Merge pull request #174 from ODM2/development

Merge development into master to issue new 0.72 release. See #165

Author: emiliom

Examples/TimeSeries_RetrieveVisualize.ipynb

@@ -7,12 +7,9 @@ dependencies:
 - yodatools
 - requests
 - scipy
-- xarray
-- folium
 - geopandas
-- gdal=2.2
-- owslib
-- ulmo
+- gdal
+- folium
 # Jupyter notebook
 - ipykernel
 - jupyter

Examples/WaterQualityMeasurements_RetrieveVisualize.ipynb

@@ -49,6 +49,16 @@ To create a new environment "myenv" with the ``odm2api`` package:
 
     conda create -n myenv -c conda-forge python=2.7 odm2api
 
+Sample Jupyter notebooks
+------------------------
+
+These two notebooks are complete, extended examples that illustrate reading from ODM2 databases and using the resulting data and metadata. They use SQLite ODM2 file databases that can be `downloaded here <https://github.com/ODM2/ODM2PythonAPI/tree/master/Examples/data>`_. 
+A conda environment to run these notebooks can be created with the conda environment file 
+`clientenvironment.yml <https://github.com/ODM2/ODM2PythonAPI/blob/master/Examples/clientenvironment.yml>`_.
+
+1. `WaterQualityMeasurements_RetrieveVisualize.ipynb <https://nbviewer.jupyter.org/github/ODM2/ODM2PythonAPI/blob/master/Examples/WaterQualityMeasurements_RetrieveVisualize.ipynb>`_
+
+2. `TimeSeries_RetrieveVisualize.ipynb <https://nbviewer.jupyter.org/github/ODM2/ODM2PythonAPI/blob/master/Examples/TimeSeries_RetrieveVisualize.ipynb>`_
 
 Code examples
 -------------
@@ -63,12 +73,14 @@ Connect to an ODM2 database and open the connection for reading.
     from odm2api.ODMconnection import dbconnection
     import odm2api.services.readService as odm2rs
 
-    # A SQLite file-based connection
+    # -----------------------------------------------------
+    # 1. A SQLite file-based connection
     session_factory = dbconnection.createConnection('sqlite', 
                                                     '/myfilepath/odm2db.sqlite')
     read = odm2rs.ReadODM2(session_factory)
 
-    # A connection to a server-based database system
+    # -----------------------------------------------------
+    # 2. A server-based database system connection
     db_credentials = {
         'address': 'ip-or-domainname',
         'db': 'dbname',
@@ -93,21 +105,9 @@ then constructing and issuing a direct ``SQL UPDATE`` statement, like this:
     from odm2api.ODMconnection import dbconnection
 
     session_factory = dbconnection.createConnection('postgresql', 
-                                                    **db_cred)
+                                                    **db_credentials)
     DBSession = session_factory.getSession()
 
     sq_str = " UPDATE mytable SET variablecode = 'xyz' WHERE variablecode = 'abc' "
     DBSession.execute(sql_str)
     DBSession.commit()
-
-
-Sample Jupyter notebooks
-------------------------
-
-These two notebooks are complete, extended examples that illustrate reading from ODM2 databases and using the resulting data and metadata. They use SQLite ODM2 file databases that can be `downloaded here <https://github.com/ODM2/ODM2PythonAPI/tree/master/Examples/data>`_. 
-A conda environment to run these notebooks can be created with the conda environment file 
-`clientenvironment.yml <https://github.com/ODM2/ODM2PythonAPI/blob/master/Examples/clientenvironment.yml>`_.
-
-1. `WaterQualityMeasurements_RetrieveVisualize.ipynb <https://github.com/ODM2/ODM2PythonAPI/blob/master/Examples/WaterQualityMeasurements_RetrieveVisualize.ipynb>`_
-
-2. `TimeSeries_RetrieveVisualize.ipynb <https://github.com/ODM2/ODM2PythonAPI/blob/master/Examples/TimeSeries_RetrieveVisualize.ipynb>`_

Examples/clientenvironment.yml

@@ -3,9 +3,11 @@ ODM2 Python API (odm2api)
 
 A Python-based application programmer's interface for the `Observations Data Model 2 (ODM2) <http://www.odm2.org>`__. Development of ``odm2api`` is done at `<https://github.com/ODM2/ODM2PythonAPI/>`_.
 
+Contents
+--------
+
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
    getstarted
    odm2models
@@ -14,7 +16,7 @@ A Python-based application programmer's interface for the `Observations Data Mod
    credits
 
 Indices and Search
-==================
+-----------------
 
 .. toctree::
    :maxdepth: 2

docs/source/getstarted.rst

@@ -14,7 +14,7 @@
 BigIntegerType = BigIntegerType.with_variant(mysql.BIGINT(), 'mysql')
 
 DateTimeType = DateTime()
-DateTimeType = DateTimeType.with_variant(sqlite.INTEGER(), 'sqlite')
+DateTimeType = DateTimeType.with_variant(sqlite.DATETIME(), 'sqlite')
 
 
 def is_hex(s):
@@ -463,7 +463,7 @@ class DataLoggerFiles(Base):
 
 
 class EquipmentModels(Base):
-    ModelID = Column('modelid', Integer, primary_key=True, nullable=False)
+    ModelID = Column('equipmentmodelid', Integer, primary_key=True, nullable=False)
     ModelManufacturerID = Column('modelmanufacturerid', Integer,
                                  ForeignKey(Organizations.OrganizationID), nullable=False)
     ModelPartNumber = Column('modelpartnumber', String(50))
@@ -537,14 +537,15 @@ class Equipment(Base):
     EquipmentCode = Column('equipmentcode', String(50), nullable=False)
     EquipmentName = Column('equipmentname', String(255), nullable=False)
     EquipmentTypeCV = Column('equipmenttypecv', ForeignKey(CVEquipmentType.Name), nullable=False, index=True)
-    ModelID = Column('modelid', ForeignKey(EquipmentModels.ModelID), nullable=False)
-    EquipmentSerialNumber = Column('equipmentseriealnumber', String(50), nullable=False)
+    ModelID = Column('equipmentmodelid', ForeignKey(EquipmentModels.ModelID), nullable=False)
+    EquipmentSerialNumber = Column('equipmentserialnumber', String(50), nullable=False)
     EquipmentInventoryNumber = Column('equipmentinventorynumber', String(50))
     EquipmentOwnerID = Column('equipmentownerid', ForeignKey(People.PersonID), nullable=False)
     EquipmentVendorID = Column('equipmentvendorid', ForeignKey(Organizations.OrganizationID), nullable=False)
     EquipmentPurchaseDate = Column('equipmentpurchasedate', DateTime, nullable=False)
     EquipmentPurchaseOrderNumber = Column('equipmentpurchaseordernumber', String(50))
     EquipmentDescription = Column('equipmentdescription', String(500))
+    EquipmentDocumentationLink = Column('equipmentdocumentationlink', String(255))
 
     PersonObj = relationship(People)
     OrganizationObj = relationship(Organizations)
@@ -580,7 +581,7 @@ class EquipmentUsed(Base):
 
 class MaintenanceActions(Base):
     ActionID = Column('actionid', Integer, ForeignKey(Actions.ActionID), primary_key=True, nullable=False)
-    IsFactoryService = Column('isfactoryservce', Boolean, nullable=False)
+    IsFactoryService = Column('isfactoryservice', Boolean, nullable=False)
     MaintenanceCode = Column('maintenancecode', String(50))
     MantenanceReason = Column('maintenancereason', String(50))
 
@@ -836,7 +837,7 @@ class ActionAnnotations(Base):
 
 class EquipmentAnnotations(Base):
     BridgeID = Column('bridgeid', Integer, primary_key=True, nullable=False)
-    EquipmentID = Column('valueid', BigIntegerType, ForeignKey(Equipment.EquipmentID), nullable=False)
+    EquipmentID = Column('equipmentid', BigIntegerType, ForeignKey(Equipment.EquipmentID), nullable=False)
     AnnotationID = Column('annotationid', ForeignKey(Annotations.AnnotationID), nullable=False)
 
     AnnotationObj = relationship(Annotations)
@@ -906,7 +907,7 @@ class ReferenceMaterials(Base):
         nullable=False,
         index=True
     )
-    ReferenceMaterialOrganizationID = Column('referencematerialoranizationid',
+    ReferenceMaterialOrganizationID = Column('referencematerialorganizationid',
                                              ForeignKey(Organizations.OrganizationID), nullable=False)
     ReferenceMaterialCode = Column('referencematerialcode', String(50), nullable=False)
     ReferenceMaterialLotCode = Column('referencemateriallotcode', String(255))
@@ -951,7 +952,7 @@ class ReferenceMaterialValues(Base):
 
 class ResultNormalizationValues(Base):
     ResultID = Column(u'resultid', ForeignKey(Results.ResultID), primary_key=True)
-    ReferenceMaterialValueID = Column(u'referencematerialvalueid',
+    ReferenceMaterialValueID = Column(u'normalizedbyreferencematerialvalueid',
                                       ForeignKey(ReferenceMaterialValues.ReferenceMaterialValueID),
                                       nullable=False)
 
@@ -1068,8 +1069,8 @@ class CitationExternalIdentifiers(Base):
     ExternalIdentifierSystemID = Column('externalidentifiersystemid',
                                         ForeignKey(ExternalIdentifierSystems.ExternalIdentifierSystemID),
                                         nullable=False)
-    CitationExternalIdentifier = Column('citationexternaldentifier', String(255), nullable=False)
-    CitationExternalIdentifierURI = Column('citationexternaldentifieruri', String(255))
+    CitationExternalIdentifier = Column('citationexternalidentifier', String(255), nullable=False)
+    CitationExternalIdentifierURI = Column('citationexternalidentifieruri', String(255))
 
     CitationObj = relationship(Citations)
     ExternalIdentifierSystemObj = relationship(ExternalIdentifierSystems)
@@ -1678,7 +1679,7 @@ class SpectraResultValues(Base):
     ValueDateTime = Column('valuedatetime', DateTimeType, nullable=False)
     ValueDateTimeUTCOffset = Column('valuedatetimeutcoffset', Integer, nullable=False)
     ExcitationWavelength = Column('excitationwavelength', Float(53), nullable=False)
-    EmissionWavelength = Column('emmistionwavelength', Float(53), nullable=False)
+    EmissionWavelength = Column('emissionwavelength', Float(53), nullable=False)
     WavelengthUnitsID = Column('wavelengthunitsid', ForeignKey(Units.UnitsID), nullable=False)
     CensorCodeCV = Column('censorcodecv', ForeignKey(CVCensorCode.Name), nullable=False, index=True)
     QualityCodeCV = Column('qualitycodecv', ForeignKey(CVQualityCode.Name), nullable=False, index=True)

docs/source/index.rst

@@ -185,7 +185,7 @@ def getAnnotations(self, annottype=None, codes=None, ids=None, **kwargs):
         a = Annotations
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the annottype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the annottype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             annottype = kwargs['type']
         if annottype:
@@ -238,7 +238,7 @@ def getCVs(self, cvtype, **kwargs):
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the cvtype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the cvtype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             cvtype = kwargs['type']
 
@@ -430,7 +430,7 @@ def getMethods(self, ids=None, codes=None, methodtype=None, **kwargs):
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the medtype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the medtype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             methodtype = kwargs['type']
 
@@ -517,7 +517,7 @@ def getSamplingFeatures(self, ids=None, codes=None, uuids=None,
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the sftype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the sftype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             sftype = kwargs['type']
         if results:
@@ -591,7 +591,7 @@ def getActions(self, ids=None, acttype=None, sfid=None, **kwargs):
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the acttype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the acttype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             acttype = kwargs['type']
         a = Actions
@@ -641,7 +641,7 @@ def getUnits(self, ids=None, name=None, unittype=None, **kwargs):
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the unittype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the unittype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             unittype = kwargs['type']
         q = self._session.query(Units)
@@ -779,7 +779,7 @@ def getResults(self, ids=None, restype=None, uuids=None, actionid=None, simulati
         query = self._session.query(Results)
         self._check_kwargs(['type', 'sfid'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the restype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the restype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             restype = kwargs['type']
         if restype:
@@ -798,8 +798,8 @@ def getResults(self, ids=None, restype=None, uuids=None, actionid=None, simulati
         if actionid:
             query = query.join(FeatureActions).filter_by(ActionID=actionid)
         if 'sfid' in kwargs:
-            warnings.warn('The parameter \'sfid\' is deprecated. '
-                          'Please use the sfids parameter instead and send in a list.',
+            warnings.warn("The parameter 'sfid' is deprecated. " +
+                          "Please use the sfids parameter instead and send in a list.",   # noqa
                           DeprecationWarning, stacklevel=2)
             if kwargs['sfid']:
                 query = query.join(FeatureActions).filter_by(SamplingFeatureID=kwargs['sfid'])
@@ -1087,7 +1087,7 @@ def getEquipment(self, codes=None, equiptype=None, sfid=None, actionid=None, **k
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the equiptype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the equiptype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             equiptype = kwargs['type']
 
@@ -1191,7 +1191,7 @@ def getExtensionProperties(self, exptype=None, **kwargs):
         # Todo what values to use for extensionproperties type
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the exptype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the exptype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             exptype = kwargs['type']
         e = ExtensionProperties
@@ -1222,7 +1222,7 @@ def getExternalIdentifiers(self, eitype=None, **kwargs):
         """
         self._check_kwargs(['type'], kwargs)
         if 'type' in kwargs:
-            warnings.warn('The parameter \'type\' is deprecated. Please use the eitype parameter instead.',
+            warnings.warn("The parameter 'type' is deprecated. Please use the eitype parameter instead.",
                           DeprecationWarning, stacklevel=2)
             eitype = kwargs['type']
         e = ExternalIdentifierSystems
@@ -1415,9 +1415,9 @@ def getResultValues(self, resultids, starttime=None, endtime=None, lowercols=Tru
                 df.columns = [self._get_columns(ResultValues)[c] for c in df.columns]
             else:
                 warnings.warn(
-                    'In a near-future release, '
-                    'the parameter \'lowercols\' default will be changed to False, '
-                    'and later the parameter may be removed.',
+                    "In a near-future release, " +  # noqa
+                    "the parameter 'lowercols' default will be changed to False, " +
+                    "and later the parameter may be removed.",   # noqa
                     DeprecationWarning, stacklevel=2)
             return df
         except Exception as e:
@@ -1487,7 +1487,7 @@ def getRelatedModels(self, modid=None, code=None, **kwargs):
         """
         self._check_kwargs(['id'], kwargs)
         if 'id' in kwargs:
-            warnings.warn('The parameter \'id\' is deprecated. Please use the modid parameter instead.',
+            warnings.warn("The parameter 'id' is deprecated. Please use the modid parameter instead.",
                           DeprecationWarning, stacklevel=2)
             modid = kwargs['id']
         m = self._session.query(Models).select_from(RelatedModels).join(RelatedModels.ModelObj)

odm2api/models.py

@@ -1,7 +1,7 @@
 from __future__ import (absolute_import, division, print_function)
 
-from odm2api.ODM2.models import CVElevationDatum, setSchema
 from odm2api.ODMconnection import SessionFactory
+from odm2api.models import CVElevationDatum, setSchema
 
 import pytest
 
@@ -15,10 +15,10 @@
     ['mysql"root@Localhost/odm2', 'mysql', 'mysql+pymysql://root@localhost/odm2'],
     ['postgresql_marchantariats_none', 'postgresql',
      'postgresql+psycopg2://postgres:None@localhost/marchantariats',
-     'marchantariats', 'postgres',  None],
+     'marchantariats', 'postgres', None],
     ['postgresql_marchantariats_empty', 'postgresql',
      'postgresql+psycopg2://postgres@localhost/marchantariats',
-     'marchantariats', 'postgres',  None],
+     'marchantariats', 'postgres', None],
     ['sqlite_wof', 'sqlite', 'sqlite:///./tests/spatialite/wof2odm/ODM2.sqlite', None, None, None]
 ]
 

odm2api/services/readService.py

@@ -1,7 +1,7 @@
 from __future__ import (absolute_import, division, print_function)
 
-from odm2api.ODM2.models import CVElevationDatum
 from odm2api.ODMconnection import dbconnection
+from odm2api.models import CVElevationDatum
 
 import pytest
 
@@ -13,7 +13,7 @@
 dbs_readonly = [
     ['mysql_odm2_odm', 'mysql', 'localhost', 'odm2', 'ODM', 'odm'],
     ['mysql_odm2_root', 'mysql', 'localhost', 'odm2', 'root', None],
-    ['postgresql_marchantariats', 'postgresql', 'localhost', 'marchantariats', 'postgres',  'iforget'],
+    ['postgresql_marchantariats', 'postgresql', 'localhost', 'marchantariats', 'postgres', 'iforget'],
     ['sqlite_wof', 'sqlite', './tests/spatialite/wof2odm/ODM2.sqlite', None, None, None]
 ]