#293 Finishing up the get and create functions in series_service

Author: Francisco Arrieta

odmtools/odmservices/cv_service.py

@@ -29,7 +29,6 @@ def __init__(self, connection_string="", debug=False):
         self.read_service = ReadODM2(session_factory=self._session_factory, debug=self._debug)
 
     # Controlled Vocabulary get methods
-    # Returns a list of all terms in the Controller Vocabulary (CV)
 
     # From ODM1 -> ODM2 Qualifier was changed to Annotations
     def get_annotations(self, type):
@@ -48,14 +47,21 @@ def get_general_category_cvs(self):
         return result
 
     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")
 
     # From ODM1 -> ODM2 Quality Controlled Level was changed to Processing Level
     def get_all_processing_levels(self):
         self.read_service.getProcessingLevels()
 
+    def get_all_method(self): # Rename to get_method_all
+        return self.read_service.getMethods(ids=None, codes=None, type=None)
+
+    def get_method_by_id(self, method_id):
+        return self.read_service.getMethods(ids=method_id)
+
+    def get_method_by_description(self, code):
+        return self.read_service.getMethods(codes=code)
+
     def get_processing_level_by_id(self, id):
         self.read_service.getProcessingLevels(ids=id)
 
@@ -67,27 +73,29 @@ def get_samples(self):
         return result
 
     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_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")
 
     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")
 
     def get_sample_type_cvs(self):
         result = self._edit_session.query(SampleTypeCV).order_by(SampleTypeCV.term).all()
         return result
 
+    # From ODM1 -> ODM2 Site was changed to Sampling Feature
+    def get_all_sites(self):
+        return self.read_service.getSamplingFeatures(ids=None, codes=None, uuids=None, type=None, wkt=None)
+
+    def get_site_by_id(self, site_id):
+        return self.read_service.getSamplingFeatures(ids=site_id)
+
+    def get_timeseries_result_values(self, type):
+        return self.read_service.getAnnotations(type=type)
+
     def get_units(self):
-        # result = self._edit_session.query(Unit).all()
-        # return result
         self.read_service.getUnits(ids=None, name=None, type=None)
 
     def get_units_not_uni(self):
@@ -100,27 +108,19 @@ 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_value_type_cvs(self):
         result = self._edit_session.query(ValueTypeCV).order_by(ValueTypeCV.term).all()
         return result
 
     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_vertical_datum_cvs(self):
-        # result = self._edit_session.query(VerticalDatumCV).order_by(VerticalDatumCV.term).all()
-        # return result
         return self.read_service.getCVs("Elevation Datum")
 
     def get_all_variables(self):
@@ -132,31 +132,7 @@ def get_variable_by_id(self, id):
     def get_variable_by_code(self, code):
         return self.read_service.getVariables(codes=code)
 
-    # def get_all_qualifiers(self):
-    #     """
-    #
-    #     :return: List[Qualifiers]
-    #     """
-    #     result = self._edit_session.query(Qualifier).order_by(Qualifier.code).all()
-    #     return result
-    #
-    # def get_qualifier_by_code(self, code):
-    #     """
-    #
-    #     :return: Qualifiers
-    #     """
-    #     result = self._edit_session.query(Qualifier).filter(Qualifier.code==code).first()
-    #     return result
-    #
-    # def get_qualifiers_by_series_id(self, series_id):
-    #     """
-    #
-    #     :param series_id:
-    #     :return:
-    #     """
-    #     subquery = self._edit_session.query(DataValue.qualifier_id).outerjoin(
-    #         Series.data_values).filter(Series.id == series_id, DataValue.qualifier_id != None).distinct().subquery()
-    #     return self._edit_session.query(Qualifier).join(subquery).distinct().all()
+
 
 
 

odmtools/odmservices/series_service.py

@@ -29,7 +29,8 @@ def __init__(self, connection_string="", debug=False):
         self.create_service = CreateODM2(session_factory=self._session_factory, debug=self._debug)
 
     def reset_session(self):
-        self._edit_session = self._session_factory.getSession()  # Reset the session in order to prevent memory leaks
+        # self._edit_session = self._session_factory.getSession()  # Reset the session in order to prevent memory leaks
+        self._edit_session = self.create_service.getSession()
 
     def get_db_version(self):
         return self._edit_session.query(ODMVersion).first().version_number
@@ -40,15 +41,6 @@ def get_db_version(self):
 #
 #####################
 
-    # Site methods
-    def get_all_sites(self):
-        """
-
-        :return: List[Sites]
-        """
-        return self._edit_session.query(Site).order_by(Site.code).all()
-
-
     def get_used_sites(self):
         """
         Return a list of all sites that are being referenced in the Series Catalog Table
@@ -68,18 +60,6 @@ def get_used_sites(self):
 
         return Sites
 
-
-    def get_site_by_id(self, site_id):
-        """
-        return a Site object that has an id=site_id
-        :param site_id: integer- the identification number of the site
-        :return: Sites
-        """
-        try:
-            return self._edit_session.query(Site).filter_by(id=site_id).first()
-        except:
-            return None
-
     # Variables methods
     def get_used_variables(self):
         """
@@ -103,43 +83,6 @@ def get_used_variables(self):
 
         return Variables
 
-    def get_variables_by_site_code(self, site_code):  # covers NoDV, VarUnits, TimeUnits
-        """
-        Finds all of variables at a site
-        :param site_code: str
-        :return: List[Variables]
-        """
-        try:
-            var_ids = [x[0] for x in self._edit_session.query(distinct(Series.variable_id)).filter_by(
-                site_code=site_code).all()]
-        except:
-            var_ids = None
-
-        variables = []
-        for var_id in var_ids:
-            variables.append(self._edit_session.query(Variable).filter_by(id=var_id).first())
-
-        return variables
-
-    # Method methods
-    def get_all_methods(self):
-        return self._edit_session.query(Method).all()
-
-    def get_method_by_id(self, method_id):
-        try:
-            result = self._edit_session.query(Method).filter_by(id=method_id).first()
-        except:
-            result = None
-        return result
-
-    def get_method_by_description(self, method_code):
-        try:
-            result = self._edit_session.query(Method).filter_by(description=method_code).first()
-        except:
-            result = None
-            logger.error("method not found")
-        return result
-
     def get_offset_types_by_series_id(self, series_id):
         """
 
@@ -215,6 +158,31 @@ def get_series_from_filter(self):
         # Pass in probably a Series object, match it against the database
         pass
 
+    def get_all_qualifiers(self):
+        """
+
+        :return: List[Qualifiers]
+        """
+        result = self._edit_session.query(Qualifier).order_by(Qualifier.code).all()
+        return result
+
+    def get_qualifier_by_code(self, code):
+        """
+
+        :return: Qualifiers
+        """
+        result = self._edit_session.query(Qualifier).filter(Qualifier.code==code).first()
+        return result
+
+    def get_qualifiers_by_series_id(self, series_id):
+        """
+
+        :param series_id:
+        :return:
+        """
+        subquery = self._edit_session.query(DataValue.qualifier_id).outerjoin(
+            Series.data_values).filter(Series.id == series_id, DataValue.qualifier_id != None).distinct().subquery()
+        return self._edit_session.query(Qualifier).join(subquery).distinct().all()
 
     #Data Value Methods
     def get_values_by_series(self, series_id):
@@ -430,7 +398,6 @@ def save_values(self, values):
 
     def create_new_series(self, data_values, site_id, variable_id, method_id, source_id, qcl_id):
         """
-
         :param data_values:
         :param site_id:
         :param variable_id:
@@ -451,9 +418,8 @@ def create_new_series(self, data_values, site_id, variable_id, method_id, source
         self._edit_session.commit()
         return series
 
-    def create_method(self, description, link):
+    def create_method(self, description, link):  # DONE
         """
-
         :param description:
         :param link:
         :return:
@@ -467,25 +433,19 @@ def create_method(self, description, link):
 
         return meth
 
-    def create_variable_by_var(self, var):
+    def create_variable_by_var(self, var):  # DONE
         """
-
         :param var:  Variable Object
         :return:
         """
-        # try:
-        #     self._edit_session.add(var)
-        #     self._edit_session.commit()
-        #     return var
-        # except:
-        #     return None
+
         self.create_service.createVariable(var)
         return var
 
     def create_variable(
             self, code, name, speciation, variable_unit_id, sample_medium,
             value_type, is_regular, time_support, time_unit_id, data_type,
-            general_category, no_data_value):
+            general_category, no_data_value):  # DONE
         """
 
         :param code:
@@ -519,7 +479,7 @@ def create_variable(
         self.create_variable_by_var(var)
         return var
 
-    def create_qcl(self, code, definition, explanation):
+    def create_qcl(self, code, definition, explanation):  # DONE
         """
 
         :param code:
@@ -532,8 +492,7 @@ def create_qcl(self, code, definition, explanation):
         qcl.definition = definition
         qcl.explanation = explanation
 
-        self._edit_session.add(qcl)
-        self._edit_session.commit()
+        self.create_service.createProcessingLevel(qcl)
         return qcl