def testSingleFile(filename):
"""
Extra Test Routine going over some entries in the NMR Restraints Grid
"""
strf = File()
strf.filename = filename
nTdebug("reading file ", strf.filename)
strf.read()
strf.filename = strf.filename + "_new.str"
nTdebug("writing file ", strf.filename)
strf.write()
def testSingleFile(filename):
"""
Extra Test Routine going over some entries in the NMR Restraints Grid
"""
strf = File()
strf.filename = filename
nTdebug("reading file ", strf.filename)
strf.read()
strf.filename = strf.filename + "_new.str"
nTdebug("writing file ", strf.filename)
strf.write()
def testEntry(entry):
"""
Extra Test Routine going over some entries in the NMR Restraints Grid
"""
# Put a check in for internet availability.
nTmessage("Testing Entry")
strf = File()
# Freely available on the web so not included in package.
stage = "2-parsed"
# stage = "3-converted-DOCR"
urlLocation = ("http://www.bmrb.wisc.edu/NRG/MRGridServlet?" +
"block_text_type=%s&file_detail=%s&pdb_id=%s" +
"&program=STAR&request_type=archive&subtype=full&type=entry"
) % (stage, stage, entry)
fnamezip = entry + ".zip"
# print "DEBUG: downloading url:", urlLocation
# TODO: wrap this in a try so the test is less invulnerable to network outages.
try:
urllib.urlretrieve(urlLocation, fnamezip)
except:
# not a real error since there might not be a network connection.
nTwarning("Failed to get; " + urlLocation)
return
# print "DEBUG: opening local zip file:", fnamezip
zfobj = zipfile.ZipFile(fnamezip)
fname = None
for name in zfobj.namelist():
if name.endswith('.str'):
fname = name
orgWattosWrittenFile = entry + "_org.str"
pystarlibWrittenFile = entry + "_pystar.str"
wattosWrittenFile = entry + "_wattos.str"
diffOrgPystarFile = entry + "_diff_org_pystar.str"
diffPystarWattosFile = entry + "_diff_pystar_wattos.str"
diffOrgWattosWattosFile = entry + "_diff_org_wattos_wattos.str"
outfile = open(orgWattosWrittenFile, 'w')
outfile.write(zfobj.read(fname))
outfile.close()
zfobj.close()
strf.filename = orgWattosWrittenFile
strf.read()
strf.filename = pystarlibWrittenFile
strf.write()
nTmessage(
"Most likely the below diff will fail because it depends on diff being installed"
)
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (
orgWattosWrittenFile, pystarlibWrittenFile, diffOrgPystarFile)
os.system(cmd)
if not os.path.exists(diffOrgPystarFile):
nTwarning("failed to diff files: " + orgWattosWrittenFile + ", " +
pystarlibWrittenFile)
nTdebug(
"Most likely the below check will fail because it depends on Wattos being installed"
)
nTdebug("rewrite to Java formating for comparison")
cmd = "%s Wattos.Star.STARFilter %s %s ." % (
JVM_CMD_STD, pystarlibWrittenFile, wattosWrittenFile)
logFileName = "wattos_STARFilter.log"
wattosProgram = ExecuteProgram(cmd, redirectOutputToFile=logFileName)
wattosExitCode = wattosProgram()
if wattosExitCode:
nTwarning("failed to execute Wattos")
return
if not os.path.exists(wattosWrittenFile):
nTerror("failed to rewrite file: " + pystarlibWrittenFile)
return
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (
pystarlibWrittenFile, wattosWrittenFile, diffPystarWattosFile)
os.system(cmd)
if not os.path.exists(diffPystarWattosFile):
nTwarning("failed to diff file: " + pystarlibWrittenFile + ", " +
wattosWrittenFile)
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (
orgWattosWrittenFile, wattosWrittenFile, diffOrgWattosWattosFile)
os.system(cmd)
if not os.path.exists(diffOrgWattosWattosFile):
nTwarning("failed to diff file: ",
orgWattosWrittenFile + ", " + wattosWrittenFile)
if 1:
try:
os.unlink(entry + ".zip")
os.unlink(orgWattosWrittenFile)
os.unlink(pystarlibWrittenFile)
except:
pass
def testEntry(entry):
"""
Extra Test Routine going over some entries in the NMR Restraints Grid
"""
# Put a check in for internet availability.
nTmessage("Testing Entry")
strf = File()
# Freely available on the web so not included in package.
stage = "2-parsed"
# stage = "3-converted-DOCR"
urlLocation = ("http://www.bmrb.wisc.edu/NRG/MRGridServlet?" +
"block_text_type=%s&file_detail=%s&pdb_id=%s" +
"&program=STAR&request_type=archive&subtype=full&type=entry") % (stage, stage, entry)
fnamezip = entry + ".zip"
# print "DEBUG: downloading url:", urlLocation
# TODO: wrap this in a try so the test is less invulnerable to network outages.
try:
urllib.urlretrieve(urlLocation, fnamezip)
except:
# not a real error since there might not be a network connection.
nTwarning("Failed to get; " + urlLocation)
return
# print "DEBUG: opening local zip file:", fnamezip
zfobj = zipfile.ZipFile(fnamezip)
fname = None
for name in zfobj.namelist():
if name.endswith('.str'):
fname = name
orgWattosWrittenFile = entry + "_org.str"
pystarlibWrittenFile = entry + "_pystar.str"
wattosWrittenFile = entry + "_wattos.str"
diffOrgPystarFile = entry + "_diff_org_pystar.str"
diffPystarWattosFile = entry + "_diff_pystar_wattos.str"
diffOrgWattosWattosFile = entry + "_diff_org_wattos_wattos.str"
outfile = open(orgWattosWrittenFile, 'w')
outfile.write(zfobj.read(fname))
outfile.close()
zfobj.close()
strf.filename = orgWattosWrittenFile
strf.read()
strf.filename = pystarlibWrittenFile
strf.write()
nTmessage("Most likely the below diff will fail because it depends on diff being installed")
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (orgWattosWrittenFile, pystarlibWrittenFile, diffOrgPystarFile)
os.system(cmd)
if not os.path.exists(diffOrgPystarFile):
nTwarning("failed to diff files: " + orgWattosWrittenFile + ", " + pystarlibWrittenFile)
nTdebug("Most likely the below check will fail because it depends on Wattos being installed")
nTdebug("rewrite to Java formating for comparison")
cmd = "%s Wattos.Star.STARFilter %s %s ." % (JVM_CMD_STD, pystarlibWrittenFile, wattosWrittenFile)
logFileName = "wattos_STARFilter.log"
wattosProgram = ExecuteProgram(cmd, redirectOutputToFile = logFileName)
wattosExitCode = wattosProgram()
if wattosExitCode:
nTwarning("failed to execute Wattos")
return
if not os.path.exists(wattosWrittenFile):
nTerror("failed to rewrite file: " + pystarlibWrittenFile)
return
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (pystarlibWrittenFile, wattosWrittenFile, diffPystarWattosFile)
os.system(cmd)
if not os.path.exists(diffPystarWattosFile):
nTwarning("failed to diff file: " + pystarlibWrittenFile + ", " + wattosWrittenFile)
cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % (orgWattosWrittenFile, wattosWrittenFile, diffOrgWattosWattosFile)
os.system(cmd)
if not os.path.exists(diffOrgWattosWattosFile):
nTwarning("failed to diff file: ", orgWattosWrittenFile + ", " + wattosWrittenFile)
if 1:
try:
os.unlink(entry + ".zip")
os.unlink(orgWattosWrittenFile)
os.unlink(pystarlibWrittenFile)
except:
pass
