def __init__(self):
dataDir = Settings.dataDir + "WorkingWithText/ExtractTextFromAllPages/"
# Open the target document
pdf = Document(dataDir + "input1.pdf")
# create TextAbsorber object to extract text
text_absorber = TextAbsorber()
# accept the absorber for all the pages
pdf.getPages().accept(text_absorber)
# In order to extract text from specific page of document, we need to specify the particular page using its index against accept(..) method.
# accept the absorber for particular PDF page
# pdfDocument.getPages().get_Item(1).accept(textAbsorber)
# get the extracted text
extracted_text = text_absorber.getText()
# create a writer and open the file
writer = FileWriter(File(dataDir + "extracted_text.out.txt"))
writer.write(extracted_text)
# write a line of text to the file
# tw.WriteLine(extractedText)
# close the stream
writer.close()
print "Text extracted successfully. Check output file."
def writePeakList(peakList, listName=None, folder="genpeaks"):
if listName == None:
listName = peakList.getName()
fileName = os.path.join(folder, listName + '.xpk2')
writer = FileWriter(fileName)
peakWriter = PeakWriter()
peakWriter.writePeaksXPK2(writer, peakList)
writer.close()
def runTestsWithXMLResultAsFile(suite, file="jython_test.xml"):
# Create writer
fileWriter = FileWriter(file)
pyFileWriter = PyFileWriter(fileWriter)
# Run test
runTestsWithXMLResult(suite, pyFileWriter)
# Close writer
pyFileWriter.close()
fileWriter.close()
def export_calibration(imp, path):
cal = imp.getCalibration()
meta = dict(w=cal.pixelWidth,
w_unit=cal.getXUnit(),
h=cal.pixelHeight,
h_unit=cal.getYUnit(),
t=cal.frameInterval,
t_unit=cal.getTimeUnit())
writer = FileWriter(path)
Gson().toJson(meta, writer)
writer.close() # important
def runTestsWithXMLResultAsFile(suite, file='jython_test.xml'): # Create writer fileWriter = FileWriter(file) pyFileWriter = PyFileWriter(fileWriter) # Run test runTestsWithXMLResult(suite, pyFileWriter) # Close writer pyFileWriter.close() fileWriter.close()
def run(file='jython_test.xml'): # Create writer fileWriter = FileWriter(file) pyFileWriter = PyFileWriter(fileWriter) # Run test suite = unittest.TestSuite([unittest.TestLoader().loadTestsFromTestCase(Test1)]) runner = xmlrunner.XMLTestRunner(pyFileWriter) s = runner.run(suite) # Close writer pyFileWriter.close() fileWriter.close()
def ig_dump_dot(dmuid, filename):
igm = project.getIGM()
uid = DMUID.parse(dmuid)
module = igm.findModule(Toplevel(uid, None))
if module == None:
printf('DM %s not found', dmuid)
else:
printf('Dumping %s...', module)
dot = IG2DOT(module)
dot.blacklistField("fImportedLibs")
dot.blacklistField("fImportedPackages")
dot.blacklistField("fZPrjID")
dot.blacklistField("fSFDBID")
dot.blacklistField("fLine")
dot.blacklistField("fCol")
dot.blacklistField("fScore")
dot.blacklistField("fFailed")
dot.blacklistField("fReject")
dot.blacklistField("fInertial")
dot.blacklistField("fDelay")
out = PrintWriter(BufferedWriter(FileWriter(filename)))
dot.convert(out)
out.close()
printf("python: wrote dot file to %s", filename)
def rtl_dump_svg(dmuid, filename):
rtlmanager = project.getRTLM()
uid = DMUID.parse(dmuid)
rtlm = rtlmanager.findModule(Toplevel(uid, None))
if rtlm == None:
printf('RTLM %s not found', dmuid)
else:
printf('Dumping %s...', rtlm)
out = PrintWriter(BufferedWriter(FileWriter(filename)))
gc = VGGCSVG(out)
contentProvider = RTLVisualGraphContentProvider(rtlm)
labelProvider = RTLVisualGraphLabelProvider(rtlm)
selectionProvider = RTLVisualGraphSelectionProvider()
layout = VGLayout(contentProvider, labelProvider, gc)
layout.paint(selectionProvider)
out.close()
printf("python: wrote svg file to %s", filename)
def export_rois(rm, is_hyperstack, path):
frame = (lambda roi: roi.getTPosition()) if is_hyperstack else (
lambda roi: roi.getPosition())
rois = rm.getRoisAsArray()
polys = {}
for roi in rois:
fp = roi.getFloatPolygon()
polys[roi.getName()] = {
't': frame(roi),
'x': fp.xpoints,
'y': fp.ypoints
}
writer = FileWriter(path)
Gson().toJson(polys, writer)
writer.close() # important
def testCSVPipe(self):
"""testing the CSV pipe"""
from java.io import PrintWriter, FileWriter
from com.ziclix.python.sql.pipe import Pipe
from com.ziclix.python.sql.pipe.db import DBSource
from com.ziclix.python.sql.pipe.csv import CSVSink
try:
src = self.connect()
fn = tempfile.mktemp(suffix="csv")
writer = PrintWriter(FileWriter(fn))
csvSink = CSVSink(writer)
c = self.cursor()
try:
c.execute("insert into zxtesting (id, name, state) values (?, ?, ?)", [(1000, 'this,has,a,comma', 'and a " quote')])
c.execute("insert into zxtesting (id, name, state) values (?, ?, ?)", [(1001, 'this,has,a,comma and a "', 'and a " quote')])
# ORACLE has a problem calling stmt.setObject(index, null)
c.execute("insert into zxtesting (id, name, state) values (?, ?, ?)", [(1010, '"this,has,a,comma"', None)], {2:zxJDBC.VARCHAR})
self.db.commit()
finally:
self.db.rollback()
c.close()
dbSource = DBSource(src, c.datahandler.__class__, "zxtesting", None, None, None)
cnt = Pipe().pipe(dbSource, csvSink) - 1 # ignore the header row
finally:
writer.close()
src.close()
os.remove(fn)
def dm_dump_dot(dmuid, filename):
dmm = project.getDUM()
uid = DMUID.parse(dmuid)
dm = dmm.getDM(uid)
if dm == None:
printf('DM %s not found', dmuid)
else:
printf('Dumping %s...', dm)
dot = AST2DOT(dm, project.getZDB())
dot.blacklistField("fParent")
# dot.blacklistField("fSource")
# dot.blacklistField("fStartCol")
# dot.blacklistField("fStartLine")
dot.blacklistField("fEndCol")
dot.blacklistField("fEndLine")
dot.blacklistField("fDeclarationMap")
out = PrintWriter(BufferedWriter(FileWriter(filename)))
dot.convert(out)
out.close()
printf("python: wrote dot file to %s", filename)
def rawPython(a, b, c):
"""Execute the text as a new CPython process"""
tmpFile = File.createTempFile("fieldRawPython", ".py", None)
writer = BufferedWriter(FileWriter(tmpFile))
writer.write(b, 0, len(b))
writer.close()
com = ExecuteCommand(".", (
"/System/Library/Frameworks/Python.framework/Versions/Current/bin/python",
tmpFile.getAbsolutePath()), 1)
com.waitFor(1)
print com.getOutput()
def saveToFile(self, event):
fileChooser = JFileChooser()
if not (self.targetURL is None):
fileChooser.setSelectedFile(File("Burp_SSL_Scanner_Result_%s.html" \
% (self.targetURL.getHost())))
else:
fileChooser.setSelectedFile(File("Burp_SSL_Scanner_Result.html"))
if (fileChooser.showSaveDialog(self.getUiComponent()) == JFileChooser.APPROVE_OPTION):
fw = FileWriter(fileChooser.getSelectedFile())
fw.write(self.textPane.getText())
fw.flush()
fw.close()
print "Saved results to disk"
def run(self):
import tempfile
import os
try:
ps = PySelection(editor)
doc = ps.getDoc()
startLine = ps.getStartLineIndex()
p1 = tempfile.mktemp()
p2 = tempfile.mktemp()
f1 = FileWriter(p1)
formatAll = False
if ps.getTextSelection().getLength() == 0:
# format all.
c = doc.get()
f1.write(c)
formatAll = True
else:
# format selection.
#c = ps.getSelectedText()
#f1.write(ps.getSelectedText())
print("Format selected text is not supported yet.")
f1.write("")
# A kind of solution is to insert a special comment in
# front and end of selection text, pythontidy it, and
# extract text according that comment.
f1.close()
os.system('PythonTidy.py "%s" "%s"' % (p1, p2))
f2 = open(p2, "r")
result = f2.read()
f2.close()
os.remove(p1)
os.remove(p2)
if startLine >= doc.getNumberOfLines():
startLine = doc.getNumberOfLines() - 1
if formatAll:
doc.set(result)
else:
#doc.replace(doc.getLineOffset(startLine), 0, result)
pass
sel = TextSelection(doc, doc.getLineOffset(startLine), 0)
self.getTextEditor().getSelectionProvider().setSelection(sel)
except java.lang.Exception as e:
self.beep(e)
def save_xml(self, path , pretty = True):
"""
Saves the xml document to file
"""
self.backup_xml(path)
format = None
xmlwriter = None
if pretty == True:
format = OutputFormat.createPrettyPrint()
format.setIndent(" ")
format.setLineSeparator("\r\n")
if format is None:
xmlwriter = XMLWriter(FileWriter(path))
else:
xmlwriter = XMLWriter(FileWriter(path), format)
xmlwriter.write(self.xmldoc)
xmlwriter.close()
def __init__(self):
dataDir = Settings.dataDir + 'WorkingWithText/ExtractTextFromAllPages/'
# Open the target document
pdf = Document(dataDir + 'input1.pdf')
# create TextAbsorber object to extract text
text_absorber = TextAbsorber()
# accept the absorber for all the pages
pdf.getPages().accept(text_absorber)
# In order to extract text from specific page of document, we need to specify the particular page using its index against accept(..) method.
# accept the absorber for particular PDF page
# pdfDocument.getPages().get_Item(1).accept(textAbsorber)
#get the extracted text
extracted_text = text_absorber.getText()
# create a writer and open the file
writer = FileWriter(File(dataDir + "extracted_text.out.txt"))
writer.write(extracted_text)
# write a line of text to the file
# tw.WriteLine(extractedText)
# close the stream
writer.close()
print "Text extracted successfully. Check output file."
def GenernateIndex(self):
fileIndex = JitarRequestContext.getRequestContext().getServletContext().getRealPath("/")
fileIndex = fileIndex + "index.html"
try:
file = File(fileIndex)
fw = FileWriter(file, False)
fw.write("<!doctype html>")
fw.write("<html><head><meta http-equiv=\"content-type\" content=\"text/html; charset=UTF-8\"><title></title>")
fw.close()
finally:
fw = None
print fileIndex
def run(self):
import tempfile
import os
try:
ps = PySelection(editor)
doc = ps.getDoc()
startLine = ps.getStartLineIndex()
p1 = tempfile.mktemp()
p2 = tempfile.mktemp()
f1 = FileWriter(p1)
formatAll = False
if ps.getTextSelection().getLength() == 0:
# format all.
c = doc.get()
f1.write(c)
formatAll = True
else:
# format selection.
#c = ps.getSelectedText()
#f1.write(ps.getSelectedText())
print "Format selected text is not supported yet."
f1.write("")
# A kind of solution is to insert a special comment in
# front and end of selection text, pythontidy it, and
# extract text according that comment.
f1.close()
os.system('PythonTidy.py "%s" "%s"' % (p1, p2))
f2 = open(p2, "r")
result = f2.read()
f2.close()
os.remove(p1)
os.remove(p2)
if startLine >= doc.getNumberOfLines():
startLine = doc.getNumberOfLines() - 1
if formatAll:
doc.set(result)
else:
#doc.replace(doc.getLineOffset(startLine), 0, result)
pass
sel = TextSelection(doc, doc.getLineOffset(startLine), 0)
self.getTextEditor().getSelectionProvider().setSelection(sel)
except java.lang.Exception, e:
self.beep(e)
def writeLocations(self):
f = Files.createExternalFile(Environment.DIRECTORY_DOWNLOADS,
"WeatherForecast", "locations.txt", None,
None)
try:
stream = FileWriter(f)
for key in self.order:
stream.write(self.locations[key] + "\n")
stream.flush()
stream.close()
except FileNotFoundException:
pass
def run():
print
base = raw_input('Base file, eg. config/templates/wl_as_template.properties? ')
env = raw_input('Environment, eg. local? ')
print
new_cfg = 'config/' + env + '/new_config.properties'
input = BufferedReader(FileReader(base))
output = BufferedWriter(FileWriter(new_cfg))
output.write('base=' + base + '\n\n')
line = input.readLine()
while line is not None:
if re.match('.*\?', line):
output.write(line)
output.newLine()
line = input.readLine()
input.close()
output.close()
log.info('new configuration file written to: ' + new_cfg)
def saveModels(mol, files, type):
active = mol.getActiveStructures()
if type == 'cif':
mol.resetActiveStructures()
if 'final' not in files[
-1]: #don't write out reference structure if in file list
sNums = [i for i in range(len(files) - 1)]
treeSet = TreeSet(sNums)
mol.setActiveStructures(treeSet)
molName = mol.getName()
cifFile = os.path.join(os.getcwd(), molName + "_all.cif")
out = FileWriter(cifFile)
MMcifWriter.writeAll(out, molName)
elif type == 'pdb':
for (i, file) in zip(active, files):
(dir, fileName) = os.path.split(file)
newFileName = 'sup_' + fileName
newFile = os.path.join(dir, newFileName)
molio.savePDB(mol, newFile, i)
def actionPerformed(self,actionEvent):
self.scl_long_tuneup_controller.getMessageTextField().setText("")
fc = JFileChooser(constants_lib.const_path_dict["LINAC_WIZARD_FILES_DIR_PATH"])
fc.setDialogTitle("Save SCL Table data into ASCII file")
fc.setApproveButtonText("Save")
fl_filter = FileNameExtensionFilter("ASCII *.dat File",["dat",])
fc.setFileFilter(fl_filter)
returnVal = fc.showOpenDialog(self.scl_long_tuneup_controller.linac_wizard_document.linac_wizard_window.frame)
if(returnVal == JFileChooser.APPROVE_OPTION):
fl_out = fc.getSelectedFile()
fl_path = fl_out.getPath()
if(fl_path.rfind(".dat") != (len(fl_path) - 4)):
fl_out = File(fl_out.getPath()+".dat")
buffer_out = BufferedWriter(FileWriter(fl_out))
txt = "# cav pos cav_amp_epics cav_amp_model cav_phase rf_gap_avg_phase"
txt += " phase_offset real_offset eKin_in eKin_out "
txt += " delta_eKin_in_out_keV bpm_eKin_out model_eKin_out delta_eKin_fit_keV E0TL_MeV"
buffer_out.write(txt)
buffer_out.newLine()
buffer_out.flush()
cav_wrappers = self.scl_long_tuneup_controller.cav_wrappers
for cav_ind in range(len(cav_wrappers)):
cav_wrapper = cav_wrappers[cav_ind]
txt = str(cav_ind+1)+" "
txt += cav_wrapper.cav.getId()+" %8.3f "%cav_wrapper.pos+" %12.5g "%cav_wrapper.initLiveAmp
txt += " %12.5g "%cav_wrapper.designAmp + " %8.3f "%cav_wrapper.designPhase
txt += " %8.3f "%cav_wrapper.avg_gap_phase + " %8.3f "%cav_wrapper.scanPhaseShift
txt += " %8.3f "%cav_wrapper.real_scanPhaseShift
txt += " %12.5g "%cav_wrapper.eKin_in + " %12.5g "%cav_wrapper.eKin_out
dE = 0.
if(cav_ind != 0):
dE = (cav_wrapper.eKin_in - cav_wrappers[cav_ind-1].eKin_out)*1000.
txt += " %12.5g "%dE + " %12.5g "%cav_wrapper.bpm_eKin_out+ " %12.5g "%cav_wrapper.model_eKin_out
txt += "% 6.1f"%(1000.*cav_wrapper.eKin_err)
E0TL = 0.
if(len(cav_wrapper.energy_guess_harm_funcion.getParamArr()) > 1):
E0TL = cav_wrapper.energy_guess_harm_funcion.getParamArr()[1]
txt += " %12.5g "%E0TL
buffer_out.write(txt)
buffer_out.newLine()
#---- end of writing
buffer_out.flush()
buffer_out.close()
def _testXMLPipe(self):
"""testing the XML pipe"""
from java.io import PrintWriter, FileWriter
from com.ziclix.python.sql.pipe import Pipe
from com.ziclix.python.sql.pipe.db import DBSource
from com.ziclix.python.sql.pipe.xml import XMLSink
try:
src = self.connect()
fn = tempfile.mktemp(suffix="csv")
writer = PrintWriter(FileWriter(fn))
xmlSink = XMLSink(writer)
dbSource = DBSource(src, self.datahandler, "zxtesting", None, None,
None)
cnt = Pipe().pipe(dbSource, xmlSink) - 1 # ignore the header row
finally:
writer.close()
src.close()
os.remove(fn)
filename = sys.argv[1]
print "Try to parse %s" % filename
# Create a Parser of specified format
format = sys.argv[2]
builder = ChannelBuilder()
if format == "0.91":
parser = RSS_0_91_Parser(builder)
else:
parser = RSS_1_0_Parser(builder)
# Read in Channel from File
channel = parser.parse(File(filename).toURL())
# Create a File to marshal to
writer = FileWriter("test-persist-channel.xml")
# Load the mapping information from the file
mapping = Mapping()
mapping.loadMapping("../../src/de/nava/informa/impl/jdo/mapping.xml")
# Marshal the channel object
marshaller = Marshaller(writer)
marshaller.setMapping(mapping)
marshaller.marshal(channel)
# ---- Unmarshalling
# Create a Reader to the file to unmarshal from
# reader = FileReader("test-persist-channel.xml")
import de.embl.cba.metadata.MetaData as MetaData import de.embl.cba.metadata.MetadataCreator as MetadataCreator import ij.IJ as IJ import org.yaml.snakeyaml.DumperOptions as DumperOptions import org.yaml.snakeyaml.Yaml as Yaml import java.io.FileWriter as FileWriter file = "/Volumes/cba/exchange/OeyvindOedegaard/yaml_project/01_TestFiles/20180627_LSM780M2_208_ibidi1_fcs_B_Posx96.lsm" metadataCreator = MetadataCreator(file) metadata = metadataCreator.getMetadata() dumperOptions = DumperOptions() dumperOptions.setDefaultFlowStyle(DumperOptions.FlowStyle.BLOCK) outputPath = "/Volumes/cba/exchange/OeyvindOedegaard/yaml_project/test.yaml" yaml = Yaml(dumperOptions) writer = FileWriter(outputPath) yaml.dump(metadata, writer) writer.flush() writer.close() IJ.open(outputPath)
def process(self):
print " * settings.py: formData=%s" % self.vc("formData")
result = "{}"
portalManager = Services.getPortalManager()
portal = portalManager.get(self.vc("portalId"))
func = self.vc("formData").get("func")
if func == "view-update":
portal.setDescription(self.vc("formData").get("view-description"))
portal.setQuery(self.vc("formData").get("view-query"))
portal.setSearchQuery(self.vc("formData").get("view-search-query"))
portal.setRecordsPerPage(int(self.vc("formData").get("view-records-per-page")))
portal.setFacetCount(int(self.vc("formData").get("view-facet-count")))
portal.setFacetDisplay(int(self.vc("formData").get("view-facet-display")))
portal.setFacetSort(self.vc("formData").get("view-facet-sort") is not None)
portalManager.save(portal)
elif func == "general-update":
config = JsonSimpleConfig()
email = StringUtils.trimToEmpty(self.vc("formData").get("general-email"))
systemEmail = StringUtils.trimToEmpty(config.getString(None, ["email"]))
if systemEmail != email:
obj = config.writableSystemConfig()
obj.put("email", self.vc("formData").get("general-email"))
obj.put("configured", "true")
config.storeSystemConfig()
# mark restart
Services.getHouseKeepingManager().requestUrgentRestart()
else:
print " * settings.py: email not updated: did not change"
self.throw_error("Email address is the same! No change saved.")
elif func == "facets-update":
portal.getObject(["portal"]).remove("facet-fields")
fields = self.vc("formData").getValues("field")
labels = self.vc("formData").getValues("label")
displays = self.vc("formData").getValues("display")
deletes = self.vc("formData").getValues("delete")
for i in range(0, len(fields)):
field = fields[i]
if deletes[i] == "false":
node = portal.writeObject(["portal", "facet-fields", field])
node.put("label", labels[i])
node.put("display", displays[i])
portalManager.save(portal)
elif func == "sort-update":
portal.getObject(["portal"]).remove("sort-fields")
default = self.vc("formData").get("default")
if default:
portal.setSortFieldDefault(default)
order = self.vc("formData").get("order")
if order:
portal.setSortFieldDefaultOrder(order)
fields = self.vc("formData").getValues("field")
labels = self.vc("formData").getValues("label")
deletes = self.vc("formData").getValues("delete")
for i in range(0, len(fields)):
field = fields[i]
if deletes[i] == "false":
node = portal.writeObject(["portal", "sort-fields"])
node.put(field, labels[i])
portalManager.save(portal)
elif func == "watcher-update":
configFile = self.getWatcherFile()
if configFile is not None:
json = JsonSimpleConfig(configFile)
pathIds = self.vc("formData").get("pathIds").split(",")
actives = self.vc("formData").getValues("watcher-active")
if actives is None:
actives = []
deletes = self.vc("formData").getValues("watcher-delete")
if deletes is None:
deletes = []
for pathId in pathIds:
if pathId not in deletes:
path = self.vc("formData").get("%s-path" % pathId)
stopped = str(pathId not in actives).lower()
watchDir = json.writeObject(["watcher", "watchDirs", path])
watchDir.put("ignoreFileFilter", self.vc("formData").get("%s-file" % pathId))
watchDir.put("ignoreDirectories", self.vc("formData").get("%s-dir" % pathId))
watchDir.put("stopped", stopped)
json.writeArray(["watcher", "watchDirs", path, "cxtTags"])
writer = FileWriter(configFile)
writer.write(json.toString(True))
writer.close()
else:
result = "The Watcher is not installed properly."
elif func == "restore-default-config":
# backup the file
JsonSimpleConfig.backupSystemFile()
# delete the file
JsonSimpleConfig.getSystemFile().delete()
# restore default
JsonSimpleConfig.getSystemFile()
# mark restart
Services.getHouseKeepingManager().requestUrgentRestart()
elif func == "housekeeping-update":
config = JsonSimpleConfig()
freq = StringUtils.trimToEmpty(self.vc("formData").get("housekeeping-timeout"))
systemFreq = StringUtils.trimToEmpty(config.getString(None, ["portal", "houseKeeping", "config", "frequency"]))
result = "House Keeper refreshed"
if systemFreq != freq:
# Get writeable access to underlying system
sysConfig = JsonSimple(config.writableSystemConfig())
# Modify the house keeping node
hkConfig = sysConfig.writeObject(["portal", "houseKeeping", "config"])
hkConfig.put("frequency", freq)
# Write the underlying config back to disk
config.storeSystemConfig()
result = "Frequency updated, refreshing House Keeper"
# Refresh the HouseKeeper
message = JsonObject()
message.put("type", "refresh")
Services.getHouseKeepingManager().sendMessage(message.toString())
self.writer.println(result)
self.writer.close()
def __processRequest(self):
depositUrl = "%s/sword/deposit.post" % portalPath
sword = SwordSimpleServer(depositUrl)
try:
p = self.vc("request").path.split(
self.vc("portalId") + "/" + self.vc("pageName") +
"/")[1] # portalPath
except:
p = ""
if p == "post":
print "\n--- post ---"
c = sword.getClient()
c.clearProxy()
c.clearCredentials()
postMsg = sword.getPostMessage()
postMsg.filetype = "application/zip"
postMsg.filepath = "/home/ward/Desktop/Test.zip"
depositResponse = c.postFile(postMsg)
return str(depositResponse)
elif p == "servicedocument":
#print "\n--- servicedocument ---"
sdr = sword.getServiceDocumentRequest()
sdr.username = self.vc("formData").get("username", "test")
sdr.password = self.vc("formData").get("password", "test")
if self.vc("formData").get("test"):
depositUrl += "?test=1"
sd = sword.doServiceDocument(sdr) # get a serviceDocument
out = self.vc("response").getPrintWriter("text/xml; charset=UTF-8")
out.println(str(sd))
out.close()
self.velocityContext["pageName"] = "-noTemplate-"
return sd
elif p == "deposit.post":
#print "\n--- deposit --- formData='%s'" % str(formData)
inputStream = self.vc("formData").getInputStream()
headers = {}
for x in self.vc("formData").getHeaders().entrySet():
headers[x.getKey()] = x.getValue()
deposit = sword.getDeposit()
noOp = headers.get("X-No-Op") or "false"
deposit.noOp = (noOp.lower()=="true") or \
(formData.get("test") is not None)
contentDisposition = headers.get("Content-Disposition", "")
filename = ""
if contentDisposition != "":
try:
filename = contentDisposition.split("filename=")[1]
deposit.filename = filename
except:
pass
slug = headers.get("Slug")
if slug is not None and slug != "":
deposit.slug = slug
#elif filename!="":
# deposit.slug = filename
deposit.username = "******"
deposit.password = deposit.username
try:
file = File.createTempFile("tmptf", ".zip")
file.deleteOnExit()
fos = FileOutputStream(file.getAbsolutePath())
IOUtils.copy(inputStream, fos)
fos.close()
print "copied posted data to '%s'" % file.getAbsolutePath()
except Exception, e:
print "--- Exception - '%s'" % str(e)
deposit.contentDisposition = file.getAbsolutePath() #????
deposit.file = inputStream
depositResponse = sword.doDeposit(deposit)
id = str(depositResponse.getEntry().id)
try:
print
#imsPlugin = PluginManager.getTransformer("ims")
jsonConfig = JsonConfig()
#imsPlugin.init(jsonConfig.getSystemFile())
#harvestClient = HarvestClient(jsonConfig.getSystemFile());
storagePlugin = PluginManager.getStorage(
jsonConfig.get("storage/type"))
#storagePlugin.init(jsonConfig.getSystemFile())
setConfigUri = self.__getPortal().getClass().getResource(
"/swordRule.json").toURI()
configFile = File(setConfigUri)
harvestConfig = JsonConfigHelper(configFile)
tFile = File.createTempFile("harvest", ".json")
tFile.deleteOnExit()
harvestConfig.set("configDir", configFile.getParent())
harvestConfig.set("sourceFile", file.getAbsolutePath())
harvestConfig.store(FileWriter(tFile))
zipObject = GenericDigitalObject(id)
zipObject.addPayload(FilePayload(file, id))
#digitalObject = imsPlugin.transform(zipObject, file)
qStorage = QueueStorage(storagePlugin, tFile)
qStorage.init(jsonConfig.getSystemFile())
qStorage.addObject(zipObject)
if deposit.noOp:
print "-- Testing noOp='true' --"
else:
# deposit the content
pass
except Exception, e:
print "---"
print " -- Exception - '%s'" % str(e)
print "---"
if i.strip() != ''
]
de_vocab = [
i.strip()
for i in codecs.open(options.de_vocab, 'r', 'utf8').readlines()
if i.strip() != ''
]
for env in en_vocab:
add_to_tags(env)
uc_training = UnCachedFgList(training_instanes=training_ti,
en_vocab=en_vocab)
for idx, ti in enumerate(training_ti):
print idx, uc_training.get(idx)
trainer = CrfTrainer(get_trainer_prm())
exit(1)
feature_ids, feature_labels = zip(
*sorted([(v, k) for k, v in feature_label2id.iteritems()]))
# initialize weight for each feature
factor_graph_model = FgModel(len(feature_label2id), list(feature_labels))
for fid in list(feature_ids):
factor_graph_model.add(fid, 0.0)
trainer.train(factor_graph_model, uc_training)
sw = FileWriter('feature.weights')
factor_graph_model.printModel(sw)
sw = codecs.open('feature.names', 'w', 'utf8')
for k, i in feature_label2id.iteritems():
sw.write(str(i) + '\t' + str(k) + '\n')
sw.flush()
sw.close()
def process(self):
self.log.debug(" * settings.py: formData={}", self.vc("formData"))
valid = self.vc("page").csrfSecurePage()
if not valid:
self.throw_error("Invalid request")
return
result = "{}"
portalManager = self.vc("Services").getPortalManager()
portal = portalManager.get(self.vc("portalId"))
func = self.vc("formData").get("func")
if func == "view-update":
portal.setDescription(self.vc("formData").get("view-description"))
portal.setQuery(self.vc("formData").get("view-query"))
portal.setSearchQuery(self.vc("formData").get("view-search-query"))
portal.setRecordsPerPage(
int(self.vc("formData").get("view-records-per-page")))
portal.setFacetCount(
int(self.vc("formData").get("view-facet-count")))
portal.setFacetDisplay(
int(self.vc("formData").get("view-facet-display")))
portal.setFacetSort(
self.vc("formData").get("view-facet-sort") is not None)
portalManager.save(portal)
elif func == "general-update":
config = JsonSimpleConfig()
email = StringUtils.trimToEmpty(
self.vc("formData").get("general-email"))
systemEmail = StringUtils.trimToEmpty(
config.getString(None, ["email"]))
if systemEmail != email:
obj = config.writableSystemConfig()
obj.put("email", self.vc("formData").get("general-email"))
obj.put("configured", "true")
config.storeSystemConfig()
# mark restart
self.vc("Services").getHouseKeepingManager(
).requestUrgentRestart()
else:
self.log.debug(
" * settings.py: email not updated: did not change")
self.throw_error("Email address is the same! No change saved.")
elif func == "facets-update":
portal.getObject(["portal"]).remove("facet-fields")
fields = self.vc("formData").getValues("field")
labels = self.vc("formData").getValues("label")
displays = self.vc("formData").getValues("display")
deletes = self.vc("formData").getValues("delete")
for i in range(0, len(fields)):
field = fields[i]
if deletes[i] == "false":
node = portal.writeObject(
["portal", "facet-fields", field])
node.put("label", labels[i])
node.put("display", displays[i])
portalManager.save(portal)
elif func == "sort-update":
portal.getObject(["portal"]).remove("sort-fields")
default = self.vc("formData").get("default")
if default:
portal.setSortFieldDefault(default)
order = self.vc("formData").get("order")
if order:
portal.setSortFieldDefaultOrder(order)
fields = self.vc("formData").getValues("field")
labels = self.vc("formData").getValues("label")
deletes = self.vc("formData").getValues("delete")
for i in range(0, len(fields)):
field = fields[i]
if deletes[i] == "false":
node = portal.writeObject(["portal", "sort-fields"])
node.put(field, labels[i])
portalManager.save(portal)
elif func == "watcher-update":
configFile = self.getWatcherFile()
if configFile is not None:
json = JsonSimpleConfig(configFile)
pathIds = self.vc("formData").get("pathIds").split(",")
actives = self.vc("formData").getValues("watcher-active")
if actives is None:
actives = []
deletes = self.vc("formData").getValues("watcher-delete")
if deletes is None:
deletes = []
for pathId in pathIds:
if pathId not in deletes:
path = self.vc("formData").get("%s-path" % pathId)
stopped = str(pathId not in actives).lower()
watchDir = json.writeObject(
["watcher", "watchDirs", path])
watchDir.put(
"ignoreFileFilter",
self.vc("formData").get("%s-file" % pathId))
watchDir.put(
"ignoreDirectories",
self.vc("formData").get("%s-dir" % pathId))
watchDir.put("stopped", stopped)
json.writeArray(
["watcher", "watchDirs", path, "cxtTags"])
writer = FileWriter(configFile)
writer.write(json.toString(True))
writer.close()
else:
result = "The Watcher is not installed properly."
elif func == "restore-default-config":
# backup the file
JsonSimpleConfig.backupSystemFile()
# delete the file
JsonSimpleConfig.getSystemFile().delete()
# restore default
JsonSimpleConfig.getSystemFile()
# mark restart
self.vc("Services").getHouseKeepingManager().requestUrgentRestart()
elif func == "housekeeping-update":
config = JsonSimpleConfig()
freq = StringUtils.trimToEmpty(
self.vc("formData").get("housekeeping-timeout"))
systemFreq = StringUtils.trimToEmpty(
config.getString(
None, ["portal", "houseKeeping", "config", "frequency"]))
result = "House Keeper refreshed"
if systemFreq != freq:
# Get writeable access to underlying system
sysConfig = JsonSimple(config.writableSystemConfig())
# Modify the house keeping node
hkConfig = sysConfig.writeObject(
["portal", "houseKeeping", "config"])
hkConfig.put("frequency", freq)
# Write the underlying config back to disk
config.storeSystemConfig()
result = "Frequency updated, refreshing House Keeper"
# Refresh the HouseKeeper
message = JsonObject()
message.put("type", "refresh")
self.vc("Services").getHouseKeepingManager().sendMessage(
message.toString())
self.writer.println(result)
self.writer.close()
ti, obs, guess = get_instance(line)
training_ti.append(ti)
for line in open(options.test_file).readlines():
ti, obs, guess = get_instance(line)
testing_ti.append(ti)
en_vocab = [i.strip() for i in codecs.open(options.en_vocab, 'r', 'utf8').readlines() if i.strip() != '']
de_vocab = [i.strip() for i in codecs.open(options.de_vocab, 'r', 'utf8').readlines() if i.strip() != '']
for env in en_vocab:
add_to_tags(env)
uc_training = UnCachedFgList(training_instanes=training_ti, en_vocab=en_vocab)
for idx, ti in enumerate(training_ti):
print idx, uc_training.get(idx)
trainer = CrfTrainer(get_trainer_prm())
exit(1)
feature_ids, feature_labels = zip(*sorted([(v, k) for k, v in feature_label2id.iteritems()]))
# initialize weight for each feature
factor_graph_model = FgModel(len(feature_label2id), list(feature_labels))
for fid in list(feature_ids):
factor_graph_model.add(fid, 0.0)
trainer.train(factor_graph_model, uc_training)
sw = FileWriter('feature.weights')
factor_graph_model.printModel(sw)
sw = codecs.open('feature.names', 'w', 'utf8')
for k, i in feature_label2id.iteritems():
sw.write(str(i) + '\t' + str(k) + '\n')
sw.flush()
sw.close()
from java.io import FileWriter
from java.io import File
from java.io import FileReader
f1 = File("file2.txt")
fr = FileReader(f1)
f2 = File("file3.txt")
fw = FileWriter(f2)
while True:
ch = fr.read()
if ch != -1:
fw.write(ch)
else:
break
fr.close()
fw.close()
def run(self):
import tempfile
import os
import traceback
logger = FormatterLogger(
self._editor.getEditorFile().getName())
try:
# PySelection(editor)
ps = self._editor.createPySelection()
doc = ps.getDoc()
startLine = ps.getStartLineIndex()
tmp_src = tempfile.mktemp()
tmp_src_fileWriter = FileWriter(tmp_src)
formatAll = False
if ps.getTextSelection().getLength() == 0:
# format all.
c = doc.get()
tmp_src_fileWriter.write(c)
formatAll = True
else:
# format selection.
# c = ps.getSelectedText()
# tmp_src_fileWriter.write(ps.getSelectedText())
logger.warn(
'Format selected text is not supported yet.')
tmp_src_fileWriter.write('')
# A kind of solution is to insert a special comment in
# front and end of selection text, pythontidy it, and
# extract text according that comment.
tmp_src_fileWriter.close()
PythonTidyAction.apply_formatting(
tmp_src,
self._editor.getEditorFile().getName(), logger)
resulting_file = open(tmp_src, 'r')
result = resulting_file.read()
resulting_file.close()
os.remove(tmp_src)
if startLine >= doc.getNumberOfLines():
startLine = doc.getNumberOfLines() - 1
if formatAll:
doc.set(result)
else:
# doc.replace(doc.getLineOffset(startLine), 0, result)
pass
if startLine >= doc.getNumberOfLines():
startLine = doc.getNumberOfLines() - 1
self._editor.selectAndReveal(
doc.getLineOffset(startLine),
0)
except java.lang.Exception as e:
self.beep(e)
logger.error(traceback.format_exc())
except:
logger.error(traceback.format_exc())
val minDate = LocalDate.of(2003, 1, 1)
val maxDate = LocalDate.of(2015, 5, 14)
val dateFormatter = DateTimeFormatter.ISO_LOCAL_DATE
val urlTemplate =
"https://www.wunderground.com/history/airport/KSFO/%d/%d/%d/DailyHistory.html?format=1"
val urlsQeueue = mutable.Queue(
Util.daysBetween(minDate, maxDate)
.map { d =>
val formattedDate = d.format(dateFormatter)
(formattedDate, urlTemplate.format(d.getYear, d.getMonthValue, d.getDayOfMonth))
}: _*
)
require(urlsQeueue.nonEmpty, "there should be URLs to query")
val fileWriter = new FileWriter("sfCrime/src/main/resources/weather.json")
fileWriter.write("[\n")
val timer = new JavaTimer(isDaemon = false)
lazy val task: TimerTask = timer.schedule(Duration.fromSeconds(5)) {
val (date, url) = urlsQeueue.dequeue()
Try(Source.fromURL(url).getLines().drop(2)) match {
case Success(lines) =>
val wds = lines.map(WeatherData.parseWeatherData).toSeq
val wdd = WeatherDataDate.buildWeatherDataDate(date, wds)
val json = wdd.asJson.spaces2
if (urlsQeueue.isEmpty) {
task.cancel()
timer.stop()
fileWriter.write(s"$json\n")
fileWriter.write("]")
fileWriter.close()
# A gl user testing framework
#
import java
from java.io import PrintWriter, FileReader, FileWriter, File
from java.lang import System
from org.fenfire.swamp import Graphs
from com.hp.hpl.mesa.rdf.jena.model import Model
from com.hp.hpl.mesa.rdf.jena.mem import ModelMem
model = ModelMem()
file = "exper.rdf"
if File(file).exists():
print "Reading", file
model.read(FileReader(file), "")
else:
print file, "not found"
# TODO: read a graph from a file
graph = Graphs.toGraph(model)
model = Graphs.toModel(graph)
print "Writing", file
model.write(FileWriter(file))
result = pluginsTreeToString()
if uploadToWiki or compareToWiki:
from fiji import MediaWikiClient
client = MediaWikiClient(URL)
wiki = client.sendRequest(['title', PAGE, 'action', 'edit'], None)
begin = wiki.find('<textarea')
begin = wiki.find('>', begin) + 1
end = wiki.find('</textarea>', begin)
wiki = wiki[begin:end].replace('<', '<')
if wiki != result:
if compareToWiki:
from fiji import SimpleExecuter
from java.io import File, FileWriter
file1 = File.createTempFile('PluginList', '.wiki')
writer1 = FileWriter(file1)
writer1.write(wiki)
writer1.close()
file2 = File.createTempFile('PluginList', '.wiki')
writer2 = FileWriter(file2)
writer2.write(result)
writer2.close()
diff = SimpleExecuter(['git', 'diff', '--patience', '--no-index', '--src-prefix=wiki/', '--dst-prefix=local/', file1.getAbsolutePath(), file2.getAbsolutePath()])
file1.delete()
file2.delete()
print diff.getOutput()
else:
# get username and password
user = None
password = None
from os import getenv, path
import java.io.FileWriter
import scala.io.Source
val in = "/Users/daria/Downloads/C-small-attempt3.in"
//val in = "/Users/daria/Downloads/in.txt"
val out = new FileWriter("/Users/daria/Downloads/out.txt")
val lines = Source.fromFile(in).getLines().toList
var T = lines(0).toInt
for (i <- 1 to T) {
val offset = 1 + (i - 1) * 2
val t = lines(offset).split(" ")
val L = t(0).toInt
val X = t(1).toInt
val ch = lines(offset+1).toArray.map(c => c.toString)
val r = "\nCase #%d: %s\n".format(i, if (process(L, X, ch)) "YES" else "NO")
out.write(r)
println(r)
}
out.close()
val step = Map(
"1" -> Map("1" -> "1", "i" -> "i", "j" -> "j", "k" -> "k"),
"i" -> Map("1" -> "i", "i" -> "-1", "j" -> "k", "k" -> "-j"),
"j" -> Map("1" -> "j", "i" -> "-k", "j" -> "-1", "k" -> "i"),
"k" -> Map("1" -> "k", "i" -> "j", "j" -> "-i", "k" -> "-1"),
"-1" -> Map("1" -> "-1", "i" -> "-i", "j" -> "-j", "k" -> "-k"),
"-i" -> Map("1" -> "-i", "i" -> "1", "j" -> "-k", "k" -> "j"),
"-j" -> Map("1" -> "-j", "i" -> "k", "j" -> "1", "k" -> "-i"),
"-k" -> Map("1" -> "-k", "i" -> "-j", "j" -> "i", "k" -> "1")
)
def process(L:Int, X: Int, ch: Array[String]): Boolean = {
