def RunJob(infile, outpath, tmpdir, email, jobid, g_params): #{{{
all_begin_time = time.time()
rootname = os.path.basename(os.path.splitext(infile)[0])
starttagfile = "%s/runjob.start" % (outpath)
runjob_errfile = "%s/runjob.err" % (outpath)
runjob_logfile = "%s/runjob.log" % (outpath)
app_logfile = "%s/app.log" % (outpath)
finishtagfile = "%s/runjob.finish" % (outpath)
failedtagfile = "%s/runjob.failed" % (outpath)
query_parafile = "%s/query.para.txt" % (outpath)
query_para = ""
content = myfunc.ReadFile(query_parafile)
if content != "":
query_para = json.loads(content)
rmsg = ""
resultpathname = jobid
outpath_result = "%s/%s" % (outpath, resultpathname)
tmp_outpath_result = "%s/%s" % (tmpdir, resultpathname)
tarball = "%s.tar.gz" % (resultpathname)
zipfile = "%s.zip" % (resultpathname)
tarball_fullpath = "%s.tar.gz" % (outpath_result)
zipfile_fullpath = "%s.zip" % (outpath_result)
resultfile_text = "%s/%s" % (outpath_result, "query.result.txt")
mapfile = "%s/seqid_index_map.txt" % (outpath_result)
finished_seq_file = "%s/finished_seqs.txt" % (outpath_result)
for folder in [outpath_result, tmp_outpath_result]:
try:
os.makedirs(folder)
except OSError:
msg = "Failed to create folder %s" % (folder)
myfunc.WriteFile(msg + "\n", gen_errfile, "a")
return 1
try:
open(finished_seq_file, 'w').close()
except:
pass
#first getting result from caches
# ==================================
maplist = []
maplist_simple = []
toRunDict = {}
hdl = myfunc.ReadFastaByBlock(infile, method_seqid=0, method_seq=0)
if hdl.failure:
isOK = False
else:
webcom.WriteDateTimeTagFile(starttagfile, runjob_logfile,
runjob_errfile)
recordList = hdl.readseq()
cnt = 0
origpath = os.getcwd()
while recordList != None:
for rd in recordList:
isSkip = False
# temp outpath for the sequence is always seq_0, and I feed
# only one seq a time to the workflow
tmp_outpath_this_seq = "%s/%s" % (tmp_outpath_result,
"seq_%d" % 0)
outpath_this_seq = "%s/%s" % (outpath_result, "seq_%d" % cnt)
subfoldername_this_seq = "seq_%d" % (cnt)
if os.path.exists(tmp_outpath_this_seq):
try:
shutil.rmtree(tmp_outpath_this_seq)
except OSError:
pass
maplist.append(
"%s\t%d\t%s\t%s" %
("seq_%d" % cnt, len(rd.seq), rd.description, rd.seq))
maplist_simple.append(
"%s\t%d\t%s" %
("seq_%d" % cnt, len(rd.seq), rd.description))
if not g_params['isForceRun']:
md5_key = hashlib.md5(
(rd.seq +
str(query_para)).encode('utf-8')).hexdigest()
subfoldername = md5_key[:2]
cachedir = "%s/%s/%s" % (path_cache, subfoldername,
md5_key)
zipfile_cache = cachedir + ".zip"
if os.path.exists(cachedir) or os.path.exists(
zipfile_cache):
if os.path.exists(cachedir):
try:
shutil.copytree(cachedir, outpath_this_seq)
except Exception as e:
msg = "Failed to copytree %s -> %s" % (
cachedir, outpath_this_seq)
date_str = time.strftime(FORMAT_DATETIME)
myfunc.WriteFile(
"[%s] %s with errmsg=%s\n" %
(date_str, msg, str(e)), runjob_errfile,
"a")
elif os.path.exists(zipfile_cache):
cmd = [
"unzip", zipfile_cache, "-d", outpath_result
]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
shutil.move("%s/%s" % (outpath_result, md5_key),
outpath_this_seq)
if os.path.exists(outpath_this_seq):
info_finish = webcom.GetInfoFinish_PRODRES(
outpath_this_seq,
cnt,
len(rd.seq),
rd.description,
source_result="cached",
runtime=0.0)
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
isSkip = True
if not isSkip:
# first try to delete the outfolder if exists
if os.path.exists(outpath_this_seq):
try:
shutil.rmtree(outpath_this_seq)
except OSError:
pass
origIndex = cnt
numTM = 0
toRunDict[origIndex] = [rd.seq, numTM, rd.description
] #init value for numTM is 0
cnt += 1
recordList = hdl.readseq()
hdl.close()
myfunc.WriteFile("\n".join(maplist_simple) + "\n", mapfile)
if not g_params['isOnlyGetCache']:
torun_all_seqfile = "%s/%s" % (tmp_outpath_result, "query.torun.fa")
dumplist = []
for key in toRunDict:
top = toRunDict[key][0]
dumplist.append(">%s\n%s" % (str(key), top))
myfunc.WriteFile("\n".join(dumplist) + "\n", torun_all_seqfile, "w")
del dumplist
sortedlist = sorted(list(toRunDict.items()),
key=lambda x: x[1][1],
reverse=True)
#format of sortedlist [(origIndex: [seq, numTM, description]), ...]
# submit sequences one by one to the workflow according to orders in
# sortedlist
for item in sortedlist:
origIndex = item[0]
seq = item[1][0]
description = item[1][2]
subfoldername_this_seq = "seq_%d" % (origIndex)
outpath_this_seq = "%s/%s" % (outpath_result,
subfoldername_this_seq)
tmp_outpath_this_seq = "%s/%s" % (tmp_outpath_result, "seq_%d" %
(0))
if os.path.exists(tmp_outpath_this_seq):
try:
shutil.rmtree(tmp_outpath_this_seq)
except OSError:
pass
seqfile_this_seq = "%s/%s" % (tmp_outpath_result, "query_%d.fa" %
(origIndex))
seqcontent = ">query_%d\n%s\n" % (origIndex, seq)
myfunc.WriteFile(seqcontent, seqfile_this_seq, "w")
if not os.path.exists(seqfile_this_seq):
msg = "failed to generate seq index %d" % (origIndex)
date_str = time.strftime(g_params['FORMAT_DATETIME'])
myfunc.WriteFile("[%s] %s\n" % (date_str, msg), runjob_errfile,
"a", True)
continue
cmd = [
"python", runscript, "--input", seqfile_this_seq, "--output",
tmp_outpath_this_seq, "--pfam-dir", path_pfamdatabase,
"--pfamscan-script", path_pfamscanscript,
"--fallback-db-fasta", blastdb
]
if 'second_method' in query_para and query_para[
'second_method'] != "":
cmd += ['--second-search', query_para['second_method']]
if 'pfamscan_evalue' in query_para and query_para[
'pfamscan_evalue'] != "":
cmd += ['--pfamscan_e-val', query_para['pfamscan_evalue']]
elif 'pfamscan_bitscore' in query_para and query_para[
'pfamscan_bitscore'] != "":
cmd += ['--pfamscan_bitscore', query_para['pfamscan_bitscore']]
if 'pfamscan_clanoverlap' in query_para:
if query_para['pfamscan_clanoverlap'] == False:
cmd += ['--pfamscan_clan-overlap', 'no']
else:
cmd += ['--pfamscan_clan-overlap', 'yes']
if 'jackhmmer_iteration' in query_para and query_para[
'jackhmmer_iteration'] != "":
cmd += [
'--jackhmmer_max_iter', query_para['jackhmmer_iteration']
]
if 'jackhmmer_threshold_type' in query_para and query_para[
'jackhmmer_threshold_type'] != "":
cmd += [
'--jackhmmer-threshold-type',
query_para['jackhmmer_threshold_type']
]
if 'jackhmmer_evalue' in query_para and query_para[
'jackhmmer_evalue'] != "":
cmd += ['--jackhmmer_e-val', query_para['jackhmmer_evalue']]
elif 'jackhmmer_bitscore' in query_para and query_para[
'jackhmmer_bitscore'] != "":
cmd += [
'--jackhmmer_bit-score', query_para['jackhmmer_bitscore']
]
if 'psiblast_iteration' in query_para and query_para[
'psiblast_iteration'] != "":
cmd += ['--psiblast_iter', query_para['psiblast_iteration']]
if 'psiblast_outfmt' in query_para and query_para[
'psiblast_outfmt'] != "":
cmd += ['--psiblast_outfmt', query_para['psiblast_outfmt']]
(t_success,
runtime_in_sec) = webcom.RunCmd(cmd, runjob_logfile,
runjob_errfile, True)
aaseqfile = "%s/seq.fa" % (tmp_outpath_this_seq + os.sep +
"query_0")
if not os.path.exists(aaseqfile):
seqcontent = ">%s\n%s\n" % (description, seq)
myfunc.WriteFile(seqcontent, aaseqfile, "w")
if os.path.exists(tmp_outpath_this_seq):
cmd = [
"mv", "-f", tmp_outpath_this_seq + os.sep + "query_0",
outpath_this_seq
]
isCmdSuccess = False
(isCmdSuccess,
t_runtime) = webcom.RunCmd(cmd, runjob_logfile,
runjob_errfile, True)
if not 'isKeepTempFile' in query_para or query_para[
'isKeepTempFile'] == False:
try:
temp_result_folder = "%s/temp" % (outpath_this_seq)
shutil.rmtree(temp_result_folder)
except:
msg = "Failed to delete the folder %s" % (
temp_result_folder)
date_str = time.strftime(g_params['FORMAT_DATETIME'])
myfunc.WriteFile("[%s] %s\n" % (date_str, msg),
runjob_errfile, "a", True)
flist = [
"%s/outputs/%s" % (outpath_this_seq, "Alignment.txt"),
"%s/outputs/%s" % (outpath_this_seq, "tableOut.txt"),
"%s/outputs/%s" % (outpath_this_seq, "fullOut.txt")
]
for f in flist:
if os.path.exists(f):
try:
os.remove(f)
except:
msg = "Failed to delete the file %s" % (f)
date_str = time.strftime(
g_params['FORMAT_DATETIME'])
myfunc.WriteFile("[%s] %s\n" % (date_str, msg),
runjob_errfile, "a", True)
if isCmdSuccess:
timefile = "%s/time.txt" % (outpath_this_seq)
runtime = webcom.ReadRuntimeFromFile(timefile,
default_runtime=0.0)
info_finish = webcom.GetInfoFinish_PRODRES(
outpath_this_seq,
origIndex,
len(seq),
description,
source_result="newrun",
runtime=runtime)
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
# now write the text output for this seq
info_this_seq = "%s\t%d\t%s\t%s" % (
"seq_%d" % origIndex, len(seq), description, seq)
resultfile_text_this_seq = "%s/%s" % (outpath_this_seq,
"query.result.txt")
#webcom.WriteSubconsTextResultFile(resultfile_text_this_seq,
# outpath_result, [info_this_seq], runtime_in_sec, g_params['base_www_url'])
# create or update the md5 cache
# create cache only on the front-end
if webcom.IsFrontEndNode(g_params['base_www_url']):
md5_key = hashlib.md5(
(seq +
str(query_para)).encode('utf-8')).hexdigest()
subfoldername = md5_key[:2]
md5_subfolder = "%s/%s" % (path_cache, subfoldername)
cachedir = "%s/%s/%s" % (path_cache, subfoldername,
md5_key)
# copy the zipped folder to the cache path
origpath = os.getcwd()
os.chdir(outpath_result)
shutil.copytree("seq_%d" % (origIndex), md5_key)
cmd = ["zip", "-rq", "%s.zip" % (md5_key), md5_key]
webcom.RunCmd(cmd, runjob_logfile, runjob_logfile)
if not os.path.exists(md5_subfolder):
os.makedirs(md5_subfolder)
shutil.move("%s.zip" % (md5_key),
"%s.zip" % (cachedir))
shutil.rmtree(
md5_key
) # delete the temp folder named as md5 hash
os.chdir(origpath)
# Add the finished date to the database
date_str = time.strftime(FORMAT_DATETIME)
webcom.InsertFinishDateToDB(date_str, md5_key, seq,
finished_date_db)
all_end_time = time.time()
all_runtime_in_sec = all_end_time - all_begin_time
if not g_params['isOnlyGetCache'] or len(toRunDict) == 0:
# now write the text output to a single file
statfile = "%s/%s" % (outpath_result, "stat.txt")
#webcom.WriteSubconsTextResultFile(resultfile_text, outpath_result, maplist,
# all_runtime_in_sec, g_params['base_www_url'], statfile=statfile)
# now making zip instead (for windows users)
# note that zip rq will zip the real data for symbolic links
os.chdir(outpath)
# cmd = ["tar", "-czf", tarball, resultpathname]
cmd = ["zip", "-rq", zipfile, resultpathname]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
# write finish tag file
if os.path.exists(finished_seq_file):
webcom.WriteDateTimeTagFile(finishtagfile, runjob_logfile,
runjob_errfile)
isSuccess = False
if (os.path.exists(finishtagfile)
and os.path.exists(zipfile_fullpath)):
isSuccess = True
else:
isSuccess = False
webcom.WriteDateTimeTagFile(failedtagfile, runjob_logfile,
runjob_errfile)
# send the result to email
# do not sendmail at the cloud VM
if webcom.IsFrontEndNode(g_params['base_www_url']
) and myfunc.IsValidEmailAddress(email):
if isSuccess:
finish_status = "success"
else:
finish_status = "failed"
webcom.SendEmail_on_finish(
jobid,
g_params['base_www_url'],
finish_status,
name_server="PRODRES",
from_email="*****@*****.**",
to_email=email,
contact_email=contact_email,
logfile=runjob_logfile,
errfile=runjob_errfile)
if os.path.exists(runjob_errfile) and os.path.getsize(runjob_errfile) > 1:
return 1
else:
try:
shutil.rmtree(tmpdir)
msg = "rmtree(%s)" % (tmpdir)
webcom.loginfo("rmtree(%s)" % (tmpdir), runjob_logfile)
except Exception as e:
msg = "Failed to rmtree(%s)" % (tmpdir)
webcom.loginfo(
"Failed to rmtree(%s) with error message: %s" %
(tmpdir, str(e)), runjob_errfile)
return 0
def RunJob(infile, outpath, tmpdir, email, jobid, g_params): #{{{
all_begin_time = time.time()
rootname = os.path.basename(os.path.splitext(infile)[0])
starttagfile = "%s/runjob.start" % (outpath)
runjob_errfile = "%s/runjob.err" % (outpath)
runjob_logfile = "%s/runjob.log" % (outpath)
app_logfile = "%s/app.log" % (outpath)
finishtagfile = "%s/runjob.finish" % (outpath)
rmsg = ""
resultpathname = jobid
outpath_result = "%s/%s" % (outpath, resultpathname)
tmp_outpath_result = "%s/%s" % (tmpdir, resultpathname)
tarball = "%s.tar.gz" % (resultpathname)
zipfile = "%s.zip" % (resultpathname)
tarball_fullpath = "%s.tar.gz" % (outpath_result)
zipfile_fullpath = "%s.zip" % (outpath_result)
resultfile_text = "%s/%s" % (outpath_result, "query.top")
mapfile = "%s/seqid_index_map.txt" % (outpath_result)
finished_seq_file = "%s/finished_seqs.txt" % (outpath_result)
finished_idx_file = "%s/finished_seqindex.txt" % (outpath)
for folder in [outpath_result, tmp_outpath_result]:
try:
os.makedirs(folder)
except OSError:
msg = "Failed to create folder %s" % (folder)
myfunc.WriteFile(msg + "\n", gen_errfile, "a")
return 1
try:
open(finished_seq_file, 'w').close()
except:
pass
#first getting result from caches
# ==================================
maplist = []
maplist_simple = []
toRunDict = {}
hdl = myfunc.ReadFastaByBlock(infile, method_seqid=0, method_seq=0)
if hdl.failure:
isOK = False
else:
webcom.WriteDateTimeTagFile(starttagfile, runjob_logfile,
runjob_errfile)
recordList = hdl.readseq()
cnt = 0
origpath = os.getcwd()
while recordList != None:
for rd in recordList:
isSkip = False
# temp outpath for the sequence is always seq_0, and I feed
# only one seq a time to the workflow
tmp_outpath_this_seq = "%s/%s" % (tmp_outpath_result,
"seq_%d" % 0)
outpath_this_seq = "%s/%s" % (outpath_result, "seq_%d" % cnt)
subfoldername_this_seq = "seq_%d" % (cnt)
if os.path.exists(tmp_outpath_this_seq):
try:
shutil.rmtree(tmp_outpath_this_seq)
except OSError:
pass
maplist.append(
"%s\t%d\t%s\t%s" %
("seq_%d" % cnt, len(rd.seq), rd.description, rd.seq))
maplist_simple.append(
"%s\t%d\t%s" %
("seq_%d" % cnt, len(rd.seq), rd.description))
if not g_params['isForceRun']:
md5_key = hashlib.md5(rd.seq.encode('utf-8')).hexdigest()
subfoldername = md5_key[:2]
cachedir = "%s/%s/%s" % (path_cache, subfoldername,
md5_key)
zipfile_cache = cachedir + ".zip"
if os.path.exists(cachedir) or os.path.exists(
zipfile_cache):
if os.path.exists(cachedir):
try:
shutil.copytree(cachedir, outpath_this_seq)
except Exception as e:
msg = "Failed to copytree %s -> %s" % (
cachedir, outpath_this_seq)
date_str = time.strftime(FORMAT_DATETIME)
myfunc.WriteFile(
"[%s] %s with errmsg=%s\n" %
(date_str, msg, str(e)), runjob_errfile,
"a")
elif os.path.exists(zipfile_cache):
cmd = [
"unzip", zipfile_cache, "-d", outpath_result
]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
shutil.move("%s/%s" % (outpath_result, md5_key),
outpath_this_seq)
checkfile = "%s/query.predict.png" % (outpath_this_seq)
fafile_this_seq = '%s/seq.fa' % (outpath_this_seq)
if os.path.exists(outpath_this_seq) and os.path.exists(
checkfile):
info_finish = webcom.GetInfoFinish_Boctopus2(
outpath_this_seq,
cnt,
len(rd.seq),
rd.description,
source_result="cached",
runtime=0.0)
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
myfunc.WriteFile("%d\n" % (cnt),
finished_idx_file,
"a",
isFlush=True)
isSkip = True
if not isSkip:
# first try to delete the outfolder if exists
if os.path.exists(outpath_this_seq):
try:
shutil.rmtree(outpath_this_seq)
except OSError:
pass
origIndex = cnt
numTM = 0
toRunDict[origIndex] = [rd.seq, numTM, rd.description
] #init value for numTM is 0
cnt += 1
recordList = hdl.readseq()
hdl.close()
myfunc.WriteFile("\n".join(maplist_simple) + "\n", mapfile)
if not g_params['isOnlyGetCache']:
torun_all_seqfile = "%s/%s" % (tmp_outpath_result, "query.torun.fa")
dumplist = []
for key in toRunDict:
top = toRunDict[key][0]
dumplist.append(">%s\n%s" % (str(key), top))
myfunc.WriteFile("\n".join(dumplist) + "\n", torun_all_seqfile, "w")
del dumplist
sortedlist = sorted(list(toRunDict.items()),
key=lambda x: x[1][1],
reverse=True)
#format of sortedlist [(origIndex: [seq, numTM, description]), ...]
# submit sequences one by one to the workflow according to orders in
# sortedlist
for item in sortedlist:
origIndex = item[0]
seq = item[1][0]
description = item[1][2]
subfoldername_this_seq = "seq_%d" % (origIndex)
outpath_this_seq = "%s/%s" % (outpath_result,
subfoldername_this_seq)
tmp_outpath_this_seq = "%s/%s" % (tmp_outpath_result, "seq_%d" %
(0))
if os.path.exists(tmp_outpath_this_seq):
try:
shutil.rmtree(tmp_outpath_this_seq)
except OSError:
pass
seqfile_this_seq = "%s/%s" % (tmp_outpath_result, "query_%d.fa" %
(origIndex))
seqcontent = ">query_%d\n%s\n" % (origIndex, seq)
myfunc.WriteFile(seqcontent, seqfile_this_seq, "w")
if not os.path.exists(seqfile_this_seq):
msg = "Failed to generate seq file for index %d" % (origIndex)
date_str = time.strftime(FORMAT_DATETIME)
myfunc.WriteFile("[%s] %s\n" % (date_str, msg), runjob_errfile,
"a", True)
continue
cmd = [runscript, seqfile_this_seq, tmp_outpath_result]
(t_success,
runtime_in_sec) = webcom.RunCmd(cmd, runjob_logfile,
runjob_errfile, True)
aaseqfile = "%s/seq.fa" % (tmp_outpath_this_seq)
if not os.path.exists(aaseqfile):
seqcontent = ">%s\n%s\n" % (description, seq)
myfunc.WriteFile(seqcontent, aaseqfile, "w")
if os.path.exists(tmp_outpath_this_seq):
cmd = ["mv", "-f", tmp_outpath_this_seq, outpath_this_seq]
(isCmdSuccess,
t_runtime) = webcom.RunCmd(cmd, runjob_logfile,
runjob_errfile)
timefile = "%s/time.txt" % (tmp_outpath_result)
targetfile = "%s/time.txt" % (outpath_this_seq)
if os.path.exists(timefile) and os.path.exists(
outpath_this_seq):
try:
shutil.move(timefile, targetfile)
except:
msg = "Failed to move %s/time.txt" % (
tmp_outpath_result)
date_str = time.strftime(FORMAT_DATETIME)
myfunc.WriteFile("[%s] %s\n" % (date_str, msg),
runjob_errfile, "a", True)
pass
if isCmdSuccess:
runtime = runtime_in_sec #in seconds
info_finish = webcom.GetInfoFinish_Boctopus2(
outpath_this_seq,
origIndex,
len(seq),
description,
source_result="newrun",
runtime=runtime)
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
# now write the text output for this seq
info_this_seq = "%s\t%d\t%s\t%s" % (
"seq_%d" % origIndex, len(seq), description, seq)
resultfile_text_this_seq = "%s/%s" % (outpath_this_seq,
"query.result.txt")
webcom.WriteBoctopusTextResultFile(
resultfile_text_this_seq, outpath_result,
[info_this_seq], runtime_in_sec,
g_params['base_www_url'])
# create or update the md5 cache
# create cache only on the front-end
figurefile = "%s/plot/query_0.png" % (outpath_this_seq)
# Note: do not create cache is figure file does not exist
if webcom.IsFrontEndNode(g_params['base_www_url']
) and os.path.exists(figurefile):
md5_key = hashlib.md5(seq.encode('utf-8')).hexdigest()
subfoldername = md5_key[:2]
md5_subfolder = "%s/%s" % (path_cache, subfoldername)
cachedir = "%s/%s/%s" % (path_cache, subfoldername,
md5_key)
if os.path.exists(cachedir):
try:
shutil.rmtree(cachedir)
except:
msg = "Failed to shutil.rmtree(%s)" % (
cachedir)
date_str = time.strftime(FORMAT_DATETIME)
myfunc.WriteFile("[%s] %s\n" % (date_str, msg),
runjob_errfile, "a", True)
pass
if not os.path.exists(md5_subfolder):
try:
os.makedirs(md5_subfolder)
except:
pass
if os.path.exists(md5_subfolder
) and not os.path.exists(cachedir):
cmd = ["mv", "-f", outpath_this_seq, cachedir]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
if not os.path.exists(
outpath_this_seq) and os.path.exists(cachedir):
rela_path = os.path.relpath(
cachedir, outpath_result) #relative path
try:
os.chdir(outpath_result)
os.symlink(rela_path, subfoldername_this_seq)
except:
pass
all_end_time = time.time()
all_runtime_in_sec = all_end_time - all_begin_time
if not g_params['isOnlyGetCache'] or len(toRunDict) == 0:
# now write the text output to a single file
statfile = "%s/%s" % (outpath_result, "stat.txt")
webcom.WriteBoctopusTextResultFile(resultfile_text,
outpath_result,
maplist,
all_runtime_in_sec,
g_params['base_www_url'],
statfile=statfile)
# now making zip instead (for windows users)
# note that zip rq will zip the real data for symbolic links
os.chdir(outpath)
cmd = ["zip", "-rq", zipfile, resultpathname]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
# write finish tag file
if os.path.exists(finished_seq_file):
webcom.WriteDateTimeTagFile(finishtagfile, runjob_logfile,
runjob_errfile)
isSuccess = False
if (os.path.exists(finishtagfile)
and os.path.exists(zipfile_fullpath)):
isSuccess = True
else:
isSuccess = False
failedtagfile = "%s/runjob.failed" % (outpath)
webcom.WriteDateTimeTagFile(failedtagfile, runjob_logfile,
runjob_errfile)
# send the result to email
# do not sendmail at the cloud VM
if webcom.IsFrontEndNode(g_params['base_www_url']
) and myfunc.IsValidEmailAddress(email):
if isSuccess:
finish_status = "success"
else:
finish_status = "failed"
webcom.SendEmail_on_finish(
jobid,
g_params['base_www_url'],
finish_status,
name_server="BOCTOPUS2",
from_email="[email protected])",
to_email=email,
contact_email=contact_email,
logfile=runjob_logfile,
errfile=runjob_errfile)
if os.path.exists(runjob_errfile) and os.path.getsize(runjob_errfile) > 1:
return 1
else:
date_str = time.strftime(FORMAT_DATETIME)
try:
shutil.rmtree(tmpdir)
msg = "rmtree(%s)" % (tmpdir)
myfunc.WriteFile("[%s] %s\n" % (date_str, msg), runjob_logfile,
"a", True)
except Exception as e:
msg = "Failed to rmtree(%s)" % (tmpdir)
myfunc.WriteFile("[%s] %s\n" % (date_str, msg), runjob_errfile,
"a", True)
pass
return 0
def RunJob_msa(infile, outpath, tmpdir, email, jobid, g_params): #{{{
all_begin_time = time.time()
rootname = os.path.basename(os.path.splitext(infile)[0])
runjob_errfile = "%s/runjob.err" % (outpath)
runjob_logfile = "%s/runjob.log" % (outpath)
starttagfile = "%s/runjob.start" % (outpath)
finishtagfile = "%s/runjob.finish" % (outpath)
failtagfile = "%s/runjob.failed" % (outpath)
rmsg = ""
qdinit_start_tagfile = "%s/runjob.qdinit.start" % (outpath)
# if the daemon starts to process the job before the run_job.py running
# in the local queue, skip it
if os.path.exists(qdinit_start_tagfile):
return 0
resultpathname = jobid
outpath_result = "%s/%s" % (outpath, resultpathname)
tmp_outpath_result = "%s/%s" % (tmpdir, resultpathname)
tarball = "%s.tar.gz" % (resultpathname)
zipfile = "%s.zip" % (resultpathname)
tarball_fullpath = "%s.tar.gz" % (outpath_result)
zipfile_fullpath = "%s.zip" % (outpath_result)
resultfile_text = "%s/%s" % (outpath_result, "query.result.txt")
mapfile = "%s/seqid_index_map.txt" % (outpath_result)
finished_seq_file = "%s/finished_seqs.txt" % (outpath_result)
finished_idx_file = "%s/finished_seqindex.txt" % (outpath)
for folder in [outpath_result, tmp_outpath_result]:
try:
os.makedirs(folder)
except OSError:
msg = "Failed to create folder %s" % (folder)
myfunc.WriteFile(msg + "\n", gen_errfile, "a")
return 1
try:
open(finished_seq_file, 'w').close()
except:
pass
#first getting result from caches
# ==================================
maplist = []
toRunDict = {}
hdl = myfunc.ReadFastaByBlock(infile, method_seqid=0, method_seq=0)
if hdl.failure:
isOK = False
else:
webcom.WriteDateTimeTagFile(starttagfile, runjob_logfile,
runjob_errfile)
cnt = 0
origpath = os.getcwd()
con = sqlite3.connect(db_cache_SCAMPI2MSA)
with con:
cur = con.cursor()
cur.execute("""
CREATE TABLE IF NOT EXISTS %s
(
md5 VARCHAR(100),
seq VARCHAR(30000),
top VARCHAR(30000),
PRIMARY KEY (md5)
)""" % (dbmsa_tablename))
recordList = hdl.readseq()
while recordList != None:
for rd in recordList:
isSkip = False
if not g_params['isForceRun']:
md5_key = hashlib.md5(
rd.seq.encode('utf-8')).hexdigest()
cmd = "SELECT md5, seq, top FROM %s WHERE md5 = \"%s\"" % (
dbmsa_tablename, md5_key)
cur.execute(cmd)
rows = cur.fetchall()
for row in rows:
top = row[2]
numTM = myfunc.CountTM(top)
# info_finish has 8 items
info_finish = [
"seq_%d" % cnt,
str(len(rd.seq)),
str(numTM), "cached",
str(0.0), rd.description, rd.seq, top
]
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
myfunc.WriteFile("%d\n" % (cnt),
finished_idx_file,
"a",
isFlush=True)
isSkip = True
if not isSkip:
# first try to delete the outfolder if exists
origIndex = cnt
numTM = 0
toRunDict[origIndex] = [rd.seq, numTM, rd.description
] #init value for numTM is 0
cnt += 1
recordList = hdl.readseq()
hdl.close()
if not g_params['isOnlyGetCache']:
torun_all_seqfile = "%s/%s" % (tmp_outpath_result, "query.torun.fa")
dumplist = []
for key in toRunDict:
top = toRunDict[key][0]
dumplist.append(">%s\n%s" % (str(key), top))
myfunc.WriteFile("\n".join(dumplist) + "\n", torun_all_seqfile, "w")
del dumplist
sortedlist = sorted(list(toRunDict.items()),
key=lambda x: x[1][1],
reverse=True)
#format of sortedlist [(origIndex: [seq, numTM, description]), ...]
# submit sequences one by one to the workflow according to orders in
# sortedlist
for item in sortedlist:
origIndex = item[0]
seq = item[1][0]
description = item[1][2]
outpath_this_seq = "%s/%s" % (outpath_result, "seq_%d" % origIndex)
tmp_outpath_this_seq = "%s/%s" % (tmp_outpath_result, "seq_%d" %
(0))
if os.path.exists(tmp_outpath_this_seq):
try:
shutil.rmtree(tmp_outpath_this_seq)
except OSError:
pass
try:
os.makedirs(tmp_outpath_this_seq)
except OSError:
g_params['runjob_err'].append(
"Failed to create the tmp_outpath_this_seq %s" %
(tmp_outpath_this_seq))
continue
seqfile_this_seq = "%s/%s" % (tmp_outpath_result, "query_%d.fa" %
(origIndex))
seqcontent = ">%d\n%s\n" % (origIndex, seq)
myfunc.WriteFile(seqcontent, seqfile_this_seq, "w")
if not os.path.exists(seqfile_this_seq):
g_params['runjob_err'].append(
"failed to generate seq index %d" % (origIndex))
continue
if not os.path.exists("%s/seq.fa" % (tmp_outpath_this_seq)):
try:
shutil.copyfile(seqfile_this_seq,
"%s/seq.fa" % (tmp_outpath_this_seq))
except OSError:
pass
numCPU = 4
outtopfile = "%s/query.top" % (tmp_outpath_this_seq)
cmd = [
runscript_msa, seqfile_this_seq, outtopfile, blastdir, blastdb
]
(t_success, runtime_in_sec) = webcom.RunCmd(cmd,
runjob_logfile,
runjob_errfile,
verbose=True)
if os.path.exists(tmp_outpath_this_seq):
cmd = ["mv", "-f", tmp_outpath_this_seq, outpath_this_seq]
(isCmdSuccess, t_runtime) = webcom.RunCmd(cmd,
runjob_logfile,
runjob_errfile,
verbose=True)
if isCmdSuccess:
runtime = runtime_in_sec #in seconds
predfile = "%s/query.top" % (outpath_this_seq)
(seqid, seqanno, top) = myfunc.ReadSingleFasta(predfile)
numTM = myfunc.CountTM(top)
# info_finish has 8 items
info_finish = [
"seq_%d" % origIndex,
str(len(seq)),
str(numTM), "newrun",
str(runtime), description, seq, top
]
myfunc.WriteFile("\t".join(info_finish) + "\n",
finished_seq_file,
"a",
isFlush=True)
all_end_time = time.time()
all_runtime_in_sec = all_end_time - all_begin_time
if len(g_params['runjob_log']) > 0:
rt_msg = myfunc.WriteFile("\n".join(g_params['runjob_log']) + "\n",
runjob_logfile, "a")
if rt_msg:
g_params['runjob_err'].append(rt_msg)
if not g_params['isOnlyGetCache'] or len(toRunDict) == 0:
if os.path.exists(finished_seq_file):
webcom.WriteDateTimeTagFile(finishtagfile, runjob_logfile,
runjob_errfile)
# now write the text output to a single file
dumped_resultfile = "%s/%s" % (outpath_result, "query.top")
statfile = "%s/%s" % (outpath_result, "stat.txt")
webcom.WriteSCAMPI2MSATextResultFile(dumped_resultfile,
outpath_result,
maplist,
all_runtime_in_sec,
g_params['base_www_url'],
statfile=statfile)
# now making zip instead (for windows users)
pwd = os.getcwd()
os.chdir(outpath)
cmd = ["zip", "-rq", zipfile, resultpathname]
webcom.RunCmd(cmd, runjob_logfile, runjob_errfile)
os.chdir(pwd)
isSuccess = False
if (os.path.exists(finishtagfile)
and os.path.exists(zipfile_fullpath)):
isSuccess = True
# delete the tmpdir if succeeded
shutil.rmtree(tmpdir) #DEBUG, keep tmpdir
else:
isSuccess = False
webcom.WriteDateTimeTagFile(failtagfile, runjob_logfile,
runjob_errfile)
finish_status = "" #["success", "failed", "partly_failed"]
if isSuccess:
finish_status = "success"
else:
finish_status = "failed"
# send the result to email
# do not sendmail at the cloud VM
if webcom.IsFrontEndNode(g_params['base_www_url']
) and myfunc.IsValidEmailAddress(email):
webcom.SendEmail_on_finish(jobid,
g_params['base_www_url'],
finish_status,
name_server="SCAMPI2-msa",
from_email="*****@*****.**",
to_email=email,
contact_email=contact_email,
logfile=runjob_logfile,
errfile=runjob_errfile)
return 0