def dumpYamlWin(yamlFile):
yaml = Yaml()
win = {}
win['geometry'] = nw.geometry()
win['title'] = "Test"
win['grid'] = nw.getGrid()
win['sconfig'] = nw.sconfig()
(rows, cols) = win['grid']
spectra = []
win['spectra'] = spectra
nCharts = nw.nCharts()
for iSpectrum in range(nCharts):
nw.active(iSpectrum)
sd = {}
spectra.append(sd)
iRow = iSpectrum / cols
iCol = iSpectrum % cols
sd['grid'] = [iRow, iCol]
sd['lim'] = nw.lim()
sd['cconfig'] = nw.cconfig()
sd['datasets'] = []
datasets = nw.datasets()
for dataset in datasets:
dset = {}
dset['name'] = dataset
dset['config'] = nw.config(dataset)
dset['dims'] = nw.getDims(dataset)
sd['datasets'].append(dset)
sd['peaklists'] = []
peakLists = nw.peakLists()
for peakList in peakLists:
pset = {}
pset['name'] = peakList
pset['config'] = nw.pconfig(peakList)
sd['peaklists'].append(pset)
print win
yamlDump = yaml.dump(win)
with open(yamlFile, 'w') as fOut:
fOut.write(yamlDump)
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)
class nomjyc (HttpServlet):
"""
This is the sandbox of the nomjyc web interface. Please refer to
<a href="http://nomjyc.ath.cx:8080">nomjyc.ath.cx:8080</a> for the main game.
Called without parameters, it will most probably just display the nomjyc rules,
read from the main nomjyc game. Send a GET or POST parameter called "test" to
add an arbitrary rule to be executed at the end of the rule list.
"""
def __init__(self):
self.yaml = Yaml()
self.yamlLexer = YamlLexer()
self.pythonLexer = PythonLexer()
self.pythonTBLexer = PythonTracebackLexer()
self.htmlFormatter = HtmlFormatter()
def dumpData(self,c):
rules = c.data["rules"]
c.data["rules"] = "omitted"
code = highlight(self.yaml.dump(c.data), self.yamlLexer, self.htmlFormatter)
c.data["rules"] = rules
return code
def dumpYaml(self, anything):
return highlight(self.yaml.dump(anything), self.yamlLexer, self.htmlFormatter)
def dumpPython(self, code):
return highlight(code, self.pythonLexer, self.htmlFormatter)
def dumpPythonTB(self, code):
return highlight(code, self.pythonTBLexer, self.htmlFormatter)
def explainException(self, title):
nruter = "<div class=\"erroroutput\"><span class=\"gu\">%s</span>" % title
exc_type, exc_value, exc_tb = sys.exc_info()
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
nruter += "\n%s" % self.dumpPythonTB(line)
return nruter + "</div>"
def doGet(self, request, response):
# Treat GET and POST equally
self.doPost(request, response)
DIV_HIDEOUS_BOX = "<div class=\"%s\"><div class=\"gh\">%s - <a href=\"javascript:ReverseDisplay('%s')\">show/hide %s</a></div><div id=\"%s\" style=\"display:%s\">%s</div>%s"
def divHideCode(self, claz, title, id, data, visible=False, content="", openend=False):
return self.DIV_HIDEOUS_BOX % (claz, title, id, content, id, visible and "show" or "none", data, openend and " " or "</div>")
def doPost(self, request, response):
c = NomjycContainer()
c.parameters = request.getParameterMap()
log = open("/var/log/nomjyc/sandbox.log","a")
safelog = dict(c.parameters)
if "pass" in safelog:
safelog["pass"]=len(safelog["pass"])
log.write(("[[%s]] %s %s\n" % (request.getRemoteAddr(), datetime.utcnow(), self.yaml.dump(safelog))).encode("utf-8"))
log.close()
output = "<div class=\"infobox\"><span class=\"gh\">nomjyc 0.1</span>\n"
c.session = {}
if len(c.parameters)==0:
output += "<pre>%s</pre>" % self.__doc__
output += "</div>"
c.salt="dckx"
try:
c.data = self.yaml.load(FileInputStream("/var/lib/tomcat6/webapps/nomjyc/data/nomjyc.yaml"))
except:
output += self.explainException("Error while initiating game state")
# Print some debug information - for now.
output += self.divHideCode("infobox", "Request", "reqi", self.dumpYaml(c.parameters), visible=True)
output += self.divHideCode("infobox", "Data read", "dri", self.dumpYaml(c.data))
# Add a final rule, if the test parameter is set
if "test" in c.parameters:
for code in c.parameters["test"]:
c.data["rules"].add({"author":"impromptu", "code":code, "creation":datetime.utcnow(), "title":"test rule"})
cycles = 1
if "cycles" in c.parameters:
try:
cycles = int(c.parameters["cycles"][0])
except:
pass
if cycles<0 or cycles>3:
cycles = 1
# Execute all rules against the user input
brain = PythonInterpreter()
c.sandbox = True # a flag that gives away that we are in a sandbox
for i in range(cycles):
c.cycle = i # a counter for the cycle we are in
for rule in c.data["rules"][:]: # we are going to modify the rules. a lot. this prevents concurrent modification.
try:
output += self.divHideCode("rulebox", "Executing rule '%s'" % rule["title"], "id"+str(random()), self.dumpPython(rule["code"]), openend=True)
err = StringWriter()
out = StringWriter()
checksum = hashlib.md5(self.yaml.dump(c.data)).hexdigest()
brain.set("self", c)
brain.setErr(err)
brain.setOut(out)
before = time.time()
timeout (brain.exec,(rule["code"],),timeout_duration=30)
runtime = int((time.time()-before) * 1000)
changes = (checksum != hashlib.md5(self.yaml.dump(c.data)).hexdigest())
output += "<div class=\"ruleoutput\">"
if changes: output += "<div class=\"erroroutput\">This rule changed the game data.</div>"
if (err.getBuffer().length()): output += "<div class=\"erroroutput\">Err:<br />%s</div>" % self.dumpPythonTB(err.toString().strip())
if (out.getBuffer().length()): output += "<div class=\"gu\">Out:</div>"+out.toString().strip()
output += "<div>(runtime: %sms)</div></div></div>" % runtime
except Exception, ex:
output += self.explainException("Execution failed") + "</div>"
# Dump the data back to file - but not in the sandbox
#try:
# self.yaml.dump(c.data, FileWriter("/var/lib/tomcat6/webapps/sandbox/data/nomjyc.yaml"))
#except:
# output += self.explainException("Error while storing game state")
# Print some debug information - for now.
output += self.divHideCode("infobox", "Session data", "sess", self.dumpYaml(c.session), visible=True)
output += self.divHideCode("infobox", "Data stored", "dsf", self.dumpYaml(c.data))
# Send all output to the user (xml or html?)
toClient = response.getWriter()
response.setContentType("text/html")
toClient.println("""
<html>
<head>
<title>Nomjyc</title>
<link rel="stylesheet" type="text/css" href="pygments.css" />
<script type="text/javascript" src="nomjyc.js"></script>
</head>
<body>%s</body>
</html>
""" % output)
class nomjyc (HttpServlet):
"""
This is the nomjyc web interface. Nomic is a game where the players change the rules.
Nomjyc is the same game, except that the rules are written in jython.
Called without parameters, it will most probably just display its own rules.
Call it with GET or POST parameters to execute and change them.
Read the code to understand how.
Just kidding. We have a wiki at <a href="http://nomjyc.ath.cx:8080/cgi/fossil">http://nomjyc.ath.cx:8080/cgi/fossil</a>
"""
def __init__(self):
self.yaml = Yaml()
self.yamlLexer = YamlLexer()
self.pythonLexer = PythonLexer()
self.pythonTBLexer = PythonTracebackLexer()
self.htmlFormatter = HtmlFormatter()
def dumpData(self,c):
rules = c.data["rules"]
c.data["rules"] = "omitted"
code = highlight(self.yaml.dump(c.data), self.yamlLexer, self.htmlFormatter)
c.data["rules"] = rules
return code
def dumpYaml(self, anything):
#return highlight(self.yaml.dump(anything), self.yamlLexer, self.htmlFormatter)
return "<pre>%s</pre>" % self.yaml.dump(anything)
def dumpPython(self, code):
return highlight(code, self.pythonLexer, self.htmlFormatter)
def dumpPythonTB(self, code):
return highlight(code, self.pythonTBLexer, self.htmlFormatter)
def explainException(self, title):
nruter = "<div class=\"erroroutput\"><span class=\"gu\">%s</span>" % title
exc_type, exc_value, exc_tb = sys.exc_info()
for line in traceback.format_exception(exc_type, exc_value, exc_tb):
nruter += "\n%s" % self.dumpPythonTB(line)
return nruter + "</div>"
def doGet(self, request, response):
# Treat GET and POST equally
self.doPost(request, response)
DIV_HIDEOUS_BOX = "<div class=\"%s\"><div class=\"gh\">%s - <a href=\"javascript:ReverseDisplay('%s')\">show/hide %s</a></div><div id=\"%s\" style=\"display:%s\">%s</div>%s"
def divHideCode(self, claz, title, id, data, visible=False, content="", openend=False):
return self.DIV_HIDEOUS_BOX % (claz, title, id, content, id, visible and "show" or "none", data, openend and " " or "</div>")
def doPost(self, request, response):
c = NomjycContainer() # re-initialized container upon every request
c.parameters = request.getParameterMap()
log = open("/var/log/nomjyc/nomjyc.log","a")
safelog = dict(c.parameters)
if "pass" in safelog:
safelog["pass"]=len(safelog["pass"])
log.write(("[[%s]] %s %s\n" % (request.getRemoteAddr(), datetime.utcnow(), self.yaml.dump(safelog))).encode("utf-8"))
log.close()
output = "<div class=\"infobox\"><span class=\"gh\">nomjyc 0.1</span>\n"
c.session = {}
if len(c.parameters)==0:
output += "<pre>%s</pre>" % self.__doc__
output += "</div>"
c.salt="dckx"
try:
c.data = self.yaml.load(FileInputStream("/var/lib/tomcat6/webapps/nomjyc/data/nomjyc.yaml"))
except:
output += self.explainException("Error while initiating game state - trying to load backup.")
c.data = self.yaml.load(FileInputStream("/var/lib/tomcat6/webapps/nomjyc/data/nomjyc.bak"))
# Print some debug information - for now.
output += self.divHideCode("infobox", "Request", "reqi", self.dumpYaml(c.parameters), visible=True)
output += self.divHideCode("infobox", "Data read", "dri", self.dumpYaml(c.data))
# If we have come so far, we assume that it is safe to write a backup.
try:
self.yaml.dump(c.data, FileWriter("/var/lib/tomcat6/webapps/nomjyc/data/nomjyc.bak"))
except:
output += self.explainException("Error while storing backup game state")
# Execute all rules against the user input
brain = PythonInterpreter()
c.sandbox = False # a flag that tells that we are not in a sandbox
checksum = hashlib.md5(self.yaml.dump(c.data)).hexdigest()
for rule in c.data["rules"][:]: # we are going to modify the rules. a lot. this prevents concurrent modification.
try:
output += self.divHideCode("rulebox", "Executing rule '%s'" % rule["title"], "id"+str(random()), self.dumpPython(rule["code"]), openend=True)
err = StringWriter()
out = StringWriter()
# Compile the rule into a jython/java class
brain.set("self", c) # expose the container to the rules
brain.setErr(err)
brain.setOut(out)
before = time.time()
timeout (brain.exec,(rule["code"],),timeout_duration=30)
runtime = int((time.time()-before) * 1000)
newsum = hashlib.md5(self.yaml.dump(c.data)).hexdigest()
changes = (checksum != newsum)
checksum = newsum
output += "<div class=\"ruleoutput\">"
if changes: output += "<div class=\"erroroutput\">This rule changed the game data.</div>"
if (err.getBuffer().length()): output += "<div class=\"erroroutput\">Err:<br />%s</div>" % self.dumpPythonTB(err.toString())
if (out.getBuffer().length()): output += "<div class=\"gu\">Out:</div>"+out.toString()
output += "<div>(runtime: %sms)</div></div></div>" % runtime
except Exception, ex:
output += self.explainException("Execution failed") + "</div>"
# Dump the data back to file
try:
self.yaml.dump(c.data, FileWriter("/var/lib/tomcat6/webapps/nomjyc/data/nomjyc.yaml"))
except:
output += self.explainException("Error while storing game state")
# Print some debug information - for now.
output += self.divHideCode("infobox", "Session data", "sess", self.dumpYaml(c.session), visible=True)
output += self.divHideCode("infobox", "Data stored", "dsf", self.dumpYaml(c.data))
# Send all output to the user (xml or html?)
toClient = response.getWriter()
response.setContentType("text/html")
toClient.println("""
<html>
<head>
<title>Nomjyc</title>
<link rel="stylesheet" type="text/css" href="pygments.css" />
<script type="text/javascript" src="nomjyc.js"></script>
</head>
<body>%s</body>
</html>
""" % output)