Merge branch 'odmtools' of http://github.com/ODM2/ODM2PythonAPI into odmtools

Author: stephanie

Examples/Sample.py

@@ -17,8 +17,8 @@
 #connect to database
 # createconnection (dbtype, servername, dbname, username, password)
 # session_factory = dbconnection.createConnection('connection type: sqlite|mysql|mssql|postgresql', '/your/path/to/db/goes/here', 2.0)#sqlite
-session_factory = dbconnection.createConnection('mysql', 'localhost', 'odm2', 'ODM', 'odm')#mysql
-# session_factory= dbconnection.createConnection('mssql', "(local)", "ODM2", "ODM", "odm")#win MSSQL
+# session_factory = dbconnection.createConnection('mysql', 'localhost', 'odm2', 'ODM', 'odm')#mysql
+session_factory= dbconnection.createConnection('mssql', "(local)", "ODM2", "ODM", "odm")#win MSSQL
 # session_factory= dbconnection.createConnection('mssql', "arroyoodm2", "", "ODM", "odm")#mac/linux MSSQL
 
 
@@ -32,7 +32,7 @@
 
 #_session = session_factory.getSession()
 read = ReadODM2(session_factory)
-create =CreateODM2(session_factory)
+create = CreateODM2(session_factory)
 
 
 

distribution_notes.txt doc/distribution_notes.txtdistribution_notes.txt renamed to doc/distribution_notes.txt

@@ -11,7 +11,7 @@
 
 
 # import logging
-# from odmtools.common.logger import LoggerTool
+# from odmtools.utils.logger import LoggerTool
 
 # tool = LoggerTool()
 # logger = tool.setupLogger(__name__, __name__ + '.log', 'w', logging.DEBUG)

notes_sqlacodegen.txt doc/notes_sqlacodegen.txtnotes_sqlacodegen.txt renamed to doc/notes_sqlacodegen.txt

@@ -444,6 +444,12 @@ def get_all_sources(self):
         except:
             return None
 
+    def get_source_by_organization(self):
+        try:
+            return self._session.query(sour)
+        except:
+            return None
+
 
 #####################
 #

odm2api/ODM1_1_1/services/edit_service.py

@@ -1,17 +1,17 @@
 
-'''from model import CensorCodeCV
-from model import DataTypeCV
-from model import DataValue
-from model import GeneralCategoryCV
-from model import ISOMetadata
-from model import LabMethod
-from model import Method
-from model import ODMVersion
-from model import OffsetType
-from model import Qualifier
-from model import QualityControlLevel
-from model import Sample
-from model import SampleMediumCV
+'''from converter import CensorCodeCV
+from converter import DataTypeCV
+from converter import DataValue
+from converter import GeneralCategoryCV
+from converter import ISOMetadata
+from converter import LabMethod
+from converter import Method
+from converter import ODMVersion
+from converter import OffsetType
+from converter import Qualifier
+from converter import QualityControlLevel
+from converter import Sample
+from converter import SampleMediumCV
 from sample_type_cv import SampleTypeCV
 from series import Series
 from session_factory import SessionFactory

odm2api/ODM1_1_1/services/series_service.py

@@ -72,7 +72,7 @@ class Site(Base):
     comments = None
 
     # relationships
-    # TODO @sreeder, Please take a look at this line as it throws: sqlalchemy.exc.InvalidRequestError: Class <class 'ODM2.LikeODM1.model.Site2'> does not have a mapped column named 'lat_long_datum_id'
+    # TODO @sreeder, Please take a look at this line as it throws: sqlalchemy.exc.InvalidRequestError: Class <class 'ODM2.LikeODM1.converter.Site2'> does not have a mapped column named 'lat_long_datum_id'
     # :)
     # spatial_ref = relationship(SpatialReference, primaryjoin=("SpatialReference.id==Site2.lat_long_datum_id"))
     # spatial_ref = relationship(SpatialReference)

odm2api/ODM2/LikeODM1/__init__.py

@@ -78,6 +78,7 @@ class CVElevationDatum(Base, CV):
 class CVEquipmentType(Base, CV):
     __tablename__ = 'cv_equipmenttype'
 
+
 class CVMediumType(Base, CV):
     __tablename__ = 'cv_medium'
 
@@ -97,6 +98,7 @@ class CVPropertyDataType(Base, CV):
 class CVQualityCode(Base, CV):
     __tablename__ = 'cv_qualitycode'
 
+
 class CVResultType(Base, CV):
     __tablename__ = 'cv_resulttype'
 
@@ -116,6 +118,7 @@ class CVSamplingFeatureType(Base, CV):
 class CVSpatialOffsetType(Base, CV):
     __tablename__ = 'cv_spatialoffsettype'
 
+
 class CVSpeciation(Base, CV):
     __tablename__ = 'cv_speciation'
 
@@ -157,7 +160,6 @@ class CVReferenceMaterialMedium(Base, CV):
 # ################################################################################
 class People(Base):
 
-
     PersonID = Column('personid', Integer, primary_key=True, nullable=False)
     PersonFirstName = Column('personfirstname', String(255), nullable=False)
     PersonMiddleName = Column('personmiddlename', String(255))
@@ -170,7 +172,6 @@ def __repr__(self):
 
 class Organizations(Base):
 
-
     OrganizationID = Column('organizationid', Integer, primary_key=True, nullable=False)
     OrganizationTypeCV = Column('organizationtypecv', ForeignKey(CVOrganizationType.Name), nullable=False,
                                 index=True)
@@ -191,7 +192,6 @@ def __repr__(self):
 
 class Affiliations(Base):
 
-
     AffiliationID = Column('affiliationid', Integer, primary_key=True, nullable=False)
     PersonID = Column('personid', ForeignKey(People.PersonID), nullable=False)
     OrganizationID = Column('organizationid', ForeignKey(Organizations.OrganizationID))
@@ -209,7 +209,6 @@ class Affiliations(Base):
 
 class Methods(Base):
 
-
     MethodID = Column('methodid', Integer, primary_key=True, nullable=False)
     MethodTypeCV = Column('methodtypecv', ForeignKey(CVMethodType.Name), nullable=False, index=True)
     MethodCode = Column('methodcode', String(50), nullable=False)
@@ -247,7 +246,6 @@ def __repr__(self):
 
 class ActionBy(Base):
 
-
     BridgeID = Column('bridgeid', Integer, primary_key=True, nullable=False)
     ActionID = Column('actionid', Integer, ForeignKey(Actions.ActionID), nullable=False)
     AffiliationID = Column('affiliationid', ForeignKey(Affiliations.AffiliationID), nullable=False)
@@ -260,7 +258,6 @@ class ActionBy(Base):
 
 class SamplingFeatures(Base):
 
-
     SamplingFeatureID = Column('samplingfeatureid', Integer, primary_key=True, nullable=False)
     SamplingFeatureUUID = Column('samplingfeatureuuid', String(36), nullable=False)
     SamplingFeatureTypeCV = Column('samplingfeaturetypecv', ForeignKey(CVSamplingFeatureType.Name),
@@ -284,16 +281,13 @@ class SamplingFeatures(Base):
 
     }
 
-
     def __repr__(self):
-
         return "<SamplingFeatures('%s', '%s', '%s', '%s', '%s')>" % (
             self.SamplingFeatureCode, self.SamplingFeatureName, self.SamplingFeatureDescription,
             # self.Elevation_m, geomkt)
             self.Elevation_m, self.FeatureGeometryWKT)
 
 
-
 class FeatureActions(Base):
     __tablename__ = u'featureactions'
     __table_args__ = {u'schema': 'odm2'}
@@ -509,7 +503,6 @@ class EquipmentModels(Base):
     OrganizationObj = relationship(Organizations)
 
 
-
 class InstrumentOutputVariables(Base):
     __tablename__ = u'instrumentoutputvariables'
     __table_args__ = {u'schema': 'odm2'}
@@ -529,7 +522,6 @@ class InstrumentOutputVariables(Base):
     VariableObj = relationship(Variables)
 
 
-
 class DataLoggerFileColumns(Base):
     __tablename__ = u'dataloggerfilecolumns'
     __table_args__ = {u'schema': 'odm2'}
@@ -557,6 +549,7 @@ class DataLoggerFileColumns(Base):
     ScanIntervalUnitsObj = relationship(Units, primaryjoin='DataLoggerFileColumns.ScanIntervalUnitsID == Units.UnitsID')
     RecordingIntervalUnitsObj = relationship(Units, primaryjoin='DataLoggerFileColumns.RecordingIntervalUnitsID == Units.UnitsID')
 
+
 class Equipment(Base):
     __tablename__ = u'equipment'
     __table_args__ = {u'schema': 'odm2'}
@@ -581,6 +574,7 @@ class Equipment(Base):
 
     # parent = relationship(u'Equipment', remote_side=[EquipmentID])
 
+
 class CalibrationReferenceEquipment(Base):
     __tablename__ = u'calibrationreferenceequipment'
     __table_args__ = {u'schema': 'odm2'}
@@ -592,6 +586,7 @@ class CalibrationReferenceEquipment(Base):
     ActionObj = relationship(Actions)
     EquipmentObj = relationship(Equipment)
 
+
 class EquipmentActions(Base):
     __tablename__ = u'equipmentactions'
     __table_args__ = {u'schema': 'odm2'}
@@ -659,6 +654,8 @@ class CalibrationActions(Base):
 # ################################################################################
 # Lab Analyses
 # ################################################################################
+
+
 class Directives(Base):
     __tablename__ = u'directives'
     __table_args__ = {u'schema': 'odm2'}
@@ -679,6 +676,7 @@ class ActionDirectives(Base):
     ActionObj = relationship(Actions)
     DirectiveObj = relationship(Directives)
 
+
 class SpecimenBatchPositions(Base):
     #todo fix misspelling
     __tablename__ = u'specimenbatchpostions'
@@ -723,10 +721,12 @@ class Specimens(SamplingFeatures):
     __mapper_args__ = {
         'polymorphic_identity':'Specimen',
     }
+
     def __repr__(self):
         return "<Specimens('%s', '%s', '%s',  '%s',)>" \
                % (self.SamplingFeatureID, self.SamplingFeatureCode, self.SpecimenTypeCV,self.SamplingFeatureCode)
 
+
 class SpatialOffsets(Base):
     __tablename__ = u'spatialoffsets'
     __table_args__ = {u'schema': 'odm2'}
@@ -958,8 +958,6 @@ class SamplingFeatureAnnotations(Base):
     SamplingFeatureObj = relationship(SamplingFeatures)
 
 
-
-
 # ################################################################################
 # Data Quality
 # ################################################################################
@@ -1010,6 +1008,7 @@ class ReferenceMaterials(Base):
     OrganizationObj = relationship(Organizations)
     SamplingFeatureObj = relationship(SamplingFeatures)
 
+
 class CalibrationStandards(Base):
     __tablename__ = u'calibrationstandards'
     __table_args__ = {u'schema': 'odm2'}
@@ -1403,7 +1402,7 @@ class MethodCitations(Base):
     MethodObj = relationship(Methods)
 
 
-# from odm2.Annotations.model import Annotation
+# from odm2.Annotations.converter import Annotation
 class RelatedAnnotations(Base):
     __tablename__ = u'relatedannotations'
     __table_args__ = {u'schema': 'odm2'}
@@ -1468,8 +1467,6 @@ class RelatedResults(Base):
 # ################################################################################
 # Results
 # ################################################################################
-
-
 class PointCoverageResults(Results):
     __tablename__ = u'pointcoverageresults'
     __table_args__ = {u'schema': 'odm2'}
@@ -1495,7 +1492,6 @@ class PointCoverageResults(Results):
     __mapper_args__ = {'polymorphic_identity':'Point coverage'}
 
 
-
 class ProfileResults(Results):
     __tablename__ = u'profileresults'
     __table_args__ = {u'schema': 'odm2'}
@@ -2037,6 +2033,7 @@ class TransectResultValueAnnotations(Base):
     AnnotationObj = relationship(Annotations)
     ValueObj = relationship(TransectResultValues)
 
+
 def _changeSchema(schema):
     import inspect
     import sys
@@ -2065,13 +2062,12 @@ def _getSchema(engine):
 
     return insp.default_schema_name
 
+
 def setSchema(engine):
-    # import datetime
-    # start = datetime.datetime.now()
+
     s = _getSchema(engine)
-    if s is None:
-        s = ''
+    # if s is None:
+    #     s = ''
     _changeSchema(s)
-    # end = datetime.datetime.now()
-    # print end-start, ": elapsed time to change schema"
+
 

odm2api/ODM2/LikeODM1/models.py

@@ -3,7 +3,7 @@
 import datetime as dt
 import uuid
 
-# from src.api.ODM2.LikeODM1.model import Site
+# from src.api.ODM2.LikeODM1.converter import Site
 from odm2api.ODM2.models import *
 from odm2api.ODM2 import serviceBase
 

odm2api/ODM2/models.py

@@ -9,8 +9,8 @@
 
 class DeleteODM2(serviceBase):
 
-    def test(self):
-        return None
+    def remove(self, obj):
+        self._session.delete(obj)
 
 # ################################################################################
 # CV