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"""Basic functional stuff, I guess.
"""
import logging
import os
LOG = logging.getLogger(__name__)
def getIpdModelFilename(ipdModel, majorityChem, paramsPath):
"""
ipdModel: str
majorityChem: str
"""
# In order of precedence they are:
# 1. Explicit path passed to --ipdModel
# 2. In-order through each directory listed in --paramsPath
if ipdModel:
LOG.info("Using passed-in kinetics model: {!r}".format(ipdModel))
return ipdModel
if majorityChem == 'unknown':
msg = "Chemistry cannot be identified---cannot perform kinetic analysis"
LOG.error(msg)
raise Exception(msg)
# Route any pre-Kiwi / pre-SSB Sequel chemistries to Seabiscuit training
if majorityChem.startswith("S/P1") or majorityChem.startswith("S/P2"):
majorityChem = "SP2-C2"
# Route any post-SSB Sequel chemistries to Kiwi training (for now)
elif majorityChem.startswith("S/"):
majorityChem = "SP3-C3"
# '/' is not a valid character in a file, unescaped--remove it
majorityChem = majorityChem.replace("/", "")
# go through each paramsPath in-order, checking if the model exists there
# or no
for paramPath in paramsPath:
ipdModel = os.path.join(paramPath, majorityChem + ".npz.gz")
if os.path.isfile(ipdModel):
LOG.info(
"Using chemistry-matched kinetics model: {!r}".format(ipdModel))
return ipdModel
msg = "No kinetics model available for this chemistry ({!r}) on paramsPath {!r}".format(
ipdModel, paramsPath)
LOG.error(msg)
raise Exception(msg)
def getResourcePathSpec(default_dir):
"""Create list of [${SMRT_CHEMISTRY_BUNDLE_DIR}/kineticsTools, {default_dir}].
Return colon-separated string.
"""
pths = []
smrtChemBundlePath = os.environ.get("SMRT_CHEMISTRY_BUNDLE_DIR", None)
if smrtChemBundlePath:
LOG.info("found SMRT_CHEMISTRY_BUNDLE_DIR, prepending to default paramsPath")
pths.append(os.path.join(smrtChemBundlePath, "kineticsTools"))
pths.append(default_dir)
return ':'.join(pths)
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