def run(self, *args, **kwargs):
""" Run the command: Acquire USGS DEM data.
Arguments:
auth hs_restclient.HydroShareAuth object
title string representing the title of the resource
hydroshare_host string representing DNS name of the HydroShare
server in which to create the resource
hydroshare_port int representing the TCP port of the HydroShare
server
use_https True if HTTPS should be used. Default: False
resource_type string representing the HydroShare resource type
that should be used to create the resource
abstract string representing the abstract of the resource
keywords list of strings representing the keywords to assign
to the resource
create_callback user-defined callable that takes as input a
file size in bytes, and generates a callable to provide feedback
to the user about the progress of the upload of resource_file.
For more information, see:
http://toolbelt.readthedocs.org/en/latest/uploading-data.html#monitoring-your-streaming-multipart-upload
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
auth = kwargs.get('auth', None)
if auth is None:
raise RunException("No HydroShare authentication mechanism was defined.")
title = kwargs.get('title', None)
if title is None:
raise RunException("Title for new HydroShare resource was not specified.")
hydroshare_host = kwargs.get('hydroshare_host', None)
hydroshare_port = kwargs.get('hydroshare_port', None)
use_https = kwargs.get('use_https', False)
resource_type = kwargs.get('resource_type', 'GenericResource')
abstract = kwargs.get('abstract', None)
keywords = kwargs.get('keywords', None)
create_callback = kwargs.get('create_callback', None)
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
self.checkMetadata(overwrite=overwrite)
resource_id = create_hydroshare_resource(self.context, auth, title,
hydroshare_host=hydroshare_host,
hydroshare_port=hydroshare_port, use_https=use_https,
resource_type=resource_type, abstract=abstract,
keywords=keywords, create_callback=create_callback,
verbose=verbose)
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
# Write metadata
GenericMetadata.writeHydroShareEntry(self.context, 'resource_id', resource_id)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
def deleteRHESSysEntry(context, key):
""" Delete a RHESSys entry from the metadata store for a given project.
@param context Context object containing projectDir, the path of the project whose
metadata store is to be deleted from
@param key The key to be deleted from the RHESSys section of the project metadata
@exception IOError(errno.EACCES) if the metadata store for the project is not writable
"""
GenericMetadata.deleteEntryFromSection(context, RHESSysMetadata.RHESSYS_SECTION, key, \
RHESSysMetadata._writeWorkflowVersionToMetadata)
def deleteRHESSysEntry(context, key):
""" Delete a RHESSys entry from the metadata store for a given project.
@param context Context object containing projectDir, the path of the project whose
metadata store is to be deleted from
@param key The key to be deleted from the RHESSys section of the project metadata
@exception IOError(errno.EACCES) if the metadata store for the project is not writable
"""
GenericMetadata.deleteEntryFromSection(context, RHESSysMetadata.RHESSYS_SECTION, key, \
RHESSysMetadata._writeWorkflowVersionToMetadata)
def test_empty_read(self):
manifest = GenericMetadata.readManifestEntries(self.context)
self.assertTrue(len(manifest) == 0)
studyArea = GenericMetadata.readStudyAreaEntries(self.context)
self.assertTrue(len(studyArea) == 0)
climatePoint = GenericMetadata.readClimatePointEntries(self.context)
self.assertTrue(len(climatePoint) == 0)
climateGrid = GenericMetadata.readClimateGridEntries(self.context)
self.assertTrue(len(climateGrid) == 0)
def writeRHESSysEntry(context, key, value):
""" Write a RHESSys entry to the metadata store for a given project.
@note Will overwrite the value for a key that already exists
@param context Context object containing projectDir, the path of the project whose
metadata store is to be written to
@param key The key to be written to the RHESSys section of the project metadata
@param value The value to be written for key stored in the RHESSys section of the project metadata
@exception IOError(errno.EACCES) if the metadata store for the project is not writable
"""
GenericMetadata.writeEntryToSection(context, RHESSysMetadata.RHESSYS_SECTION, key, value, \
RHESSysMetadata._writeWorkflowVersionToMetadata)
def writeRHESSysEntry(context, key, value):
""" Write a RHESSys entry to the metadata store for a given project.
@note Will overwrite the value for a key that already exists
@param context Context object containing projectDir, the path of the project whose
metadata store is to be written to
@param key The key to be written to the RHESSys section of the project metadata
@param value The value to be written for key stored in the RHESSys section of the project metadata
@exception IOError(errno.EACCES) if the metadata store for the project is not writable
"""
GenericMetadata.writeEntryToSection(context, RHESSysMetadata.RHESSYS_SECTION, key, value, \
RHESSysMetadata._writeWorkflowVersionToMetadata)
def test_write_climate_point1_overwrite(self):
""" Test case where there is a single data file the station, the entry is overwritten """
station = ClimatePointStation()
station.type = "GHCN"
station.id = "US1MDBL0027"
station.longitude = -76.716
station.latitude = 39.317
station.elevation = 128.0
station.name = "My station name"
station.data = "clim.txt"
station.startDate = datetime.strptime("201007", "%Y%m")
station.endDate = datetime.strptime("201110", "%Y%m")
station.variables = [ClimatePointStation.VAR_PRECIP, \
ClimatePointStation.VAR_SNOW]
station.writeToMetadata(self.context)
climatePointStation = GenericMetadata.readClimatePointStations(self.context)[0]
self.assertTrue(station.type.lower() == climatePointStation.type)
self.assertTrue(station.id.lower() == climatePointStation.id)
self.assertTrue(station.longitude == climatePointStation.longitude)
self.assertTrue(station.latitude == climatePointStation.latitude)
self.assertTrue(station.elevation == climatePointStation.elevation)
self.assertTrue(station.name == climatePointStation.name)
self.assertTrue(station.data == climatePointStation.data)
self.assertTrue(station.startDate == climatePointStation.startDate)
self.assertTrue(station.endDate == climatePointStation.endDate)
self.assertTrue(station.variables == climatePointStation.variables)
station.longitude = -76.716
station.latitude = 39.317
station.elevation = 128.0
station.name = "My (longer) station name"
station.data = "clim.dat"
station.startDate = datetime.strptime("201006", "%Y%m")
station.endDate = datetime.strptime("201310", "%Y%m")
station.variables = [ClimatePointStation.VAR_PRECIP, \
ClimatePointStation.VAR_SNOW]
station.writeToMetadata(self.context)
climatePointStation = GenericMetadata.readClimatePointStations(self.context)[0]
self.assertTrue(station.type.lower() == climatePointStation.type)
self.assertTrue(station.id.lower() == climatePointStation.id)
self.assertTrue(station.longitude == climatePointStation.longitude)
self.assertTrue(station.latitude == climatePointStation.latitude)
self.assertTrue(station.elevation == climatePointStation.elevation)
self.assertTrue(station.name == climatePointStation.name)
self.assertTrue(station.data == climatePointStation.data)
self.assertTrue(station.startDate == climatePointStation.startDate)
self.assertTrue(station.endDate == climatePointStation.endDate)
self.assertTrue(station.variables == climatePointStation.variables)
def checkMetadata(self, *args, **kwargs):
""" Check to make sure the project directory has the necessary metadata to run this command.
@note Concrete commands must call this super class method in their own
implementation of checkMetadata(), and must call their implementation
near the beginning of their run method.
"""
super(GrassCommand, self).checkMetadata()
self.grassMetadata = GenericMetadata.readGRASSEntries(self.context)
if not "grass_dbase" in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS Dbase" % (self.context.projectDir,)
)
if not "grass_location" in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS location" % (self.context.projectDir,)
)
if not "grass_mapset" in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS mapset" % (self.context.projectDir,)
)
self.setupGrassEnv()
def checkMetadata(self, *args, **kwargs):
""" Check to make sure the project directory has the necessary metadata to run this command.
@note Concrete commands must call this super class method in their own
implementation of checkMetadata(), and must call their implementation
near the beginning of their run method.
"""
super(GrassCommand, self).checkMetadata()
self.grassMetadata = GenericMetadata.readGRASSEntries(self.context)
if not 'grass_dbase' in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS Dbase"
% (self.context.projectDir, ))
if not 'grass_location' in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS location"
% (self.context.projectDir, ))
if not 'grass_mapset' in self.metadata:
raise MetadataException(
"Metadata in project directory %s does not contain a GRASS mapset"
% (self.context.projectDir, ))
self.setupGrassEnv()
def run(self, *args, **kwargs):
""" Run the command: Acquire Australian soils data.
Arguments:
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
self.checkMetadata()
bbox = bboxFromString(self.studyArea['bbox_wgs84'])
try:
rasters = getSoilsRasterDataForBoundingBox(
self.context.config,
self.context.projectDir,
bbox,
srs=self.studyArea['dem_srs'],
resx=self.studyArea['dem_res_x'],
resy=self.studyArea['dem_res_y'],
overwrite=overwrite,
verbose=verbose,
outfp=self.outfp)
except Exception as e:
traceback.print_exc(file=self.outfp)
raise RunException(e)
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
for attr in list(rasters.keys()):
(filepath, url) = rasters[attr]
filename = os.path.basename(filepath)
asset = AssetProvenance(GenericMetadata.MANIFEST_SECTION)
asset.name = attr
asset.dcIdentifier = filename
asset.dcSource = url
asset.dcTitle = attr
asset.dcPublisher = soilwcs.DC_PUBLISHER
asset.dcDescription = cmdline
asset.writeToMetadata(self.context)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
def checkMetadata(self, *args, **kwargs):
""" Check to make sure the project directory has the necessary metadata to run this command.
@note Concrete commands must call this super class method in their own
implementation of checkMetadata(), and must call their implementation
near the beginning of their run method.
"""
self.studyArea = GenericMetadata.readStudyAreaEntries(self.context)
def readRHESSysEntries(context):
""" Read all RHESSys entries from the metadata store for a given project
@param context Context object containing projectDir, the path of the project whose
metadata store is to be read from
@exception A dictionary of key/value pairs from the RHESSys section of the project metadata
"""
return GenericMetadata._readEntriesForSection(context.projectDir, RHESSysMetadata.RHESSYS_SECTION)
def test_version_conflict(self):
""" Induce a version conflict """
step1 = "mkdir foo; cd foo"
step2 = "touch README.txt"
GenericMetadata.appendProcessingHistoryItem(self.context, step1)
# For testing purposes only, users should not modify
# GenericMetadata._ecohydrolibVersion
_prevVersion = GenericMetadata._ecohydrolibVersion
GenericMetadata._ecohydrolibVersion = '11'
caughtMetadataVersionError = False
try:
GenericMetadata.appendProcessingHistoryItem(self.context, step2)
except MetadataVersionError:
caughtMetadataVersionError = True
self.assertTrue(caughtMetadataVersionError, "Expected metadata version mismatch, but none found.")
GenericMetadata._ecohydrolibVersion = _prevVersion
def checkMetadata(self, *args, **kwargs):
""" Check to make sure the project directory has the necessary metadata to run this command.
@note Concrete commands must call this super class method in their own
implementation of checkMetadata(), and must call their implementation
near the beginning of their run method.
"""
self.studyArea = GenericMetadata.readStudyAreaEntries(self.context)
def run(self, *args, **kwargs):
""" Run the command: Acquire Australian soils data.
Arguments:
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
self.checkMetadata()
bbox = bboxFromString(self.studyArea['bbox_wgs84'])
try:
rasters = getSoilsRasterDataForBoundingBox(self.context.config,
self.context.projectDir,
bbox,
srs=self.studyArea['dem_srs'],
resx=self.studyArea['dem_res_x'],
resy=self.studyArea['dem_res_y'],
overwrite=overwrite,
verbose=verbose,
outfp=self.outfp)
except Exception as e:
traceback.print_exc(file=self.outfp)
raise RunException(e)
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
for attr in rasters.keys():
(filepath, url) = rasters[attr]
filename = os.path.basename(filepath)
asset = AssetProvenance(GenericMetadata.MANIFEST_SECTION)
asset.name = attr
asset.dcIdentifier = filename
asset.dcSource = url
asset.dcTitle = attr
asset.dcPublisher = soilwcs.DC_PUBLISHER
asset.dcDescription = cmdline
asset.writeToMetadata(self.context)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
def readRHESSysEntries(context):
""" Read all RHESSys entries from the metadata store for a given project
@param context Context object containing projectDir, the path of the project whose
metadata store is to be read from
@exception A dictionary of key/value pairs from the RHESSys section of the project metadata
"""
return GenericMetadata._readEntriesForSection(
context.projectDir, RHESSysMetadata.RHESSYS_SECTION)
def checkMetadata(self, *args, **kwargs):
""" Check to make sure the project directory has the necessary metadata to run this command.
"""
super(HydroShareCreateResource, self).checkMetadata(args, kwargs)
overwrite = kwargs.get('overwrite', False)
self.hydroshare = GenericMetadata.readHydroShareEntries(self.context)
if not overwrite and 'resource_id' in self.hydroshare:
raise MetadataException("HydroShare resource ID is already defined, but overwrite was not specified")
def __init__(self, projectDir, configFile=None):
""" Constructor for Context class
@param projectDir Path of the project whose metadata store is to be read from
@param configFile Path of ecohydrolib configuration file to use. If none,
will attempt to read configuration from a file named in the environment
variable Context.CONFIG_FILE_ENV
@raise IOError if project directory path is not a directory
@raise IOError if project directory is not writable
@raise MetadataVersionError if a version already exists in the
metadata store and is different than GenericMetadata._ecohydrolibVersion
@raise EnvironmentError if configuration file name could not be read from the
environment
@raise IOError if configuration file could not be read
"""
if not os.path.isdir(projectDir):
raise IOError(errno.ENOTDIR, "Specified project directory %s is not a directory" % \
(projectDir,))
if not os.access(projectDir, os.W_OK):
raise IOError(errno.EACCES, "Unable to write to project directory %s" % \
(projectDir,))
self.projectDir = os.path.abspath(projectDir)
# Make sure metadata version is compatible with this version of ecohydrolib
# will raise MetadataVersionError if there is a version mismatch
GenericMetadata.checkMetadataVersion(projectDir)
if not configFile:
try:
self._configFile = os.environ[CONFIG_FILE_ENV]
except KeyError:
raise EnvironmentError("Configuration file not specified via environmental variable %s" %\
CONFIG_FILE_ENV)
else:
self._configFile = configFile
if not os.access(self._configFile, os.R_OK):
raise IOError(errno.EACCES, "Unable to read configuration file %s" %
self._configFile)
self.config = ConfigParser.RawConfigParser()
self.config.read(self._configFile)
def __init__(self, projectDir, configFile=None):
""" Constructor for Context class
@param projectDir Path of the project whose metadata store is to be read from
@param configFile Path of ecohydrolib configuration file to use. If none,
will attempt to read configuration from a file named in the environment
variable Context.CONFIG_FILE_ENV
@raise IOError if project directory path is not a directory
@raise IOError if project directory is not writable
@raise MetadataVersionError if a version already exists in the
metadata store and is different than GenericMetadata._ecohydrolibVersion
@raise EnvironmentError if configuration file name could not be read from the
environment
@raise IOError if configuration file could not be read
"""
if not os.path.isdir(projectDir):
raise IOError(errno.ENOTDIR, "Specified project directory %s is not a directory" % \
(projectDir,))
if not os.access(projectDir, os.W_OK):
raise IOError(errno.EACCES, "Unable to write to project directory %s" % \
(projectDir,))
self.projectDir = os.path.abspath(projectDir)
# Make sure metadata version is compatible with this version of ecohydrolib
# will raise MetadataVersionError if there is a version mismatch
GenericMetadata.checkMetadataVersion(projectDir)
if not configFile:
try:
self._configFile = os.environ[CONFIG_FILE_ENV]
except KeyError:
raise EnvironmentError("Configuration file not specified via environmental variable %s" %\
CONFIG_FILE_ENV)
else:
self._configFile = configFile
if not os.access(self._configFile, os.R_OK):
raise IOError(errno.EACCES, "Unable to read configuration file %s" %
self._configFile)
self.config = configparser.RawConfigParser()
self.config.read(self._configFile)
def test_provenance_overwrite(self):
""" Test case writing provenance metadata, with overwrite """
asset = AssetProvenance()
asset.section = GenericMetadata.MANIFEST_SECTION
asset.name = "dem"
asset.dcIdentifier = "dem.tif"
asset.dcSource = "http://www.demexplorer.com/..."
asset.dcTitle = "Study area DEM"
asset.dcDate = datetime.strptime("201303", "%Y%m")
asset.dcPublisher = "USGS"
asset.dcDescription = "RegisterDEM.py ..."
asset.writeToMetadata(self.context)
assetProvenance = GenericMetadata.readAssetProvenanceObjects(self.context)[0]
self.assertTrue(asset.section == assetProvenance.section)
self.assertTrue(asset.name == assetProvenance.name)
self.assertTrue(asset.dcIdentifier == assetProvenance.dcIdentifier)
self.assertTrue(asset.dcSource == assetProvenance.dcSource)
self.assertTrue(asset.dcTitle == assetProvenance.dcTitle)
self.assertTrue(asset.dcDate == assetProvenance.dcDate)
self.assertTrue(asset.dcPublisher == assetProvenance.dcPublisher)
self.assertTrue(asset.dcDescription == assetProvenance.dcDescription)
asset.dcIdentifier = 'foo.img'
asset.dcSource = "http://a.different.url/..."
asset.dcTitle = "A different study area DEM"
asset.dcDate = datetime.strptime("201304", "%Y%m")
asset.dcPublisher = "NASA"
asset.dcDescription = "GetDEMExplorerDEM.py ..."
asset.writeToMetadata(self.context)
assetProvenance = GenericMetadata.readAssetProvenanceObjects(self.context)[0]
self.assertTrue(asset.section == assetProvenance.section)
self.assertTrue(asset.name == assetProvenance.name)
self.assertTrue(asset.dcIdentifier == assetProvenance.dcIdentifier)
self.assertTrue(asset.dcSource == assetProvenance.dcSource)
self.assertTrue(asset.dcTitle == assetProvenance.dcTitle)
self.assertTrue(asset.dcDate == assetProvenance.dcDate)
self.assertTrue(asset.dcPublisher == assetProvenance.dcPublisher)
self.assertTrue(asset.dcDescription == assetProvenance.dcDescription)
def checkMetadata(self):
""" Check to make sure the project directory has the necessary metadata to run this command.
"""
super(USGSWCSNLCD, self).checkMetadata()
# Check for necessary information in metadata
self.manifest = GenericMetadata.readManifestEntries(self.context)
if not 'dem' in self.manifest:
raise MetadataException("Metadata in project directory %s does not contain a DEM" % (self.context.projectDir,))
if not 'dem_srs' in self.studyArea:
raise MetadataException("Metadata in project directory %s does not contain a spatial reference system" % (self.context.projectDir,))
if not 'dem_res_x' in self.studyArea:
raise MetadataException("Metadata in project directory %s does not contain a raster X resolution" % (self.context.projectDir,))
if not 'dem_res_y' in self.studyArea:
raise MetadataException("Metadata in project directory %s does not contain a raster Y resolution" % (self.context.projectDir,))
def test_write_climate_point2(self):
""" Test case where there are separate data files for each variable and there are two climate stations """
station = ClimatePointStation()
station.type = "GHCN"
station.id = "US1MDBL0027"
station.longitude = -76.716
station.latitude = 39.317
station.elevation = 128.0
station.name = "My station name"
station.startDate = datetime.strptime("201007", "%Y%m")
station.endDate = datetime.strptime("201110", "%Y%m")
station.variables = [ClimatePointStation.VAR_PRECIP, \
ClimatePointStation.VAR_SNOW]
station.variablesData[ClimatePointStation.VAR_PRECIP] = ClimatePointStation.VAR_PRECIP + '.txt'
station.variablesData[ClimatePointStation.VAR_SNOW] = ClimatePointStation.VAR_SNOW + '.txt'
station.writeToMetadata(self.context)
station2 = ClimatePointStation()
station2.type = "GHCN"
station2.id = "US1MDBL4242"
station2.longitude = -42.716
station2.latitude = 42.317
station2.elevation = 42.0
station2.name = "My 42 station"
station2.startDate = datetime.strptime("199907", "%Y%m")
station2.endDate = datetime.strptime("200110", "%Y%m")
station2.variables = [ClimatePointStation.VAR_PRECIP, \
ClimatePointStation.VAR_SNOW]
station2.variablesData[ClimatePointStation.VAR_PRECIP] = ClimatePointStation.VAR_PRECIP + '.txt'
station2.variablesData[ClimatePointStation.VAR_SNOW] = ClimatePointStation.VAR_SNOW + '.txt'
station2.writeToMetadata(self.context)
climatePointStation = GenericMetadata.readClimatePointStations(self.context)[0]
self.assertTrue(station.type.lower() == climatePointStation.type)
self.assertTrue(station.id.lower() == climatePointStation.id)
self.assertTrue(station.longitude == climatePointStation.longitude)
self.assertTrue(station.latitude == climatePointStation.latitude)
self.assertTrue(station.elevation == climatePointStation.elevation)
self.assertTrue(station.name == climatePointStation.name)
self.assertTrue(station.startDate == climatePointStation.startDate)
self.assertTrue(station.endDate == climatePointStation.endDate)
self.assertTrue(station.variables == climatePointStation.variables)
self.assertTrue(station.variablesData[ClimatePointStation.VAR_PRECIP] == climatePointStation.variablesData[ClimatePointStation.VAR_PRECIP])
self.assertTrue(station.variablesData[ClimatePointStation.VAR_SNOW] == climatePointStation.variablesData[ClimatePointStation.VAR_SNOW])
def test_processing_history(self):
""" Test processing history metadata """
projectDir = "/tmp"
step1 = "mkdir foo; cd foo"
step2 = "touch README.txt"
step3 = "git init"
GenericMetadata.appendProcessingHistoryItem(self.context, step1)
GenericMetadata.appendProcessingHistoryItem(self.context, step2)
GenericMetadata.appendProcessingHistoryItem(self.context, step3)
history = GenericMetadata.getProcessingHistoryList(self.context)
self.assertTrue(len(history) == 3, "Expected history length to be 3, but it is %d" % (len(history),) )
self.assertTrue(history[0] == step1)
self.assertTrue(history[1] == step2)
self.assertTrue(history[2] == step3)
def checkMetadata(self):
""" Check to make sure the project directory has the necessary metadata to run this command.
"""
super(USGSWCSNLCD, self).checkMetadata()
# Check for necessary information in metadata
self.manifest = GenericMetadata.readManifestEntries(self.context)
if not 'dem' in self.manifest:
raise MetadataException(
"Metadata in project directory %s does not contain a DEM" %
(self.context.projectDir, ))
if not 'dem_srs' in self.studyArea:
raise MetadataException(
"Metadata in project directory %s does not contain a spatial reference system"
% (self.context.projectDir, ))
if not 'dem_res_x' in self.studyArea:
raise MetadataException(
"Metadata in project directory %s does not contain a raster X resolution"
% (self.context.projectDir, ))
if not 'dem_res_y' in self.studyArea:
raise MetadataException(
"Metadata in project directory %s does not contain a raster Y resolution"
% (self.context.projectDir, ))
def test_check_metadata_version(self):
""" Test check metadata version """
step1 = "mkdir foo; cd foo"
GenericMetadata.appendProcessingHistoryItem(self.context, step1)
GenericMetadata.checkMetadataVersion(self.context.projectDir)
# For testing purposes only, users should not modify
# GenericMetadata._ecohydrolibVersion
_prevVersion = GenericMetadata._ecohydrolibVersion
GenericMetadata._ecohydrolibVersion = '11'
caughtMetadataVersionError = False
try:
GenericMetadata.checkMetadataVersion(self.context.projectDir)
except MetadataVersionError:
caughtMetadataVersionError = True
self.assertTrue(caughtMetadataVersionError, "Expected metadata version mismatch, but none found.")
GenericMetadata._ecohydrolibVersion = _prevVersion
from ecohydrolib.metadata import GenericMetadata
from ecohydrolib.metadata import AssetProvenance
from ecohydrolib.hydro1k.basins import getCatchmentShapefileForHYDRO1kBasins
# Handle command line options
parser = argparse.ArgumentParser(description='Get shapefile for the drainage area of an NHDPlus2 streamflow gage')
parser.add_argument('-i', '--configfile', dest='configfile', required=False,
help='The configuration file')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-f', '--outfile', dest='outfile', required=False,
help='The name of the catchment shapefile to be written. File extension ".shp" will be added. If a file of this name exists, program will silently exit.')
parser.add_argument('-b', '--basins', dest='basins', nargs='+', required=True,
help='HYDRO1k basins to extract')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_OGR2OGR'):
sys.exit("Config file %s does not define option %s in section %s" % \
(args.configfile, 'GDAL/OGR', 'PATH_OF_OGR2OGR'))
if not context.config.has_option('HYDRO1k', 'PATH_OF_HYDRO1K_BAS'):
sys.exit("Config file %s does not define option %s in section %s" % \
(args.configfile, 'HYDRO1k', 'PATH_OF_HYDRO1K_BAS'))
if not context.config.has_option('HYDRO1k', 'HYDRO1k_BAS_LAYER_NAME'):
sys.exit("Config file %s does not define option %s in section %s" % \
def run(self, *args, **kwargs):
""" Run the command: Acquire NLCD data from USGS WCS web service.
Arguments:
lctype -- string Source dataset from which NLCD tile should be extracted.
outfile -- string The name of the NLCD file to be written. File extension ".tif" will be added.
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
lctype = kwargs.get('lctype', DEFAULT_LC_TYPE)
outfile = kwargs.get('outfile', None)
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
if lctype not in ecohydrolib.usgs.nlcdwcs.LC_TYPE_TO_COVERAGE:
msg = "Land cover type {lctype} is not in the list of supported types {types}"
raise CommandException(msg.format(lctype=lctype,
types=ecohydrolib.usgs.nlcdwcs.LC_TYPE_TO_COVERAGE))
self.checkMetadata()
demFilename = self.manifest['dem']
demFilepath = os.path.join(self.context.projectDir, demFilename)
demFilepath = os.path.abspath(demFilepath)
bbox = getRasterExtentAsBbox(demFilepath)
if not outfile:
outfile = 'NLCD'
try:
(resp, urlFetched, fname) = getNLCDRasterDataForBoundingBox(self.context.config,
self.context.projectDir,
bbox,
coverage=LC_TYPE_TO_COVERAGE[lctype],
filename=outfile,
srs=self.studyArea['dem_srs'],
resx=self.studyArea['dem_res_x'],
resy=self.studyArea['dem_res_y'],
overwrite=overwrite,
verbose=verbose,
outfp=self.outfp)
except Exception as e:
traceback.print_exc(file=self.outfp)
raise RunException(e)
if not resp:
raise RunException("Failed to download NLCD data from URL {0}".format(urlFetched))
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
GenericMetadata.writeStudyAreaEntry(self.context, "landcover_type", lctype)
# Write provenance
asset = AssetProvenance(GenericMetadata.MANIFEST_SECTION)
asset.name = 'landcover'
asset.dcIdentifier = fname
asset.dcSource = urlFetched
asset.dcTitle = "The National Landcover Database: {0}".format(lctype)
asset.dcPublisher = 'USGS'
asset.dcDescription = cmdline
asset.writeToMetadata(self.context)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
'--demResolution',
dest='demResolution',
required=False,
nargs=2,
type=float,
help=
'Two floating point numbers representing the desired X and Y output resolution of soil property raster maps; unit: meters'
)
parser.add_argument(
'-t',
'--t_srs',
dest='t_srs',
required=False,
help='Target spatial reference system of output, in EPSG:num format')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" % \
(configFile, 'PATH_OF_GDAL_WARP', 'GDAL/OGR'))
if args.outfile:
outfile = args.outfile
else:
outfile = "DEM"
parser.add_argument(
"-p",
"--projectDir",
dest="projectDir",
required=True,
help="The directory to which metadata, intermediate, and final files should be saved",
)
parser.add_argument(
"-d",
"--outdir",
dest="outdir",
required=False,
help="The name of the subdirectory within the project directory to write the climate data to.",
)
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option("GHCND", "PATH_OF_STATION_DB"):
sys.exit("Config file %s does not define option %s in section %s" % (configFile, "PATH_OF_STATION_DB", "GHCND"))
if args.outdir:
outDir = args.outdir
else:
outDir = "climate"
outDirPath = os.path.join(context.projectDir, outDir)
'--projectDir',
dest='projectDir',
required=True,
help=
'The directory to which metadata, intermediate, and final files should be saved'
)
parser.add_argument(
'-d',
'--outdir',
dest='outdir',
required=False,
help=
'The name of the subdirectory within the project directory to write the climate data to.'
)
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GHCND', 'PATH_OF_STATION_DB'):
sys.exit("Config file %s does not define option %s in section %s" % \
(configFile, 'PATH_OF_STATION_DB', 'GHCND'))
if args.outdir:
outDir = args.outdir
else:
outDir = 'climate'
def run(self, *args, **kwargs):
""" Run the command: Acquire USGS DEM data.
Arguments:
coverage -- string Source dataset from which DEM tile should be extracted.
outfile -- string The name of the DEM file to be written. File extension ".tif" will be added.
demResolution list<float>[2] Two floating point numbers representing the desired X and Y output resolution of soil property raster maps; unit: meters.
srs -- string Target spatial reference system of output, in EPSG:num format.
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
coverage = kwargs.get('coverage', self.DEFAULT_COVERAGE)
outfile = kwargs.get('outfile', None)
demResolution = kwargs.get('demResolution', None)
srs = kwargs.get('srs', None)
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
self.checkMetadata()
bbox = bboxFromString(self.studyArea['bbox_wgs84'])
if not outfile:
outfile = 'DEM'
demFilename = "%s.tif" % (outfile)
demResolutionX = demResolutionY = None
if demResolution:
demResolutionX = demResolution[0]
demResolutionY = demResolution[1]
if srs:
if not isValidSrs(srs):
msg = "ERROR: '%s' is not a valid spatial reference. Spatial reference must be of the form 'EPSG:XXXX', e.g. 'EPSG:32617'. For more information, see: http://www.spatialreference.org/" % (srs,)
raise RunException(msg)
else:
# Default for UTM
(centerLon, centerLat) = calculateBoundingBoxCenter(bbox)
(utmZone, isNorth) = getUTMZoneFromCoordinates(centerLon, centerLat)
srs = getEPSGStringForUTMZone(utmZone, isNorth)
try:
(dataFetched, urlFetched) = ecohydrolib.usgs.demwcs.getDEMForBoundingBox(self.context.config,
self.context.projectDir,
demFilename,
bbox,
srs,
coverage=coverage,
resx=demResolutionX,
resy=demResolutionY,
scale=0.01,
overwrite=overwrite,
verbose=verbose,
outfp=self.outfp)
except Exception as e:
traceback.print_exc(file=self.outfp)
raise RunException(e)
if not dataFetched:
raise RunException("Failed to download DEM data from URL {0}".format(urlFetched))
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
# Write metadata
demFilepath = os.path.join(self.context.projectDir, demFilename)
demSrs = getSpatialReferenceForRaster(demFilepath)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_res_x', demSrs[0])
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_res_y', demSrs[1])
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_srs', srs)
# Get rows and columns for DEM
(columns, rows) = getDimensionsForRaster(demFilepath)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_columns', columns)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_rows', rows)
# Write provenance
asset = AssetProvenance(GenericMetadata.MANIFEST_SECTION)
asset.name = 'dem'
asset.dcIdentifier = demFilename
asset.dcSource = urlFetched
asset.dcTitle = "Digital Elevation Model ({0})".format(coverage)
asset.dcPublisher = 'U.S. Geological Survey'
asset.dcDescription = cmdline
asset.processingNotes = "Elevation values rescaled from centimeters to meters. "
asset.processingNotes += "Spatial grid resampled to {srs} with X resolution {xres} and Y resolution {yres}."
asset.processingNotes = asset.processingNotes.format(srs=srs,
xres=demSrs[0],
yres=demSrs[1])
asset.writeToMetadata(self.context)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
required=True,
help=
'The directory to which metadata, intermediate, and final files should be saved'
)
parser.add_argument('command')
parser.add_argument('args', nargs=argparse.REMAINDER)
args = parser.parse_args()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
# Run command
cmd = ecohydrolib.util.getAbsolutePathOfExecutable(args.command)
if cmd == None:
sys.exit("Enable able to find command '%s'" % (args.command, ))
result = subprocess.call([cmd] + args.args)
if result != 0:
sys.exit("Command '%s' failed returning %d" % (args.command, result))
# Build representation of command with absolute path of all command arguments
cmdline = cmd
for arg in args.args:
cmdline += ' ' + ecohydrolib.util.getAbsolutePathOfItem(arg)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(context, cmdline)
help='The iRODS collection corresponding to the project directory')
args = parser.parse_args()
context = Context(args.projectDir, None)
# Make sure there's no trailing PATH_SEP_IRODS on the collection
collection = args.collection.rstrip(PATH_SEP_IRODS)
outfilePath = os.path.join(context.projectDir, OUTFILE_NAME)
outfile = codecs.getwriter('utf-8')(open(outfilePath, 'w'))
outfile.write('<?xml version="1.0" encoding="UTF-8" ?>\n')
outfile.write('<metadata>\n')
# Write study area metadata to collection root
writeDictToXMLFile(outfile, collection,
GenericMetadata.readStudyAreaEntries(context))
# Write processing history to collection root
history = GenericMetadata.getProcessingHistoryList(context)
i = 1
for entry in history:
attribute = "processing_step_%d" % (i, )
i += 1
writeAVUToXMLFile(outfile, collection, attribute, entry)
# Write provenance to each item in the manifest
provenance = GenericMetadata.readAssetProvenanceObjects(context)
for entry in provenance:
target = collection + PATH_SEP_IRODS + entry.dcIdentifier
writeAVUToXMLFile(outfile, target, 'name', entry.name)
writeAVUToXMLFile(outfile, target, 'dc.source', entry.dcSource)
def run(self, *args, **kwargs):
""" Run the command: Acquire USGS DEM data.
Arguments:
coverage -- string Source dataset from which DEM tile should be extracted.
outfile -- string The name of the DEM file to be written. File extension ".tif" will be added.
demResolution list<float>[2] Two floating point numbers representing the desired X and Y output resolution of soil property raster maps; unit: meters.
srs -- string Target spatial reference system of output, in EPSG:num format.
verbose -- boolean Produce verbose output. Default: False.
overwrite -- boolean Overwrite existing output. Default: False.
"""
coverage = kwargs.get('coverage', self.DEFAULT_COVERAGE)
outfile = kwargs.get('outfile', None)
demResolution = kwargs.get('demResolution', None)
srs = kwargs.get('srs', None)
verbose = kwargs.get('verbose', False)
overwrite = kwargs.get('overwrite', False)
self.checkMetadata()
bbox = bboxFromString(self.studyArea['bbox_wgs84'])
if not outfile:
outfile = 'DEM'
demFilename = "%s.tif" % (outfile)
demResolutionX = demResolutionY = None
if demResolution:
demResolutionX = demResolution[0]
demResolutionY = demResolution[1]
if srs:
if not isValidSrs(srs):
msg = "ERROR: '%s' is not a valid spatial reference. Spatial reference must be of the form 'EPSG:XXXX', e.g. 'EPSG:32617'. For more information, see: http://www.spatialreference.org/" % (srs,)
raise RunException(msg)
else:
# Default for UTM
(centerLon, centerLat) = calculateBoundingBoxCenter(bbox)
(utmZone, isNorth) = getUTMZoneFromCoordinates(centerLon, centerLat)
srs = getEPSGStringForUTMZone(utmZone, isNorth)
try:
(dataFetched, urlFetched) = ecohydrolib.usgs.demwcs.getDEMForBoundingBox(self.context.config,
self.context.projectDir,
demFilename,
bbox,
srs,
coverage=coverage,
resx=demResolutionX,
resy=demResolutionY,
scale=0.01,
overwrite=overwrite,
verbose=verbose,
outfp=self.outfp)
except Exception as e:
traceback.print_exc(file=self.outfp)
raise RunException(e)
if not dataFetched:
raise RunException("Failed to download DEM data from URL {0}".format(urlFetched))
# Write metadata entries
cmdline = GenericMetadata.getCommandLine()
# Write metadata
demFilepath = os.path.join(self.context.projectDir, demFilename)
demSrs = getSpatialReferenceForRaster(demFilepath)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_res_x', demSrs[0])
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_res_y', demSrs[1])
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_srs', srs)
# Get rows and columns for DEM
(columns, rows) = getDimensionsForRaster(demFilepath)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_columns', columns)
GenericMetadata.writeStudyAreaEntry(self.context, 'dem_rows', rows)
# Write provenance
asset = AssetProvenance(GenericMetadata.MANIFEST_SECTION)
asset.name = 'dem'
asset.dcIdentifier = demFilename
asset.dcSource = urlFetched
asset.dcTitle = "Digital Elevation Model ({0})".format(coverage)
asset.dcPublisher = 'U.S. Geological Survey'
asset.dcDescription = cmdline
asset.processingNotes = "Elevation values rescaled from centimeters to meters. "
asset.processingNotes += "Spatial grid resampled to {srs} with X resolution {xres} and Y resolution {yres}."
asset.processingNotes = asset.processingNotes.format(srs=srs,
xres=demSrs[0],
yres=demSrs[1])
asset.writeToMetadata(self.context)
# Write processing history
GenericMetadata.appendProcessingHistoryItem(self.context, cmdline)
help='Target spatial reference system of output, in EPSG:num format')
parser.add_argument(
'-s',
'--resampleMethod',
dest='resampleMethod',
required=False,
choices=RASTER_RESAMPLE_METHOD,
default='bilinear',
help='Method to use to resample DEM (if necessary). Defaults to bilinear.')
parser.add_argument('--scale',
dest='scale',
required=False,
type=float,
help='Amount to scale input DEM by')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'GDAL/OGR', 'PATH_OF_GDAL_WARP'))
if not os.access(args.demfile, os.R_OK):
raise IOError(errno.EACCES,
"Not allowed to read input DEM %s" (args.demfile, ))
inDEMPath = os.path.abspath(args.demfile)
from ecohydrolib.spatialdata.utils import getRasterExtentAsBbox
from ecohydrolib.nlcd.daacquery import getNLCDForBoundingBox
from ecohydrolib.nlcd.daacquery import HOST
# Handle command line options
parser = argparse.ArgumentParser(description='Get NLCD data (in GeoTIFF format) for DEM extent from a local copy of the entire NLCD 2006 dataset.')
parser.add_argument('-i', '--configfile', dest='configfile', required=False,
help='The configuration file')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-s', '--source', dest='source', required=False, choices=['local', 'wcs'], default='wcs',
help='Source for NLCD data')
parser.add_argument('-f', '--outfile', dest='outfile', required=False,
help='The name of the NLCD file to be written. File extension ".tif" will be added.')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'GDAL/OGR', 'PATH_OF_GDAL_WARP'))
if args.outfile:
outfile = args.outfile
else:
outfile = "NLCD"
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-g', '--gageFile', dest='gageFile', required=True,
help='The name of the gage shapefile to be registered.')
parser.add_argument('-l', '--layerName', dest='layerName', required=True,
help='The name of the layer within the gage shapefile where gage points are located.')
parser.add_argument('-a', '--idAttribute', dest='idAttribute', required=True,
help='The name of the attribute field that uniquely identifies gage points.')
parser.add_argument('-d', '--idValue', dest='idValue', required=True,
help='The gage ID that uniquely identifies the gage point.')
parser.add_argument('-f', '--outfile', dest='outfile', required=False,
help='The name of the gage shapefile to be written to the project directory. File extension ".shp" will be added.')
parser.add_argument('-b', '--publisher', dest='publisher', required=False,
help="The publisher of the stream flow gage location dataset, if not supplied 'SELF PUBLISHED' will be used")
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not os.access(args.gageFile, os.R_OK):
raise IOError(errno.EACCES, "Not allowed to read input gage shapefile %s" %
args.gageFile)
inGagePath = os.path.abspath(args.gageFile)
if args.publisher:
publisher = args.publisher
else:
parser.add_argument(
'-p',
'--projectDir',
dest='projectDir',
required=True,
help=
'The directory to which metadata, intermediate, and final files should be saved'
)
parser.add_argument(
'-b',
'--buffer',
dest='buffer',
required=False,
help='Number of WGS84 degrees by which to buffer the bounding box')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
context = Context(args.projectDir, None)
buffer = 0.01
if args.buffer:
buffer = float(args.buffer)
# Get name of study area shapefile
manifest = GenericMetadata.readManifestEntries(context)
shapefileName = manifest['study_area_shapefile']
shapefilePath = os.path.join(context.projectDir, shapefileName)
if not os.access(shapefilePath, os.R_OK):
raise IOError(errno.EACCES, "Unable to read shapefile %s" % args.shapefile)
def test_delete(self):
GenericMetadata.writeManifestEntry(self.context, "key1", "value_one")
manifest = GenericMetadata.readManifestEntries(self.context)
self.assertTrue(manifest["key1"] == "value_one")
GenericMetadata.deleteManifestEntry(self.context, "key1")
manifest = GenericMetadata.readManifestEntries(self.context)
self.assertTrue(not 'key1' in manifest)
GenericMetadata.writeStudyAreaEntry(self.context, "key1", "value_one")
studyArea = GenericMetadata.readStudyAreaEntries(self.context)
self.assertTrue(studyArea["key1"] == "value_one")
GenericMetadata.deleteStudyAreaEntry(self.context, 'key1')
studyArea = GenericMetadata.readStudyAreaEntries(self.context)
self.assertTrue(not 'key1' in studyArea)
GenericMetadata.writeClimatePointEntry(self.context, "key1", "value_one")
climatePoint = GenericMetadata.readClimatePointEntries(self.context)
self.assertTrue(climatePoint["key1"] == "value_one")
GenericMetadata.deleteClimatePointEntry(self.context, 'key1')
climatePoint = GenericMetadata.readClimatePointEntries(self.context)
self.assertTrue(not 'key1' in climatePoint)
GenericMetadata.writeClimateGridEntry(self.context, "key1", "value_one")
climateGrid = GenericMetadata.readClimateGridEntries(self.context)
self.assertTrue(climateGrid["key1"] == "value_one")
GenericMetadata.deleteClimateGridEntry(self.context, 'key1')
climateGrid = GenericMetadata.readClimateGridEntries(self.context)
self.assertTrue(not 'key1' in climateGrid)
# Delete and empty entry
GenericMetadata.deleteClimateGridEntry(self.context, "not_in_store")
GenericMetadata.writeHydroShareEntry(self.context, "resource_id", "fae3688aa1354fb2a558380669229a66")
hydroshare = GenericMetadata.readHydroShareEntries(self.context)
self.assertTrue(hydroshare["resource_id"] == "fae3688aa1354fb2a558380669229a66")
GenericMetadata.deleteHydroShareEntry(self.context, "resource_id")
hydroshare = GenericMetadata.readHydroShareEntries(self.context)
self.assertTrue(not 'resource_id' in hydroshare)
# Handle command line options
parser = argparse.ArgumentParser(description='Get DEM raster (in GeoTIFF format) for a bounding box from GeoBrain WCS4DEM')
parser.add_argument('-i', '--configfile', dest='configfile', required=False,
help='The configuration file')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-d', '--demType', dest='demType', required=False, choices=demquery.SUPPORTED_COVERAGE, default=demquery.SUPPORTED_COVERAGE[0],
help='Source dataset from which DEM tile should be extracted.')
parser.add_argument('-f', '--outfile', dest='outfile', required=False,
help='The name of the DEM file to be written. File extension ".tif" will be added.')
parser.add_argument('-c', '--demResolution', dest='demResolution', required=False, nargs=2, type=float,
help='Two floating point numbers representing the desired X and Y output resolution of soil property raster maps; unit: meters')
parser.add_argument('-t', '--t_srs', dest='t_srs', required=False,
help='Target spatial reference system of output, in EPSG:num format')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" % \
(configFile, 'PATH_OF_GDAL_WARP', 'GDAL/OGR'))
if args.outfile:
outfile = args.outfile
else:
outfile = "DEM"
'The directory to which metadata, intermediate, and final files should be saved'
)
parser.add_argument('-s',
'--source',
dest='source',
required=False,
choices=['local', 'webservice'],
default='webservice',
help='Source to query NHDPlusV2 dataset')
parser.add_argument('-g',
'--gageid',
dest='gageid',
required=True,
help='An integer representing the USGS site identifier')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if args.source == 'local':
sys.stdout.write(
'Getting identifiers and location from local NHDPlus dataset...')
sys.stdout.flush()
if not context.config.has_option('NHDPLUS2', 'PATH_OF_NHDPLUS2_DB'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'NHDPLUS2', 'PATH_OF_NHDPLUS2_DB'))
parser.add_argument(
'-f',
'--outfile',
dest='outfile',
required=False,
help=
'The name of the catchment shapefile to be written. File extension ".shp" will be added. If a file of this name exists, program will silently exit.'
)
parser.add_argument('-b',
'--basins',
dest='basins',
nargs='+',
required=True,
help='HYDRO1k basins to extract')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_OGR2OGR'):
sys.exit("Config file %s does not define option %s in section %s" % \
(args.configfile, 'GDAL/OGR', 'PATH_OF_OGR2OGR'))
if not context.config.has_option('HYDRO1k', 'PATH_OF_HYDRO1K_BAS'):
sys.exit("Config file %s does not define option %s in section %s" % \
(args.configfile, 'HYDRO1k', 'PATH_OF_HYDRO1K_BAS'))
if not context.config.has_option('HYDRO1k', 'HYDRO1k_BAS_LAYER_NAME'):
sys.exit("Config file %s does not define option %s in section %s" % \
parser = argparse.ArgumentParser(
description=
'Dump point climate station information from EcohydroLib metadata to standard output'
)
parser.add_argument('-p',
'--projectDir',
dest='projectDir',
required=True,
help='The directory from which metadata should be read')
parser.add_argument('-s',
'--separator',
dest='separator',
required=False,
default=',',
help='Field separator for output')
args = parser.parse_args()
context = Context(args.projectDir, None)
s = args.separator
sys.stderr.write("Getting stations from metadata... ")
stations = GenericMetadata.readClimatePointStations(context)
sys.stderr.write("done\n")
for station in stations:
output = station.id.upper() + s + str(station.latitude) + s + str(
station.longitude) + s + str(
station.elevation) + s + station.name + os.linesep
sys.stdout.write(output)
help='The name of the DEM file to be registered.')
parser.add_argument('-f', '--outfile', dest='outfile', required=False,
help='The name of the DEM file to be written to the project directory. File extension ".tif" will be added.')
parser.add_argument('-b', '--publisher', dest='publisher', required=False,
help="The publisher of the DEM dataset, if not supplied 'SELF PUBLISHED' will be used")
parser.add_argument('-c', '--demResolution', dest='demResolution', required=False, nargs=2, type=float,
help='Two floating point numbers representing the desired X and Y output resolution of soil property raster maps; unit: meters')
parser.add_argument('-t', '--t_srs', dest='t_srs', required=False,
help='Target spatial reference system of output, in EPSG:num format')
parser.add_argument('-s', '--resampleMethod', dest='resampleMethod', required=False,
choices=RASTER_RESAMPLE_METHOD, default='bilinear',
help='Method to use to resample DEM (if necessary). Defaults to bilinear.')
parser.add_argument('--scale', dest='scale', required=False, type=float,
help='Amount to scale input DEM by')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'GDAL/OGR', 'PATH_OF_GDAL_WARP'))
if not os.access(args.demfile, os.R_OK):
raise IOError(errno.EACCES, "Not allowed to read input DEM %s" (args.demfile,))
inDEMPath = os.path.abspath(args.demfile)
inSpatialMetadata = getSpatialReferenceForRaster(inDEMPath)
def test_write_and_read(self):
GenericMetadata.writeManifestEntry(self.context, "key1", "value_one")
GenericMetadata.writeManifestEntry(self.context, "key2", "value_two")
manifest = GenericMetadata.readManifestEntries(self.context)
self.assertTrue(manifest["key1"] == "value_one")
GenericMetadata.writeStudyAreaEntry(self.context, "key1", "value_one")
GenericMetadata.writeStudyAreaEntry(self.context, "key2", "value_two")
studyArea = GenericMetadata.readStudyAreaEntries(self.context)
self.assertTrue(studyArea["key1"] == "value_one")
GenericMetadata.writeClimatePointEntry(self.context, "key1", "value_one")
GenericMetadata.writeClimatePointEntry(self.context, "key2", "value_two")
climatePoint = GenericMetadata.readClimatePointEntries(self.context)
self.assertTrue(climatePoint["key1"] == "value_one")
GenericMetadata.writeClimateGridEntry(self.context, "key1", "value_one")
GenericMetadata.writeClimateGridEntry(self.context, "key2", "value_two")
climateGrid = GenericMetadata.readClimateGridEntries(self.context)
self.assertTrue(climateGrid["key1"] == "value_one")
GenericMetadata.writeHydroShareEntry(self.context, "resource_id", "fae3688aa1354fb2a558380669229a66")
hydroshare = GenericMetadata.readHydroShareEntries(self.context)
self.assertTrue(hydroshare["resource_id"] == "fae3688aa1354fb2a558380669229a66")
import argparse
from ecohydrolib.context import Context
from ecohydrolib.metadata import GenericMetadata
from ecohydrolib.metadata import AssetProvenance
import ecohydrolib.ssurgo.attributequery
from ecohydrolib.solim.inference import inferSoilPropertiesForSSURGOAndTerrainData
# Handle command line options
parser = argparse.ArgumentParser(description='Get SSURGO features for a bounding box')
parser.add_argument('-i', '--configfile', dest='configfile', required=False,
help='The configuration file')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('SOLIM', 'PATH_OF_SOLIM'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'SOLIM', 'PATH_OF_SOLIM'))
# Get provenance data for SSURGO
ssurgoProvenance = [i for i in GenericMetadata.readAssetProvenanceObjects(context) if i.name == 'soil_features'][0]
if ssurgoProvenance is None:
sys.exit("Unable to load SSURGO provenance information from metadata")
import os
import errno
import argparse
from ecohydrolib.context import Context
from ecohydrolib.metadata import GenericMetadata
from ecohydrolib.spatialdata.utils import getBoundingBoxForShapefile
# Handle command line options
parser = argparse.ArgumentParser(description='Get bounding box from study area shapefile')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-b', '--buffer', dest='buffer', required=False,
help='Number of WGS84 degrees by which to buffer the bounding box')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
context = Context(args.projectDir, None)
buffer = 0.01
if args.buffer:
buffer = float(args.buffer)
# Get name of study area shapefile
manifest = GenericMetadata.readManifestEntries(context)
shapefileName = manifest['study_area_shapefile']
shapefilePath = os.path.join(context.projectDir, shapefileName)
if not os.access(shapefilePath, os.R_OK):
raise IOError(errno.EACCES, "Unable to read shapefile %s" %
args.shapefile)
from ecohydrolib.metadata import GenericMetadata
from ecohydrolib.metadata import AssetProvenance
from ecohydrolib.nhdplus2.networkanalysis import getNHDReachcodeAndMeasureForGageSourceFea
from ecohydrolib.nhdplus2.networkanalysis import getLocationForStreamGageByGageSourceFea
from ecohydrolib.spatialdata.utils import writeCoordinatePairsToPointShapefile
# Handle command line options
parser = argparse.ArgumentParser(description='Get NHDPlus2 streamflow gage identifiers for a USGS gage.')
parser.add_argument('-i', '--configfile', dest='configfile', required=False,
help='The configuration file')
parser.add_argument('-p', '--projectDir', dest='projectDir', required=True,
help='The directory to which metadata, intermediate, and final files should be saved')
parser.add_argument('-g', '--gageid', dest='gageid', required=True,
help='An integer representing the USGS site identifier')
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('NHDPLUS2', 'PATH_OF_NHDPLUS2_DB'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'NHDPLUS2', 'PATH_OF_NHDPLUS2_DB'))
if not context.config.has_option('NHDPLUS2', 'PATH_OF_NHDPLUS2_GAGELOC'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'NHDPLUS2', 'PATH_OF_NHDPLUS2_GAGELOC'))
dest='clip',
required=False,
action='store_true',
help=
'Clip raster to DEM extent. Will re-sample raster using method specified by resamplingMethod option'
)
parser.add_argument(
'-b',
'--publisher',
dest='publisher',
required=False,
help=
"The publisher of the raster, if not supplied 'SELF PUBLISHED' will be used"
)
args = parser.parse_args()
cmdline = GenericMetadata.getCommandLine()
configFile = None
if args.configfile:
configFile = args.configfile
context = Context(args.projectDir, configFile)
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_WARP'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'GDAL/OGR', 'PATH_OF_GDAL_WARP'))
if not context.config.has_option('GDAL/OGR', 'PATH_OF_GDAL_TRANSLATE'):
sys.exit("Config file %s does not define option %s in section %s" & \
(args.configfile, 'GDAL/OGR', 'PATH_OF_GDAL_TRANSLATE'))