1
2 """
3 script plugin
4
5 Plugin read by omero.cli.Cli during initialization. The method(s)
6 defined here will be added to the Cli class for later use.
7
8 The script plugin is used to run arbitrary blitz scripts which
9 take as their sole input Ice configuration arguments, including
10 --Ice.Config=file1,file2.
11
12 The first parameter, the script itself, should be natively executable
13 on a given platform. I.e. invokable by subprocess.call([file,...])
14
15 Copyright 2008 Glencoe Software, Inc. All rights reserved.
16 Use is subject to license terms supplied in LICENSE.txt
17
18 """
19
20 import exceptions, subprocess, re, os, sys, signal, time, atexit
21
22 from omero.cli import CLI
23 from omero.cli import BaseControl
24
25 from omero.util.sessions import SessionsStore
26
27 from omero_ext.argparse import Action
28 from omero_ext.strings import shlex
29 from omero_ext.functional import wraps
30
31 from path import path
32
33 HELP = """Support for launching, uploading and otherwise managing OMERO.scripts"""
34
35 DEMO_SCRIPT = """#!/usr/bin/env python
36 import omero
37 import omero.rtypes as rtypes
38 import omero.scripts as scripts
39
40 o = scripts.Long("opt", min=0, max=5)
41 a = scripts.String("a", values=("foo", "bar"), optional=False)
42 b = scripts.Long("b").out()
43
44 client = scripts.client("length of input string",
45 \"\"\"
46 Trivial example script which calculates the length
47 of the string passed in as the "a" input, and returns
48 the value as the long "b"
49 \"\"\", a, b, o,
50
51 authors = ["OME Team"],
52 institutions = ["openmicroscopy.org"])
53
54 print "Starting script"
55
56 try:
57 a = client.getInput("a").getValue()
58 b = len(a)
59 client.setOutput("b", rtypes.rlong(b))
60 client.setOutput("unregistered-output-param", rtypes.wrap([1,2,3]))
61 finally:
62 client.closeSession()
63
64 print "Finished script"
65 """
66
67 RE0 = re.compile("\s*script\s+upload\s*")
68 RE1 = re.compile("\s*script\s+upload\s+--official\s*")
69
71
72 - def _complete(self, text, line, begidx, endidx):
73 """
74 Returns a file after "upload" and otherwise delegates to the BaseControl
75 """
76 for RE in (RE1, RE0):
77 m = RE.match(line)
78 if m:
79 replaced = RE.sub('', line)
80 suggestions = self._complete_file(replaced, os.getcwd())
81 if False:
82 add = "--official"
83 parts = line.split(" ")
84 if "--official".startswith(parts[-1]):
85 new = add[len(parts[-1]):]
86 if new:
87 add = new
88 suggestions.insert(0, add)
89 return suggestions
90 return BaseControl._complete(self, text, line, begidx, endidx)
91
95
96 sub = parser.sub()
97
98
99
100 demo = parser.add(sub, self.demo, "Runs a short demo of the scripting system")
101
102 list = parser.add(sub, self.list, help = "List files for user or group")
103 _who(list)
104
105 cat = parser.add(sub, self.cat, "Prints a script to standard out")
106 edit = parser.add(sub, self.edit, "Opens a script in $EDITOR and saves it back to the server")
107 params = parser.add(sub, self.params, help="Print the parameters for a given script")
108 launch = parser.add(sub, self.launch, help = "Launch a script with parameters")
109 disable = parser.add(sub, self.disable, help = "Makes script non-executable by setting the mimetype")
110 disable.add_argument("--mimetype", default="text/plain", help="Use a mimetype other than the default (%(default)s)")
111 enable = parser.add(sub, self.enable, help = "Makes a script non-executable (sets mimetype to text/x-python)")
112 enable.add_argument("--mimetype", default="text/x-python", help="Use a mimetype other than the default (%(default)s)")
113
114 for x in (launch, params, cat, disable, enable, edit):
115 x.add_argument("original_file", help="Id or path of a script file stored in OMERO")
116 launch.add_argument("input", nargs="*", help="Inputs for the script of the form 'param=value'")
117
118 jobs = parser.add(sub, self.jobs, help = "List current jobs for user or group")
119 jobs.add_argument("--all", action="store_true", help="Show all jobs, not just running ones")
120 _who(jobs)
121
122 serve = parser.add(sub, self.serve, help = "Start a usermode processor for scripts")
123 serve.add_argument("--verbose", action="store_true", help="Enable debug logging on processor")
124 serve.add_argument("-b", "--background", action="store_true", help="Run processor in background. Used in demo")
125 serve.add_argument("-t", "--timeout", default=0, type=long, help="Seconds that the processor should run. 0 means no timeout")
126 _who(serve)
127
128 upload = parser.add(sub, self.upload, help = "Upload a script")
129 upload.add_argument("--official", action="store_true", help = "If set, creates a system script. Must be an admin")
130 upload.add_argument("file", help = "Local script file to upload to OMERO")
131
132 replace = parser.add(sub, self.replace, help = "Replace an existing script with a new value")
133 replace.add_argument("id", type=long, help = "Id of the original file which is to be replaced")
134 replace.add_argument("file", help = "Local script which should overwrite the existing one")
135
136 run = parser.add(sub, self.run, help = "Run a script with the OMERO libraries loaded and current login")
137 run.add_argument("file", help = "Local script file to run")
138 run.add_argument("input", nargs="*", help="Inputs for the script of the form 'param=value'")
139
140
141
142 - def help(self, args):
143 self.ctx.out("""
144
145 Available or planned(*) commands:
146 ================================
147 demo
148
149 set
150 set file=[id|name]
151 set user=[id|name]
152 set group=[id|name]
153 set user=
154
155 Note: Some of the other actions call set internally.
156
157
158 cat
159 cat file=[id|name]
160 mv
161 rm
162 cp
163 --replace / --overwrite
164
165 register
166 publish
167 processors
168 chain
169 edit
170
171 jobs
172 jobs user
173 jobs group
174
175 launch
176 launch file=[id|name]
177
178 list
179 list user
180 list group
181 list user=[id|name]
182 list group=[id|name]
183 list publication=[regex]
184 list ofifical
185 list namespace=[]
186
187 log
188 log file
189 log user
190 log group
191 log file=[id|name]
192 log user=[id|name]
193 log group=[id|name]
194
195 params
196 params file=[id|name]
197
198 serve
199 serve --background
200 serve --timeout={min}
201 serve --verbose
202 serve user
203 serve group
204 serve user=[id|name]
205 serve group=[id|name]
206 serve group=[id|name] user=[id|name]
207 serve count=1
208 serve log
209 serve log=some/file/somewhere
210
211 upload file=/tmp/my_script.py
212 replace
213 delete
214
215 #
216 # Other
217 #
218
219 run
220 """)
221
222
223 - def demo(self, args):
224 from omero.util.temp_files import create_path
225 t = create_path("Demo_Script", ".py")
226
227 try:
228 from hashlib import sha1 as sha_new
229 except ImportError:
230 from sha import new as sha_new
231
232 digest = sha_new()
233 digest.update(DEMO_SCRIPT)
234 sha1 = digest.hexdigest()
235
236 self.ctx.out("\nExample script writing session")
237 self.ctx.out("="*80)
238
239 def msg(title, method = None, *arguments):
240 self.ctx.out("\n")
241 self.ctx.out("\t+" + ("-"*68) + "+")
242 title = "\t| %-66.66s | " % title
243 self.ctx.out(title)
244 if method:
245 cmd = "%s %s" % (method.__name__, " ".join(arguments))
246 cmd = "\t| COMMAND: bin/omero script %-40.40s | " % cmd
247 self.ctx.out(cmd)
248 self.ctx.out("\t+" + ("-"*68) + "+")
249 self.ctx.out(" ")
250 if method:
251 try:
252 self.ctx.invoke(['script', method.__name__] + list(arguments))
253 except exceptions.Exception, e:
254 import traceback
255 self.ctx.out("\nEXECUTION FAILED: %s" % e)
256 self.ctx.dbg(traceback.format_exc())
257
258 client = self.ctx.conn(args)
259 admin = client.sf.getAdminService()
260 current_user = self.ctx._event_context.userId
261 query = "select o from OriginalFile o where o.sha1 = '%s' and o.details.owner.id = %s" % (sha1, current_user)
262 files = client.sf.getQueryService().findAllByQuery(query, None)
263 if len(files) == 0:
264 msg("Saving demo script to %s" % t)
265 t.write_text(DEMO_SCRIPT)
266
267 msg("Uploading script", self.upload, str(t))
268 id = self.ctx.get("script.file.id")
269 else:
270 id = files[0].id.val
271 msg("Reusing demo script %s" % id)
272
273 msg("Listing available scripts for user", self.list, "user")
274 msg("Printing script content for file %s" % id, self.cat, str(id))
275 msg("Serving file %s in background" % id, self.serve, "user", "--background")
276 msg("Printing script params for file %s" % id, self.params, "file=%s" % id)
277 msg("Launching script with parameters: a=bad-string (fails)", self.launch, "file=%s" % id, "a=bad-string")
278 msg("Launching script with parameters: a=bad-string opt=6 (fails)", self.launch, "file=%s" % id, "a=bad-string", "opt=6")
279 msg("Launching script with parameters: a=foo opt=1 (passes)", self.launch, "file=%s" % id, "a=foo", "opt=1")
280 try:
281 for p in list(getattr(self, "_processors", [])):
282 p.cleanup()
283 self._processors.remove(p)
284 except exceptions.Exception, e:
285 self.ctx.err("Failed to clean processors: %s" % e)
286
287
288
289
290 - def cat(self, args):
291 client = self.ctx.conn(args)
292 script_id, ofile = self._file(args, client)
293 try:
294 self.ctx.out(client.sf.getScriptService().getScriptText(script_id))
295 except exceptions.Exception, e:
296 self.ctx.err("Failed to find script: %s (%s)" % (script_id, e))
297
298 - def edit(self, args):
311
312 - def jobs(self, args):
313 client = self.ctx.conn(args)
314 cols = ("username", "groupname", "started", "finished")
315 query = "select j, %s, s.value from Job j join j.status s" % (",".join(["j.%s" % j for j in cols]))
316 if not args.all:
317 query += " where j.finished is null"
318
319 self.ctx.out("Running query via 'hql' subcommand: %s" % query)
320 self.ctx.invoke("""hql "%s" """ % query)
321
323 """
324 """
325
326 client = self.ctx.conn(args)
327 script_id, ofile = self._file(args, client)
328
329 import omero
330 import omero.scripts
331 import omero.rtypes
332 svc = client.sf.getScriptService()
333 try:
334 params = svc.getParams(script_id)
335 except omero.ValidationException, ve:
336 self.ctx.die(502, "ValidationException: %s" % ve.message)
337
338 m = self._parse_inputs(args, params)
339
340 try:
341 proc = svc.runScript(script_id, m, None)
342 job = proc.getJob()
343 except omero.ValidationException, ve:
344 self.ctx.err("Bad parameters:\n%s" % ve)
345 return
346
347
348 cb = omero.scripts.ProcessCallbackI(client, proc)
349 try:
350 self.ctx.out("Job %s ready" % job.id.val)
351 self.ctx.out("Waiting....")
352 count = 0
353 while proc.poll() is None:
354 cb.block(1000)
355 self.ctx.out("Callback received: %s" % cb.block(0))
356 rv = proc.getResults(3)
357 finally:
358 cb.close()
359
360 def p(m):
361 class handle(object):
362 def write(this, val):
363 val = "\t* %s" % val
364 val = val.replace("\n","\n\t* ")
365 self.ctx.out(val, newline=False)
366 def close(this):
367 pass
368
369 f = rv.get(m, None)
370 if f and f.val:
371 self.ctx.out("\n\t*** start %s ***" % m)
372 try:
373 client.download(ofile=f.val, filehandle=handle())
374 except:
375 self.ctx.err("Failed to display %s" % m)
376 self.ctx.out("\n\t*** end %s ***\n" % m)
377
378 p("stdout")
379 p("stderr")
380 self.ctx.out("\n\t*** out parameters ***")
381 for k, v in rv.items():
382 if k not in ("stdout", "stderr", "omero.scripts.parse"):
383 self.ctx.out("\t* %s=%s" % (k, omero.rtypes.unwrap(v)))
384 self.ctx.out("\t*** done ***")
385
386 - def list(self, args):
387 import omero_api_IScript_ice
388 client = self.ctx.conn(args)
389 sf = client.sf
390 svc = sf.getScriptService()
391 ec = self.ctx._event_context
392 if args.who:
393 who = [self._parse_who(w) for w in args.who]
394 scripts = svc.getUserScripts(who)
395 banner = "Scripts for %s" % ", ".join(args.who)
396 else:
397 scripts = svc.getScripts()
398 banner = "Official scripts"
399 self._parse_scripts(scripts, banner)
400
401 - def log(self, args):
404
406 client = self.ctx.conn(args)
407 script_id, ofile = self._file(args, client)
408 import omero
409 import omero_api_IScript_ice
410 svc = client.sf.getScriptService()
411
412 try:
413 job_params = svc.getParams(script_id)
414 except omero.ResourceError, re:
415 self.ctx.die(455, "Could not get params: %s" % re.message)
416
417 if job_params:
418 self.ctx.out("")
419 self.ctx.out("id: %s" % script_id)
420 self.ctx.out("name: %s" % job_params.name)
421 self.ctx.out("version: %s" % job_params.version)
422 self.ctx.out("authors: %s" % ", ".join(job_params.authors))
423 self.ctx.out("institutions: %s" % ", ".join(job_params.institutions))
424 self.ctx.out("description: %s" % job_params.description)
425 self.ctx.out("namespaces: %s" % ", ".join(job_params.namespaces))
426 self.ctx.out("stdout: %s" % job_params.stdoutFormat)
427 self.ctx.out("stderr: %s" % job_params.stderrFormat)
428 def print_params(which, params):
429 import omero
430 self.ctx.out(which)
431 for k, v in params.items():
432 self.ctx.out(" %s - %s" % (k, (v.description and v.description or "(no description)")))
433 self.ctx.out(" Optional: %s" % v.optional)
434 self.ctx.out(" Type: %s" % v.prototype.ice_staticId())
435 if isinstance(v.prototype, omero.RCollection):
436 coll = v.prototype.val
437 if len(coll) == 0:
438 self.ctx.out(" Subtype: (empty)")
439 else:
440 self.ctx.out(" Subtype: %s" % coll[0].ice_staticId())
441
442 elif isinstance(v.prototype, omero.RMap):
443 try:
444 proto_value = v.prototype.val.values[0].ice_staticId()
445 except:
446 proto_value = None
447
448 self.ctx.out(" Subtype: %s" % proto_value)
449 self.ctx.out(" Min: %s" % (v.min and v.min.val or ""))
450 self.ctx.out(" Max: %s" % (v.max and v.max.val or ""))
451 values = omero.rtypes.unwrap(v.values)
452 self.ctx.out(" Values: %s" % (values and ", ".join(values) or ""))
453 print_params("inputs:", job_params.inputs)
454 print_params("outputs:", job_params.outputs)
455
457
458
459 if not hasattr(self, "_processors"):
460 self._processors = []
461
462 debug = args.verbose
463 background = args.background
464 timeout = args.timeout
465 client = self.ctx.conn(args)
466 sf = client.sf
467 who = [self._parse_who(w) for w in args.who]
468 if not who:
469 who = []
470
471
472 import logging
473 original = list(logging._handlerList)
474 roots = list(logging.getLogger().handlers)
475 logging._handlerList = []
476 logging.getLogger().handlers = []
477
478 from omero.util import configure_logging
479 from omero.processor import usermode_processor
480 lvl = debug and 10 or 20
481 configure_logging(loglevel=lvl)
482
483 try:
484 try:
485 impl = usermode_processor(client, serverid = "omer.scripts.serve", accepts_list = who, omero_home=self.ctx.dir)
486 self._processors.append(impl)
487 except exceptions.Exception, e:
488 self.ctx.die(100, "Failed initialization: %s" % e)
489
490 if background:
491 def cleanup():
492 impl.cleanup()
493 logging._handlerList = original
494 logging.getLogger().handlers = roots
495 atexit.register(cleanup)
496 else:
497 try:
498 def handler(signum, frame):
499 raise SystemExit()
500 old = signal.signal(signal.SIGALRM, handler)
501 signal.alarm(timeout)
502 self.ctx.input("Press any key to exit...\n")
503 signal.alarm(0)
504 finally:
505 self.ctx.dbg("DONE")
506 signal.signal(signal.SIGTERM, old)
507 impl.cleanup()
508 finally:
509 if not background:
510 logging._handlerList = original
511 logging.getLogger().handlers = roots
512
513 return impl
514
515
517
518 p = path(args.file)
519 if not p.exists():
520 self.ctx.die(502, "File does not exist: %s" % p.abspath())
521
522 import omero
523 c = self.ctx.conn(args)
524 scriptSvc = c.sf.getScriptService()
525
526 if args.official:
527 try:
528 id = scriptSvc.uploadOfficialScript(args.file, p.text())
529 except omero.ApiUsageException, aue:
530 if "editScript" in aue.message:
531 self.ctx.die(502, "%s already exists; use 'replace' instead" % args.file)
532 else:
533 self.ctx.die(504, "ApiUsageException: %s" % aue.message)
534 except omero.SecurityViolation, sv:
535 self.ctx.die(503, "SecurityViolation: %s" % sv.message)
536 else:
537 id = scriptSvc.uploadScript(args.file, p.text())
538
539 self.ctx.out("Uploaded %sscript as original file #%s" % ((args.official and "official " or ""), id))
540 self.ctx.set("script.file.id", id)
541
555
557 if len(args) != 1:
558 self.ctx.die(123, "Usage: <original file id>")
559
560 ofile = long(args.args[0])
561 import omero_api_IScript_ice
562 client = self.ctx.conn(args)
563 try:
564 client.sf.getScriptService().deleteScript(ofile)
565 except exceptions.Exception, e:
566 self.ctx.err("Failed to delete script: %s (%s)" % (ofile, e))
567
569 ofile = self.setmimetype(args)
570 self.ctx.out("Disabled %s by setting mimetype to %s" % (ofile.id.val, args.mimetype))
571
573 ofile = self.setmimetype(args)
574 self.ctx.out("Enabled %s by setting mimetype to %s" % (ofile.id.val, args.mimetype))
575
582
583
584
585
586 - def run(self, args):
587 if not os.path.exists(args.file):
588 self.ctx.die(670, "No such file: %s" % args.file)
589 else:
590 client = self.ctx.conn(args)
591 store = SessionsStore()
592 srv, usr, uuid = store.get_current()
593 props = store.get(srv, usr, uuid)
594
595 from omero.scripts import parse_file
596 from omero.util.temp_files import create_path
597 path = create_path()
598 text = """
599 omero.host=%(omero.host)s
600 omero.user=%(omero.sess)s
601 omero.pass=%(omero.sess)s
602 """
603 path.write_text(text % props)
604
605 params = parse_file(args.file)
606 m = self._parse_inputs(args, params)
607 for k, v in m.items():
608 if v is not None:
609 client.setInput(k, v)
610
611 p = self.ctx.popen([sys.executable, args.file], stdout=sys.stdout, stderr=sys.stderr,\
612 ICE_CONFIG = str(path))
613 p.wait()
614 if p.poll() != 0:
615 self.ctx.die(p.poll(), "Execution failed.")
616
617
618
619
630
640
641 - def _file(self, args, client):
642 import omero
643 f = args.original_file
644 q = client.sf.getQueryService()
645 svc = client.sf.getScriptService()
646
647 if f is None:
648 self.ctx.die(100, "No script provided")
649 elif f.startswith("file="):
650 f = f[5:]
651
652 try:
653 script_id = long(f)
654 except:
655 script_path = str(f)
656 script_id = svc.getScriptID(script_path)
657 ofile = q.get("OriginalFile", script_id)
658
659 return script_id, ofile
660
662 """
663 Parses who items of the form: "user", "group", "user=1", "group=6"
664 """
665
666 import omero
667 WHO_FACTORY = {"user":omero.model.ExperimenterI, "group":omero.model.ExperimenterGroupI}
668 WHO_CURRENT = { "user":lambda ec: ec.userId,
669 "group":lambda ec: ec.groupId}
670
671 for key, factory in WHO_FACTORY.items():
672 if who.startswith(key):
673 if who == key:
674 id = WHO_CURRENT[key](self.ctx._event_context)
675 return factory(id, False)
676 else:
677 parts = who.split("=")
678 if len(parts) != 2:
679 continue
680 else:
681 id = long(parts[1])
682 return factory(id, False)
683
684 try:
685 register("script", ScriptControl, HELP)
686 except NameError:
687 if __name__ == "__main__":
688 cli = CLI()
689 cli.register("script", ScriptControl, HELP)
690 cli.invoke(sys.argv[1:])
691