impl.seasons_get(year=None, pageSize=None, page=None)
-    return "Not implemented"
+    return StudiesController_impl.seasons_get(year, pageSize, page)
 
 
 def studies_search_get(studyType=None, programDbId=None, locationDbId=None, seasonDbId=None, trialDbId=None, studyDbId=None, germplasmDbIds=None, observationVariableDbIds=None, pageSize=None, page=None, active=None, sortBy=None, sortOrder=None):  # noqa: E501

bety_brapi/controllers_impl/CallsController_impl.py

@@ -0,0 +1,57 @@
+from bety_brapi import helper
+
+VERSIONS_ALL = ["1.0", "1.1", "1.2"]
+VERSIONS_LATEST = ["1.2"]
+
+
+def calls_get(datatype, pageSize, page):
+    """
+    Return a list of all calls that are implemented
+    """
+
+    # create the full list of all calls implemented.
+    data = [
+        calls_get_helper('calls'),
+        calls_get_helper('commonCropNames', versions=['1.2']),
+        calls_get_helper('crops'),
+        calls_get_helper('germplasm-search'),
+        calls_get_helper('locations'),
+        calls_get_helper('locations/{locationDbId}'),
+        calls_get_helper('phenotypes-search'),
+        calls_get_helper('seasons')
+    ]
+
+    # filter on datatype
+    if datatype:
+        data = [d for d in data if datatype in d['datatypes']]
+
+    # total number of rows
+    count = len(data)
+
+    # add a limit
+    if not pageSize:
+        pageSize = len(data)
+    if not page:
+        page = 0
+    data = data[page * pageSize:(page+1) * pageSize]
+
+    # return the resulting data
+    return helper.create_result({"data": data}, count, pageSize, page)
+
+
+def calls_get_helper(api_call, datatypes=None, methods=None, versions=None):
+    """
+    Helper function to return a brapi call information.
+    """
+    if not datatypes:
+        datatypes = ["json"]
+    if not methods:
+        methods = ['GET']
+    if not versions:
+        versions = VERSIONS_ALL
+    return {
+            "call": api_call,
+            "datatypes": datatypes,
+            "methods": methods,
+            "versions": versions
+        }

bety_brapi/controllers_impl/CropsController_impl.py

@@ -0,0 +1,15 @@
+from bety_brapi import helper
+
+def common_crop_names_get(pageSize=None, page=None):
+
+    query = "SELECT DISTINCT commonname FROM species ORDER BY commonname"
+    count = helper.query_count(query)
+    res = helper.query_result(query, [], pageSize, page)
+
+    data = [r[0] for r in res]
+
+    return helper.create_result({"data": data}, count, pageSize, page)
+
+def crops_get(pageSize=None, page=None):
+    # deprecated function name
+    return common_crop_names_get(pageSize, page)

bety_brapi/controllers_impl/GermplasmController_impl.py

@@ -0,0 +1,41 @@
+import json
+
+from bety_brapi import helper
+
+def germplasm_search_get(germplasmPUI, germplasmDbId, germplasmName, commonCropName, pageSize, page):
+    """
+    Search for a specific germplasm. Right now this will use an external file to get all the information.
+    :param germplasmPUI:
+    :param germplasmDbId:
+    :param germplasmName:
+    :param commonCropName:
+    :param pageSize:
+    :param page:
+    :return:
+    """
+
+    # load all the data
+    # TODO this does not work if pakcage is installed, need to use pkgutil
+    file = 'data/germplasm.json'
+    data = json.load(open(file, 'r'))
+
+    # filter the data
+    if germplasmPUI:
+        data = [x for x in data if x.get('germplasmPUI', '') == germplasmPUI]
+    if germplasmDbId:
+        data = [x for x in data if x.get('germplasmDbId', '') == int(germplasmDbId)]
+    if germplasmName:
+        data = [x for x in data if x.get('germplasmName', '') == germplasmName]
+    if commonCropName:
+        data = [x for x in data if x.get('commonCropName', '') == commonCropName]
+
+    # split data if needed, remembering total number
+    count = len(data)
+    if not pageSize:
+        pageSize = helper.DEFAULT_PAGE_SIZE
+    if not page:
+        page = 0
+    data = data[page * pageSize:(page+1) * pageSize]
+
+    # return the resulting data
+    return helper.create_result({"data": data}, count, pageSize, page)

bety_brapi/controllers_impl/LocationsController_impl.py

@@ -0,0 +1,102 @@
+from bety_brapi import helper
+
+
+def locations_get(locationType, pageSize, page):
+    """
+
+    :param locationType:
+    :param pageSize: number of elements to return
+    :param page: which page to return
+    :return: all locations in the page
+    """
+
+    # TODO map locationType to something
+    params = list()
+
+    # get all sitegroups and sites
+    query = "SELECT sitegroups.id AS locationDbId, " \
+            "       sitegroups.name AS name, " \
+            "       sites.geometry AS geometry " \
+            "FROM sites, sitegroups, sitegroups_sites " \
+            "WHERE sitegroups_sites.site_id = sites.id " \
+            "      AND sitegroups_sites.sitegroup_id = sitegroups.id "
+    # compute the bounding box
+    query = "SELECT locationDbId, " \
+            "       name, " \
+            "       ST_Extent(geometry) AS geometry " \
+            "FROM (" + query + ") ss1 " \
+            "GROUP BY locationDbId, name "
+    # compute center point
+    query = "SELECT locationDbId::text, " \
+            "       name, " \
+            "       ST_X(ST_CENTROID(geometry)) AS longitude, " \
+            "       ST_Y(ST_CENTROID(geometry)) AS latitude " \
+            "FROM (" + query + ") ss2"
+
+    # order query
+    query += "   ORDER BY locationDbId"
+
+    # TODO add a filter on the locationType
+    # if locationType:
+    #     # wrap query in a sub select to allow us to use locationType in WHERE clause
+    #     query = "SELECT * FROM (" + query + ") locations WHERE locationType = %s "
+    #     params.append(locationType)
+
+    # count first
+    count = helper.query_count(query, params)
+
+    # execute query
+    results = helper.query_result(query, params, pageSize, page)
+
+    # wrap result
+    data = []
+    for row in results:
+        data.append({k: v for k, v in row.items() if v})
+    return helper.create_result({"data": data}, count, pageSize, page)
+
+
+def locations_location_db_id_get(locationDbId):
+    """
+
+    :param locationDbId:
+    :return:
+    """
+
+    params = list()
+
+    # get all sitegroups and sites
+    query = "SELECT sitegroups.id AS locationDbId, " \
+            "       sitegroups.name AS name, " \
+            "       sites.geometry AS geometry " \
+            "FROM sites, sitegroups, sitegroups_sites " \
+            "WHERE sitegroups.id = %s " \
+            "      AND sitegroups_sites.site_id = sites.id " \
+            "      AND sitegroups_sites.sitegroup_id = sitegroups.id "
+    params.append(int(locationDbId))
+    # compute the bounding box
+    query = "SELECT locationDbId, " \
+            "       name, " \
+            "       ST_Extent(geometry) AS geometry " \
+            "FROM (" + query + ") ss1 " \
+            "GROUP BY locationDbId, name "
+    # compute center point
+    query = "SELECT locationDbId::text, " \
+            "       name, " \
+            "       ST_X(ST_CENTROID(geometry)) AS longitude, " \
+            "       ST_Y(ST_CENTROID(geometry)) AS latitude " \
+            "FROM (" + query + ") ss2"
+
+    # order query
+    query += "   ORDER BY locationDbId"
+
+    # count first
+    count = helper.query_count(query, params)
+
+    # execute query
+    results = helper.query_result(query, params)
+
+    # wrap result
+    data = []
+    for row in results:
+        data.append({k: v for k, v in row.items() if v})
+    return helper.create_result({"location": data}, count)