Skip to content

V0.68 Temporarily skip DrugBank data processing #48

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
piehld merged 1 commit into from
May 15, 2026
Merged

V0.68 Temporarily skip DrugBank data processing #48

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions HISTORY.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,3 +62,4 @@
2-Mar-2026 - V0.66 Add refstats subpackage for ligand and RSCC reference generation;
Update test pipelines to python 3.13
7-May-2026 - V0.67 Configure logging at start of CLI executable scripts
11-May-2026 - V0.68 Temporarily skip DrugBank data processing until dataset becomes available
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ build-backend = "hatchling.build"
[project]
name = "rcsb.workflow"
description = "RCSB Python data processing and ETL/ELT workflow entry points"
version = "0.67"
version = "0.68"
readme = "README.md"
authors = [
{ name="John Westbrook", email="john.westbrook@rcsb.org" }
Expand Down
15 changes: 10 additions & 5 deletions rcsb/workflow/targets/ProteinTargetSequenceExecutionWorkflow.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,8 @@ def exportFasta(self, reloadPharos=True, fromDbPharos=True):
addTaxonomy=True,
reloadPharos=reloadPharos,
fromDbPharos=fromDbPharos,
resourceNameList=["sabdab", "card", "drugbank", "chembl", "pharos"],
# resourceNameList=["sabdab", "card", "drugbank", "chembl", "pharos"],
resourceNameList=["sabdab", "card", "chembl", "pharos"],
backupPharos=True,
remotePrefix=self.__stashRemotePrefix
)
Expand All @@ -199,7 +200,8 @@ def createSearchDatabases(self):
ok = False
try:
ptsW = ProteinTargetSequenceWorkflow(self.__cfgOb, self.__cachePath)
ok = ptsW.createSearchDatabases(resourceNameList=["sabdab", "card", "drugbank", "chembl", "pharos", "pdbprent"], addTaxonomy=True, timeOutSeconds=3600, verbose=False)
# ok = ptsW.createSearchDatabases(resourceNameList=["sabdab", "card", "drugbank", "chembl", "pharos", "pdbprent"], addTaxonomy=True, timeOutSeconds=3600, verbose=False)
ok = ptsW.createSearchDatabases(resourceNameList=["sabdab", "card", "chembl", "pharos", "pdbprent"], addTaxonomy=True, timeOutSeconds=3600, verbose=False)
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok
Expand Down Expand Up @@ -234,7 +236,8 @@ def searchDatabases(self):
ptsW = ProteinTargetSequenceWorkflow(self.__cfgOb, self.__cachePath)
ok1 = ptsW.search(
referenceResourceName="pdbprent",
resourceNameList=["sabdab", "drugbank", "chembl", "pharos"],
# resourceNameList=["sabdab", "drugbank", "chembl", "pharos"],
resourceNameList=["sabdab", "chembl", "pharos"],
identityCutoff=0.95,
sensitivity=4.5,
timeOutSeconds=1000,
Expand Down Expand Up @@ -288,7 +291,8 @@ def buildCofactorData(self):
ok = False
try:
ptsW = ProteinTargetSequenceWorkflow(self.__cfgOb, self.__cachePath)
ok = ptsW.buildCofactorData(referenceResourceName="pdbprent", resourceNameList=["chembl", "pharos", "drugbank"], backup=True, remotePrefix=self.__stashRemotePrefix)
# ok = ptsW.buildCofactorData(referenceResourceName="pdbprent", resourceNameList=["chembl", "pharos", "drugbank"], backup=True, remotePrefix=self.__stashRemotePrefix)
ok = ptsW.buildCofactorData(referenceResourceName="pdbprent", resourceNameList=["chembl", "pharos"], backup=True, remotePrefix=self.__stashRemotePrefix)
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok
Expand All @@ -299,7 +303,8 @@ def loadTargetCofactorData(self):
ok = False
try:
ptsW = ProteinTargetSequenceWorkflow(self.__cfgOb, self.__cachePath)
ok = ptsW.loadTargetCofactorData(resourceNameList=["chembl", "pharos", "drugbank"])
# ok = ptsW.loadTargetCofactorData(resourceNameList=["chembl", "pharos", "drugbank"])
ok = ptsW.loadTargetCofactorData(resourceNameList=["chembl", "pharos"])
except Exception as e:
logger.exception("Failing with %s", str(e))
return ok
Expand Down
3 changes: 2 additions & 1 deletion rcsb/workflow/targets/ProteinTargetSequenceWorkflow.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,8 @@ def __init__(self, cfgOb, cachePath, **kwargs):
self.__configName = cfgOb.getDefaultSectionName()
self.__cachePath = os.path.abspath(cachePath)
self.__umP = None
self.__defaultResourceNameList = ["sabdab", "card", "drugbank", "chembl", "pdbprent"]
# self.__defaultResourceNameList = ["sabdab", "card", "drugbank", "chembl", "pdbprent"]
self.__defaultResourceNameList = ["sabdab", "card", "chembl", "pdbprent"]

def testCache(self):
return True
Expand Down
Loading