-
Notifications
You must be signed in to change notification settings - Fork 0
/
querystatus.cgi
625 lines (564 loc) · 27.2 KB
/
querystatus.cgi
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
#!C:\Python27\python.exe
"""
CGI Module for checking on the status of an OPAL job
"""
__date__ = "4 January 2010"
__author__ = "Wes Goodman, Samir Unni, Yong Huang"
import sys
import cgi
import cgitb
import os,shutil,glob,string,time,urllib
from src.server import *
from src.aconf import *
from src.utilities import getTrackingScriptString, getEventTrackingString
cgitb.enable()
form = cgi.FieldStorage()
def printheader(pagetitle,refresh=None,jobid=None):
str = ""
str+= "<html>\n"
str+= "<HEAD>\n"
if refresh:
str+= "\t<META HTTP-EQUIV=\"Refresh\" CONTENT=\"%s\">\n" % refresh
str+= "\t<TITLE>%s</TITLE>\n" % pagetitle
str+= "\t<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % STYLESHEET
str+= getTrackingScriptString(jobid)
str+= "</HEAD>\n"
return str
#def getloads():
# """
# get the system load information for output and logging
#
# returns
# loads: a three entry list containing the 1, 5, and
# 15 minute loads. if the load file is not found,
# return none.
# """
# if loadpath == "": return none
# try:
# file = open(loadpath, 'ru')
# except ioerror:
# return none
#
# line = file.readline()
# words = string.split(line)
# loads = words[:3]
#
# return loads
#def cleantmpdir():
# """
# clean up the temp directory for cgi. if the size of the directory
# is greater than limit, delete the older half of the files. since
# the files are stored by system time of creation, this is an
# easier task.
# """
# newdir = []
# size = 0.0
# count = 0
# path = INSTALLDIR + tmpdir
#
# dir = os.listdir(path)
# for filename in dir:
# size = size + os.path.getsize("%s%s" % (path, filename))
# period = string.find(filename,".")
# id = filename[:period]
# if id not in newdir:
# newdir.append(id)
# count += 1
#
# newdir.sort()
# size = size / (1024.0 * 1024.0)
#
# newcount = 0
# if size >= limit:
# for filename in newdir:
# if newcount > count/2.0: break
# try:
# os.remove("%s%s.pqr" % (path, filename))
# except oserror: pass
# try:
# os.remove("%s%s.in" % (path, filename))
# except oserror: pass
# try:
# os.remove("%s%s.html" % (path, filename))
# except oserror: pass
# newcount += 1
#
#def getquote(path):
# """
# get a quote to display for the refresh page.
# uses fortune to generate a quote.
#
# parameters:
# path: the path to the fortune script (str)
# returns:
# quote: the quote to display (str)
# """
# fortune = os.popen(path)
# quote = fortune.read()
# quote = string.replace(quote, "\n", "<br>")
# quote = string.replace(quote, "\t", " "*5)
# quote = "%s<p>" % quote
# return quote
#
#def printprogress(name, refreshname, reftime, starttime):
# """
# print the progress of the server
#
# parameters
# name: the id of the html page to write to (string)
# refreshname: the name of the html page to refresh to (string)
# reftime: the length of time to set the refresh wait to (int)
# starttime: the time as returned by time.time() that the run started (float)
# """
# elapsedtime = time.time() - starttime + refreshtime/2.0 # add in time offset
# filename = "%s%s%s/%s-tmp.html" % (INSTALLDIR, tmpdir, jobid, name)
# file = open(filename,"w")
# file.write("<html>\n")
# file.write("<head>\n")
# file.write("<title>pdb2pqr progress</title>\n")
# file.write("<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % stylesheet)
# file.write("<meta http-equiv=\"refresh\" content=\"%s; url=%s\">\n" % \
# (reftime, refreshname))
# file.write("</head>\n")
# file.write("<body>\n")
# file.write("<h2>pdb2pqr progress</h2><p>\n")
# file.write("the pdb2pqr server is generating your results - this page will automatically \n")
# file.write("refresh every %s seconds.<p>\n" % refreshtime)
# file.write("thank you for your patience!<p>\n")
# file.write("server progress:<p>\n")
# file.write("<blockquote>\n")
# file.write("<font size=2>elapsed time:</font> <code>%.2f seconds</code><br>\n" % elapsedtime)
# file.write("</blockquote>\n")
# file.write("server information:<p>\n")
# file.write("<blockquote>\n")
# loads = getloads()
# if loads != none:
# file.write("<font size=2>server load:</font> <code>%s (1min) %s (5min) %s (15min)</code><br>\n" % (loads[0], loads[1], loads[2]))
#
# file.write("<font size=2>server time:</font> <code>%s</code><br>\n" % (time.asctime(time.localtime())))
# file.write("</blockquote>\n")
# file.write("<script type=\"text/javascript\">")
# file.write("var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");")
# file.write("document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));")
# file.write("</script>")
# file.write("<script type=\"text/javascript\">")
# file.write("try {")
# file.write("var pageTracker = _gat._getTracker(\"UA-11026338-3\");")
# file.write("pageTracker._trackPageview();")
# file.write("} catch(err) {}</script>")
# file.write("</body></html>")
# file.close()
#
#def createresults(header, input, name, time, missedligands=[]):
# """
# create the results web page for cgi-based runs
#
# parameters
# header: the header of the pqr file (string)
# input: a flag whether an input file has been created (int)
# tmpdir: the resulting file directory (string)
# name: the result file root name, based on local time (string)
# time: the time taken to run the script (float)
# missedligands: a list of ligand names whose parameters could
# not be assigned. optional. (list)
# """
# newheader = string.replace(header, "\n", "<br>")
# newheader = string.replace(newheader," "," ")
#
# filename = "%s%s%s/%s.html" % (INSTALLDIR, tmpdir, jobid, name)
# file = open(filename, "w")
#
# file.write("<html>\n")
# file.write("<head>\n")
# file.write("<title>pdb2pqr results</title>\n")
# file.write("<link rel=\"stylesheet\" href=\"%s\" type=\"text/css\">\n" % stylesheet)
# file.write("</head>\n")
#
# file.write("<body>\n")
# file.write("<h2>pdb2pqr results</h2>\n")
# file.write("<p>\n")
# file.write("here are the results from pdb2pqr. the files will be available on the ")
# file.write("server for a short period of time if you need to re-access the results.<p>\n")
#
# file.write("<a href=\"%s%s%s.pqr\">%s.pqr</a><br>\n" % (website, tmpdir, name, name))
# if input:
# file.write("<a href=\"%s%s%s.in\">%s.in</a><br>\n" % (website, tmpdir, name, name))
# pkaname = "%s%s%s/%s.propka" % (INSTALLDIR, tmpdir, jobid, name)
# if os.path.isfile(pkaname):
# file.write("<a href=\"%s%s%s.propka\">%s.propka</a><br>\n" % (website, tmpdir, name, name))
# typename = "%s%s%s/%s-typemap.html" % (INSTALLDIR, tmpdir, jobid, name)
# if os.path.isfile(typename):
# file.write("<a href=\"%s%s%s-typemap.html\">%s-typemap.html</a><br>\n" % (website, tmpdir, name, name))
# file.write("<p>the header for your pqr file, including any warnings generated, is:<p>\n")
# file.write("<blockquote><code>\n")
# file.write("%s<p>\n" % newheader)
# file.write("</code></blockquote>\n")
# if missedligands != []:
# file.write("the forcefield that you have selected does not have ")
# file.write("parameters for the following ligands in your pdb file. please visit ")
# file.write("<a href=\"http://davapc1.bioch.dundee.ac.uk/programs/prodrg/\">prodrg</a> ")
# file.write("to convert these ligands into mol2 format. this ligand can the be ")
# file.write("parameterized in your pdb2pqr calculation using the peoe_pb methodology via ")
# file.write("the 'assign charges to the ligand specified in a mol2 file' checkbox:<p>\n")
# file.write("<blockquote><code>\n")
# for item in missedligands:
# file.write("%s<br>\n" % item)
# file.write("<p></code></blockquote>\n")
# file.write("if you would like to run pdb2pqr again, please click <a href=\"%s%s\">\n" % (website, webname))
# file.write("here</a>.<p>\n")
# file.write("if you would like to run apbs with these results, please click <a href=\"%s../apbs/index.py?pdb2pqr-id=%s\">here</a>.<p>\n" % (website[:-1], name))
# file.write("<p>thank you for using the pdb2pqr server!<p>\n")
# file.write("<font size=\"-1\"><p>total time on server: %.2f seconds</font><p>\n" % time)
# file.write("<font size=\"-1\"><center><i>last updated %s</i></center></font>\n" % __date__)
# file.write("<script type=\"text/javascript\">")
# file.write("var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");")
# file.write("document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));")
# file.write("</script>")
# file.write("<script type=\"text/javascript\">")
# file.write("try {")
# file.write("var pageTracker = _gat._getTracker(\"UA-11026338-3\");")
# file.write("pageTracker._trackPageview();")
# file.write("} catch(err) {}</script>")
# file.write("</body>\n")
# file.write("</html>\n")
def checkprogress(jobid=None,appServicePort=None,calctype=None):
"""
Finds out if the job has been completed
"""
if have_opal:
# construct soap request
try:
status=appServicePort.queryStatus(queryStatusRequest(jobid))
except Exception, e:
return ["error"]
if status._code == 4:
return ["error"]
if status._code == 8:
return ["complete",status]
else:
return ["running",status]
else:
progress = []
file = open('%s%s%s/%s_status' % (INSTALLDIR,TMPDIR,jobid, form["calctype"].value))
for line in file.readlines():
progress.append(string.strip(line))
file.close()
return progress
def mainCGI():
"""
Main method for determining the query page output
"""
logopts = {}
print "Content-type: text/html\n\n"
calctype = form["calctype"].value
# prints version error, if it exists
if form["jobid"].value == 'False':
print printheader("%s Job Status Page" % calctype.upper())
progress = "version_mismatch"
runtime = 0
elif form["jobid"].value == 'notenoughmem':
print printheader("%s Job Status Page" % calctype.upper())
progress = "not_enough_memory"
runtime = 0
else:
progress = None
#Check for error html
errorpath = '%s%s%s.html' % (INSTALLDIR, TMPDIR, form["jobid"].value)
if os.path.isfile(errorpath):
string = ""
string+= "<html>\n"
string+= "\t<head>\n"
string+= "\t\t<meta http-equiv=\"Refresh\" content=\"0; url=%s%s%s.html\">\n" % (WEBSITE, TMPDIR, form["jobid"].value)
string+= "\t</head>\n"
string+= "</html>\n"
print string
return
# prepares for Opal query, if necessary
if have_opal:
if calctype=="pdb2pqr":
opal_url = PDB2PQR_OPAL_URL
elif calctype=="apbs":
opal_url = APBS_OPAL_URL
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(opal_url)
else:
appServicePort = None
# if PDB2PQR, determines if link to APBS calculation should be shown
if calctype=="pdb2pqr":
#if(form["apbsinput"].value=="True"): # change to use a file
# apbs_input = True
#else:
# apbs_input = False
apbsInputFile = open('%s%s%s/apbs_input' % (INSTALLDIR, TMPDIR, form["jobid"].value))
apbs_input = apbsInputFile.read()
apbsInputFile.close()
if apbs_input=="True":
apbs_input = True
else:
apbs_input = False
typemapInputFile = open('%s%s%s/typemap' % (INSTALLDIR, TMPDIR, form["jobid"].value))
typemap = typemapInputFile.read()
typemapInputFile.close()
if typemap=="True":
typemap = True
else:
typemap = False
if have_opal and progress == None:
if form["calctype"].value=="pdb2pqr":
pdb2pqrJobIDFile = open('%s%s%s/pdb2pqr_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = pdb2pqrJobIDFile.read()
pdb2pqrJobIDFile.close()
elif form["calctype"].value=="apbs":
apbsJobIDFile = open('%s%s%s/apbs_opal_job_id' % (INSTALLDIR, TMPDIR, form["jobid"].value))
jobid = apbsJobIDFile.read()
apbsJobIDFile.close()
else:
jobid = form["jobid"].value
if progress == None:
cp = checkprogress(jobid,appServicePort,calctype) # finds out status of job
progress = cp[0]
#initialize with bogus value just in case
starttime = time.time()
if progress == "running" or progress == "complete":
timefile = open('%s%s%s/%s_start_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value))
starttime = float(timefile.read())
timefile.close()
if progress == "running" or (have_opal and progress not in ("version_mismatch",
"not_enough_memory",
"error",
"complete")):
runtime = time.time()-starttime
elif progress == "complete":
endTimeFileString = '%s%s%s/%s_end_time' % (INSTALLDIR, TMPDIR, form["jobid"].value, form["calctype"].value)
if have_opal and not os.path.isfile(endTimeFileString):
runtime = time.time()-starttime
with open(endTimeFileString, 'w') as endTimeFile:
endTimeFile.write(str(time.time()))
else:
with open(endTimeFileString, 'r') as endTimeFile:
runtime = float(endTimeFile.read())-starttime
else:
runtime = -1
if progress == "running":
#if have_opal:
# resultsurl = cp[1]._baseURL
#else:
if calctype=="pdb2pqr":
resultsurl = '%squerystatus.cgi?jobid=%s&apbsinput=%s&calctype=pdb2pqr' % (WEBSITE, form["jobid"].value, apbs_input)
else:
resultsurl = '%squerystatus.cgi?jobid=%s&calctype=apbs' % (WEBSITE, form["jobid"].value)
if progress == "complete":
print printheader("%s Job Status Page" % calctype.upper(), jobid=form["jobid"].value)
elif progress == "error":
print printheader("%s Job Status Page - Error" % calctype.upper(),0, jobid=form["jobid"].value)
elif progress == "running": # job is not complete, refresh in 30 seconds
print printheader("%s Job Status Page" % calctype.upper(), refresh, jobid=form["jobid"].value)
print "<BODY>\n<P>"
print "<h3>Status"
print "</h3>"
print "Message: %s<br />" % progress
print "Run time: %s seconds<br />" % int(runtime)
print "Current time: %s<br />" % time.asctime()
print "</P>\n<HR>\n<P>"
if progress == "complete":
if calctype=="pdb2pqr":
nexturl = 'apbs_cgi.cgi?jobid=%s' % form["jobid"].value
else:
nexturl = 'visualize.cgi?jobid=%s' % form["jobid"].value
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
filelist = resp._outputFile
print "Here are the results:<ul>"
print "<li>Input files<ul>"
if calctype=="pdb2pqr":
# this code should be cleaned up once local PDB2PQR runs output the PDB file with the .pdb extension
if have_opal:
for i in range(0,len(filelist)):
if len(filelist[i]._name) == 4:
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/%s.pdb>%s.pdb</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid)
elif calctype=="apbs":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name == "apbsinput.in" or filelist[i]._name[-4:] == ".pqr":
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
else:
print "<li><a href=%s%s%s/apbsinput.in>apbsinput.in</a></li>" % (WEBSITE, TMPDIR, jobid)
print "<li><a href=%s%s%s/%s.pqr>%s.pqr</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, jobid)
print "</ul></li>"
print "<li>Output files<ul>"
queryString = [str(os.environ["REMOTE_ADDR"])]
# Getting PDB2PQR run log info
if os.path.isfile('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid)):
pdb2pqrLogFile=open('%s%s%s/pdb2pqr_log' % (INSTALLDIR, TMPDIR, jobid), 'r')
logstr=pdb2pqrLogFile.read().split('\n')
templogopts = eval(logstr[0])
pdb2pqrLogFile.close()
queryString.insert(0, templogopts.get('pdb',''))
if calctype=="pdb2pqr":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name.endswith((".propka", "-typemap.html", ".pqr", ".in")):
# if filelist[i]._name[-4:]==".pqr":
# # Getting pqr file length for PDB2PQR Opal run
# f=urllib.urlopen(filelist[i]._url)
# #pqrOpalFileLength = len(f.readlines())
# f.close()
print "<li><a href=%s>%s</a></li>" % (filelist[i]._url, filelist[i]._name)
#Get the first line of the summary file.
if filelist[i]._name.endswith(".summary"):
f=urllib.urlopen(filelist[i]._url)
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
f.close()
# logRun(logopts, runtime, pqrOpalFileLength, logff, REMOTE_ADDR)
else:
#Get the first line of the summary file.
summaryFile = '%s%s%s/%s%s' % (INSTALLDIR, TMPDIR, jobid, jobid, ".summary")
if os.path.isfile(summaryFile):
with open(summaryFile) as f:
summaryLine = f.readline().strip()
#logopts["pdb"]=logopts.get("pdb", "") + "|" + summaryLine
queryString.append(summaryLine)
outputfilelist = glob.glob('%s%s%s/*.propka' % (INSTALLDIR, TMPDIR, jobid))
for i in range(0,len(outputfilelist)):
outputfilelist[i] = os.path.basename(outputfilelist[i])
for extension in ["-typemap.html", ".pqr", ".in"]:
if extension != ".in" or apbs_input != False:
if extension == "-typemap.html" and typemap == False:
continue
outputfilelist.append('%s%s' % (jobid, extension))
for outputfile in outputfilelist:
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, outputfile, outputfile)
logopts['queryPDB2PQR'] = '|'.join(queryString)
#for extension in ["-typemap.html", ".pqr", ".in"]:
# print "<li><a href=%s%s%s/%s%s>%s%s</a></li>" % (WEBSITE, TMPDIR, jobid, jobid, extension, jobid, extension)
elif calctype=="apbs":
if have_opal:
for i in range(0,len(filelist)):
if filelist[i]._name[-3:]==".dx":
# compressing APBS OpenDX output files
currentpath = os.getcwd()
zipjobid = filelist[i]._name.split("-")[0]
urllib.urlretrieve(filelist[i]._url, '%s%s%s/%s' % (INSTALLDIR, TMPDIR, zipjobid, filelist[i]._name))
os.chdir('%s%s%s' % (INSTALLDIR, TMPDIR, zipjobid))
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (filelist[i]._name)
os.system(syscommand)
syscommand = 'gzip -9 ' + filelist[i]._name
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (filelist[i]._name)
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = filelist[i]._name + '.gz'
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, zipjobid, outputfilezip, outputfilezip)
else:
outputfilelist = glob.glob('%s%s%s/%s-*.dx' % (INSTALLDIR, TMPDIR, jobid, jobid))
for outputfile in outputfilelist:
# compressing APBS OpenDX output files
currentpath = os.getcwd()
workingpath = os.path.dirname(outputfile)
os.chdir(workingpath)
# making both the dx file and the compressed file (.gz) available in the directory
syscommand = 'cp %s dxbkupfile' % (os.path.basename(outputfile))
os.system(syscommand)
syscommand = 'gzip -9 ' + os.path.basename(outputfile)
os.system(syscommand)
syscommand = 'mv dxbkupfile %s' % (os.path.basename(outputfile))
os.system(syscommand)
os.chdir(currentpath)
outputfilezip = outputfile+".gz"
print "<li><a href=%s%s%s/%s>%s</a></li>" % (WEBSITE, TMPDIR, jobid, os.path.basename(outputfilezip), os.path.basename(outputfilezip))
logopts['queryAPBS'] = '|'.join(queryString)
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
#if have_opal:
# resp = appServicePort.getOutputs(getOutputsRequest(jobid))
# for opalfile in resp._outputFile:
# if opalfile._name[-8:]!="-input.p":
# print "<li><a href=%s>%s</a></li>" % (opalfile._url, opalfile._name)
# print "<li><a href=%s>Standard output</a></li>" % (resp._stdOut)
# print "<li><a href=%s>Standard error</a></li>" % (resp._stdErr)
#else:
# for line in cp[1:]:
# line = os.path.basename(line)
# if line[-8:]!="-input.p":
# if line[-11:]=="_stdout.txt":
# printname = "Standard output"
# elif line[-11:]=="_stderr.txt":
# printname = "Standard error"
# else:
# printname = line
# print "<li><a href=%s>%s</a></li>" % (WEBSITE+TMPDIR+jobid+"/"+line,printname)
if calctype=="pdb2pqr" and apbs_input and HAVE_APBS:
print "</ul></p><hr><p><b><a href=%s>Click here</a> to run APBS with your results.</b></p>" % nexturl
elif calctype=="apbs":
print "</ul></p><hr><p><b><a href=%s>Click here</a> to visualize your results.</b></p>" % nexturl
elif progress == "error":
print "There was an error with your query request. This page will not refresh."
print "</ul></li>"
print "<li>Runtime and debugging information<ul>"
if have_opal:
resp = appServicePort.getOutputs(getOutputsRequest(jobid))
stdouturl = resp._stdOut
stderrurl = resp._stdErr
else:
stdouturl = "%s%s%s/%s_stdout.txt" % (WEBSITE, TMPDIR, jobid, calctype)
stderrurl = "%s%s%s/%s_stderr.txt" % (WEBSITE, TMPDIR, jobid, calctype)
print "<li><a href=%s>Program output (stdout)</a></li>" % stdouturl
print "<li><a href=%s>Program errors and warnings (stderr)</a></li>" % stderrurl
print "</ul></li></ul>"
elif progress == "running":
print "Page will refresh in %d seconds<br />" % refresh
print "<HR>"
print "<small>Your results will appear at <a href=%s>this page</a>. If you want, you can bookmark it and come back later (note: results are only stored for approximately 12-24 hours).</small>" % resultsurl
elif progress == "version_mismatch":
print "The versions of APBS on the local server and on the Opal server do not match, so the calculation could not be completed"
print "</P>"
print "<script type=\"text/javascript\">"
for key in logopts:
print getEventTrackingString('queryData', key, logopts[key]),
#print "_gaq.push(['_trackPageview', '/main_cgi/has_%s_%s.html']);" % (key, logopts[key])
print "</script>"
print "</BODY>"
print "</HTML>"
if __name__ == "__main__" and os.environ.has_key("REQUEST_METHOD"):
""" Determine if called from command line or CGI """
refresh=30
if not form.has_key("jobid") and form["calctype"].value=="pdb2pqr":
print "Content-type: text/html\n\n"
print printheader("PDB2PQR Job Status - Error")
text="<BODY>\n"
text+="\t<H2>Missing jobid field</H2>\n"
text+="\t<P>Your request url is missing the jobid field</P>\n"
text += "<script type=\"text/javascript\">"
text += "var gaJsHost = ((\"https:\" == document.location.protocol) ? \"https://ssl.\" : \"http://www.\");"
text += "document.write(unescape(\"%3Cscript src=\'\" + gaJsHost + \"google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E\"));"
text += "</script>"
text += "<script type=\"text/javascript\">"
text += "try {"
text += "var pageTracker = _gat._getTracker(\"UA-11026338-3\");"
text += "pageTracker._trackPageview();"
text += "} catch(err) {}</script>"
text+="</BODY>\n</HTML>"
print text
sys.exit(2)
if (form["calctype"].value=="pdb2pqr" and HAVE_PDB2PQR_OPAL=="1") or (form["calctype"].value=="apbs" and APBS_OPAL_URL!=""):
have_opal = True
from AppService_client import AppServiceLocator, getAppMetadataRequest, launchJobRequest, launchJobBlockingRequest, getOutputAsBase64ByNameRequest, queryStatusRequest, getOutputsRequest
from AppService_types import ns0
from ZSI.TC import String
else:
have_opal = False
mainCGI()