def output_module_html(webpage_path):
'''Output an HTML page for each module'''
icons_relpath = relpath(cellprofiler.icons.__path__[0])
all_png_icons = glob(os.path.join(icons_relpath, "*.png"))
icon_names = [os.path.basename(f)[:-4] for f in all_png_icons]
help_text = """
<h2>Help for CellProfiler Modules</a></h2>
<ul>\n"""
d = {}
module_path = webpage_path
if not (os.path.exists(module_path) and os.path.isdir(module_path)):
try:
os.mkdir(module_path)
except IOError:
raise ValueError("Could not create directory %s" % module_path)
for module_name in sorted(get_module_names()):
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
if isinstance(module.category, (str,unicode)):
module.category = [module.category]
for category in module.category:
if not d.has_key(category):
d[category] = {}
d[category][module_name] = module
result = module.get_help()
if result is None:
continue
result = result.replace('<body><h1>','<body><h1>Module: ')
# Replace refs to icons in memory with the relative path to the image dir (see above)
result = re.sub("memory:",os.path.join("images","").encode('string-escape'),result)
# Check if a corresponding image exists for the module
if module_name in icon_names:
# Strip out end html tags so I can add more stuff
result = result.replace('</body>','').replace('</html>','')
# Include images specific to the module, relative to html files ('images' dir)
LOCATION_MODULE_IMAGES = os.path.join('images','%s.png'%(module_name))
result += '\n\n<div><p><img src="%s", width="50%%"></p></div>\n'%LOCATION_MODULE_IMAGES
# Now end the help text
result += '</body></html>'
fd = open(os.path.join(module_path,"%s.html" % module_name), "w")
fd.write(result)
fd.close()
for category in sorted(d.keys()):
sub_d = d[category]
help_text += "<li><b>%s</b><br><ul>\n"%category
for module_name in sorted(sub_d.keys()):
help_text += "<li><a href='%s.html'>%s</a></li>\n" % (module_name, module_name)
help_text += "</ul></li>\n"
help_text += "</ul>\n"
return help_text
def output_module_html(webpage_path):
'''Output an HTML page for each module'''
icons_relpath = relpath(cellprofiler.icons.__path__[0])
all_png_icons = glob(os.path.join(icons_relpath, "*.png"))
icon_names = [os.path.basename(f)[:-4] for f in all_png_icons]
help_text = """
<h2>Help for CellProfiler Modules</a></h2>
<ul>\n"""
d = {}
module_path = webpage_path
if not (os.path.exists(module_path) and os.path.isdir(module_path)):
try:
os.mkdir(module_path)
except IOError:
raise ValueError("Could not create directory %s" % module_path)
for module_name in sorted(get_module_names()):
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
if isinstance(module.category, (str,unicode)):
module.category = [module.category]
for category in module.category:
if not d.has_key(category):
d[category] = {}
d[category][module_name] = module
result = module.get_help()
if result is None:
continue
result = result.replace('<body><h1>','<body><h1>Module: ')
# Replace refs to icons in memory with the relative path to the image dir (see above)
result = re.sub("memory:",os.path.join("images","").encode('string-escape'),result)
# Check if a corresponding image exists for the module
if module_name in icon_names:
# Strip out end html tags so I can add more stuff
result = result.replace('</body>','').replace('</html>','')
# Include images specific to the module, relative to html files ('images' dir)
LOCATION_MODULE_IMAGES = os.path.join('images','%s.png'%(module_name))
result += '\n\n<div><p><img src="%s", width="50%%"></p></div>\n'%LOCATION_MODULE_IMAGES
# Now end the help text
result += '</body></html>'
fd = open(os.path.join(module_path,"%s.html" % module_name), "w")
fd.write(result)
fd.close()
for category in sorted(d.keys()):
sub_d = d[category]
help_text += "<li><b>%s</b><br><ul>\n"%category
for module_name in sorted(sub_d.keys()):
help_text += "<li><a href='%s.html'>%s</a></li>\n" % (module_name, module_name)
help_text += "</ul></li>\n"
help_text += "</ul>\n"
return help_text
def plugin_list():
plugin_dir = cpprefs.get_plugin_directory()
if plugin_dir is not None and os.path.isdir(plugin_dir):
file_list = glob.glob(os.path.join(plugin_dir, '*.py'))
return [os.path.basename(f)[:-3] for f in file_list
if not f.endswith('__init__.py')]
return []
def plugin_list():
plugin_dir = cpprefs.get_plugin_directory()
if plugin_dir is not None and os.path.isdir(plugin_dir):
file_list = glob.glob(os.path.join(plugin_dir, '*.py'))
return [os.path.basename(f)[:-3] for f in file_list
if not f.endswith('__init__.py')]
return []
def find_module(self, fullname, path=None):
if not fullname.startswith('cellprofiler.modules.plugins'):
return None
prefix, modname = fullname.rsplit('.', 1)
if prefix != 'cellprofiler.modules.plugins':
return None
if os.path.exists(os.path.join(cpprefs.get_plugin_directory(), modname + '.py')):
return self
return None
def find_module(self, fullname, path=None):
if not fullname.startswith('cellprofiler.modules.plugins'):
return None
prefix, modname = fullname.rsplit('.', 1)
if prefix != 'cellprofiler.modules.plugins':
return None
if os.path.exists(os.path.join(cpprefs.get_plugin_directory(), modname + '.py')):
return self
return None
def load_module(self, fullname):
if fullname in sys.modules:
return sys.modules[fullname]
prefix, modname = fullname.rsplit('.', 1)
assert prefix == 'cellprofiler.modules.plugins'
try:
mod = imp.new_module(fullname)
sys.modules[fullname] = mod
mod.__loader__ = self
mod.__file__ = os.path.join(cpprefs.get_plugin_directory(), modname + '.py')
contents = open(mod.__file__, "r").read()
exec compile(contents, mod.__file__, "exec") in mod.__dict__
return mod
except:
if fullname in sys.module:
del sys.modules[fullname]
def load_module(self, fullname):
if fullname in sys.modules:
return sys.modules[fullname]
prefix, modname = fullname.rsplit('.', 1)
assert prefix == 'cellprofiler.modules.plugins'
try:
mod = imp.new_module(fullname)
sys.modules[fullname] = mod
mod.__loader__ = self
mod.__file__ = os.path.join(cpprefs.get_plugin_directory(), modname + '.py')
contents = open(mod.__file__, "r").read()
exec compile(contents, mod.__file__, "exec") in mod.__dict__
return mod
except:
if fullname in sys.module:
del sys.modules[fullname]
def search_module_help(text):
'''Search the help for a string
text - find text in the module help using case-insensitive matching
returns an html document of all the module help pages that matched or
None if no match found.
'''
matching_help = []
for item in MAIN_HELP:
matching_help += __search_menu_helper(
item, lambda x:__search_fn(x, text))
count = sum([len(x[2]) for x in matching_help])
for module_name in get_module_names():
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
help_text = module.get_help()
matches = __search_fn(help_text, text)
if len(matches) > 0:
matching_help.append((module_name, help_text, matches))
count += len(matches)
if len(matching_help) == 0:
return None
top = """<html style="font-family:arial">
<head><title>%s found</title></head>
<body><h1>Matches found</h1><br><ul>
""" % ("1 match" if len(matching_help) == 1 else "%d matches" % len(matching_help))
body = "<br>"
match_num = 1
prev_link = (
'<a href="#match%d" title="Previous match">'
'<img src="memory:previous.png" alt="previous match"></a>')
anchor = '<a name="match%d"><u>%s</u></a>'
next_link = ('<a href="#match%d" title="Next match">'
'<img src="memory:next.png" alt="next match"></a>')
for title, help_text, pairs in matching_help:
top += """<li><a href="#match%d">%s</a></li>\n""" % (
match_num, title)
if help_text.find("<h1>") == -1:
body += "<h1>%s</h1>" % title
start_match = re.search(r"<\s*body[^>]*?>", help_text, re.IGNORECASE)
if start_match is None:
start = 0
else:
start = start_match.end()
end_match = re.search(r"<\\\s*body", help_text, re.IGNORECASE)
if end_match is None:
end = len(help_text)
else:
end = end_match.start()
for begin_pos, end_pos in pairs:
body += help_text[start:begin_pos]
if match_num > 1:
body += prev_link % (match_num - 1)
body += anchor % (match_num, help_text[begin_pos:end_pos])
if match_num != count:
body += next_link % (match_num + 1)
start = end_pos
match_num += 1
body += help_text[start:end] + "<br>"
result = "%s</ul><br>\n%s</body></html>" % (top, body)
return result
def fill_modules():
del pymodules[:]
del badmodules[:]
del datatools[:]
all_modules.clear()
svn_revisions.clear()
def add_module(mod, check_svn):
try:
m = __import__(mod, globals(), locals(), ['__all__'], 0)
cp_module = find_cpmodule(m)
name = cp_module.module_name
except Exception as e:
logger.warning("Could not load %s", mod, exc_info=True)
badmodules.append((mod, e))
return
try:
pymodules.append(m)
if name in all_modules:
logger.warning(
"Multiple definitions of module %s\n\told in %s\n\tnew in %s",
name, sys.modules[all_modules[name].__module__].__file__,
m.__file__)
all_modules[name] = cp_module
check_module(cp_module, name)
# attempt to instantiate
if not hasattr(cp_module, 'do_not_check'):
cp_module()
if hasattr(cp_module, "run_as_data_tool"):
datatools.append(name)
if check_svn and hasattr(m, '__version__'):
match = re.match('^\$Revision: ([0-9]+) \$$', m.__version__)
if match is not None:
svn_revisions[name] = match.groups()[0]
if not hasattr(all_modules[name], "settings"):
# No settings = pure data tool
pure_datatools[name] = all_modules[name]
del all_modules[name]
except Exception as e:
logger.warning("Failed to load %s", name, exc_info=True)
badmodules.append((mod, e))
if name in all_modules:
del all_modules[name]
del pymodules[-1]
for mod in builtin_modules:
add_module('cellprofiler.modules.' + mod, True)
plugin_directory = get_plugin_directory()
if plugin_directory is not None:
old_path = sys.path
sys.path.insert(0, plugin_directory)
try:
for mod in plugin_list():
add_module(mod, False)
finally:
sys.path = old_path
datatools.sort()
if len(badmodules) > 0:
logger.warning("could not load these modules: %s",
",".join([x[0] for x in badmodules]))
svn_revisions[name] = match.groups()[0]
if not hasattr(all_modules[name], "settings"):
# No settings = pure data tool
pure_datatools[name] = all_modules[name]
del all_modules[name]
except Exception, e:
logger.warning("Failed to load %s", name, exc_info=True)
badmodules.append((mod, e))
if name in all_modules:
del all_modules[name]
del pymodules[-1]
for mod in builtin_modules:
add_module('cellprofiler.modules.' + mod, True)
plugin_directory = get_plugin_directory()
if plugin_directory is not None:
old_path = sys.path
sys.path.insert(0, plugin_directory)
try:
for mod in plugin_list():
add_module(mod, False)
finally:
sys.path = old_path
datatools.sort()
if len(badmodules) > 0:
logger.warning("could not load these modules: %s",
",".join([x[0] for x in badmodules]))
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.analysis_worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP, CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
# sys.argv[0] points at
# CellProfiler.app/Contents/Resources/CellProfiler.py
# We want
# CellProfiler.app/Contents/MacOS/CellProfiler
#
contents_resources_dir = os.path.split(sys.argv[0])[0]
contents_dir = os.path.split(contents_resources_dir)[0]
cp_executable = os.path.join(contents_dir, "MacOS", "CellProfiler")
assert os.path.isfile(cp_executable), \
"Did not find CellProfiler in its expected place: %s" % cp_executable
assert os.access(cp_executable, os.EX_OK), \
"%s is not executable" % cp_executable
args = ["arch", "-x86_64", "-i386", cp_executable,
"--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
else:
aw_path = os.path.join(
os.path.split(
os.path.abspath(sys.argv[0]))[0],
"analysis_worker")
args = [aw_path,
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
worker = subprocess.Popen(args,
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source(),
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()],
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
def run_logger(workR, widx):
while(True):
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.analysis_worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP, CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
# sys.argv[0] points at
# CellProfiler.app/Contents/Resources/CellProfiler.py
# We want
# CellProfiler.app/Contents/MacOS/CellProfiler
#
contents_resources_dir = os.path.split(sys.argv[0])[0]
contents_dir = os.path.split(contents_resources_dir)[0]
cp_executable = os.path.join(contents_dir, "MacOS", "CellProfiler")
assert os.path.isfile(cp_executable), \
"Did not find CellProfiler in its expected place: %s" % cp_executable
assert os.access(cp_executable, os.EX_OK), \
"%s is not executable" % cp_executable
args = ["arch", "-x86_64", cp_executable,
"--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
else:
aw_path = os.path.join(
os.path.split(
os.path.abspath(sys.argv[0]))[0],
"analysis_worker")
args = [aw_path,
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
worker = subprocess.Popen(args,
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source(),
'--work-announce',
cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()],
env=find_worker_env(),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds = close_fds)
def run_logger(workR, widx):
while(True):
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def fill_modules():
del pymodules[:]
del badmodules[:]
del datatools[:]
all_modules.clear()
svn_revisions.clear()
def add_module(mod, check_svn):
try:
m = __import__(mod, globals(), locals(), ['__all__'], 0)
cp_module = find_cpmodule(m)
name = cp_module.module_name
except Exception as e:
logger.warning("Could not load %s", mod, exc_info=True)
badmodules.append((mod, e))
return
try:
pymodules.append(m)
if name in all_modules:
logger.warning(
"Multiple definitions of module %s\n\told in %s\n\tnew in %s",
name, sys.modules[all_modules[name].__module__].__file__,
m.__file__)
all_modules[name] = cp_module
check_module(cp_module, name)
# attempt to instantiate
if not hasattr(cp_module, 'do_not_check'):
cp_module()
if hasattr(cp_module, "run_as_data_tool"):
datatools.append(name)
if check_svn and hasattr(m, '__version__'):
match = re.match('^\$Revision: ([0-9]+) \$$', m.__version__)
if match is not None:
svn_revisions[name] = match.groups()[0]
if not hasattr(all_modules[name], "settings"):
# No settings = pure data tool
pure_datatools[name] = all_modules[name]
del all_modules[name]
except Exception as e:
logger.warning("Failed to load %s", name, exc_info=True)
badmodules.append((mod, e))
if name in all_modules:
del all_modules[name]
del pymodules[-1]
for mod in builtin_modules:
add_module('cellprofiler.modules.' + mod, True)
plugin_directory = get_plugin_directory()
if plugin_directory is not None:
old_path = sys.path
sys.path.insert(0, plugin_directory)
try:
for mod in plugin_list():
add_module(mod, False)
finally:
sys.path = old_path
datatools.sort()
if len(badmodules) > 0:
logger.warning("could not load these modules: %s",
",".join([x[0] for x in badmodules]))
def test_01_01_output_module_html(self):
from cellprofiler.modules import get_module_names, instantiate_module
M.output_module_html(self.temp_dir)
for module_name in sorted(get_module_names()):
fd = None
try:
fd = open(os.path.join(self.temp_dir, module_name + ".html"))
except:
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
traceback.print_exc()
self.assert_("Failed to open %s.html" % module_name)
data = fd.read()
fd.close()
#
# Make sure that some nesting rules are obeyed.
#
tags_we_care_about = ("i", "b", "ul", "ol", "li", "table", "tr",
"td", "th", "h1", "h2", "h3", "html", "head",
"body")
pattern = r"<\s*([a-zA-Z0-9]+).[^>]*>"
anti_pattern = r"</\s*([a-zA-Z0-9]+)[^>]*>"
d = {}
anti_d = {}
COUNT = 0
LIST = 1
for tag in tags_we_care_about:
for dd in (d, anti_d):
dd[tag] = [0, []]
for p, dd in ((pattern, d), (anti_pattern, anti_d)):
pos = 0
while (True):
m = re.search(p, data[pos:])
if m is None:
break
tag = m.groups()[0].lower()
pos = pos + m.start(1) + 1
if dd.has_key(tag):
dd[tag][COUNT] += 1
dd[tag][LIST].append(pos)
#
# Check table nesting rules
#
T_TABLE = 0
T_ANTI_TABLE = 1
T_TR = 2
T_ANTI_TR = 3
T_TH = 4
T_ANTI_TH = 5
T_TD = 6
T_ANTI_TD = 7
T_UL = 8
T_ANTI_UL = 9
T_OL = 10
T_ANTI_OL = 11
T_LI = 12
T_ANTI_LI = 13
T_I = 14
T_ANTI_I = 15
T_B = 16
T_ANTI_B = 17
tokens = []
for tag, token, anti_token in (('table', T_TABLE, T_ANTI_TABLE),
('tr', T_TR, T_ANTI_TR),
('td', T_TD, T_ANTI_TD),
('th', T_TH,
T_ANTI_TH), ('ul', T_UL,
T_ANTI_UL),
('ol', T_OL,
T_ANTI_OL), ('li', T_LI,
T_ANTI_LI),
('i', T_I, T_ANTI_I), ('b', T_B,
T_ANTI_B)):
tokens += [(pos, token) for pos in d[tag][LIST]]
tokens += [(pos, anti_token) for pos in anti_d[tag][LIST]]
tokens = sorted(tokens)
S_INIT = 0
S_AFTER_TABLE = 1
S_AFTER_TR = 2
S_AFTER_TD = 3
S_AFTER_TH = 4
S_AFTER_OL = 5
S_AFTER_UL = 6
S_AFTER_LI = 7
S_AFTER_I = 8
S_AFTER_B = 9
state_transitions = {
S_INIT: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_I: S_AFTER_I,
T_B: S_AFTER_B
},
S_AFTER_TABLE: {
T_ANTI_TABLE: S_INIT,
T_TR: S_AFTER_TR
},
S_AFTER_TR: {
T_ANTI_TR: S_INIT,
T_TD: S_AFTER_TD,
T_TH: S_AFTER_TH
},
S_AFTER_TD: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TD: S_INIT
},
S_AFTER_TH: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TH: S_INIT
},
S_AFTER_OL: {
T_LI: S_AFTER_LI,
T_ANTI_OL: S_INIT
},
S_AFTER_UL: {
T_LI: S_AFTER_LI,
T_ANTI_UL: S_INIT
},
S_AFTER_LI: {
T_ANTI_LI: S_INIT,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I
},
S_AFTER_I: {
T_ANTI_I: S_INIT,
T_I: S_AFTER_I, # Stupid but legal <i><i>Foo</i></i>
T_B: S_AFTER_B,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
},
S_AFTER_B: {
T_ANTI_B: S_INIT,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
}
}
state = []
for pos, token in tokens:
self.assertTrue(
len(state) >= 0, "Error in %s near position %d (%s)" %
(module_name, pos,
data[max(0, pos - 30):max(pos + 30, len(data))]))
top_state, start_pos = (S_INIT,
0) if len(state) == 0 else state[-1]
self.assertTrue(
state_transitions[top_state].has_key(token),
"Nesting error in %s near position %d (%s)" %
(module_name, pos, data[max(0, pos - 50):pos] + "^^^" +
data[pos:min(pos + 50, len(data))]))
next_state = state_transitions[top_state][token]
if next_state == S_INIT:
state.pop()
else:
state.append((next_state, pos))
if len(state) > 0:
self.assertEqual(
len(state), 0,
"Couldn't find last closing tag in %s. Last tag position = %d (%s)"
% (module_name, state[-1][1],
data[(state[-1][1] - 30):(state[-1][1] + 30)]))
#
# Check begin/end tag counts
#
for tag in tags_we_care_about:
if d.has_key(tag):
self.assertTrue(
anti_d.has_key(tag),
"Missing closing </%s> tag in %s" % (tag, module_name))
self.assertEqual(
d[tag][COUNT], anti_d[tag][COUNT],
"Found %d <%s>, != %d </%s> in %s" %
(d[tag][COUNT], tag, anti_d[tag][COUNT], tag,
module_name))
else:
self.assertFalse(
anti_d.has_key(tag),
"Missing opening <%s> tag in %s" % (tag, module_name))
svn_revisions[name] = match.groups()[0]
if not hasattr(all_modules[name], "settings"):
# No settings = pure data tool
pure_datatools[name] = all_modules[name]
del all_modules[name]
except Exception, e:
logger.warning("Failed to load %s", name, exc_info=True)
badmodules.append((mod, e))
if name in all_modules:
del all_modules[name]
del pymodules[-1]
for mod in builtin_modules:
add_module("cellprofiler.modules." + mod, True)
plugin_directory = get_plugin_directory()
if plugin_directory is not None:
old_path = sys.path
sys.path.insert(0, plugin_directory)
try:
for mod in plugin_list():
add_module(mod, False)
finally:
sys.path = old_path
datatools.sort()
if len(badmodules) > 0:
logger.warning("could not load these modules: %s", ",".join([x[0] for x in badmodules]))
def add_module_for_tst(module_class):
def start_workers(cls, num=None):
if cls.workers:
return
try:
num = multiprocessing.cpu_count() if num is None else num
except NotImplementedError:
num = 4
cls.work_announce_address = get_announcer_address()
logger.info("Starting workers on address %s" % cls.work_announce_address)
if 'CP_DEBUG_WORKER' in os.environ:
if os.environ['CP_DEBUG_WORKER'] == 'NOT_INPROC':
return
from cellprofiler.worker import \
AnalysisWorker, NOTIFY_ADDR, NOTIFY_STOP
from cellprofiler.pipeline import CancelledException
class WorkerRunner(threading.Thread):
def __init__(self, work_announce_address):
threading.Thread.__init__(self)
self.work_announce_address = work_announce_address
self.notify_socket = zmq.Context.instance().socket(zmq.PUB)
self.notify_socket.bind(NOTIFY_ADDR)
def run(self):
with AnalysisWorker(self.work_announce_address) as aw:
try:
aw.run()
except CancelledException:
logger.info("Exiting debug worker thread")
def wait(self):
self.notify_socket.send(NOTIFY_STOP)
self.join()
thread = WorkerRunner(cls.work_announce_address)
thread.setDaemon(True)
thread.start()
cls.workers.append(thread)
return
close_fds = False
# start workers
for idx in range(num):
if sys.platform == 'darwin':
close_all_on_exec()
aw_args = ["--work-announce", cls.work_announce_address,
"--plugins-directory", cpprefs.get_plugin_directory(),
"--ij-plugins-directory", cpprefs.get_ij_plugin_directory()]
jvm_arg = "%dm" % cpprefs.get_jvm_heap_mb()
aw_args.append("--jvm-heap-size=%s" % jvm_arg)
# stdin for the subprocesses serves as a deadman's switch. When
# closed, the subprocess exits.
if hasattr(sys, 'frozen'):
if sys.platform == 'darwin':
executable = os.path.join(
os.path.dirname(sys.executable), "CellProfiler")
args = ([executable] + aw_args)
elif sys.platform.startswith('linux'):
aw_path = os.path.join(os.path.dirname(__file__),
"worker.py")
args = [sys.executable, aw_path] + aw_args
else:
args = [sys.executable] + aw_args
worker = subprocess.Popen(args,
env=find_worker_env(idx),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds=close_fds)
else:
worker = subprocess.Popen(
[find_python(),
'-u', # unbuffered
find_analysis_worker_source()] + aw_args,
env=find_worker_env(idx),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
close_fds=close_fds)
def run_logger(workR, widx):
while True:
try:
line = workR.stdout.readline()
if not line:
break
logger.info("Worker %d: %s", widx, line.rstrip())
except:
break
start_daemon_thread(target=run_logger, args=(worker, idx,), name='worker stdout logger')
cls.workers += [worker]
cls.deadman_switches += [worker.stdin] # closing stdin will kill subprocess
def test_01_01_output_module_html(self):
from cellprofiler.modules import get_module_names, instantiate_module
M.output_module_html(self.temp_dir)
for module_name in sorted(get_module_names()):
fd = None
try:
fd = open(os.path.join(self.temp_dir, module_name + ".html"))
except:
module = instantiate_module(module_name)
location = os.path.split(
module.create_settings.im_func.func_code.co_filename)[0]
if location == cpprefs.get_plugin_directory():
continue
traceback.print_exc()
self.assert_("Failed to open %s.html" %module_name)
data = fd.read()
fd.close()
#
# Make sure that some nesting rules are obeyed.
#
tags_we_care_about = ("i","b","ul","ol","li","table","tr","td","th",
"h1","h2","h3","html","head", "body")
pattern = r"<\s*([a-zA-Z0-9]+).[^>]*>"
anti_pattern = r"</\s*([a-zA-Z0-9]+)[^>]*>"
d = {}
anti_d = {}
COUNT = 0
LIST = 1
for tag in tags_we_care_about:
for dd in (d, anti_d):
dd[tag] = [0, []]
for p, dd in ((pattern, d),
(anti_pattern, anti_d)):
pos = 0
while(True):
m = re.search(p, data[pos:])
if m is None:
break
tag = m.groups()[0].lower()
pos = pos + m.start(1)+1
if dd.has_key(tag):
dd[tag][COUNT] += 1
dd[tag][LIST].append(pos)
#
# Check table nesting rules
#
T_TABLE = 0
T_ANTI_TABLE = 1
T_TR = 2
T_ANTI_TR = 3
T_TH = 4
T_ANTI_TH = 5
T_TD = 6
T_ANTI_TD = 7
T_UL = 8
T_ANTI_UL = 9
T_OL = 10
T_ANTI_OL = 11
T_LI = 12
T_ANTI_LI = 13
T_I = 14
T_ANTI_I = 15
T_B = 16
T_ANTI_B = 17
tokens = []
for tag, token, anti_token in (
('table', T_TABLE, T_ANTI_TABLE),
('tr', T_TR, T_ANTI_TR),
('td', T_TD, T_ANTI_TD),
('th', T_TH, T_ANTI_TH),
('ul', T_UL, T_ANTI_UL),
('ol', T_OL, T_ANTI_OL),
('li', T_LI, T_ANTI_LI),
('i', T_I, T_ANTI_I),
('b', T_B, T_ANTI_B)
):
tokens += [(pos, token) for pos in d[tag][LIST]]
tokens += [(pos, anti_token) for pos in anti_d[tag][LIST]]
tokens = sorted(tokens)
S_INIT = 0
S_AFTER_TABLE = 1
S_AFTER_TR = 2
S_AFTER_TD = 3
S_AFTER_TH = 4
S_AFTER_OL = 5
S_AFTER_UL = 6
S_AFTER_LI = 7
S_AFTER_I = 8
S_AFTER_B = 9
state_transitions = {
S_INIT: { T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_I: S_AFTER_I,
T_B: S_AFTER_B },
S_AFTER_TABLE: {
T_ANTI_TABLE: S_INIT,
T_TR: S_AFTER_TR
},
S_AFTER_TR: {
T_ANTI_TR: S_INIT,
T_TD: S_AFTER_TD,
T_TH: S_AFTER_TH
},
S_AFTER_TD: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TD: S_INIT
},
S_AFTER_TH: {
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_ANTI_TH: S_INIT
},
S_AFTER_OL: {
T_LI: S_AFTER_LI,
T_ANTI_OL: S_INIT
},
S_AFTER_UL: {
T_LI: S_AFTER_LI,
T_ANTI_UL: S_INIT
},
S_AFTER_LI: {
T_ANTI_LI: S_INIT,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL,
T_B: S_AFTER_B,
T_I: S_AFTER_I
},
S_AFTER_I: {
T_ANTI_I: S_INIT,
T_I: S_AFTER_I, # Stupid but legal <i><i>Foo</i></i>
T_B: S_AFTER_B,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
},
S_AFTER_B: {
T_ANTI_B: S_INIT,
T_B: S_AFTER_B,
T_I: S_AFTER_I,
T_TABLE: S_AFTER_TABLE,
T_OL: S_AFTER_OL,
T_UL: S_AFTER_UL
}
}
state = []
for pos, token in tokens:
self.assertTrue(
len(state) >= 0,
"Error in %s near position %d (%s)" %
(module_name, pos, data[max(0,pos - 30):
max(pos + 30, len(data))])
)
top_state, start_pos = (S_INIT,0) if len(state) == 0 else state[-1]
self.assertTrue(
state_transitions[top_state].has_key(token),
"Nesting error in %s near position %d (%s)" %
(module_name, pos, data[max(0,pos - 50):pos]+"^^^"+
data[pos:min(pos + 50, len(data))]))
next_state = state_transitions[top_state][token]
if next_state == S_INIT:
state.pop()
else:
state.append((next_state, pos))
if len(state) > 0:
self.assertEqual(
len(state), 0,
"Couldn't find last closing tag in %s. Last tag position = %d (%s)" %
(module_name, state[-1][1], data[(state[-1][1] - 30):
(state[-1][1] + 30)]))
#
# Check begin/end tag counts
#
for tag in tags_we_care_about:
if d.has_key(tag):
self.assertTrue(anti_d.has_key(tag),
"Missing closing </%s> tag in %s" %
(tag, module_name))
self.assertEqual(
d[tag][COUNT], anti_d[tag][COUNT],
"Found %d <%s>, != %d </%s> in %s" %
(d[tag][COUNT], tag,
anti_d[tag][COUNT], tag, module_name))
else:
self.assertFalse(anti_d.has_key(tag),
"Missing opening <%s> tag in %s" %
(tag, module_name))
