def feed(self, data):
if self.__last_was_cr and data[0:1] == '\n':
data = data[1:]
self.__last_was_cr = data[-1:] == '\r'
data = string.replace(data, '\r\n', '\n')
data = string.replace(data, '\r', '\n')
self.__parser.feed(data)
def callRiger(rigerTableFile,scoring='KSbyScore',output='',callRiger = True):
'''
calls riger using the KS scoring metric (default)
'''
rigerDirectory = '/raider/temp/riger/'
rigerTableAbsFile = os.path.abspath(rigerTableFile)
outputFolder = utils.getParentFolder(rigerTableAbsFile)
if len(output) == 0:
output = string.replace(rigerTableAbsFile,'_friger.txt','_friger_%s_out.txt' % (scoring))
rigerBashFileName = string.replace(rigerTableAbsFile,'_friger.txt','_callRiger.sh')
rigerBashFile = open(rigerBashFileName,'w')
rigerBashFile.write('#!/usr/bin/bash\n')
rigerBashFile.write('cd %s\n\n' % (rigerDirectory))
rigerCmd = 'java -cp commons-cli-1.2.jar:rigerj-1.6.2.jar org.broadinstitute.rnai.rigerj.RigerJMain -scoringMethod %s -inputFile %s -outputFile %s' % (scoring,rigerTableAbsFile,output)
rigerBashFile.write(rigerCmd)
rigerBashFile.write('\n')
rigerBashFile.close()
print("WROTE RIGER CMD TO %s" % (rigerBashFileName))
if callRiger == True:
print("Calling RIGER with %s scoring method" % (scoring))
print("RIGER CMD: %s" % (rigerCmd))
os.system(rigerBashFileName)
return rigerBashFileName
def expand_macros(feed, item, conf_items):
macro_defns = {}
macro_defns["%{host}"] = "TODO"
macro_defns["%{user}"] = "TODO"
macro_defns["%{rss-link}"] = feed.setdefault("href", None)
macro_defns["%{last-modified}"] = "TODO"
macro_defns["%{item:link}"] = item.setdefault("link", None)
macro_defns["%{item:title}"] = item.setdefault("title", None)
macro_defns["%{item:description}"] = item.setdefault("description", None)
macro_defns["%{item:dc:date}"] = item.setdefault("date", None)
macro_defns["%{item:dc:subject}"] = "TODO"
macro_defns["%{item:dc:creator}"] = "TODO"
macro_defns["%{channel:link}"] = feed.setdefault("feed", None).setdefault("link", None)
macro_defns["%{channel:title}"] = feed.setdefault("feed", None).setdefault("title", None)
macro_defns["%{channel:description}"] = feed.setdefault("feed", None).setdefault("description", None)
macro_defns["%{channel:dc:date}"] = feed.setdefault("feed", None).setdefault("date", None)
expanded_config = {}
for key, val in conf_items.items():
regex = re.compile("(?P<macro>%{.*})")
matches = regex.search(val)
if matches is not None:
macro_label = matches.groupdict()["macro"]
# need to escape folders
if key == "folder":
macro_defns[macro_label] = string.replace(macro_defns[macro_label], ".", ":")
expanded_config[key] = string.replace(conf_items[key], macro_label, macro_defns[macro_label])
else:
expanded_config[key] = conf_items[key]
return expanded_config
def main():
print "in main"
usage = "%prog -i inifile -o outputfile -s servers"
parser = OptionParser(usage)
parser.add_option("-s", "--servers", dest="servers")
parser.add_option("-i", "--inifile", dest="inifile")
parser.add_option("-o", "--outputFile", dest="outputFile")
parser.add_option("-p", "--os", dest="os")
options, args = parser.parse_args()
print "the ini file is", options.inifile
print "the server info is", options.servers
servers = json.loads(options.servers)
f = open(options.inifile)
data = f.readlines()
for i in range(len(data)):
if "dynamic" in data[i]:
data[i] = string.replace(data[i], "dynamic", servers[0])
servers.pop(0)
if options.os == "windows":
if "root" in data[i]:
data[i] = string.replace(data[i], "root", "Administrator")
if "couchbase" in data[i]:
data[i] = string.replace(data[i], "couchbase", "Membase123")
for d in data:
print d,
f = open(options.outputFile, "w")
f.writelines(data)
def parseFileName(name):
nameString = dropInsideContent(name,"[","]" )
nameString = dropInsideContent(nameString,"{","}" )
nameString = dropInsideContent(nameString,"(",")" )
nameString = nameString.strip('()_{}[]!@#$^&*+=|\\/"\'?<>~`')
nameString = nameString.lstrip(' ')
nameString = nameString.rstrip(' ')
nameString = dropInsideContent(nameString,"{","}" )
nameString = nameString.lower()
nameString = string.replace(nameString,"\t"," ")
nameString = string.replace(nameString," "," ")
try:
nameString = unicodedata.normalize('NFKD',nameString).encode()
nameString = nameString.encode()
except:
try:
nameString = nameString.encode('latin-1', 'ignore')
nameString = unicodedata.normalize('NFKD',nameString).encode("ascii")
nameString = str(nameString)
except:
nameString = "unknown"
if len(nameString)==0: nameString=" "
return nameString
def get_cast(self):
self.cast = "<%s" % gutils.trim(self.page, '/ob.gif"',"<br/>\n\t")
self.cast = string.replace(self.cast, "\n",'')
self.cast = string.replace(self.cast, "\t",'')
self.cast = string.replace(self.cast, '<div class="filmActor">', "\n")
self.cast = string.replace(self.cast, ":", _(" as "))
self.cast = gutils.strip_tags(self.cast)
def find(self, string, pattern):
word = string.replace(pattern,'*','\*')
words = string.replace(word,' ','\s*')
if re.search(words,string):
pass
else:
raise log.err(string)
def genmenu(start, directory):
# get a directory list
dirlist = os.listdir(directory)
for d in dirlist:
# set di to overall directory
di = directory + "/" + d
# if we get a dir, generate a menu
if isdir(di):
print ""
print ' <menu id="' + di + '" label="' + d + '" >'
genmenu(start, di)
print " </menu>"
# if we get a file, check if it is a valid type
else:
if re.search(filetypes, string.lower(di)) > 0:
# make fi variable just filename, without extension
fi = string.replace(string.replace(di, directory, ""), "/", "")
fi = fi[: string.rfind(fi, ".")]
# if so, add it to the pipe menu
print ' <item label="' + fi + '">'
# execute line to set wallpaper
print ' <action name="Execute"><execute>' + program + ' "' + di + '"</execute></action>'
# if we want to update config file, do so
if config == "yes":
print ' <action name="Execute"><execute>~/.config/openbox/wallmenu.py ' + di + "</execute></action>"
print " </item>"
def get_director(self): self.director = re.findall(r'yseria\t+(.*)\t+scenariusz', self.page) if len(self.director)>0: self.director = self.director[0] self.director = string.replace(self.director, "\t",'') self.director = string.replace(self.director, ",",", ") self.director = string.replace(self.director, ", (wi\xeacej ...)",'')
def regexp_escape (a_string): import string; r = a_string r = string.replace (r, '\\', '\\\\') r = string.replace (r, '/', '\\/') r = string.replace (r, '.', '\\.') return r
def filter_message(message):
"""
Filter a message body so it is suitable for learning from and
replying to. This involves removing confusing characters,
padding ? and ! with ". " so they also terminate lines
and converting to lower case.
"""
# to lowercase
message = string.lower(message)
# remove garbage
message = string.replace(message, "\"", "") # remove "s
message = string.replace(message, "\n", " ") # remove newlines
message = string.replace(message, "\r", " ") # remove carriage returns
# remove matching brackets (unmatched ones are likely smileys :-) *cough*
# should except out when not found.
index = 0
try:
while 1:
index = string.index(message, "(", index)
# Remove matching ) bracket
i = string.index(message, ")", index+1)
message = message[0:i]+message[i+1:]
# And remove the (
message = message[0:index]+message[index+1:]
except ValueError, e:
pass
def createLSFScript(cfgfile):
file=os.path.basename(cfgfile)
absDir=os.path.abspath(os.path.dirname(cfgfile))
outScript="runlsf_" + string.replace(file,".py",".csh")
outLog="runlsf_" + string.replace(file,".py",".log")
inScript=os.path.join(file)
outScript=os.path.join(absDir,outScript)
outLog=os.path.join(absDir,outLog)
oFile = open(outScript,'w')
oFile.write("#!/bin/csh" + "\n")
#oFile.write("\n")
oFile.write("cd " + absDir + "\n")
oFile.write("eval `scram runtime -csh`" + "\n")
#oFile.write("\n")
oFile.write("cmsRun " + inScript + "\n")
#oFile.write("date" + "\n")
oFile.close()
return
def sanitize(text):
"""
Sanitizes text for referral URLS and for not found errors
"""
text = string.replace(text, "<", "")
text = string.replace(text, ">", "")
return text
def CleanFileData(self, data):
""" clean the read file data and return it """
fresh = []
for i in data:
if string.strip(string.replace(i, '\012', '')) != '':
fresh.append(string.strip(string.replace(i, '\012', '')))
return fresh
def createCFGFiles(i,orgFile,basename,dir):
newFile=basename + "_" + str(i) + ".py"
newFile=os.path.join(dir,newFile)
print(newFile)
outFile = open(newFile,'w')
for iline in orgFile:
indx=string.find(iline,INPUTSTARTSWITH)
if (indx == 0):
indx2=string.find(iline,searchInput)
if (indx2 < 0):
print("Problem")
sys.exit(1)
else:
iline=string.replace(iline,searchInput,str(i))
indx=string.find(iline,OUTPUTSTARTSWITH)
if (indx == 0):
indx2=string.find(iline,searchOutput)
if (indx2 < 0):
print("Problem")
sys.exit(1)
else:
replString="_" + str(i) + searchOutput
iline=string.replace(iline,searchOutput,replString)
outFile.write(iline + "\n")
CloseFile(outFile)
return newFile
def formatElement(el,path):
if (el.find("{http://www.w3.org/2001/XMLSchema}annotation") is not None):
splitPath=string.split(path,'/')
#set default component to "scenario", i.e. write to the "Scenario" worksheet below
component="scenario"
printPath=string.replace(path,"/"+component,"")
#update component if a know child element of scenario, i.e. write to another worksheet below
if (len(splitPath)>2):
if (splitPath[2] in worksheets):
component=splitPath[2]
printPath=string.replace(printPath,"/"+component,"")
sheet= worksheets[component][0]
row=worksheets[component][1]
sheet.write(row,0,string.lstrip(printPath,"/"))
annotation=el.find("{http://www.w3.org/2001/XMLSchema}annotation")
docuElem=annotation.find("{http://www.w3.org/2001/XMLSchema}documentation")
if (docuElem is not None):
docu=docuElem.text
else:
docu="TODO"
content=string.strip(docu)
sheet.write(row,1,normalizeNewlines(content),docu_xf)
appInfoElem=el.find("{http://www.w3.org/2001/XMLSchema}annotation").find("{http://www.w3.org/2001/XMLSchema}appinfo")
if (appInfoElem is not None):
appInfo=string.strip(appInfoElem.text)
else:
appInfo="name:TODO"
appInfoList=string.split(appInfo,";")[0:-1]
for keyValue in appInfoList:
splitPair=string.split(keyValue,":")
colIndex=appinfoOrder.index(string.strip(str(splitPair[0])))+2
sheet.write(row,colIndex,splitPair[1],docu_xf)
#update next row to be written in that sheet
worksheets[component][1]=worksheets[component][1]+1
def get_rendereable_badgeset(account):
"""
Will return a badgset as follows:
theme
-badgeset
name
description
alt
key
perm(issions)
"""
badges = get_all_badges_for_account(account)
badgeset = []
for b in badges:
""" Badge id is theme-name-perm. spaces and " " become "-" """
name_for_id = string.replace(b.name, " ", "_")
name_for_id = string.replace(name_for_id, "-", "_")
theme_for_id = string.replace(b.theme, " ", "_")
theme_for_id = string.replace(theme_for_id, "-", "_")
badge_id = theme_for_id + "-" + name_for_id + "-" + b.permissions
item = {"name": b.name,
"description": b.description,
"alt":b.altText,
"key":b.key().name(),
"perm":b.permissions,
"theme" : b.theme,
"id": badge_id,
"downloadLink":b.downloadLink}
badgeset.append(item)
return badgeset
def get_cast(self):
self.cast = ''
tmp = gutils.trim(self.page_cast, '<h2>cast</h2>', '</table>')
elements = string.split(tmp, '<td class="name">')
for element in elements:
element = string.replace(element, '</a>', '$$$')
self.cast = self.cast + string.replace(re.sub('[$][$][$]$', '', re.sub('[ ]+', ' ', string.replace(gutils.clean(element), '\n', ''))), '$$$', _(' as ')) + '\n'
def lurk(bot):
print('lurink...')
handler = LabAPIHandler(bot.config.labstatus.api_url)
if handler.update_data():
lab_is_open = handler.get_lab_state()
lab_was_open = bot.memory['lab_was_open']
status_str = ''
if( lab_is_open and not lab_was_open ): # state changed to 'open'
status_str = 'geöffnet!'
elif( not lab_is_open and lab_was_open ): # state changed to 'closed'
status_str = 'geschlossen.'
else: # nothing happend
return
topic = string.replace(bot.config.labstatus.topic_draft, '$STATUS', status_str)
for channel in bot.channels:
bot.write(('TOPIC', channel + ' :' + string.replace(topic, '$CHANNEL', channel)))
bot.msg(channel, '+++ NEUER LAB-STATUS: ' + status_str + ' +++')
bot.memory['lab_was_open'] = lab_is_open
else:
print('API call failed');
def loadFile(fileName, width, height):
"""
Loads skin xml file and resolves embedded #include directives.
Returns completely loaded file as a string.
"""
log.debug("loadFile(%s, %d, %d)"%(fileName, width, height ) )
s = ""
f = file( fileName )
for l in f.readlines():
# log.debug(fileName + ":" + l)
m = sre.match( '^#include (.*)$', l )
if m:
incFile = m.group(1)
incFile = incFile.strip()
if sre.match( '^\w+\.xml$', incFile ):
# need to find skin file
incFile = findSkinFile( incFile, width, height )
elif sre.match( '\%SKINDIR\%', incFile ):
incFile = string.replace(incFile, "%SKINDIR%", getSkinDir())
else:
# convert path separators to proper path separator - just in case
incFile = string.replace( incFile, "/", os.sep )
incFile = string.replace( incFile, "\\", os.sep )
# assume relative path provided
path = os.path.dirname( fileName )
path += os.sep + incFile
incFile = path
s += loadFile( incFile, width, height )
else:
s += l
f.close()
return s
def get_payload(self):
s = self.firewall.to_json()
s = string.replace(s, 'inlist', "in")
s = string.replace(s, 'outlist', "out")
payload = {self._mn3: json.loads(s)}
return json.dumps(payload, default=lambda o: o.__dict__,
sort_keys=True, indent=4)
def get_plot(self):
self.plot = gutils.trim(self.page,"<td valign=\"top\" align=\"left\">","</td>")
self.plot = string.strip(self.plot.decode('latin-1'))
self.plot = string.replace(self.plot,"<br>", " ")
self.plot = string.replace(self.plot,"<p>", " ")
self.plot = string.replace(self.plot,"'","_")
self.plot = string.strip(gutils.strip_tags(self.plot))
def four11Path(self, filename411): """Translates 411 file names into UNIX absolute filenames.""" # Warning this is UNIX dependant n = string.replace(filename411, ".", "/") n = string.replace(n, "//", ".") return os.path.normpath(os.path.join(self.rootdir, n))
def render(self):
form = self.request.params
if not form.has_key("id"):
return "ERROR No job specified"
id = string.atoi(form["id"])
if form.has_key("prefix"):
prefix = form["prefix"]
prefix = string.replace(prefix, '<', '')
prefix = string.replace(prefix, '>', '')
prefix = string.replace(prefix, '/', '')
prefix = string.replace(prefix, '&', '')
prefix = string.replace(prefix, '\\', '')
elif form.has_key("phase") and form.has_key("test"):
id = self.lookup_detailid(id, form["phase"], form["test"])
if id == -1:
return "ERROR Specified test not found"
prefix = "test"
else:
prefix = ""
try:
filename = app.utils.results_filename(prefix, id)
self.request.response.body_file = file(filename, "r")
self.request.response.content_type="application/octet-stream"
self.request.response.content_disposition = "attachment; filename=\"%d.tar.bz2\"" % (id)
return self.request.response
except Exception, e:
if isinstance(e, IOError):
# We can still report error to client at this point
return "ERROR File missing"
else:
return "ERROR Internal error"
def precmd(self, line): """Handle alias expansion and ';;' separator.""" if not line: return line args = string.split(line) while self.aliases.has_key(args[0]): line = self.aliases[args[0]] ii = 1 for tmpArg in args[1:]: line = string.replace(line, "%" + str(ii), tmpArg) ii = ii + 1 line = string.replace(line, "%*", string.join(args[1:], ' ')) args = string.split(line) # split into ';;' separated commands # unless it's an alias command if args[0] != 'alias': marker = string.find(line, ';;') if marker >= 0: # queue up everything after marker next = string.lstrip(line[marker+2:]) self.cmdqueue.append(next) line = string.rstrip(line[:marker]) return line
def search(self, pattern='', context=''):
pattern = string.replace(string.lower(pattern),'*','%')
pattern = string.replace(string.lower(pattern),'?','_')
if pattern:
return self.select("context LIKE '%s'" % pattern, orderBy="context")
else:
return self.select(orderBy="context")
def render_admin_panel(self, req, cat, page, path_info):
req.perm.require('TRAC_ADMIN')
status, message = init_admin(self.gitosis_user, self.gitosis_server, self.admrepo, self.env.path)
data = {}
if status != 0:
add_warning(req, _('Error while cloning gitosis-admin repository. Please check your settings and/or passphrase free connection to this repository for the user running trac (in most cases, the web server user)'))
message = 'return code: '+str(status)+'\nmessage:\n'+message
if message:
add_warning(req, _(message))
repo = replace(os.path.basename(self.config.get('trac', 'repository_dir')), '.git', '')
if req.method == 'POST':
config = {}
self.log.debug('description: '+req.args.get('description'))
for option in ('daemon', 'gitweb', 'description', 'owner'):
config[option] = req.args.get(option)
self.set_config(repo, config)
req.redirect(req.href.admin(cat, page))
repo = replace(os.path.basename(self.config.get('trac', 'repository_dir')), '.git', '')
if repo != '':
data = self.get_config(repo)
self.log.debug('data: %s', str(data))
if not data:
data = {}
for option in ('daemon', 'gitweb', 'description', 'owner'):
if option not in data:
data[option] = ''
data['gitweb'] = data['gitweb'] in _TRUE_VALUES
data['daemon'] = data['daemon'] in _TRUE_VALUES
return 'admin_tracgitosis_repo.html', {'repo': data}
def __normalize_dell_charset(self, page_content):
page_content = replace(page_content, "<sc'+'ript", '')
page_content = replace(page_content, "</sc'+'ript", '')
t = ''.join(map(chr, range(256)))
d = ''.join(map(chr, range(128, 256)))
page_content = page_content.translate(t, d)
return page_content
def normalize(string):
string = string.replace(u"Ä", "Ae").replace(u"ä", "ae")
string = string.replace(u"Ö", "Oe").replace(u"ö", "oe")
string = string.replace(u"Ü", "Ue").replace(u"ü", "ue")
string = string.replace(u"ß", "ss")
string = string.encode("ascii", "ignore")
return string
def get_genre(self):
self.genre = gutils.trim(self.page,"Genre(s):","</table>")
self.genre = string.replace(self.genre, "<br>", ", ")
self.genre = gutils.strip_tags(self.genre)
self.genre = string.replace(self.genre, "/", ", ")
self.genre = gutils.clean(self.genre)
self.genre = self.genre[0:-1]
def _stringSource(target, source, env):
import string
return (str(target[0]) + ' <-\n |' +
string.replace(source[0].get_contents(), '\n', "\n |"))
def format_prize_amount(payout):
payout = string.replace(payout, ',', '')
payout = string.replace(payout, '$', '')
return float(payout)
def wild2regex(string):
"""Convert a Unix wildcard glob into a regular expression"""
return string.replace('.',
'\.').replace('*',
'.*').replace('?',
'.').replace('!', '^')
#! python
# -*- coding: utf-8 -*-
# (c) 2006 Werner Mayer LGPL
# FreeCAD report memory leaks script to get provide the log file of Visual Studio in more readable file.
import string, re
# Open the memory leak file
file = open("MemLog.txt")
lines = file.readlines()
file.close()
d = dict()
l = list()
for line in lines:
r = re.search("\\(#\\s*\\d+\\)", line)
if r is not None:
s = line[r.start():r.end()]
t = re.search("^Leak", line)
if t is not None:
m = d[s]
l.append(m)
else:
d[s] = line
file = open("MemLog_leaks.txt", "w")
for line in l:
line = string.replace(line, 'Alloc', 'Leak')
file.write(line)
file.close()
def str_attribute(self, k):
kt = replace(k, '_', '-')
if self.attlist[k]: return '%s: %s' % (kt, str(self[k]))
else: return self[k] and kt or ''
def strip_nick(message, sender):
return string.replace(string.strip(message),
nickname, sender)
def get_right_sep(fullPath):
return string.replace(fullPath, "\\", os.sep)
def get_genre(self):
self.genre = string.replace(
gutils.regextrim(self.page, 'Genre[s]*:<[^>]+>', '</div>'), '\n',
'')
self.genre = self.__before_more(self.genre)
def findFileName(filename):
filename = string.replace(filename, '\\', '/')
dataset_name = string.split(filename, '/')[-1]
return dataset_name
return mg, mg_c, cr1, cr2, cr3, cr4, cr5
countnuv = np.vectorize(countnuv)
# Function to find seperation in celestial coordinates.
cc = SkyCoord(RA, DEC, unit=(u.hourangle, u.deg))
def cel_separation(a, b):
coo = SkyCoord(a, b, frame='icrs', unit='deg')
return coo.separation(cc)
# To get on with MAST website queries.
ra = string.replace(RA, ':', '+')
dec = string.replace(DEC, ':', '+')
# Mast website form data.
mastdata = {
'__EVENTTARGET': '""',
'__EVENTARGUMENT': '""',
'__VIEWSTATE':
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',
'__VIEWSTATEGENERATOR': 'C84C2718',
'__EVENTVALIDATION':
'/wEdAAue+6xrb6xgp2ityzurA/pfWsTF2CBs9ziYHlDmus7EnHXVqisK/ch+FuYDN4RJj9bNygAwoalISibjyjYgoB7/Pb1PMsXU2LG7o+i6/zoft2ZmqVWZEJyWTGlJer/5/ymk9SeG9Y8RLbkbyiuf4BcRXP2SoyGCMZyu6LfyUjL5ZgAB13huDNxtBirRDFLR6zW3raPnQUy5sK21W/3eiEs/KUQOVtp9GallVy/IsFMIp4yMEruOYx0KrV7GUndYi0m5y40+',
'_ctl10:txtTargetName': '',
'_ctl10:resolverDropList': 'SIMBAD',
'_ctl10:txtRadius': '0.4',
'_ctl10:txtRA': ra,
def Hopach(self, cluster_method, metric_gene, force_gene, metric_array,
force_array):
print_out = r('library("hopach")')
if "Error" in print_out:
print 'Installing the R package "hopach" in Config/R'
print_out = r(
'source("http://bioconductor.org/biocLite.R"); biocLite("hopach")'
)
if "Error" in print_out:
print 'unable to download the package "hopach"'
forceError
print_out = r('library("hopach")')
filename = self.File()
#r('memory.limit(2000)')
print "Begining to process", filename, "using HOPACH"
metric_g = self.format_value_for_R(metric_gene)
metric_a = self.format_value_for_R(metric_array)
parse_line = 'data<-read.table(%s,sep="\t",as.is=T,row.names=1,header=T)' % filename
checklinelengths(self._file)
print_out = r(parse_line)
#print parse_line
dat = r['data']
#print "Number of columns in input file:",len(dat)
print_out = r('data<-as.matrix(data)')
dat = r['data']
#print "Number of columns in matrix:",len(dat)
force1 = ''
force2 = ''
hopg = 'NULL'
hopa = 'NULL'
distmatg = 'NULL'
distmata = 'NULL' ### defaults for tree export
if force_gene != '' and force_gene != 0:
force1 = ',kmax=' + str(force_gene) + ', khigh=' + str(force_gene)
if force_array != '' and force_array != 0:
force2 = ',kmax=' + str(force_array) + ', khigh=' + str(
force_array)
if cluster_method == 'both' or cluster_method == 'gene':
distance_matrix_line = 'distmatg<-distancematrix(data,d=%s)' % metric_g
#print distance_matrix_line
if len(dat) > 1:
print_out1 = r(distance_matrix_line)
print_out2 = r('hopg<-hopach(data,dmat=distmatg,ord="own"' +
force1 + ')')
#print 'hopg<-hopach(data,dmat=distmatg,ord="own"'+force1+')'
try:
hopach_run = r['hopg']
except Exception:
print print_out1
print print_out2
sys.exit()
hopg = 'hopg'
distmatg = 'distmatg'
gene_output = self.HopachGeneOutputFilename(
metric_gene, str(force_gene))
output = 'out<-makeoutput(data,hopg,file=%s)' % gene_output
#print output
print_out = r(output)
output_file = r['out']
status = 'stop'
if 'clustering' in hopach_run:
if 'order' in hopach_run['clustering']:
try:
if len(hopach_run['clustering']['order']) > 10:
status = 'continue'
except TypeError:
error = 'file: ' + filename + ": Hopach returned the array of cluster orders as blank while clustering GENES... can not process cluster... continuing with other files"
print error
errors.append(error)
if status == 'continue':
r(output_file)
print 'hopach output written'
else:
error = 'file: ' + filename + " Hopach returned data-matrix length zero...ARRAY clusters can not be generated"
print error
errors.append(error)
if cluster_method == 'both' or cluster_method == 'array':
distance_matrix_line = 'distmata<-distancematrix(t(data),d=%s)' % metric_a
if len(dat) > 1:
dist = r(distance_matrix_line)
#print distance_matrix_line
print_out = r('hopa<-hopach(t(data),dmat=distmata,ord="own"' +
force2 + ')')
#print 'hopa<-hopach(t(data),dmat=distmata,ord="own"'+force2+')'
hopach_run = r['hopa']
hopa = 'hopa'
distmata = 'distmata'
array_output = self.HopachArrayOutputFilename(
metric_array, str(force_array))
output = 'out<-makeoutput(t(data),hopa,file=%s)' % array_output
#print output
print_out = r(output)
output_file = r['out']
status = 'stop'
if 'clustering' in hopach_run:
if 'order' in hopach_run['clustering']:
try:
if len(hopach_run['clustering']['order']) > 10:
status = 'continue'
except TypeError:
error = 'file: ' + filename + ": Hopach returned the array of cluster orders as blank while clustering ARRAYS... can not process cluster"
print error
errors.append(error)
if status == 'continue':
r(output_file)
print 'hopach output written'
else:
error = 'file: ' + filename + "data-matrix length zero...ARRAY clusters can not be generated...continuing analysis"
print error
errors.append(error)
if len(metric_g) == 0: metric_g = 'NULL'
if len(metric_a) == 0: metric_a = 'NULL'
try:
output_filename = string.replace(gene_output, 'rows.', '')
cdt_output_line = 'hopach2tree(data, file = %s, hopach.genes = %s, hopach.arrays = %s, dist.genes = %s, dist.arrays = %s, d.genes = %s, d.arrays = %s, gene.wts = NULL, array.wts = NULL, gene.names = NULL)' % (
output_filename, hopg, hopa, distmatg, distmata, metric_g,
metric_a) ###7 values
except Exception:
None
#make_tree_line = 'makeTree(labels, ord, medoids, dist, side = "GENE")' ### Used internally by HOPACH
#print cdt_output_line
try:
print_out = r(cdt_output_line)
except Exception:
None
def findParentDir(filename):
filename = string.replace(filename, '//', '/')
filename = string.replace(filename, '\\', '/')
x = string.find(filename[::-1], '/') * -1
return filename[:x]
import math
import random
import copy
import os
import os.path
try:
from rpy import r
print "\n---------Using RPY---------\n"
except Exception:
from pyper import *
print "\n---------Using PypeR---------\n"
r = R(use_numpy=True)
### Create a Directory for R packages in the AltAnalyze program directory (in non-existant)
r_package_path = string.replace(os.getcwd() + '/Config/R', '\\',
'/') ### R doesn't link \\
try:
os.mkdir(r_package_path)
except Exception:
None
### Set an R-package installation path
command = '.libPaths("' + r_package_path + '")'
r(command) ### doesn't work with %s for some reason
#print_out = r('.libPaths()');print print_out; sys.exit()
def remoteMonocle(samplelogfile,
genes=[],
expPercent=50,
pval=0.01,
def cleanUpLine(line):
line = string.replace(line, '\n', '')
line = string.replace(line, '\c', '')
data = string.replace(line, '\r', '')
data = string.replace(data, '"', '')
return data
def _checkFunction(module, func, c=None, main=0, in_class=0):
"Return a list of Warnings found in a function/method."
# always push a new config object, so we can pop at end of function
utils.pushConfig()
code = CodeChecks.Code()
code.init(func)
if main:
for key in func.function.func_globals.keys():
code.unusedLocals[key] = -1
codeSource = CodeChecks.CodeSource(module, func, c, main, in_class, code)
try:
_checkCode(code, codeSource)
if not in_class:
_findUnreachableCode(code)
# handle lambdas and nested functions
codeSource.calling_code.append(func)
for func_code in code.codeObjects.values():
_handleNestedCode(func_code, code, codeSource)
del codeSource.calling_code[-1]
except (SystemExit, KeyboardInterrupt):
exc_type, exc_value, exc_tb = sys.exc_info()
raise exc_type, exc_value
except:
exc_type, exc_value, exc_tb = sys.exc_info()
exc_list = traceback.format_exception(exc_type, exc_value, exc_tb)
for index in range(0, len(exc_list)):
exc_list[index] = string.replace(exc_list[index], "\n", "\n\t")
code.addWarning(msgs.CHECKER_BROKEN % string.join(exc_list, ""))
if cfg().checkReturnValues:
_checkReturnWarnings(code)
if cfg().localVariablesUsed:
for var, line in code.unusedLocals.items():
if line is not None and line > 0 and _name_unused(var):
code.addWarning(msgs.UNUSED_LOCAL % var, line)
if cfg().argumentsUsed:
op = code.getFirstOp()
if not (OP.RAISE_VARARGS(op) or OP.RETURN_VALUE(op)):
for var, line in code.unusedLocals.items():
_checkUnusedParam(var, line, func, code)
# Check code complexity:
# loops should be counted as one branch, but there are typically 3
# branches in byte code to setup a loop, so subtract off 2/3's of them
# / 2 to approximate real branches
branches = (len(code.branches.keys()) - (2 * code.loops)) / 2
lines = (code.getLineNum() - code.func_code.co_firstlineno)
returns = len(code.returnValues)
if not main and not in_class:
args = code.func_code.co_argcount
locals = len(code.func_code.co_varnames) - args
_checkComplex(code, cfg().maxArgs, args, func, msgs.TOO_MANY_ARGS)
_checkComplex(code,
cfg().maxLocals, locals, func, msgs.TOO_MANY_LOCALS)
_checkComplex(code, cfg().maxLines, lines, func, msgs.FUNC_TOO_LONG)
_checkComplex(code, cfg().maxReturns, returns, func, msgs.TOO_MANY_RETURNS)
_checkComplex(code,
cfg().maxBranches, branches, func, msgs.TOO_MANY_BRANCHES)
if not (main or in_class):
utils.popConfig()
func.returnValues = code.returnValues
return (code.warnings, code.globalRefs, code.functionsCalled,
code.codeObjects.values(), code.returnValues)
def AffyNormalization(self, normalization_method, probe_level,
batch_effects):
print 'Loading affy package in R'
print_out = r('library("affy")')
if "Error" in print_out:
#print_out = r('install.packages("ggplot2", repos="http://cran.us.r-project.org")')
print 'Installing the R package "affy" in Config/R'
print_out = r(
'source("http://bioconductor.org/biocLite.R"); biocLite("affy")'
)
if "Error" in print_out:
print 'unable to download the package "affy"'
forceError
print_out = r('library("affy")')
if 'gcrma' in normalization_method:
print 'Loading gcrma package in R'
print_out = r('library("gcrma")')
if "Error" in print_out:
print 'Installing the R package "gcrma" in Config/R'
print_out = r(
'source("http://bioconductor.org/biocLite.R"); biocLite("gcrma")'
)
if "Error" in print_out:
print 'unable to download the package "gcrma"'
forceError
print_out = r('library("gcrma")')
if batch_effects == 'remove':
### Import or download support for SVA/Combat
print 'Loading sva package in R'
print_out = r('library("sva")')
if "Error" in print_out:
print 'Installing the R package "sva" in Config/R'
print_out = r(
'source("http://bioconductor.org/biocLite.R"); biocLite("sva")'
)
if "Error" in print_out:
print 'unable to download the package "sva"'
forceError
print_out = r('library("sva")')
print "Reading Affy files..."
print_out = r('rawdata<-ReadAffy()')
print print_out
r('setwd("ExpressionInput")')
if probe_level: ### normalize at the level of probes rahter than probeset (e.g., alt.exon analysis of 3' array)
print_out = r('PM<-probes(rawdata,which="pm")')
print print_out
print_out = r('AffyInfo<-dimnames(PM)[[1]]')
print print_out
print_out = r('cutpos<-regexpr("\\d+$",AffyInfo,perl=T)')
print print_out
print_out = r('AffyID<-substr(AffyInfo,1,cutpos-1)')
print print_out
print_out = r(
'probe<-as.numeric(substr(AffyInfo,cutpos,nchar(AffyInfo)))')
print print_out
print_out = r('data.bgc<-bg.correct(rawdata,method="rma")')
print print_out
print_out = r(
'data.bgc.q<-normalize.AffyBatch.quantiles(data.bgc,type="pmonly")'
)
print print_out
print_out = r('pm.bgc.q<-probes(data.bgc.q,which="pm")')
print print_out
print_out = r('normalized<-cbind(AffyID,probe,pm.bgc.q)')
print print_out
command = 'write.table(normalized,file=' + self.File(
) + ',sep="\t",row.names=FALSE, quote=FALSE)'
print_out = r(command)
print print_out
print 'probe-level normalization complete'
else:
print "Begining %s normalization (will install array annotations if needed)... be patient" % normalization_method
print_out = r('normalized<-%s(rawdata)') % normalization_method
print print_out
command = 'write.exprs(normalized,' + self.File() + ')'
print_out = r(command)
print print_out
print self.File(), 'written...'
if batch_effects == 'remove':
### Import data
command = 'mod = model.matrix(~as.factor(cancer) + age, data=pheno)'
print_out = r(command)
command = 'cdata = ComBat(dat=normalized, batch=as.factor(pheno$batch), mod=mod, numCov=match("age", colnames(mod)))'
print_out = r(command)
command = 'write.table(cdata,file=' + self.File(
) + ',sep="\t",row.names=FALSE, quote=FALSE)'
print_out = r(command)
output_file = string.replace(self.File(), 'exp.', 'stats.')
print_out = r('calls<-mas5calls(rawdata)')
#print_out = r('pvals<-se.exprs(calls)') ### outdated?
print_out = r('pvals<-assayData(calls)[["se.exprs"]]')
command = 'write.table(pvals,' + output_file + ',sep = "\t", col.names = NA)'
print_out = r(command)
print output_file, 'written...'
def get_platform():
"""Return a string that identifies the current platform. This is used
mainly to distinguish platform-specific build directories and
platform-specific built distributions. Typically includes the OS name
and version and the architecture (as supplied by 'os.uname()'),
although the exact information included depends on the OS; eg. for IRIX
the architecture isn't particularly important (IRIX only runs on SGI
hardware), but for Linux the kernel version isn't particularly
important.
Examples of returned values:
linux-i586
linux-alpha (?)
solaris-2.6-sun4u
irix-5.3
irix64-6.2
For non-POSIX platforms, currently just returns 'sys.platform'.
"""
if os.name != "posix" or not hasattr(os, 'uname'):
# XXX what about the architecture? NT is Intel or Alpha,
# Mac OS is M68k or PPC, etc.
return sys.platform
# Try to distinguish various flavours of Unix
(osname, host, release, version, machine) = os.uname()
# Convert the OS name to lowercase, remove '/' characters
# (to accommodate BSD/OS), and translate spaces (for "Power Macintosh")
osname = string.lower(osname)
osname = string.replace(osname, '/', '')
machine = string.replace(machine, ' ', '_')
machine = string.replace(machine, '/', '-')
if osname[:5] == "linux":
# At least on Linux/Intel, 'machine' is the processor --
# i386, etc.
# XXX what about Alpha, SPARC, etc?
return "%s-%s" % (osname, machine)
elif osname[:5] == "sunos":
if release[0] >= "5": # SunOS 5 == Solaris 2
osname = "solaris"
release = "%d.%s" % (int(release[0]) - 3, release[2:])
# fall through to standard osname-release-machine representation
elif osname[:4] == "irix": # could be "irix64"!
return "%s-%s" % (osname, release)
elif osname[:3] == "aix":
return "%s-%s.%s" % (osname, version, release)
elif osname[:6] == "cygwin":
osname = "cygwin"
rel_re = re.compile(r'[\d.]+')
m = rel_re.match(release)
if m:
release = m.group()
elif osname[:6] == "darwin":
#
# For our purposes, we'll assume that the system version from
# distutils' perspective is what MACOSX_DEPLOYMENT_TARGET is set
# to. This makes the compatibility story a bit more sane because the
# machine is going to compile and link as if it were
# MACOSX_DEPLOYMENT_TARGET.
from distutils.sysconfig import get_config_vars
cfgvars = get_config_vars()
macver = os.environ.get('MACOSX_DEPLOYMENT_TARGET')
if not macver:
macver = cfgvars.get('MACOSX_DEPLOYMENT_TARGET')
if not macver:
# Get the system version. Reading this plist is a documented
# way to get the system version (see the documentation for
# the Gestalt Manager)
try:
f = open('/System/Library/CoreServices/SystemVersion.plist')
except IOError:
# We're on a plain darwin box, fall back to the default
# behaviour.
pass
else:
m = re.search(
r'<key>ProductUserVisibleVersion</key>\s*' +
r'<string>(.*?)</string>', f.read())
f.close()
if m is not None:
macver = '.'.join(m.group(1).split('.')[:2])
# else: fall back to the default behaviour
if macver:
from distutils.sysconfig import get_config_vars
release = macver
osname = "macosx"
if (release + '.') >= '10.4.' and \
get_config_vars().get('UNIVERSALSDK', '').strip():
# The universal build will build fat binaries, but not on
# systems before 10.4
machine = 'fat'
elif machine in ('PowerPC', 'Power_Macintosh'):
# Pick a sane name for the PPC architecture.
machine = 'ppc'
return "%s-%s-%s" % (osname, release, machine)
attrlist = set()
contentHandler = parseXML(attrlist)
parser.setContentHandler(contentHandler)
if not no_comments:
parser.setProperty(property_lexical_handler, contentHandler)
for arg in sys.argv[1:]:
if os.path.isdir(arg):
for file in os.listdir(arg):
if (file.endswith(".xml")):
parser.parse(os.path.join(arg, file))
else:
parser.parse(arg)
attrlist = list(attrlist)
attrlist.sort(key=lambda a: a[0])
for (k, c) in attrlist:
print()
print('#: ' + arg)
string.replace(k, "\\n", "\"\n\"")
if c:
for l in c.split('\n'):
print("#. ", l)
print('msgid "' + str(k) + '"')
print('msgstr ""')
attrlist = set()
def cleanupWordsString(str):
str = string.replace(str, ".", " ")
str = string.replace(str, "!", " ")
str = string.replace(str, "?", " ")
str = string.replace(str, ",", " ")
str = string.replace(str, "'", " ")
str = string.replace(str, '"', " ")
str = string.replace(str, ";", " ")
str = string.replace(str, "(", " ")
str = string.replace(str, ")", " ")
str = string.replace(str, "{", " ")
str = string.replace(str, "}", " ")
str = string.replace(str, "<", " ")
str = string.replace(str, ">", " ")
str = string.replace(str, "=", " ")
str = string.replace(str, "/", " ")
str = string.replace(str, "*", " ")
str = string.replace(str, ":", " ")
str = string.replace(str, "#", " ")
str = string.replace(str, "\\", " ")
str = string.replace(str, "\n", " ")
str = string.replace(str, "\r", " ")
str = string.replace(str, "\xc2", " ")
str = string.replace(str, "\xa0", " ")
return str
#!/usr/bin/env python
import sys
import numpy as nmp
from os import system
from netCDF4 import Dataset
from string import replace
if len(sys.argv) != 2:
print 'Usage: ' + sys.argv[0] + ' <nemo_bathy.nc>'
sys.exit(0)
cf_old = sys.argv[1]
cf_new = replace(cf_old, '.nc', '_new.nc')
cv_bathy = 'Bathymetry'
# First, creating a copy:
system('rm -f ' + cf_new)
system('cp ' + cf_old + ' ' + cf_new)
print '\n'
# Opening the Netcdf file:
f_new = Dataset(cf_new, 'r+')
print 'File ', cf_new, 'is open...\n'
Xbathy = f_new.variables[cv_bathy][:, :]
# Edit zone:
def safely_replace(string: str, replaced_substring: str,
new_substring: str) -> str:
if replaced_substring not in string:
raise ValueError(f'Expecting {replaced_substring} to be in {string}.')
return string.replace(replaced_substring, new_substring)
for (extdirpath, extdirnames, extfilenames) in os.walk(extractionDir):
for extfname in extfilenames:
#TODO check for actual output name because there will be more than 1 bin file for t16
if extfname[-4:] == ".bin":
runLine = False
if (not os.path.isdir(extractionDir) or runLine) and rightTracker:
mmfFile = dirpath + os.sep + filename
pathComponents = dirpath.split(os.sep)
dirLength = len(pathComponents)
lineHandle = functions.sanitizeForFileName(lineName)
batchScriptDir = os.path.dirname(fullProjectDirPath) + os.sep + settings.batchScriptDirProjectsSuffix + os.sep + 'extraction'
if not os.path.exists(batchScriptDir):
os.makedirs(batchScriptDir)
shfile = batchScriptDir + '/' + lineHandle + '_' + tracker + '.sh'
if not os.path.isdir(extractionDir):
os.makedirs(extractionDir)
shfile = batchScriptDir + '/' + lineHandle + '_' + tracker + '.sh'
extractFile = extractionDir + os.sep + lineHandle + '.bxx'
functions.createExtractFile(extractFile, mmfFile, extractionDir, extractionOptions)
functions.createQsubExtractFile(shfile, extractFile, settings.settingsDir, os.path.dirname(mmfFile))
jobName = 'ext' + lineHandle + '_' + str(njob) ;
qsubOut = shfile[:-3] + '.log'
#qsubCommand = 'qsub -l short -N ' + settings.supplementaryQsubParams[tracker] + 'ext_' + string.replace(lineName[:11],'@','_') + ' -j y -b y -o ' + qsubOut + ' -cwd ' + shfile
qsubCommand = 'bsub -J ' + settings.supplementaryQsubParams[tracker] + 'ext_' + string.replace(lineName[:11],'@','_') + ' -o ' + qsubOut + ' ' + shfile
os.system("chmod 755 " + shfile)
#qsubCommand = shfile
njob = njob + 1
functions.addQsubToQueue(qsubCommand)
functions.runAllQsubsToCompletion()
def create(self):
self._dmplugin = PlugInManager().getPlugInInstance("DepManPlugIn")
if self._dmplugin == None:
self.reportError("PlugIn `depman` not found")
return False
#user questions
if self._is_Interactive:
self._group = raw_input("Group: ")
self._artifact = raw_input("Artifact: ")
self._version = raw_input("Version: ")
tmpstr = ""
for p in self._dmplugin.getSupportedPlatforms():
tmpstr = tmpstr + p + " "
print "( ", tmpstr, ")"
tmstr = "Platform [*]:"
self._platform = raw_input(
string.replace(tmstr, "*", self._dmplugin.getOSPlatform()))
if len(self._platform) == 0:
self._platform = self._dmplugin.getOSPlatform()
tmpstr = ""
for p in self._dmplugin.getSupportedCompilers():
tmpstr = tmpstr + p + " "
print "( ", tmpstr, ")"
tmstr = "Compiler [*]:"
self._compiler = raw_input(
string.replace(tmstr, "*", self._dmplugin.getOSCompiler()))
if len(self._compiler) == 0:
self._compiler = self._dmplugin.getOSCompiler()
tmpstr = ""
for p in self._dmplugin.getSupportedArchs():
tmpstr = tmpstr + p + " "
print "( ", tmpstr, ")"
tmstr = "Architecture [*]:"
self._arch = raw_input(
string.replace(tmstr, "*", self._dmplugin.getOSArch()))
if len(self._arch) == 0:
self._arch = self._dmplugin.getOSArch()
tmpstr = ""
for p in self._dmplugin.getSupportedLibraryTypes():
tmpstr = tmpstr + p + " "
print "( ", tmpstr, ")"
self._ltype = raw_input("Library Type: ")
upload_response = raw_input("Upload to server? (y/n): ")
if upload_response == "y" or upload_response == "yes":
self._upload = True
if self._packageNode != None:
for n in self._packageNode.childNodes:
if n.localName == "package":
processPackage = True
if n.hasAttributes():
if n.attributes.has_key("platform"):
values = n.attributes.get("platform").value.split(
",")
if self._dmplugin.getOSPlatform() in values:
processPackage = True
else:
processPackage = False
if processPackage:
print "Processing for platform..."
for p in n.childNodes:
if p.localName == "group":
self._group = p.childNodes[0].nodeValue
if p.localName == "artifact":
self._artifact = p.childNodes[0].nodeValue
if p.localName == "version":
self._version = p.childNodes[0].nodeValue
if p.localName == "platform":
self._platform = p.childNodes[0].nodeValue
if p.localName == "compiler":
self._compiler = p.childNodes[0].nodeValue
if p.localName == "arch":
self._arch = p.childNodes[0].nodeValue
if p.localName == "libraryType":
self._ltype = p.childNodes[0].nodeValue
if p.localName == "upload":
#TODO: Maybe upload should be an external plugin
for k in p.childNodes:
if k.localName == "sshserver":
self._default_ssh = k.childNodes[
0].nodeValue
if k.localName == "destdir":
self._default_destdir = k.childNodes[
0].nodeValue
if k.localName == "username":
self._default_login = k.childNodes[
0].nodeValue
if self._group == "":
self.reportError("Group cannot be empty")
return False
if self._artifact == "":
self.reportError("Artifact cannot be empty")
return False
if self._version == "":
self.reportError("Version cannog be empty")
return
self._group = self._group.replace(".", "/")
if self._platform == "default":
self._platform = self._dmplugin.getOSPlatform()
if self._compiler == "default":
self._compiler = self._dmplugin.getOSCompiler()
if self._arch == "default":
self._arch = self._dmplugin.getOSArch()
#let's check user input consistency
if self._platform not in self._dmplugin.getSupportedPlatforms():
self.reportError("Platform not supported: " + self._platform +
". Supported platforms:" +
str(self._dmplugin.getSupportedPlatforms()))
return False
if self._compiler not in self._dmplugin.getSupportedCompilers():
self.reportError("Compiler not supported: " + self._compiler +
". Supported compilers:" +
str(self._dmplugin.getSupportedCompilers()))
return False
if self._arch not in self._dmplugin.getSupportedArchs():
self.reportError("Architecture not supported: " + self._arch +
". Supported archs:" +
str(self._dmplugin.getSupportedArchs()))
return False
if self._ltype not in self._dmplugin.getSupportedLibraryTypes():
self.reportError("Library type not supported: " + self._ltype +
". Supported libraries:" +
str(self._dmplugin.getSupportedLibraryTypes()))
return False
#artifact and md5 generation
file_name = self._artifact + "-" + self._version + "-" + self._platform + "-" + self._compiler + "-" + self._arch + "-" + self._ltype
tarname = file_name + ".tar.gz"
md5name = tarname + ".md5"
dmfile = file_name + ".xml"
dmutil = BMUtil()
tmpdir = self._dmplugin.getDepManPath(
) + os.path.sep + ".cache" + os.path.sep + self._group + os.path.sep + self._artifact + os.path.sep + self._version + os.path.sep + self._platform + os.path.sep + self._compiler + os.path.sep + self._arch + os.path.sep + self._ltype
dmutil.mkdir(tmpdir)
print tmpdir + os.path.sep + tarname, self._path
dmutil.targz(os.path.join(tmpdir, tarname), self._path)
#print "targz ",tmpdir+os.path.sep+tarname
dmutil.createMD5(tmpdir + os.path.sep + tarname,
tmpdir + os.path.sep + md5name)
if self._xmlfile != "":
shutil.copyfile(self._xmlfile, tmpdir + os.path.sep + dmfile)
print "Artifact " + tarname + " created in:\n" + tmpdir
if self._upload:
dmutil.rmdir(
".dmn_tmp") # Prevent for uploading bad previous compilations!
sshtmpdir = ".dmn_tmp" + os.path.sep + self._group + os.path.sep + self._artifact + os.path.sep + self._version + os.path.sep + self._platform + os.path.sep + self._compiler + os.path.sep + self._arch + os.path.sep + self._ltype
dmutil.mkdir(sshtmpdir)
shutil.copyfile(tmpdir + os.path.sep + tarname,
sshtmpdir + os.path.sep + tarname)
shutil.copyfile(tmpdir + os.path.sep + md5name,
sshtmpdir + os.path.sep + md5name)
if self._xmlfile != "":
shutil.copyfile(tmpdir + os.path.sep + dmfile,
sshtmpdir + os.path.sep + dmfile)
url = self._default_ssh
destdir = self._default_destdir
login = self._default_login
if self._is_Interactive:
tmstr = "SSH Server [*]:"
url = raw_input(string.replace(tmstr, "*", self._default_ssh))
if len(url) == 0:
url = self._default_ssh
tmstr = "Destination Directory [*]:"
destdir = raw_input(
string.replace(tmstr, "*", self._default_destdir))
if len(destdir) == 0:
destdir = self._default_destdir
tmstr = "Login [*]:"
login = raw_input(
string.replace(tmstr, "*", self._default_login))
if len(login) == 0:
login = self._default_login
download_dir = self._group + "/" + self._artifact + "/" + self._version + "/" + self._platform + "/" + self._compiler + "/" + self._arch + "/" + self._ltype
print "* Uploading ", tarname
print "* Uploading ", md5name
#scp
base_ssh = destdir
url_ssh = url
scpcommand = "scp"
pscppath = ""
if sys.platform == "win32":
scpcommand = self._dmplugin.getDepManDataPath(
) + os.path.sep + "win32" + os.path.sep + "pscp.exe"
scpcommand = '"' + os.path.normpath(scpcommand) + '"'
cmdstr = scpcommand + " -r " + ".dmn_tmp" + os.path.sep + "*" + " " + login + "@" + url_ssh + ":" + base_ssh
print cmdstr
os.system(cmdstr)
#scp
dmutil.rmdir(".dmn_tmp")
colon_from_end = st.find(line[1][::-1], ':')
if colon_from_end >= 0:
start_i = len(line[1]) - colon_from_end
if line[1][start_i] == '0':
lookahead = 1
while line[1][start_i + lookahead] == '0':
lookahead += 1
if line[1][start_i + lookahead] == '.':
start_i += lookahead - 1
else:
start_i += lookahead
precolon = line[1][:start_i]
line[1] = line[1][start_i:]
else:
precolon = ""
params.append([line[0], np.float(st.replace(line[1], 'D', 'e')), \
np.float(st.replace(line[3], 'D', 'e')), precolon])
# Convert frequency and frequency derivatives to period and period
# derivatives if flags['-p'] = True
already_gave_F0_warning = False
f0 = 0.0
deriv = -1
if flags['-p']:
for i in range(0, len(params)):
success = True
freq = True
name = params[i][0]
ndigits = len(name) - 1
if name[0] == 'F' and (ndigits == 1 or ndigits == 2):
if ndigits == 1: deriv = np.int(name[1])
def doRun(self, PassedCommString):
"""This method is responsible for the processing of the 'run' command."""
# Tokenize!
self._commString = PassedCommString
self._commTokens = PassedCommString.split()
myCommandCount = 0
myServerGroupList = []
myServerNameList = []
myRunTarget = ''
myIsNow = False
myIsReverse = False
myIsSingle = False
myIsRunInThreads = False
#
# Step 1: Create our own tokens, and check for SSH flags and
# the special-case keywords. (i.e. now, reverse, single)
#
if (self._commString.find('"') == -1):
myError = "Command Syntax Error. Try 'help run' for more information."
self._globalConfig.getMultiLogger().LogMsgWarn(myError)
return False
# Get substr indexes.
myFirstQuoteIndex = self._commString.find('"')
myLastQuoteIndex = self._commString.rfind('"')
myPrefixStr = self._commString[0:myFirstQuoteIndex]
myBodyStr = self._commString[myFirstQuoteIndex:(myLastQuoteIndex + 1)]
mySuffixStr = self._commString[myLastQuoteIndex + 1:]
# Check for pass-through SSH flags
if (myPrefixStr.find('-') != -1):
myFlagStr = ' ' + myPrefixStr[myPrefixStr.find('-'):]
myFlagStr = myFlagStr.rstrip()
else:
myFlagStr = ''
# Check for special-case keywords.
if (mySuffixStr.find(' now') != -1):
myIsNow = True
mySuffixStr = string.replace(mySuffixStr, ' now', '')
if (mySuffixStr.find(' reverse') != -1):
myIsReverse = True
mySuffixStr = string.replace(mySuffixStr, ' reverse', '')
if (mySuffixStr.find(' single') != -1):
myIsSingle = True
mySuffixStr = string.replace(mySuffixStr, ' single', '')
if (mySuffixStr.find(' threads') != -1):
myIsRunInThreads = True
mySuffixStr = string.replace(mySuffixStr, ' threads', '')
#
# Step 2: Try to determine what the target of the command is
# and set a state-tracking variable accordingly.
#
if (len(mySuffixStr) == 0):
# run "uptime"
# run -t "uptime"
myRunTarget = 'current_server_group'
# Check for syntax errors.
elif (mySuffixStr.find(' on ') == -1):
myError = "Command Syntax Error. Try 'help run' for more information."
self._globalConfig.getMultiLogger().LogMsgWarn(myError)
return False
elif (mySuffixStr.find(',') == -1):
# run "uptime" on app
# run -t "uptime" on app
# run "uptime" on app01
# run -t "uptime" on app01
myRunTarget = 'single_server_group'
else:
# run "uptime" on app, www
# run -t "uptime" on app, www
# run "uptime" on app01, www01
# run -t "uptime" on app01, www01
myRunTarget = 'multiple_server_group'
# Assuming no error up until my point we can now
# throw out the " on " part of our command.
myGroupStr = mySuffixStr[mySuffixStr.find(' on ') + 4:]
myGroupStr = myGroupStr.strip()
#
# Step 3: Assemble two lists based on command syntax.
#
# myServerNameList will contain a list of server names.
# -or-
# myServerGroupList will contain a list of server groups.
#
if (myRunTarget == 'current_server_group'):
myGroupStr = self._globalConfig.getCurrentServerGroup().getName()
myServerGroupList.append(myGroupStr)
elif (myRunTarget == 'single_server_group'):
# Check for server name match.
myServer = self._globalConfig.getCurrentEnv().getServerByName(
myGroupStr)
if (myServer):
myServerNameList.append(myServer.getName())
else:
# Check for server group match, with and without attributes.
myServerGroup = self._globalConfig.getCurrentEnv(
).getServerGroupByName(myGroupStr)
# Validate.
if (not myServerGroup):
myError = "No matching server name or group '" + \
self._globalConfig.getCurrentEnv().getServerGroupName(myGroupStr) + "'."
self._globalConfig.getMultiLogger().LogMsgError(myError)
return False
else:
myServerGroupList.append(myGroupStr)
elif (myRunTarget == 'multiple_server_group'):
myGroupList = myGroupStr.split(',')
for myLoopStr in myGroupList:
myLoopStr = myLoopStr.strip()
# Check for server name match.
myServer = self._globalConfig.getCurrentEnv().getServerByName(
myLoopStr)
if (myServer):
myServerNameList.append(myServer.getName())
continue
# Check for server group match, with and without attributes.
myServerGroup = self._globalConfig.getCurrentEnv(
).getServerGroupByName(myLoopStr)
# Validate.
if (not myServerGroup):
if (not self._globalConfig.isBatchMode()):
myError = "No matching server name or group '" + \
self._globalConfig.getCurrentEnv().getServerGroupName(myLoopStr) + "'."
self._globalConfig.getMultiLogger().LogMsgError(
myError)
return False
else:
myServerGroupList.append(myLoopStr)
#
# Step 4: Make sure noone's trying to mix
# server hostnames and server group names together.
#
if ((len(myServerNameList) > 0) and (len(myServerGroupList) > 0)):
myError = "Mixing of server name(s) and server group(s) is unsupported."
self._globalConfig.getMultiLogger().LogMsgError(myError)
return False
#
# Step 5: Must make sure...are you sure you're sure?
#
if ((not self._globalConfig.isBatchMode()) and (not myIsNow)):
myDisplayStr = ''
if (len(myServerNameList) > 0):
for myNameStr in myServerNameList:
myDisplayStr = myDisplayStr + myNameStr + ','
myDisplayStr = myDisplayStr.rstrip(',')
# Are you sure?
myInfo = "Run command " + myBodyStr + " on server(s) " + \
myDisplayStr + "?"
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
if (not self.doAreYouSure()):
myInfo = "Aborting command."
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
return False
else:
for myGroupStr in myServerGroupList:
myDisplayStr = myDisplayStr + myGroupStr + ','
myDisplayStr = myDisplayStr.rstrip(',')
# Are you sure?
myInfo = "Run command " + myBodyStr + " on server group(s) " + \
myDisplayStr + "?"
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
if (not self.doAreYouSure()):
myInfo = "Aborting command."
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
return False
#
# Step 6: If we found server name(s), then run with that.
# Otherwise, do the same with the server group(s) given.
#
threadList = {}
threadCounter = 0
if (len(myServerNameList) > 0):
if (myIsReverse):
myServerNameList.reverse()
try:
for myNameStr in myServerNameList:
myServer = self._globalConfig.getCurrentEnv(
).getServerByName(myNameStr)
myPinger = engine.misc.HostPinger.HostPinger(
self._globalConfig)
if (myPinger.ping(myNameStr) == 0):
myExternalCommand = engine.data.ExternalCommand.ExternalCommand(
self._globalConfig)
# Build It.
if (myServer.getVersion() != None):
myExternalCommand.setCommand( \
self._globalConfig.getSshBinary() + myFlagStr + \
" -" + myServer.getVersion() + \
" -l " + myServer.getUsername() + " " + \
myServer.getName() + " " + \
myBodyStr )
else:
myExternalCommand.setCommand( \
self._globalConfig.getSshBinary() + myFlagStr + \
" -l " + myServer.getUsername() + " " + \
myServer.getName() + " " + \
myBodyStr )
# Run in threads
if myIsRunInThreads:
# set to true to prompt user before running
if (self._globalConfig.isBatchMode()):
PassedIsInteractive = False
elif (len(myFlagStr) > 0):
myExternalCommand.run(True)
else:
myExternalCommand.run()
PassedIsInteractive = False
# create the thread object
externalCommandThread = threading.Thread(
target=myExternalCommand.run,
kwargs={
'PassedIsInteractive': PassedIsInteractive
},
name=myNameStr)
# dictionary containing thread objects and their count from 0 to ... the key is the machine name
threadCounter += 1
threadList[myNameStr] = {
'thread': externalCommandThread,
'number': threadCounter
}
# join thread n to thread n - maxThreads
if threadList[myNameStr]['number'] >= maxThreads:
threadNumberToJoin = threadList[myNameStr][
'number'] - maxThreads
threadToJoin = [
threadList[ns] for ns in threadList.keys()
if threadList[ns]['number'] ==
threadNumberToJoin
][0]['thread']
threadToJoin.join()
externalCommandThread.start()
else:
if (self._globalConfig.isBatchMode()):
myExternalCommand.run()
elif (len(myFlagStr) > 0):
myExternalCommand.run(True)
else:
myExternalCommand.run()
myCommandCount = myCommandCount + 1
threadCounter += 1
if (myIsSingle):
break
else:
myError = "Server '" + myServer.getName() + \
"' appears to be down. Continuing..."
self._globalConfig.getMultiLogger().LogMsgWarn(myError)
self._globalConfig.getMultiLogger(
).LogMsgDebugSeperator()
# join the controlling thread to all the running threads so it can't exit until they are all finished
def masterThreadJoiner():
pass
masterThread = threading.Thread(target=masterThreadJoiner)
[t['thread'].join(threadTimeout) for t in threadList.values()]
masterThread.start()
except EOFError:
pass
except KeyboardInterrupt:
myInfo = "Caught CTRL-C keystroke. Attempting to abort..."
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
self._globalConifg.setBreakState(True)
return False
return True
else:
#
# If we found server group names, then run with that.
#
for myGroupStr in myServerGroupList:
# Check for server group match, with and without attributes.
myServerGroup = self._globalConfig.getCurrentEnv(
).getServerGroupByName(myGroupStr)
if (myGroupStr.find('[') == -1):
myServerList = myServerGroup.getServerList()
else:
myServerList = myServerGroup.getAttribValueServerList(
myGroupStr)
if (myIsReverse):
myServerList.reverse()
try:
for myServer in myServerList:
myPinger = engine.misc.HostPinger.HostPinger(
self._globalConfig)
if (myPinger.ping(myServer.getName()) == 0):
myExternalCommand = engine.data.ExternalCommand.ExternalCommand(
self._globalConfig)
# Build It.
if (myServer.getVersion() != None):
myExternalCommand.setCommand( \
self._globalConfig.getSshBinary() + myFlagStr + \
" -" + myServer.getVersion() + \
" -l " + myServer.getUsername() + " " + \
myServer.getName() + " " + \
myBodyStr )
else:
myExternalCommand.setCommand( \
self._globalConfig.getSshBinary() + myFlagStr + \
" -l " + myServer.getUsername() + " " + \
myServer.getName() + " " + \
myBodyStr )
# Run in threads
if myIsRunInThreads:
# set to true to prompt user before running
if (self._globalConfig.isBatchMode()):
PassedIsInteractive = False
elif (len(myFlagStr) > 0):
myExternalCommand.run(True)
else:
myExternalCommand.run()
PassedIsInteractive = False
# create the thread object
externalCommandThread = threading.Thread(
target=myExternalCommand.run,
kwargs={
'PassedIsInteractive':
PassedIsInteractive
},
name=myServer)
# dictionary containing thread objects and their count from 0 to ... the key is the machine name
threadList[myServer] = {
'thread': externalCommandThread,
'number': threadCounter
}
# join thread n to thread n - maxThreads
if threadList[myServer]['number'] >= maxThreads:
threadNumberToJoin = threadList[myServer][
'number'] - maxThreads
threadToJoin = [
threadList[ns]
for ns in threadList.keys()
if threadList[ns]['number'] ==
threadNumberToJoin
][0]['thread']
threadToJoin.join()
externalCommandThread.start()
else:
if (self._globalConfig.isBatchMode()):
myExternalCommand.run()
elif (len(myFlagStr) > 0):
myExternalCommand.run(True)
else:
myExternalCommand.run()
myCommandCount = myCommandCount + 1
threadCounter += 1
if (myIsSingle):
break
else:
myError = "Server '" + myServer.getName() + \
"' appears to be down. Continuing..."
self._globalConfig.getMultiLogger().LogMsgWarn(
myError)
self._globalConfig.getMultiLogger(
).LogMsgDebugSeperator()
# join the controlling thread to all the running threads so it can't exit until they are all finished
def masterThreadJoiner():
pass
masterThread = threading.Thread(target=masterThreadJoiner)
[
t['thread'].join(threadTimeout)
for t in threadList.values()
]
masterThread.start()
except EOFError:
pass
except KeyboardInterrupt:
myInfo = "Caught CTRL-C keystroke. Attempting to abort..."
self._globalConfig.getMultiLogger().LogMsgInfo(myInfo)
self._globalConfig.setBreakState(True)
return False
if (myIsReverse):
myServerList.sort()
return myCommandCount
def _open(self):
# Quick rejection: if there's not an LF among the first
# 100 bytes, this is (probably) not a text header.
if not "\n" in self.fp.read(100):
raise SyntaxError, "not an IM file"
self.fp.seek(0)
n = 0
# Default values
self.info[MODE] = "L"
self.info[SIZE] = (512, 512)
self.info[FRAMES] = 1
self.rawmode = "L"
while 1:
s = self.fp.read(1)
# Some versions of IFUNC uses \n\r instead of \r\n...
if s == "\r":
continue
if not s or s[0] == chr(0) or s[0] == chr(26):
break
# FIXME: this may read whole file if not a text file
s = s + self.fp.readline()
if len(s) > 100:
raise SyntaxError, "not an IM file"
if s[-2:] == '\r\n':
s = s[:-2]
elif s[-1:] == '\n':
s = s[:-1]
try:
m = split.match(s)
except re.error, v:
raise SyntaxError, "not an IM file"
if m:
k, v = m.group(1, 2)
# Convert value as appropriate
if k in [FRAMES, SCALE, SIZE]:
v = string.replace(v, "*", ",")
v = tuple(map(number, string.split(v, ",")))
if len(v) == 1:
v = v[0]
elif k == MODE and OPEN.has_key(v):
v, self.rawmode = OPEN[v]
# Add to dictionary. Note that COMMENT tags are
# combined into a list of strings.
if k == COMMENT:
if self.info.has_key(k):
self.info[k].append(v)
else:
self.info[k] = [v]
else:
self.info[k] = v
if TAGS.has_key(k):
n = n + 1
else:
raise SyntaxError, "Syntax error in IM header: " + s
test.must_match('test10' + _exe, " -c -x\nThis is a .F77 file.\n")
g77 = test.detect('F77', 'g77')
FTN_LIB = TestSCons.fortran_lib
if g77:
test.write("wrapper.py",
"""import os
import string
import sys
open('%s', 'wb').write("wrapper.py\\n")
os.system(string.join(sys.argv[1:], " "))
""" % string.replace(test.workpath('wrapper.out'), '\\', '\\\\'))
test.write('SConstruct', """
foo = Environment(LIBS = %FTN_LIBs)
f77 = foo.Dictionary('F77')
bar = foo.Clone(F77 = r'%(_python_)s wrapper.py ' + f77, F77FLAGS = '-Ix')
foo.Program(target = 'foo', source = 'foo.f')
bar.Program(target = 'bar', source = 'bar.f')
""" % locals())
test.write('foo.f', r"""
PROGRAM FOO
PRINT *,'foo.f'
STOP
END
""")
control_info = msg.split(control_sep)
assert len(control_info) == 4, 'len(control_info) = %d' % len(control_info)
control_info[2] = eval(control_info[2]) #Convert back to int
control_info[3] = eval(control_info[3]) #Convert back to tuple
return control_info
#----------------------------------------------------------------------------
# Initialise module
#----------------------------------------------------------------------------
# Take care of situation where module is part of package
import sys, os, string, os.path
dirname = os.path.dirname(string.replace(__name__, '.', os.sep)).strip()
if not dirname:
dirname = '.'
if dirname[-1] != os.sep:
dirname += os.sep
# Import MPI extension
#
# Verify existence of mpiext.so.
try:
import mpiext
except:
errmsg = 'ERROR: C extension mpiext could not be imported.\n'
def replacechars(filename, fileExt, isCrowdin):
s = open(filename, "r+")
newfilename = filename + ".tmp"
fin = open(newfilename, "w")
errorOccured = False
if fileExt != '.csv':
for line in s.readlines():
if line.startswith("<?xml"):
line = "<?xml version=\"1.0\" encoding=\"utf-8\"?> \n <!-- \n ~ Copyright (c) 2009 Andrew <andrewdubya@gmail> \n ~ Copyright (c) 2009 Edu Zamora <*****@*****.**> \n ~ Copyright (c) 2009 Daniel Svaerd <*****@*****.**> \n ~ Copyright (c) 2009 Nicolas Raoul <*****@*****.**> \n ~ Copyright (c) 2010 Norbert Nagold <*****@*****.**> \n ~ This program is free software; you can redistribute it and/or modify it under \n ~ the terms of the GNU General Public License as published by the Free Software \n ~ Foundation; either version 3 of the License, or (at your option) any later \n ~ version. \n ~ \n ~ This program is distributed in the hope that it will be useful, but WITHOUT ANY \n ~ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A \n ~ PARTICULAR PURPOSE. See the GNU General Public License for more details. \n ~ \n ~ You should have received a copy of the GNU General Public License along with \n ~ this program. If not, see <http://www.gnu.org/licenses/>. \n --> \n \n"
else:
# some people outwitted crowdin's "0"-bug by filling in "0 ", this changes it back:
if line.startswith(" <item>0 </item>"):
line = " <item>0</item>\n"
line = string.replace(line, '\'', '\\\'')
line = string.replace(line, '\\\\\'', '\\\'')
line = string.replace(line, '\n\s', '\\n')
line = string.replace(line, 'amp;', '')
if re.search('%[0-9]\\s\\$|%[0-9]\\$\\s', line) != None:
errorOccured = True
# print line
fin.write(line)
else:
fin.write(
"<?xml version=\"1.0\" encoding=\"utf-8\"?> \n <!-- \n ~ Copyright (c) 2011 Norbert Nagold <*****@*****.**> \n ~ This program is free software; you can redistribute it and/or modify it under \n ~ the terms of the GNU General Public License as published by the Free Software \n ~ Foundation; either version 3 of the License, or (at your option) any later \n ~ version. \n ~ \n ~ This program is distributed in the hope that it will be useful, but WITHOUT ANY \n ~ WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A \n ~ PARTICULAR PURPOSE. See the GNU General Public License for more details. \n ~ \n ~ You should have received a copy of the GNU General Public License along with \n ~ this program. If not, see <http://www.gnu.org/licenses/>. \n --> \n \n \n<resources> \n <string-array name=\"tutorial_questions\"> \n"
)
content = re.sub('([^\"])\n', "\\1", s.read()).split("\n")
length = len(content)
line = []
for i in range(length - 1):
if isCrowdin:
start = content[i].rfind('\",\"') + 3
else:
start = content[i].find('\"') + 1
contentLine = content[i][start:len(content[i]) - 1]
sepPos = contentLine.find('<separator>')
if sepPos == -1:
if len(contentLine) > 2:
errorOccured = True
print contentLine
continue
line.append([
"<![CDATA[" + contentLine[:sepPos] + "]]>",
"<![CDATA[" + contentLine[sepPos + 11:] + "]]>"
])
for fi in line:
fi[0] = re.sub('\"+', '\\\"', fi[0])
fi[0] = re.sub('\'+', '\\\'', fi[0])
fi[0] = re.sub('\\\\{2,}', '\\\\', fi[0])
fin.write(" <item>" + fi[0] + "</item> \n")
fin.write(
" </string-array>\n <string-array name=\"tutorial_answers\">\n")
for fi in line:
fi[1] = re.sub('\"+', '\\\"', fi[1])
fi[1] = re.sub('\'+', '\\\'', fi[1])
fi[1] = re.sub('\\\\{2,}', '\\\\', fi[1])
fin.write(" <item>" + fi[1] + "</item> \n")
fin.write(" </string-array>\n</resources>")
s.close()
fin.close()
shutil.move(newfilename, filename)
if errorOccured:
#os.remove(filename)
print 'Error in file ' + filename
return False
else:
# print 'File ' + filename + ' successfully copied' # Disabled, makes output too large.
return True
def fixEndings(str):
str = string.replace(str, '\r\n', '\n')
str = string.replace(str, '\r', '\n')
return str
