ODMconnection

class odm2api.ODMconnection.SessionFactory(connection_string, echo=True, version=2.0)

getSession()

class odm2api.ODMconnection.dbconnection(debug=False)

classmethod buildConnectionString(engine, address, db, user, password)

classmethod closeConnection(session)

constringBuilder(engine=None, address=None, db=None, user=None, password=None, driver=None)

classmethod createConnection(engine, address, db=None, user=None, password=None, dbtype=2.0, echo=False)

classmethod createConnectionFromString(conn_string, dbtype=2.0, echo=False)

classmethod isValidConnection(connection_string=None, dbtype=2.0)

classmethod testEngine(connection_string, echo=False)

classmethod testEngine1_1(connection_string, echo=False)

Read Services

class odm2api.ODM2.services.readService.DetailedAffiliation(affiliation, person, org)

class odm2api.ODM2.services.readService.DetailedResult(action, result, sc, sn, method, variable, processingLevel, unit)

class odm2api.ODM2.services.readService.ReadODM2(session_factory, debug=False)

Bases: odm2api.base.serviceBase

CalibrationReferenceEquipment(self)

• Pass nothing - return a list of all objects

CalibrationStandards(self)

• Pass nothing - return a list of all objects

DataLoggerFiles(self)

• Pass nothing - return a list of all objects

DataloggerFileColumns(self)

• Pass nothing - return a list of all objects

DataloggerProgramFiles(self)

• Pass Nothing - return a list of all objects

EquipmentModels(self)

• Pass Nothing - return a list of all objects

EquipmentUsed(self)

• Pass Nothing - return a list of all objects

InstrumentOutputVariables(self, modelid=None, variableid=None)

• Pass Nothing - return a list of all objects
• Pass ModelID
• Pass VariableID

RelatedEquipment(self, code=None)

• Pass nothing - return a list of all objects
• Pass code- return a single object with the given code

getActionDirectives(self)

• Pass nothing - return a list of all objects

getActions(self, ids=None, type=None, sfid=None)

• Pass nothing - returns a list of all Actions
• Pass a list of Action ids - returns a list of Action objects
• Pass a ActionTypeCV - returns a list of Action objects of that type
• Pass a SamplingFeature ID - returns a list of Action objects associated with that Sampling feature ID, Found through featureAction table

getAffiliations(ids=None, personfirst=None, personlast=None, orgcode=None)

Retrieve a list of Affiliation objects.

If no arguments are passed to the function, or their values are None, all Affiliation objects in the database will be returned.

Parameters:

• ids (list, optional) – List of AffiliationIDs.
• personfirst (str, optional) – Person First Name.
• personlast (str, optional) – Person Last Name.
• orgcode (str, optional) – Organization Code.

Returns:

List of Affiliation objects

Return type:

list

Examples

>>> ReadODM2.getAffiliations(ids=[39,40])
>>> ReadODM2.getAffiliations(personfirst='John',
...                      personlast='Smith')
>>> ReadODM2.getAffiliations(orgcode='Acme')

getAnnotations(type=None, codes=None, ids=None)

def getAnnotations(self, type=None, codes = None, ids = None):

• Pass Nothing - return a list of all objects
• Pass AnnotationTypeCV - return a list of all objects of the fiven type
• Pass a list of codes - return a list of objects, one for each of the given codes
• Pass a list of ids -return a list of objects, one for each of the given ids

getAuthorLists(self)

• Pass nothing - return a list of all objects

getCVs(type)

getCVs(self, type): * Pass CVType - return a list of all objects of the given type

getDataQuality(self)

• Pass nothing - return a list of all objects

getDataSets(self, codes=None, uuids=None)

• Pass nothing - returns a list of all DataSet objects
• Pass a list of DataSetCode - returns a single DataSet object for each code
• Pass a list of UUIDS - returns a single DataSet object for each UUID

getDatasetCitations(self)

• Pass nothing - return a list of all objects

getDerivationEquations(self)

• Pass nothing - return a list of all objects

getDetailedAffiliationInfo(self)

• Pass Nothing - Return a list of all Affiliations with detailed information, including Affiliation, People and Organization

getDetailedResultInfo(self, resultTypeCV=None, resultID=None, sfID=None)

Get detailed information for all selected Results including , unit info, site info, method info , ProcessingLevel info. * Pass nothing - return a list of all objects * Pass resultTypeCV - All objects of given type * Pass a result ID - single object with the given result ID * Pass a SamplingFeatureID - All objects associated with the given sampling feature.

getDirectives(self)

• Pass nothing - return a list of all objects

getEquipment(self, codes=None, type=None, sfid=None, actionid=None)

• Pass nothing - returns a list of all Equipment objects
• Pass a list of EquipmentCodes- return a list of all Equipment objects that match each of the codes
• Pass a EquipmentType - returns a single Equipment object
• Pass a SamplingFeatureID - returns a single Equipment object
• Pass an ActionID - returns a single Equipment object

getExtensionProperties(self, type=None)

• Pass nothing - return a list of all objects
• Pass type- return a list of all objects of the given type

getExternalIdentifiers(self, type=None)

• Pass nothing - return a list of all objects
• Pass type- return a list of all objects of the given type

getMethodCitations(self)

• Pass nothing - return a list of all objects

getMethods(ids=None, codes=None, type=None)

getMethods(self, ids=None, codes=None, type=None): * Pass nothing - returns full list of method objects * Pass a list of MethodIDs - returns a single method object for each given id * Pass a list of MethodCode - returns a single method object for each given code * Pass a MethodType - returns a list of method objects of the given MethodType

getModels(self, codes=None)

• Pass nothing - return a list of all Model Objects
• Pass a list of ModelCodes - get a list of converter objects related to the converter having ModeCode

getOrganizations(self, ids=None, codes=None)

• Pass nothing - returns a list of all organization objects
• Pass a list of OrganizationID - returns a single organization object
• Pass a list of OrganizationCode - returns a single organization object

getPeople(self, ids=None, firstname=None, lastname=None)

• Pass nothing - returns a list of all People objects
• Pass a list of PeopleID - returns a single People object
• Pass a First Name - returns a single People object
• Pass a Last Name - returns a single People object

getProcessingLevels(self, ids=None, codes=None)

• Pass nothing - returns full list of ProcessingLevel objects
• Pass a list of ProcessingLevelID - returns a single processingLevel object for each given id
• Pass a list of ProcessingLevelCode - returns a single processingLevel object for each given code

getReferenceMaterialValues(self)

• Pass nothing - return a list of all objects

getReferenceMaterials(self)

• Pass nothing - return a list of all objects

getRelatedActions(self, actionid=None)

• Pass an ActionID - get a list of Action objects related to the input action along with the relatinship type

getRelatedAnnotations(self)

• Pass nothing - return a list of all objects

getRelatedCitations(self)

• Pass nothing - return a list of all objects

getRelatedDatasets(self)

• Pass nothing - return a list of all objects

getRelatedModels(self, id=None, code=None)

• Pass a ModelID - get a list of converter objects related to the converter having ModelID
• Pass a ModelCode - get a list of converter objects related to the converter having ModeCode

getRelatedResults(self)

• Pass nothing - return a list of all objects

getRelatedSamplingFeatures(sfid=None, rfid=None, relationshiptype=None)

getRelatedSamplingFeatures(self, sfid=None, rfid = None, relationshiptype=None): * Pass a SamplingFeatureID - get a list of sampling feature objects related to the input sampling feature * Pass a RelatedFeatureID - get a list of Sampling features objects through the related feature * Pass a RelationshipTypeCV - get a list of sampling feature objects with the given type

getResultDerivationEquations(self)

• Pass nothing - return a list of all objects

getResultNormalizationValues(self)

• Pass nothing - return a list of all objects

getResultValues(self, resultids, starttime=None, endtime=None)

• Pass in a list of ResultID - Returns a pandas dataframe object of type that is specific to the result type -

  The resultids must be associated with the same value type

• Pass a ResultID and a date range - returns a pandas dataframe object of type that is specific to the result type with values between the input date range
• Pass a starttime - Returns a dataframe with the values after the given start time
• Pass an endtime - Returns a dataframe with the values before the given end time

getResults(ids=None, type=None, uuids=None, actionid=None, simulationid=None, sfid=None, variableid=None, siteid=None)

Retrieve a list of Result objects.

If no arguments are passed to the function, or their values are None, all Result objects in the database will be returned.

Parameters:

• ids (list, optional) – List of ResultIDs.
• type (str, optional) – Type of Result from controlled vocabulary name.
• uuids (list, optional) – List of UUIDs string.
• actionid (int, optional) – ActionID.
• simulationid (int, optional) – SimulationID.
• sfid (int, optional) – SamplingFeatureID.
• variableid (int, optional) – VariableID.
• siteid (int, optional) – SiteID.

Returns:

List of Result objects

Return type:

list

Examples

>>> ReadODM2.getResults(ids=[39,40])
>>> ReadODM2.getResults(type='Time series coverage')
>>> ReadODM2.getResults(sfid=65)
>>> ReadODM2.getResults(uuids=['a6f114f1-5416-4606-ae10-23be32dbc202',
...                            '5396fdf3-ceb3-46b6-aaf9-454a37278bb4'])
>>> ReadODM2.getResults(simulationid=50)
>>> ReadODM2.getResults(siteid=6)
>>> ReadODM2.getResults(variableid=7)
>>> ReadODM2.getResults(actionid=20)

getResultsDataQuality(self)

• Pass nothing - return a list of all objects

getSamplingFeatures(ids=None, codes=None, uuids=None, type=None, wkt=None, results=False)

getSamplingFeatures(self, ids=None, codes=None, uuids=None, type=None, wkt=None, results=False): * Pass nothing - returns a list of all sampling feature objects with each object of type specific to that sampling feature * Pass a list of SamplingFeatureID - returns a single sampling feature object for the given ids * Pass a list of SamplingFeatureCode - returns a single sampling feature object for the given code * Pass a list of SamplingFeatureUUID - returns a single sampling feature object for the given UUID’s * Pass a SamplingFeatureType - returns a list of sampling feature objects of the type passed in * Pass a SamplingFeature Well Known Text - return a list of sampling feature objects * Pass whether or not you want to return only the sampling features that have results associated with them

getSimulations(self, name=None, actionid=None)

• Pass nothing - get a list of all converter simuation objects
• Pass a SimulationName - get a single simulation object
• Pass an ActionID - get a single simulation object

getSpatialReferences(self, srsCodes=None)

• Pass nothing - return a list of all Spatial References
• Pass in a list of SRS Codes-

getSpecimenBatchPositions(self)

• Pass nothing - return a list of all objects

getTaxonomicClassifiers()

getTaxonomicClassifiers(self): * Pass nothing - return a list of all objects

getUnits(self, ids=None, name=None, type=None)

• Pass nothing - returns a list of all units objects
• Pass a list of UnitsID - returns a single units object for the given id
• Pass UnitsName - returns a single units object
• Pass a type- returns a list of all objects of the given type

getVariables(ids=None, codes=None, sitecode=None, results=False)

getVariables(self, ids=None, codes=None, sitecode=None, results= False): * Pass nothing - returns full list of variable objects * Pass a list of VariableID - returns a single variable object * Pass a list of VariableCode - returns a single variable object * Pass a SiteCode - returns a list of Variable objects that are collected at the given site. * Pass whether or not you want to return the sampling features that have results associated with them

resultExists(result)

resultExists(self, result): Check to see if a Result Object exists * Pass Result Object - return a boolean value of wether the given object exists