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Merged
sreeder merged 6 commits into from
Nov 15, 2017
Merged

Sfresults #123

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00834dd
add sfids, sfcodes and sfuuids to getResults
Nov 13, 2017
69656fa
test sfresult function
Nov 13, 2017
1559213
add todo comment
Nov 13, 2017
5ec7eb6
update warning message
Nov 13, 2017
be1a758
add restype to result function
Nov 14, 2017
817a78e
Merge branch 'development' into sfresults
sreeder Nov 14, 2017
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11 changes: 6 additions & 5 deletions Examples/Sample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,13 @@
#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('postgresql', 'localhost', 'odm2', 'ODM', 'odm')
# 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('postgresql', 'localhost', 'odm2', 'ODM', 'odm')
# 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
# session_factory = dbconnection.createConnection('sqlite', '/Users/stephanie/DEV/YODA-Tools/tests/test_files/XL_specimen.sqlite', 2.0)
# session_factory = dbconnection.createConnection('sqlite', 'path/to/ODM2.sqlite', 2.0)



Expand Down Expand Up @@ -61,6 +61,7 @@
try:
print ("\n-------- Information about Sites ---------")
siteFeatures = read.getSamplingFeatures(type= 'site')

# siteFeatures = read.getSamplingFeatures(type='Site')
numSites = len(siteFeatures)
print ("Successful query")
Expand Down Expand Up @@ -144,7 +145,7 @@
# Get the values for a particular TimeSeriesResult
print("\n-------- Example of Retrieving Time Series Result Values ---------")

tsValues = read.getResultValues(resultid = 1) # Return type is a pandas datafram
tsValues = read.getResultValues(resultids = [1]) # Return type is a pandas datafram

# Print a few Time Series Values to the console
# tsValues.set_index('ValueDateTime', inplace=True)
Expand Down
34 changes: 29 additions & 5 deletions odm2api/ODM2/services/readService.py
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Original file line number Diff line number Diff line change
Expand Up @@ -614,8 +614,8 @@ def getAffiliations(self, ids=None, personfirst=None, personlast=None, orgcode=N
return None

# Results
def getResults(self, ids=None, type=None, uuids=None, actionid=None, simulationid=None, sfid=None,
variableid=None, siteid=None):
def getResults(self, ids=None, type=None, restype = None, uuids=None, actionid=None, simulationid=None, sfid=None,
variableid=None, siteid=None, sfids=None, sfuuids=None, sfcodes=None):

# TODO what if user sends in both type and actionid vs just actionid
"""Retrieve a list of Result objects.
Expand All @@ -625,7 +625,7 @@ def getResults(self, ids=None, type=None, uuids=None, actionid=None, simulationi

Args:
ids (list, optional): List of ResultIDs.
type (str, optional): Type of Result from
restype (str, optional): Type of Result from
`controlled vocabulary name <http://vocabulary.odm2.org/resulttype/>`_.
uuids (list, optional): List of UUIDs string.
actionid (int, optional): ActionID.
Expand All @@ -634,14 +634,17 @@ def getResults(self, ids=None, type=None, uuids=None, actionid=None, simulationi
variableid (int, optional): VariableID.
siteid (int, optional): SiteID. - goes through related features table and finds all of results
recorded at the given site
sfids(list, optional): List of Sampling Feature IDs integer.
sfuuids(list, optional): List of Sampling Feature UUIDs string.
sfcodes=(list, optional): List of Sampling Feature codes string.

Returns:
list: List of Result objects

Examples:
>>> ReadODM2.getResults(ids=[39,40])
>>> ReadODM2.getResults(type='Time series coverage')
>>> ReadODM2.getResults(sfid=65)
>>> ReadODM2.getResults(restype='Time series coverage')
>>> ReadODM2.getResults(sfids=[65])
>>> ReadODM2.getResults(uuids=['a6f114f1-5416-4606-ae10-23be32dbc202',
... '5396fdf3-ceb3-46b6-aaf9-454a37278bb4'])
>>> ReadODM2.getResults(simulationid=50)
Expand All @@ -653,7 +656,12 @@ def getResults(self, ids=None, type=None, uuids=None, actionid=None, simulationi
query = self._session.query(Results)

if type:
import warnings
warnings.warn(
"The parameter 'type' is no longer be supported. Please use the restype parameter instead.")
query = query.filter_by(ResultTypeCV=type)
if restype:
query = query.filter_by(ResultTypeCV=restype)
if variableid:
query = query.filter_by(VariableID=variableid)
if ids:
Expand All @@ -668,16 +676,32 @@ def getResults(self, ids=None, type=None, uuids=None, actionid=None, simulationi
if actionid:
query = query.join(FeatureActions).filter_by(ActionID=actionid)
if sfid:
import warnings
warnings.warn("The parameter 'sfid' is no longer be supported. Please use the sfids parameter and send in a list.")
query = query.join(FeatureActions).filter_by(SamplingFeatureID=sfid)
if sfids or sfcodes or sfuuids:
sf_list = self.getSamplingFeatures(ids=sfids, codes=sfcodes, uuids=sfuuids)
sfids = []
for sf in sf_list:
sfids.append(sf.SamplingFeatureID)
query = query.join(FeatureActions).filter(FeatureActions.SamplingFeatureID.in_(sfids))

if siteid:

sfids = [x[0] for x in self._session.query(
distinct(SamplingFeatures.SamplingFeatureID))
.select_from(RelatedFeatures)
.join(RelatedFeatures.SamplingFeatureObj)
.filter(RelatedFeatures.RelatedFeatureID == siteid)
.all()
]

#TODO does this code do the same thing as the code above?
# sf_list = self.getRelatedSamplingFeatures(rfid=siteid)
# sfids = []
# for sf in sf_list:
# sfids.append(sf.SamplingFeatureID)

query = query.join(FeatureActions).filter(FeatureActions.SamplingFeatureID.in_(sfids))

try:
Expand Down
130 changes: 50 additions & 80 deletions tests/test_odm2/test_readservice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ def setup(self):
self.db = globals_vars['db']


# Sampling Features
# Sampling Features
def test_getAllSamplingFeatures(self):
# get all models from the database
res = self.engine.execute('SELECT * FROM SamplingFeatures').fetchall()
Expand All @@ -91,6 +91,14 @@ def test_getSamplingFeatureByID(self):
# get all simulations using the api
resapi = self.reader.getSamplingFeatures(ids=[sfid])
assert resapi is not None

def test_getSamplingFeatureByCode(self):
# get all models from the database
res = self.engine.execute('SELECT * FROM SamplingFeatures').fetchone()
code = res[2]
# get all simulations using the api
resapi = self.reader.getSamplingFeatures(codes=[code])
assert resapi is not None

#DataSets
def test_getDataSets(self):
Expand Down Expand Up @@ -121,8 +129,6 @@ def test_getDataSetsValues(self):
assert len(values) > 0



#ToDo figure out how to actually test this function
def test_getSamplingFeatureDataSets(self):

#find a sampling feature that is associated with a dataset
Expand Down Expand Up @@ -151,18 +157,48 @@ def test_getSamplingFeatureDataSets(self):
assert len(dsapi) > 0
assert ds[1] == dsapi[0].DataSetID

# Results
def test_getAllResults(self):
# get all results from the database
res = self.engine.execute('SELECT * FROM Results').fetchall()
print(res)
# get all results using the api
resapi = self.reader.getResults()
assert len(res) == len(resapi)

# Models
"""
TABLE Models
ModelID INTEGER NOT NULL PRIMARY KEY,
ModelCode VARCHAR (50) NOT NULL,
ModelName VARCHAR (255) NOT NULL,
ModelDescription VARCHAR (500) NULL,
Version VARCHAR (255) NULL,
ModelLink VARCHAR (255) NULL
"""
def test_getResultsByID(self):
# get a result from the database
res = self.engine.execute('SELECT * FROM Results').fetchone()
resultid = res[1]

# get the result using the api
resapi = self.reader.getResults(ids=[resultid])
assert resapi is not None

def test_getResultsBySFID(self):
sf = self.engine.execute(
'SELECT * from SamplingFeatures as sf '
'inner join FeatureActions as fa on fa.SamplingFeatureID == sf.SamplingFeatureID '
'inner join Results as r on fa.FeatureActionID == r.FeatureActionID '
).fetchone()
assert len(sf) > 0
sfid = sf[0]

res = self.engine.execute(
'SELECT * from Results as r '
'inner join FeatureActions as fa on fa.FeatureActionID == r.FeatureActionID '
'where fa.SamplingFeatureID = ' + str(sfid)
).fetchone()

assert len(res) > 0

# get the result using the api
resapi = self.reader.getResults(sfids=[sfid])
assert resapi is not None
assert len(resapi) > 0
assert resapi[0].ResultID == res[0]

# Models
def test_getAllModels(self):
# get all models from the database
res = self.engine.execute('SELECT * FROM Models').fetchall()
Expand All @@ -179,19 +215,7 @@ def test_getModelByCode(self):
assert resapi is not None


# RelatedModels
"""
TABLE RelatedModels (
RelatedID INTEGER NOT NULL PRIMARY KEY,
ModelID INTEGER NOT NULL,
RelationshipTypeCV VARCHAR (255) NOT NULL,
RelatedModelID INTEGER NOT NULL,
FOREIGN KEY (RelationshipTypeCV) REFERENCES CV_RelationshipType (Name)
ON UPDATE NO ACTION ON DELETE NO ACTION,
FOREIGN KEY (ModelID) REFERENCES Models (ModelID)
ON UPDATE NO ACTION ON DELETE NO ACTION
"""

# RelatedModels
def test_getRelatedModelsByID(self):
# get related models by id using the api
resapi = self.reader.getRelatedModels(id=1)
Expand All @@ -214,61 +238,7 @@ def test_getRelatedModelsByCode(self):
# test invalid argument
resapi = self.reader.getRelatedModels(code=234123)
assert not resapi


# Results
"""
TABLE Results (
ResultID INTEGER NOT NULL PRIMARY KEY,
ResultUUID VARCHAR(36) NOT NULL,
FeatureActionID INTEGER NOT NULL,
ResultTypeCV VARCHAR (255) NOT NULL,
VariableID INTEGER NOT NULL,
UnitsID INTEGER NOT NULL,
TaxonomicClassifierID INTEGER NULL,
ProcessingLevelID INTEGER NOT NULL,
ResultDateTime DATETIME NULL,
ResultDateTimeUTCOffset INTEGER NULL,
ValidDateTime DATETIME NULL,
ValidDateTimeUTCOffset INTEGER NULL,
StatusCV VARCHAR (255) NULL,
SampledMediumCV VARCHAR (255) NOT NULL,
ValueCount INTEGER NOT NULL
"""
def test_getAllResults(self):
# get all results from the database
res = self.engine.execute('SELECT * FROM Results').fetchall()
# print(res)
# get all results using the api
resapi = self.reader.getResults()
assert len(res) == len(resapi)

def test_getResultsByID(self):
# get a result from the database
res = self.engine.execute('SELECT * FROM Results').fetchone()
resultid = res[1]

# get the result using the api
resapi = self.reader.getResults(ids=[resultid])
assert resapi is not None

# Simulations
"""
TABLE Simulations (
SimulationID INTEGER NOT NULL PRIMARY KEY,
ActionID INTEGER NOT NULL,
SimulationName VARCHAR (255) NOT NULL,
SimulationDescription VARCHAR (500) NULL,
SimulationStartDateTime DATETIME NOT NULL,
SimulationStartDateTimeUTCOffset INTEGER NOT NULL,
SimulationEndDateTime DATETIME NOT NULL,
SimulationEndDateTimeUTCOffset INTEGER NOT NULL,
TimeStepValue FLOAT NOT NULL,
TimeStepUnitsID INTEGER NOT NULL,
InputDataSetID INTEGER NULL,
ModelID INTEGER NOT NULL,
"""

def test_getAllSimulations(self):
# get all simulation from the database
res = self.engine.execute('SELECT * FROM Simulations').fetchall()
Expand Down