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CI-WATER/gsshapy | gsshapy/orm/snw.py | OrographicGageFile._read | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Orographic Gage File Read from File Method
"""
# Set file extension property
self.fileExtension = extension
# Open file and parse into HmetRecords
... | python | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Orographic Gage File Read from File Method
"""
# Set file extension property
self.fileExtension = extension
# Open file and parse into HmetRecords
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CI-WATER/gsshapy | gsshapy/orm/snw.py | OrographicGageFile._write | def _write(self, session, openFile, replaceParamFile):
"""
Orographic Gage File Write to File Method
"""
# Write lines
openFile.write('Num_Sites: %s\n' % self.numSites)
openFile.write('Elev_Base %s\n' % self.elevBase)
openFile.write('Elev_2 %s\n' % s... | python | def _write(self, session, openFile, replaceParamFile):
"""
Orographic Gage File Write to File Method
"""
# Write lines
openFile.write('Num_Sites: %s\n' % self.numSites)
openFile.write('Elev_Base %s\n' % self.elevBase)
openFile.write('Elev_2 %s\n' % s... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile.getFluvialLinks | def getFluvialLinks(self):
"""
Retrieve only the links that represent fluvial portions of the stream. Returns a list of StreamLink instances.
Returns:
list: A list of fluvial :class:`.StreamLink` objects.
"""
# Define fluvial types
fluvialTypeKeywords = ('TRA... | python | def getFluvialLinks(self):
"""
Retrieve only the links that represent fluvial portions of the stream. Returns a list of StreamLink instances.
Returns:
list: A list of fluvial :class:`.StreamLink` objects.
"""
# Define fluvial types
fluvialTypeKeywords = ('TRA... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile.getOrderedLinks | def getOrderedLinks(self, session):
"""
Retrieve the links in the order of the link number.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
list: A list of :class:`.StreamLink` objects.... | python | def getOrderedLinks(self, session):
"""
Retrieve the links in the order of the link number.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database.
Returns:
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile.getStreamNetworkAsWkt | def getStreamNetworkAsWkt(self, session, withNodes=True):
"""
Retrieve the stream network geometry in Well Known Text format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withNodes (bool, optional): In... | python | def getStreamNetworkAsWkt(self, session, withNodes=True):
"""
Retrieve the stream network geometry in Well Known Text format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withNodes (bool, optional): In... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile.getStreamNetworkAsGeoJson | def getStreamNetworkAsGeoJson(self, session, withNodes=True):
"""
Retrieve the stream network geometry in GeoJSON format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
withNodes (bool, optional): Includ... | python | def getStreamNetworkAsGeoJson(self, session, withNodes=True):
"""
Retrieve the stream network geometry in GeoJSON format.
Args:
session (:mod:`sqlalchemy.orm.session.Session`): SQLAlchemy session object bound to PostGIS enabled database
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._read | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Channel Input File Read from File Method
"""
# Set file extension property
self.fileExtension = extension
# Dictionary of keywords/cards and parse fun... | python | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Channel Input File Read from File Method
"""
# Set file extension property
self.fileExtension = extension
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] | 00fd4af0fd65f1614d75a52fe950a04fb0867f4c | https://github.com/CI-WATER/gsshapy/blob/00fd4af0fd65f1614d75a52fe950a04fb0867f4c/gsshapy/orm/cif.py#L389-L447 | train |
CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._write | def _write(self, session, openFile, replaceParamFile):
"""
Channel Input File Write to File Method
"""
# Write lines
openFile.write('GSSHA_CHAN\n')
alpha = vwp(self.alpha, replaceParamFile)
try:
openFile.write('ALPHA%s%.6f\n' % (' ' * 7, alpha))
... | python | def _write(self, session, openFile, replaceParamFile):
"""
Channel Input File Write to File Method
"""
# Write lines
openFile.write('GSSHA_CHAN\n')
alpha = vwp(self.alpha, replaceParamFile)
try:
openFile.write('ALPHA%s%.6f\n' % (' ' * 7, alpha))
... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createLink | def _createLink(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Link Object Method
"""
link = None
# Cases
if linkResult['type'] == 'XSEC':
# Cross section link handler
link = self._createCrossSection(linkResult, replaceParamFile)
... | python | def _createLink(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Link Object Method
"""
link = None
# Cases
if linkResult['type'] == 'XSEC':
# Cross section link handler
link = self._createCrossSection(linkResult, replaceParamFile)
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createConnectivity | def _createConnectivity(self, linkList, connectList):
"""
Create GSSHAPY Connect Object Method
"""
# Create StreamLink-Connectivity Pairs
for idx, link in enumerate(linkList):
connectivity = connectList[idx]
# Initialize GSSHAPY UpstreamLink objects
... | python | def _createConnectivity(self, linkList, connectList):
"""
Create GSSHAPY Connect Object Method
"""
# Create StreamLink-Connectivity Pairs
for idx, link in enumerate(linkList):
connectivity = connectList[idx]
# Initialize GSSHAPY UpstreamLink objects
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createCrossSection | def _createCrossSection(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Cross Section Objects Method
"""
# Extract header variables from link result object
header = linkResult['header']
# Initialize GSSHAPY StreamLink object
link = StreamLink(linkNumber=i... | python | def _createCrossSection(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Cross Section Objects Method
"""
# Extract header variables from link result object
header = linkResult['header']
# Initialize GSSHAPY StreamLink object
link = StreamLink(linkNumber=i... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createStructure | def _createStructure(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Structure Objects Method
"""
# Constants
WEIRS = ('WEIR', 'SAG_WEIR')
CULVERTS = ('ROUND_CULVERT', 'RECT_CULVERT')
CURVES = ('RATING_CURVE', 'SCHEDULED_RELEASE', 'RULE_CURVE')
... | python | def _createStructure(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Structure Objects Method
"""
# Constants
WEIRS = ('WEIR', 'SAG_WEIR')
CULVERTS = ('ROUND_CULVERT', 'RECT_CULVERT')
CURVES = ('RATING_CURVE', 'SCHEDULED_RELEASE', 'RULE_CURVE')
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createReservoir | def _createReservoir(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Reservoir Objects Method
"""
# Extract header variables from link result object
header = linkResult['header']
# Cases
if linkResult['type'] == 'LAKE':
# Lake handler
... | python | def _createReservoir(self, linkResult, replaceParamFile):
"""
Create GSSHAPY Reservoir Objects Method
"""
# Extract header variables from link result object
header = linkResult['header']
# Cases
if linkResult['type'] == 'LAKE':
# Lake handler
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._createGeometry | def _createGeometry(self, session, spatialReferenceID):
"""
Create PostGIS geometric objects
"""
# Flush the current session
session.flush()
# Create geometry for each fluvial link
for link in self.getFluvialLinks():
# Retrieve the nodes for each lin... | python | def _createGeometry(self, session, spatialReferenceID):
"""
Create PostGIS geometric objects
"""
# Flush the current session
session.flush()
# Create geometry for each fluvial link
for link in self.getFluvialLinks():
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._writeConnectivity | def _writeConnectivity(self, links, fileObject):
"""
Write Connectivity Lines to File Method
"""
for link in links:
linkNum = link.linkNumber
downLink = link.downstreamLinkID
numUpLinks = link.numUpstreamLinks
upLinks = ''
for u... | python | def _writeConnectivity(self, links, fileObject):
"""
Write Connectivity Lines to File Method
"""
for link in links:
linkNum = link.linkNumber
downLink = link.downstreamLinkID
numUpLinks = link.numUpstreamLinks
upLinks = ''
for u... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._writeLinks | def _writeLinks(self, links, fileObject, replaceParamFile):
"""
Write Link Lines to File Method
"""
for link in links:
linkType = link.type
fileObject.write('LINK %s\n' % link.linkNumber)
# Cases
if 'TRAP' in linkType or 'TRAPEZO... | python | def _writeLinks(self, links, fileObject, replaceParamFile):
"""
Write Link Lines to File Method
"""
for link in links:
linkType = link.type
fileObject.write('LINK %s\n' % link.linkNumber)
# Cases
if 'TRAP' in linkType or 'TRAPEZO... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._writeCrossSectionLink | def _writeCrossSectionLink(self, link, fileObject, replaceParamFile):
"""
Write Cross Section Link to File Method
"""
linkType = link.type
# Write cross section link header
dx = vwp(link.dx, replaceParamFile)
try:
fileObject.write('DX %.6f... | python | def _writeCrossSectionLink(self, link, fileObject, replaceParamFile):
"""
Write Cross Section Link to File Method
"""
linkType = link.type
# Write cross section link header
dx = vwp(link.dx, replaceParamFile)
try:
fileObject.write('DX %.6f... | [
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CI-WATER/gsshapy | gsshapy/orm/cif.py | ChannelInputFile._writeOptionalXsecCards | def _writeOptionalXsecCards(self, fileObject, xSec, replaceParamFile):
"""
Write Optional Cross Section Cards to File Method
"""
if xSec.erode:
fileObject.write('ERODE\n')
if xSec.maxErosion != None:
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"""
Write Optional Cross Section Cards to File Method
"""
if xSec.erode:
fileObject.write('ERODE\n')
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | replace_file | def replace_file(from_file, to_file):
"""
Replaces to_file with from_file
"""
try:
os.remove(to_file)
except OSError:
pass
copy(from_file, to_file) | python | def replace_file(from_file, to_file):
"""
Replaces to_file with from_file
"""
try:
os.remove(to_file)
except OSError:
pass
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework._prepare_lsm_gag | def _prepare_lsm_gag(self):
"""
Determines whether to prepare gage data from LSM
"""
lsm_required_vars = (self.lsm_precip_data_var,
self.lsm_precip_type)
return self.lsm_input_valid and (None not in lsm_required_vars) | python | def _prepare_lsm_gag(self):
"""
Determines whether to prepare gage data from LSM
"""
lsm_required_vars = (self.lsm_precip_data_var,
self.lsm_precip_type)
return self.lsm_input_valid and (None not in lsm_required_vars) | [
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework._update_card_file_location | def _update_card_file_location(self, card_name, new_directory):
"""
Moves card to new gssha working directory
"""
with tmp_chdir(self.gssha_directory):
file_card = self.project_manager.getCard(card_name)
if file_card:
if file_card.value:
... | python | def _update_card_file_location(self, card_name, new_directory):
"""
Moves card to new gssha working directory
"""
with tmp_chdir(self.gssha_directory):
file_card = self.project_manager.getCard(card_name)
if file_card:
if file_card.value:
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.download_spt_forecast | def download_spt_forecast(self, extract_directory):
"""
Downloads Streamflow Prediction Tool forecast data
"""
needed_vars = (self.spt_watershed_name,
self.spt_subbasin_name,
self.spt_forecast_date_string,
self.ckan_eng... | python | def download_spt_forecast(self, extract_directory):
"""
Downloads Streamflow Prediction Tool forecast data
"""
needed_vars = (self.spt_watershed_name,
self.spt_subbasin_name,
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.prepare_hmet | def prepare_hmet(self):
"""
Prepare HMET data for simulation
"""
if self._prepare_lsm_hmet:
netcdf_file_path = None
hmet_ascii_output_folder = None
if self.output_netcdf:
netcdf_file_path = '{0}_hmet.nc'.format(self.project_manager.name... | python | def prepare_hmet(self):
"""
Prepare HMET data for simulation
"""
if self._prepare_lsm_hmet:
netcdf_file_path = None
hmet_ascii_output_folder = None
if self.output_netcdf:
netcdf_file_path = '{0}_hmet.nc'.format(self.project_manager.name... | [
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.prepare_gag | def prepare_gag(self):
"""
Prepare gage data for simulation
"""
if self._prepare_lsm_gag:
self.event_manager.prepare_gag_lsm(self.lsm_precip_data_var,
self.lsm_precip_type,
self.prec... | python | def prepare_gag(self):
"""
Prepare gage data for simulation
"""
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self.event_manager.prepare_gag_lsm(self.lsm_precip_data_var,
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.rapid_to_gssha | def rapid_to_gssha(self):
"""
Prepare RAPID data for simulation
"""
# if no streamflow given, download forecast
if self.path_to_rapid_qout is None and self.connection_list_file:
rapid_qout_directory = os.path.join(self.gssha_directory, 'rapid_streamflow')
... | python | def rapid_to_gssha(self):
"""
Prepare RAPID data for simulation
"""
# if no streamflow given, download forecast
if self.path_to_rapid_qout is None and self.connection_list_file:
rapid_qout_directory = os.path.join(self.gssha_directory, 'rapid_streamflow')
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.hotstart | def hotstart(self):
"""
Prepare simulation hotstart info
"""
if self.write_hotstart:
hotstart_time_str = self.event_manager.simulation_end.strftime("%Y%m%d_%H%M")
try:
os.mkdir('hotstart')
except OSError:
pass
... | python | def hotstart(self):
"""
Prepare simulation hotstart info
"""
if self.write_hotstart:
hotstart_time_str = self.event_manager.simulation_end.strftime("%Y%m%d_%H%M")
try:
os.mkdir('hotstart')
except OSError:
pass
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CI-WATER/gsshapy | gsshapy/modeling/framework.py | GSSHAFramework.run_forecast | def run_forecast(self):
"""
Updates card & runs for RAPID to GSSHA & LSM to GSSHA
"""
# ----------------------------------------------------------------------
# LSM to GSSHA
# ----------------------------------------------------------------------
self.prepare_hme... | python | def run_forecast(self):
"""
Updates card & runs for RAPID to GSSHA & LSM to GSSHA
"""
# ----------------------------------------------------------------------
# LSM to GSSHA
# ----------------------------------------------------------------------
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | get_cache_key | def get_cache_key(request, page, lang, site_id, title):
"""
Create the cache key for the current page and tag type
"""
from cms.cache import _get_cache_key
from cms.templatetags.cms_tags import _get_page_by_untyped_arg
from cms.models import Page
if not isinstance(page, Page):
page ... | python | def get_cache_key(request, page, lang, site_id, title):
"""
Create the cache key for the current page and tag type
"""
from cms.cache import _get_cache_key
from cms.templatetags.cms_tags import _get_page_by_untyped_arg
from cms.models import Page
if not isinstance(page, Page):
page ... | [
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | get_page_tags | def get_page_tags(page):
"""
Retrieves all the tags for a Page instance.
:param page: a Page instance
:return: list or queryset of attached tags
:type: List
"""
from .models import PageTags
try:
return page.pagetags.tags.all()
except PageTags.DoesNotExist:
return [] | python | def get_page_tags(page):
"""
Retrieves all the tags for a Page instance.
:param page: a Page instance
:return: list or queryset of attached tags
:type: List
"""
from .models import PageTags
try:
return page.pagetags.tags.all()
except PageTags.DoesNotExist:
return [] | [
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | page_has_tag | def page_has_tag(page, tag):
"""
Check if a Page object is associated with the given tag.
:param page: a Page instance
:param tag: a Tag instance or a slug string.
:return: whether the Page instance has the given tag attached (False if no Page or no
attached PageTags exists)
:type... | python | def page_has_tag(page, tag):
"""
Check if a Page object is associated with the given tag.
:param page: a Page instance
:param tag: a Tag instance or a slug string.
:return: whether the Page instance has the given tag attached (False if no Page or no
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | title_has_tag | def title_has_tag(page, lang, tag):
"""
Check if a Title object is associated with the given tag.
This function does not use fallbacks to retrieve title object.
:param page: a Page instance
:param lang: a language code
:param tag: a Tag instance or a slug string.
:return: whether the Title... | python | def title_has_tag(page, lang, tag):
"""
Check if a Title object is associated with the given tag.
This function does not use fallbacks to retrieve title object.
:param page: a Page instance
:param lang: a language code
:param tag: a Tag instance or a slug string.
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | get_page_tags_from_request | def get_page_tags_from_request(request, page_lookup, lang, site, title=False):
"""
Get the list of tags attached to a Page or a Title from a request from usual
`page_lookup` parameters.
:param request: request object
:param page_lookup: a valid page_lookup argument
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Get the list of tags attached to a Page or a Title from a request from usual
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nephila/djangocms-page-tags | djangocms_page_tags/utils.py | get_title_tags_from_request | def get_title_tags_from_request(request, page_lookup, lang, site):
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Get the list of tags attached to a Title from a request from usual
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:param request: request object
:param page_lookup: a valid page_lookup argument
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Get the list of tags attached to a Title from a request from usual
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CI-WATER/gsshapy | gsshapy/orm/msk.py | WatershedMaskFile.generateFromWatershedShapefile | def generateFromWatershedShapefile(self,
shapefile_path,
cell_size,
out_raster_path=None,
load_raster_to_db=True):
"""
Generates a mask from a water... | python | def generateFromWatershedShapefile(self,
shapefile_path,
cell_size,
out_raster_path=None,
load_raster_to_db=True):
"""
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CI-WATER/gsshapy | gsshapy/util/context.py | tmp_chdir | def tmp_chdir(new_path):
"""Change directory temporarily and return when done."""
prev_cwd = os.getcwd()
os.chdir(new_path)
try:
yield
finally:
os.chdir(prev_cwd) | python | def tmp_chdir(new_path):
"""Change directory temporarily and return when done."""
prev_cwd = os.getcwd()
os.chdir(new_path)
try:
yield
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CI-WATER/gsshapy | gsshapy/grid/era_to_gssha.py | ERAtoGSSHA._download | def _download(self):
"""download ERA5 data for GSSHA domain"""
# reproject GSSHA grid and get bounds
min_x, max_x, min_y, max_y = self.gssha_grid.bounds(as_geographic=True)
if self.era_download_data == 'era5':
log.info("Downloading ERA5 data ...")
download_era5_fo... | python | def _download(self):
"""download ERA5 data for GSSHA domain"""
# reproject GSSHA grid and get bounds
min_x, max_x, min_y, max_y = self.gssha_grid.bounds(as_geographic=True)
if self.era_download_data == 'era5':
log.info("Downloading ERA5 data ...")
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hellupline/flask-manager | flask_manager/views.py | View.dispatch_request | def dispatch_request(self, *args, **kwargs):
"""Dispatch the request.
Its the actual ``view`` flask will use.
"""
if request.method in ('POST', 'PUT'):
return_url, context = self.post(*args, **kwargs)
if return_url is not None:
return redirect(retu... | python | def dispatch_request(self, *args, **kwargs):
"""Dispatch the request.
Its the actual ``view`` flask will use.
"""
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bayesimpact/fex | fex/runner.py | _run_cmd_get_output | def _run_cmd_get_output(cmd):
"""Runs a shell command, returns console output.
Mimics python3's subprocess.getoutput
"""
process = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
out, err = process.communicate()
return out or err | python | def _run_cmd_get_output(cmd):
"""Runs a shell command, returns console output.
Mimics python3's subprocess.getoutput
"""
process = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
out, err = process.communicate()
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bayesimpact/fex | fex/runner.py | _remote_github_url_to_string | def _remote_github_url_to_string(remote_url):
"""Parse out the repository identifier from a github URL."""
# TODO: make this work with https URLs
match = re.search('git@github\.com:(.*)\.git', remote_url)
if not match:
raise EnvironmentError('Remote is not a valid github URL')
identifier = m... | python | def _remote_github_url_to_string(remote_url):
"""Parse out the repository identifier from a github URL."""
# TODO: make this work with https URLs
match = re.search('git@github\.com:(.*)\.git', remote_url)
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bayesimpact/fex | fex/runner.py | _get_args | def _get_args(args):
"""Argparse logic lives here.
returns: parsed arguments.
"""
parser = argparse.ArgumentParser(
description='A tool to extract features into a simple format.',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument('--no-cache', action=... | python | def _get_args(args):
"""Argparse logic lives here.
returns: parsed arguments.
"""
parser = argparse.ArgumentParser(
description='A tool to extract features into a simple format.',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
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bayesimpact/fex | fex/runner.py | run | def run(*extractor_list, **kwargs):
"""Parse arguments provided on the commandline and execute extractors."""
args = _get_args(kwargs.get('args'))
n_extractors = len(extractor_list)
log.info('Going to run list of {} FeatureExtractors'.format(n_extractors))
collection = fex.Collection(cache_path=args... | python | def run(*extractor_list, **kwargs):
"""Parse arguments provided on the commandline and execute extractors."""
args = _get_args(kwargs.get('args'))
n_extractors = len(extractor_list)
log.info('Going to run list of {} FeatureExtractors'.format(n_extractors))
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CI-WATER/gsshapy | gsshapy/orm/map.py | RasterMapFile._delete_existing | def _delete_existing(self, project_file, session):
"""
This will delete existing instances with the same extension
"""
# remove existing grid if exists
existing_elev = session.query(RasterMapFile).\
filter(RasterMapFile.projectFile == project... | python | def _delete_existing(self, project_file, session):
"""
This will delete existing instances with the same extension
"""
# remove existing grid if exists
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CI-WATER/gsshapy | gsshapy/orm/map.py | RasterMapFile._load_raster_text | def _load_raster_text(self, raster_path):
"""
Loads grass ASCII to object
"""
# Open file and read plain text into text field
with open(raster_path, 'r') as f:
self.rasterText = f.read()
# Retrieve metadata from header
lines = self.rasterText.split('\... | python | def _load_raster_text(self, raster_path):
"""
Loads grass ASCII to object
"""
# Open file and read plain text into text field
with open(raster_path, 'r') as f:
self.rasterText = f.read()
# Retrieve metadata from header
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CI-WATER/gsshapy | gsshapy/orm/map.py | RasterMapFile._read | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Raster Map File Read from File Method
"""
# Assign file extension attribute to file object
self.fileExtension = extension
self.filename = filename
... | python | def _read(self, directory, filename, session, path, name, extension, spatial, spatialReferenceID, replaceParamFile):
"""
Raster Map File Read from File Method
"""
# Assign file extension attribute to file object
self.fileExtension = extension
self.filename = filename
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CI-WATER/gsshapy | gsshapy/orm/map.py | RasterMapFile._write | def _write(self, session, openFile, replaceParamFile):
"""
Raster Map File Write to File Method
"""
# If the raster field is not empty, write from this field
if self.raster is not None:
# Configure RasterConverter
converter = RasterConverter(session)
... | python | def _write(self, session, openFile, replaceParamFile):
"""
Raster Map File Write to File Method
"""
# If the raster field is not empty, write from this field
if self.raster is not None:
# Configure RasterConverter
converter = RasterConverter(session)
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CI-WATER/gsshapy | gsshapy/orm/map.py | RasterMapFile.write | def write(self, session, directory, name, replaceParamFile=None, **kwargs):
"""
Wrapper for GsshaPyFileObjectBase write method
"""
if self.raster is not None or self.rasterText is not None:
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"""
Wrapper for GsshaPyFileObjectBase write method
"""
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hellupline/flask-manager | flask_manager/utils.py | slugify | def slugify(value):
"""Simple Slugify."""
s1 = first_cap_re.sub(r'\1_\2', value)
s2 = all_cap_re.sub(r'\1_\2', s1)
return s2.lower().replace(' _', '_').replace(' ', '_') | python | def slugify(value):
"""Simple Slugify."""
s1 = first_cap_re.sub(r'\1_\2', value)
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dssg/argcmdr | src/argcmdr.py | entrypoint | def entrypoint(cls):
"""Mark the decorated command as the intended entrypoint of the
command module.
"""
if not isinstance(cls, type) or not issubclass(cls, Command):
raise TypeError(f"inappropriate entrypoint instance of type {cls.__class__}")
cls._argcmdr_entrypoint_ = True
return cls | python | def entrypoint(cls):
"""Mark the decorated command as the intended entrypoint of the
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"""
if not isinstance(cls, type) or not issubclass(cls, Command):
raise TypeError(f"inappropriate entrypoint instance of type {cls.__class__}")
cls._argcmdr_entrypoint_ = True
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robinandeer/puzzle | puzzle/plugins/base.py | Plugin.individual_dict | def individual_dict(self, ind_ids):
"""Return a dict with ind_id as key and Individual as values."""
ind_dict = {ind.ind_id: ind for ind in self.individuals(ind_ids=ind_ids)}
return ind_dict | python | def individual_dict(self, ind_ids):
"""Return a dict with ind_id as key and Individual as values."""
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robinandeer/puzzle | tasks.py | clean | def clean():
"""clean - remove build artifacts."""
run('rm -rf build/')
run('rm -rf dist/')
run('rm -rf puzzle.egg-info')
run('find . -name __pycache__ -delete')
run('find . -name *.pyc -delete')
run('find . -name *.pyo -delete')
run('find . -name *~ -delete')
log.info('cleaned up') | python | def clean():
"""clean - remove build artifacts."""
run('rm -rf build/')
run('rm -rf dist/')
run('rm -rf puzzle.egg-info')
run('find . -name __pycache__ -delete')
run('find . -name *.pyc -delete')
run('find . -name *.pyo -delete')
run('find . -name *~ -delete')
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eleme/meepo | meepo/sub/zmq.py | zmq_sub | def zmq_sub(bind, tables, forwarder=False, green=False):
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:param bind: the zmq pub socket or zmq device socket.
:param tables: the events of tables to follow.
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:param... | python | def zmq_sub(bind, tables, forwarder=False, green=False):
"""0mq fanout sub.
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robinandeer/puzzle | puzzle/plugins/sql/mixins/case.py | CaseMixin.add_case | def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj.case_id,
name=case_obj.name,
... | python | def add_case(self, case_obj, vtype='snv', mode='vcf', ped_svg=None):
"""Load a case with individuals.
Args:
case_obj (puzzle.models.Case): initialized case model
"""
new_case = Case(case_id=case_obj.case_id,
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robinandeer/puzzle | puzzle/plugins/sql/mixins/case.py | CaseMixin.individuals | def individuals(self, ind_ids=None):
"""Fetch all individuals from the database."""
query = self.query(Individual)
if ind_ids:
query = query.filter(Individual.ind_id.in_(ind_ids))
return query | python | def individuals(self, ind_ids=None):
"""Fetch all individuals from the database."""
query = self.query(Individual)
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robinandeer/puzzle | puzzle/models/sql/models.py | Case.case_comments | def case_comments(self):
"""Return only comments made on the case."""
comments = (comment for comment in self.comments if
comment.variant_id is None)
return comments | python | def case_comments(self):
"""Return only comments made on the case."""
comments = (comment for comment in self.comments if
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return comments | [
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basecrm/basecrm-python | basecrm/http_client.py | HttpClient.put | def put(self, url, body=None, **kwargs):
"""
Send a PUT request.
:param str url: Sub URL for the request. You MUST not specify neither base url nor api version prefix.
:param dict body: (optional) Dictionary of body attributes that will be wrapped with envelope and json encoded.
... | python | def put(self, url, body=None, **kwargs):
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Send a PUT request.
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eleme/meepo | meepo/apps/replicator/queue.py | QueueReplicator.event | def event(self, *topics, **kwargs):
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callback func should receive two args: topic and pk, and then process
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Note: The callback func must return True/False. When passed a list of
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eleme/meepo | meepo/apps/replicator/queue.py | QueueReplicator.run | def run(self):
"""Run the replicator.
Main process receive messages and distribute them to worker queues.
"""
for worker_pool in self.workers.values():
worker_pool.start()
if isinstance(self.listen, list):
for i in self.listen:
self.socke... | python | def run(self):
"""Run the replicator.
Main process receive messages and distribute them to worker queues.
"""
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eleme/meepo | meepo/pub/sqlalchemy.py | sqlalchemy_pub._pk | def _pk(self, obj):
"""Get pk values from object
:param obj: sqlalchemy object
"""
pk_values = tuple(getattr(obj, c.name)
for c in obj.__mapper__.primary_key)
if len(pk_values) == 1:
return pk_values[0]
return pk_values | python | def _pk(self, obj):
"""Get pk values from object
:param obj: sqlalchemy object
"""
pk_values = tuple(getattr(obj, c.name)
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if len(pk_values) == 1:
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return pk_values | [
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eleme/meepo | meepo/pub/sqlalchemy.py | sqlalchemy_pub.session_update | def session_update(self, session, *_):
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# this may happen when there's nothing to commit
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"""Pub the events after the session committed.
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tswicegood/Dolt | dolt/helpers.py | add_basic_auth | def add_basic_auth(dolt, username, password):
"""
Send basic auth username and password.
Normally you can use httplib2.Http.add_credentials() to add username and password.
However this has two disadvantages.
1. Some poorly implemented APIs require basic auth but don't send a
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"""
Send basic auth username and password.
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robinandeer/puzzle | puzzle/plugins/gemini/mixins/variant_extras/genotypes.py | GenotypeExtras._add_genotypes | def _add_genotypes(self, variant_obj, gemini_variant, case_id,
individual_objs):
"""Add the genotypes for a variant for all individuals
Args:
variant_obj (puzzle.models.Variant)
gemini_variant (GeminiQueryRow): The gemini variant
... | python | def _add_genotypes(self, variant_obj, gemini_variant, case_id,
individual_objs):
"""Add the genotypes for a variant for all individuals
Args:
variant_obj (puzzle.models.Variant)
gemini_variant (GeminiQueryRow): The gemini variant
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## Arguments
# frames
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- if integer or integer-valued float (e.g. 1.0):
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"""
Check and process 'frames' argument
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robinandeer/puzzle | puzzle/cli/init.py | init | def init(ctx, reset, root, phenomizer):
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configs = {}
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robinandeer/puzzle | puzzle/utils/get_info.py | get_gene_symbols | def get_gene_symbols(chrom, start, stop):
"""Get the gene symbols that a interval overlaps"""
gene_symbols = query_gene_symbol(chrom, start, stop)
logger.debug("Found gene symbols: {0}".format(', '.join(gene_symbols)))
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"""Get the gene symbols that a interval overlaps"""
gene_symbols = query_gene_symbol(chrom, start, stop)
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ensembl_ids (Optional[list]): list of Ensembl gene ids
hgnc_symbols (Optional[list]): list of HGNC gene symbols
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robinandeer/puzzle | puzzle/utils/get_info.py | get_most_severe_consequence | def get_most_severe_consequence(transcripts):
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transcripts (list): A list of transcripts to evaluate
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robinandeer/puzzle | puzzle/utils/get_info.py | get_cytoband_coord | def get_cytoband_coord(chrom, pos):
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chrom(str): A chromosome
pos(int): The position
Returns:
cytoband
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chrom = chrom.strip('chr')
pos = int(pos)
result = None
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Args:
chrom(str): A chromosome
pos(int): The position
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jreese/dotlink | dotlink/dotlink.py | Dotlink.parse_mapping | def parse_mapping(self, map_path, source=None, dotfiles=None):
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include_re = r"""^\s*#include\s+(".+"|'.+')"""
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jreese/dotlink | dotlink/dotlink.py | Dotlink.run | def run(self):
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jreese/dotlink | dotlink/dotlink.py | Dotlink.load_dotfiles | def load_dotfiles(self):
"""Read in the dotfile mapping as a dictionary."""
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dotfiles_path = self.args.map
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dotfiles_path = self.source
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"""Read in the dotfile mapping as a dictionary."""
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jreese/dotlink | dotlink/dotlink.py | Dotlink.clone_repo | def clone_repo(self):
"""Clone a repository containing the dotfiles source."""
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tempdir_path = tempfile.mkdtemp()
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jreese/dotlink | dotlink/dotlink.py | Dotlink.cleanup_repo | def cleanup_repo(self):
"""Cleanup the temporary directory containing the dotfiles repo."""
if self.source and path.isdir(self.source):
self.log.debug('Cleaning up source repo from %s', self.source)
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"""Cleanup the temporary directory containing the dotfiles repo."""
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jreese/dotlink | dotlink/dotlink.py | Dotlink.deploy_dotfiles | def deploy_dotfiles(self, dotfiles):
"""Deploy dotfiles using the appropriate method."""
if self.args.server:
return self.deploy_remote(dotfiles)
else:
return self.deploy_local(dotfiles) | python | def deploy_dotfiles(self, dotfiles):
"""Deploy dotfiles using the appropriate method."""
if self.args.server:
return self.deploy_remote(dotfiles)
else:
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jreese/dotlink | dotlink/dotlink.py | Dotlink.deploy_remote | def deploy_remote(self, dotfiles):
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"""Deploy dotfiles to a remote server."""
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jreese/dotlink | dotlink/dotlink.py | Dotlink.deploy_local | def deploy_local(self, dotfiles, target_root=None):
"""Deploy dotfiles to a local path."""
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target_root = self.args.path
for source_path, target_path in dotfiles.items():
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"""Deploy dotfiles to a local path."""
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target_root = self.args.path
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inveniosoftware-contrib/json-merger | json_merger/utils.py | dedupe_list | def dedupe_list(l):
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result = []
for el in l:
if el not in... | python | def dedupe_list(l):
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ldomic/lintools | lintools/plots.py | Plots.plot_amino_diagrams | def plot_amino_diagrams(self):
"""
Plotting of amino diagrams - circles with residue name and id, colored according to the
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robinandeer/puzzle | puzzle/utils/ped.py | get_cases | def get_cases(variant_source, case_lines=None, case_type='ped',
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"""Create a cases and populate it with individuals
Args:
variant_source (str): Path to vcf files
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variant_source (str): Path to vcf files
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jalmeroth/pymusiccast | pymusiccast/zone.py | Zone.handle_message | def handle_message(self, message):
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jalmeroth/pymusiccast | pymusiccast/zone.py | Zone.update_status | def update_status(self, new_status=None):
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if self.status and new_status is None:
_LOGGER.debug("Zone: healthy.")
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jalmeroth/pymusiccast | pymusiccast/zone.py | Zone.set_power | def set_power(self, power):
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req_url = ENDPOINTS["setPower"].format(self.ip_address, self.zone_id)
params = {"power": "on" if power else "standby"}
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jalmeroth/pymusiccast | pymusiccast/zone.py | Zone.set_mute | def set_mute(self, mute):
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robinandeer/puzzle | puzzle/plugins/vcf/mixins/variant_extras/annotations.py | AnnotationExtras._add_compounds | def _add_compounds(self, variant_obj, info_dict):
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jwodder/javaproperties | javaproperties/xmlprops.py | load_xml | def load_xml(fp, object_pairs_hook=dict):
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jwodder/javaproperties | javaproperties/xmlprops.py | loads_xml | def loads_xml(s, object_pairs_hook=dict):
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:param props: A mapping or itera... | python | def dump_xml(props, fp, comment=None, encoding='UTF-8', sort_keys=False):
"""
Write a series ``props`` of key-value pairs to a binary filehandle ``fp``
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jwodder/javaproperties | javaproperties/xmlprops.py | dumps_xml | def dumps_xml(props, comment=None, sort_keys=False):
"""
Convert a series ``props`` of key-value pairs to a text string containing
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:param props: A mapping or iterable of ``(key, value)`` pairs t... | python | def dumps_xml(props, comment=None, sort_keys=False):
"""
Convert a series ``props`` of key-value pairs to a text string containing
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robinandeer/puzzle | puzzle/plugins/sql/store.py | Store.connect | def connect(self, db_uri, debug=False):
"""Configure connection to a SQL database.
Args:
db_uri (str): path/URI to the database to connect to
debug (Optional[bool]): whether to output logging information
"""
kwargs = {'echo': debug, 'convert_unicode': True}
... | python | def connect(self, db_uri, debug=False):
"""Configure connection to a SQL database.
Args:
db_uri (str): path/URI to the database to connect to
debug (Optional[bool]): whether to output logging information
"""
kwargs = {'echo': debug, 'convert_unicode': True}
... | [
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] | 9476f05b416d3a5135d25492cb31411fdf831c58 | https://github.com/robinandeer/puzzle/blob/9476f05b416d3a5135d25492cb31411fdf831c58/puzzle/plugins/sql/store.py#L62-L86 | train |
robinandeer/puzzle | puzzle/plugins/sql/store.py | Store.select_plugin | def select_plugin(self, case_obj):
"""Select and initialize the correct plugin for the case."""
if case_obj.variant_mode == 'vcf':
logger.debug("Using vcf plugin")
plugin = VcfPlugin(case_obj.variant_type)
elif case_obj.variant_mode == 'gemini':
logger.debug("... | python | def select_plugin(self, case_obj):
"""Select and initialize the correct plugin for the case."""
if case_obj.variant_mode == 'vcf':
logger.debug("Using vcf plugin")
plugin = VcfPlugin(case_obj.variant_type)
elif case_obj.variant_mode == 'gemini':
logger.debug("... | [
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robinandeer/puzzle | puzzle/server/blueprints/public/views.py | index | def index():
"""Show the landing page."""
gene_lists = app.db.gene_lists() if app.config['STORE_ENABLED'] else []
queries = app.db.gemini_queries() if app.config['STORE_ENABLED'] else []
case_groups = {}
for case in app.db.cases():
key = (case.variant_source, case.variant_type, case.variant... | python | def index():
"""Show the landing page."""
gene_lists = app.db.gene_lists() if app.config['STORE_ENABLED'] else []
queries = app.db.gemini_queries() if app.config['STORE_ENABLED'] else []
case_groups = {}
for case in app.db.cases():
key = (case.variant_source, case.variant_type, case.variant... | [
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robinandeer/puzzle | puzzle/server/blueprints/public/views.py | case | def case(case_id):
"""Show the overview for a case."""
case_obj = app.db.case(case_id)
return render_template('case.html', case=case_obj, case_id=case_id) | python | def case(case_id):
"""Show the overview for a case."""
case_obj = app.db.case(case_id)
return render_template('case.html', case=case_obj, case_id=case_id) | [
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robinandeer/puzzle | puzzle/server/blueprints/public/views.py | delete_phenotype | def delete_phenotype(phenotype_id):
"""Delete phenotype from an individual."""
ind_id = request.form['ind_id']
ind_obj = app.db.individual(ind_id)
try:
app.db.remove_phenotype(ind_obj, phenotype_id)
except RuntimeError as error:
return abort(500, error.message)
return redirect(re... | python | def delete_phenotype(phenotype_id):
"""Delete phenotype from an individual."""
ind_id = request.form['ind_id']
ind_obj = app.db.individual(ind_id)
try:
app.db.remove_phenotype(ind_obj, phenotype_id)
except RuntimeError as error:
return abort(500, error.message)
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