Updating the cv service

Rename to ReadService. Mapped the methods to use the ReadOMD2 class in OMD2api

Author: Francisco Arrieta

odmtools/odmservices/cv_service.py renamed to odmtools/odmservices/ReadService.py

@@ -1,88 +1,63 @@
-# CV imports
 from odmtools.odmdata import SessionFactory
 from odmtools.odmdata import VerticalDatumCV
-from odmtools.odmdata import SiteTypeCV
-from odmtools.odmdata import VariableNameCV
-from odmtools.odmdata import SpeciationCV
-from odmtools.odmdata import SampleMediumCV
 from odmtools.odmdata import ValueTypeCV
-from odmtools.odmdata import DataTypeCV
 from odmtools.odmdata import GeneralCategoryCV
-from odmtools.odmdata import CensorCodeCV
-from odmtools.odmdata import TopicCategoryCV
-from odmtools.odmdata import SampleTypeCV
-from odmtools.odmdata import OffsetType
-from odmtools.odmdata import Sample
-from odmtools.odmdata import Qualifier
 from odmtools.odmdata import Unit
 from sqlalchemy import not_
 from odm2api.ODM2.services.readService import ReadODM2
 
 
-class CVService(): # Rename to ReadService
+class ReadService:
     # Accepts a string for creating a SessionFactory, default uses odmdata/connection.cfg
     def __init__(self, connection_string="", debug=False):
         self._session_factory = SessionFactory(connection_string, debug)
         self._edit_session = self._session_factory.getSession()
         self._debug = debug
         self.read_service = ReadODM2(self._session_factory, debug=self._debug)
 
-
     # Controlled Vocabulary get methods
-
     #return a list of all terms in the cv
     def get_vertical_datum_cvs(self):
         result = self._edit_session.query(VerticalDatumCV).order_by(VerticalDatumCV.term).all()
         return result
 
     def get_samples(self):
-        result = self._edit_session.query(Sample).order_by(Sample.lab_sample_code).all()
-        return result
+        return self.read_service.getSamplingFeatures(ids=None, codes=None, uuids=None, type=None, wkt=None)
 
     def get_site_type_cvs(self):
-        result = self._edit_session.query(SiteTypeCV).order_by(SiteTypeCV.term).all()
-        return result
+        return self.read_service.getCVs(type="Site Type")  # OR return self.read_service.getCVs(type="Sampling Feature Type")
 
     def get_variable_name_cvs(self):
-        result = self._edit_session.query(VariableNameCV).order_by(VariableNameCV.term).all()
-        return result
+        return self.read_service.getCVs(type="Variable Name")
 
     def get_offset_type_cvs(self):
-        result = self._edit_session.query(OffsetType).order_by(OffsetType.id).all()
-        return result
+        return self.read_service.getCVs(type="Spatial Offset Type")
 
     def get_speciation_cvs(self):
-        result = self._edit_session.query(SpeciationCV).order_by(SpeciationCV.term).all()
-        return result
-        # return self.read_service.getCVs(type="Speciation") # Returns Error running Query,
+        return self.read_service.getCVs(type="Speciation")
 
     def get_sample_medium_cvs(self):
-        result = self._edit_session.query(SampleMediumCV).order_by(SampleMediumCV.term).all()
-        return result
+        return self.read_service.getCVs(type="Medium")
 
     def get_value_type_cvs(self):
         result = self._edit_session.query(ValueTypeCV).order_by(ValueTypeCV.term).all()
         return result
 
     def get_data_type_cvs(self):
-        result = self._edit_session.query(DataTypeCV).order_by(DataTypeCV.term).all()
-        return result
+        return self.read_service.getCVs(type="dataset type")
 
     def get_general_category_cvs(self):
         result = self._edit_session.query(GeneralCategoryCV).order_by(GeneralCategoryCV.term).all()
         return result
 
     def get_censor_code_cvs(self):
-        result = self._edit_session.query(CensorCodeCV).order_by(CensorCodeCV.term).all()
-        return result
+        return self.read_service.getCVs(type="censorcode")
 
     def get_sample_type_cvs(self):
-        result = self._edit_session.query(SampleTypeCV).order_by(SampleTypeCV.term).all()
-        return result
+        return self.read_service.getCVs(type="Sampling Feature Type")
 
     def get_units(self):
-        result = self._edit_session.query(Unit).all()
-        return result
+        return self.read_service.getUnits(ids=None, name=None, type=None)
 
     def get_units_not_uni(self):
         result = self._edit_session.query(Unit).filter(not_(Unit.name.contains('angstrom'))).all()
@@ -94,16 +69,13 @@ def get_units_names(self):
 
     # return a single cv
     def get_unit_by_name(self, unit_name):
-        result = self._edit_session.query(Unit).filter_by(name=unit_name).first()
-        return result
+        return self.read_service.getUnits(name=unit_name)
 
     def get_unit_by_id(self, unit_id):
-        result = self._edit_session.query(Unit).filter_by(id=unit_id).first()
-        return result
+        return self.read_service.getUnits(ids=unit_id)
 
     def get_annotation_by_code(self, code):
-        self.read_service.getAnnotations(type=code)
-        return
+        return self.read_service.getAnnotations(type=code)
 
     def get_all_annotations(self):
         return self.read_service.getAnnotations(type=None)

odmtools/odmservices/__init__.py

@@ -1,6 +1,6 @@
 from service_manager import ServiceManager
 from series_service import SeriesService
-from cv_service import CVService
+from ReadService import ReadService
 from edit_service import EditService
 from export_service import ExportService
 
@@ -11,7 +11,7 @@
 
 __all__ = [
     'EditService',
-    'CVService',
+    'ReadService',
     'SeriesService',
     'ExportService',
     'ServiceManager',

odmtools/odmservices/service_manager.py

@@ -8,7 +8,7 @@
 
 from odmtools.common.logger import LoggerTool
 from series_service import SeriesService
-from cv_service import CVService
+from ReadService import ReadService
 from edit_service import EditService
 from odmtools.controller import EditTools
 from export_service import ExportService
@@ -153,7 +153,7 @@ def get_series_service(self, conn_dict=""):
 
     def get_cv_service(self):
         conn_string = self._build_connection_string(self._current_conn_dict)
-        return CVService(conn_string, self.debug)
+        return ReadService(conn_string, self.debug)
 
     def get_edit_service(self, series_id, connection):
 

tests/test_odmservices/test_cv_service.py

@@ -1,4 +1,4 @@
-from odmtools.odmservices import CVService
+from odmtools.odmservices import ReadService
 from tests import test_util
 
 
@@ -8,7 +8,7 @@
 class TestCVService:
     def setup(self):
         self.connection_string = "sqlite:///:memory:"
-        self.cv_service = CVService(self.connection_string, debug=False)
+        self.cv_service = ReadService(self.connection_string, debug=False)
         self.session = self.cv_service._session_factory.getSession()
         engine = self.cv_service._session_factory.engine
         test_util.build_db(engine)