def serve_demo():
filename = "demo/demo-chemokine.web"
assert os.path.exists(filename)
spydertype = Spyder.AttractEasyModel
formlib = form_standard
cgiscript = "attractserver-easy.py"
model = spydertype.fromfile(filename)
import random
from spyder.formtools import embed
embed(model)
filename2 = os.path.split(filename)[0] + "-" + str(random.randint(1,1000000))
os.chdir("/tmp")
model.tofile(filename2)
f = spydertype._form()
f = formlib.webform_easy(f, model)
header = formlib.header.replace("<head>", "<head>\n <base href=\"%s\" target=\"_blank\">" % webdir, 1)
html = attracthtmlform.htmlform(
obj=model,
form=f,
cgi=cgidir+cgiscript,
header=header,
footer=formlib.footer,
header_indentation = 12,
resourcefilename=filename2,
)
return html
def serve_upload():
webform = cgi.FieldStorage()
if "protocolfile" not in webform:
raise Exception ### TODO, nice error message
data = webform["protocolfile"].value
interface = webform["interface"].value
typ, content = spyder.core.parse(data)
conversion = False
if interface == "auto":
interface = typ
else:
conversion = True
if interface == "AttractModel":
spydertype = Spyder.AttractModel
formlib = form_model
cgiscript = "attractserver.py"
elif interface == "AttractEasyModel":
spydertype = Spyder.AttractEasyModel
formlib = form_standard
cgiscript = "attractserver-easy.py"
elif interface == "AttractPeptideModel":
spydertype = Spyder.AttractPeptideModel
formlib = form_peptide
cgiscript = "attractserver-peptide.py"
else:
raise ValueError(interface) ### TODO, nice error message
if conversion:
spydertype2 = getattr(Spyder, typ)
model = spydertype2.fromdict(content)
model = model.convert(spydertype)
else:
model = spydertype.fromdict(content)
import random
from spyder.formtools import embed
embed(model)
mydir = "attract-upload" + str(random.randint(1, 1000000))
fname = "attract.web"
os.chdir("/tmp")
os.mkdir(mydir)
os.chdir(mydir)
model.tofile(fname)
f = spydertype._form()
f = formlib.webform(f, model)
header = formlib.header.replace(
"<head>",
"<head>\n <base href=\"%s\" target=\"_blank\">" % webdir, 1)
html = attracthtmlform.htmlform(
obj=model,
form=f,
cgi=cgidir + cgiscript,
header=header,
footer=formlib.footer,
header_indentation=12,
resourcefilename=mydir + "/" + fname,
)
return html
def html(form, cgi, spyderobj, newtab=False, header=header0, footer=footer0):
import random
import attracthtmlform
args = dict(
obj=spyderobj,
form=form,
cgi=cgi,
header=header,
footer=footer,
header_indentation=12,
newtab=newtab,
)
if spyderobj is not None:
from spyder.formtools import embed
embed(spyderobj)
mydir = "attractrun" + str(random.randint(1, 1000000))
fname = "attract.web"
os.chdir("/tmp/")
os.mkdir(mydir)
os.chdir(mydir)
spyderobj.tofile(fname)
args["resourcefilename"] = mydir + "/" + fname
html = attracthtmlform.htmlform(**args)
return html
#!/usr/bin/python """ Command line tool to embed a Spyder model """ import sys, os currdir = os.path.abspath(os.path.split(__file__)[0]) guidir = currdir + "/../gui" sys.path.insert(0, guidir) import spyder, Spyder import attractmodel from spyder.formtools import embed inputfile = sys.argv[1] inputdata = open(inputfile).read() inputdir = os.path.split(inputfile)[0] if len(inputdir): os.chdir(inputdir) spydertypename, spyderdict = spyder.core.parse(inputdata) spydertype = getattr(Spyder, spydertypename) model = spydertype.fromdict(spyderdict) embed(model) print repr(model)
def serve_attract(spydertype, formlib, deploy, **kwargs):
# Obtain the webdict (what the user submitted) and f, the spyderform used to generate the HTML
webdict = spyder.formtools.cgi.dict_from_fieldstorage(cgi.FieldStorage())
easy = "easy" in kwargs and kwargs["easy"]
if easy:
f = formlib.webserverform_easy(webdict, spydertype=spydertype)
else:
f = formlib.webserverform(webdict, spydertype=spydertype)
# Fill in links to embedded resources
resourceobj = None
resourcefilevar = getattr(f, "resourcefilevar", None)
if resourcefilevar is not None and resourcefilevar in webdict:
tmpf = "/tmp/" + webdict[resourcefilevar]
resourceobj = spydertype.fromfile(tmpf)
newmodel, status, delta = spyder.formtools.cgi.cgi(webdict,
f,
resourceobj,
spydertype=spydertype)
# Detect empty form
if not len(webdict) or delta is None:
raise AttractServerError(status="You didn't submit any data",
delta=None)
#Special case: use_iattract is by default False in the easy web interface, but True in the standard interface
if easy and "use_iattract" not in delta:
delta["use_iattract"] = False
if easy and delta["use_iattract"]: #bug in Spyder?
newmodel.use_iattract = True
# Create a result directory
cwd = os.getcwd()
os.chdir(localresultdir)
mydir = "run" + str(random.randint(1, 1000000))
os.mkdir(mydir)
# Detect errors in the form submission
# We will still give the user the delta file
deltamessage = format_delta(delta, mydir)
if status.splitlines()[0].find("OK") == -1:
raise AttractServerError(status=status, delta=deltamessage)
# New model was received OK, should be no bugs from here on...
try:
# Obtain a runname
runname = getattr(newmodel, "runname", None)
if runname is None or runname == "attract":
runname = "attract-" + datetime.datetime.now().date().isoformat()
runname = ''.join(
[str(char) for char in runname if char in string.printable])
runname = re.sub(r'[^a-zA-Z0-9\.]', '_', runname)
# Embed the model, and save the delta
os.chdir(cwd)
newmodel.runname = runname
embed(newmodel)
fname_embedded = "%s-embedded.web" % runname
fname = "%s.web" % runname
os.chdir(localresultdir)
deltamessage = format_delta(delta, mydir, runname)
os.chdir(mydir)
newmodel.tofile(fname_embedded)
except:
# Processing error 1
error = traceback.format_exc()
response = response_processing1_error % error
response += deltamessage
return response
try:
#Create an archive directory equal to runname
os.mkdir(runname)
os.chdir(runname)
deploy(newmodel, ".")
newmodel.tofile(fname)
except:
# Processing error 2
error = traceback.format_exc()
response = response_processing2_error % error
response += response_embedded % (webresultdir + mydir + "/" +
fname_embedded, fname_embedded)
response += deltamessage
return response
try:
#Run the generator, write the script and create the archive
if isinstance(newmodel, Spyder.AttractPeptideModel):
newmodel = newmodel.convert(Spyder.AttractEasyModel)
r = newmodel.partners[1].pdbfile
r.link("peptide.pdb")
r.save()
script = newmodel.generate()
shname = "%s.sh" % runname
f = open(shname, "w")
f.write(script)
f.close()
os.system("chmod +x %s" % shname)
os.chdir("..")
os.system("chmod a+rw %s" % mydir)
aname = "%s.tgz" % runname
os.system("tar czf %s %s" % (aname, runname))
assert os.path.exists(aname)
except:
# Generator error
error = traceback.format_exc()
response = response_generator_error % error
response += response_embedded % (webresultdir + mydir + "/" +
fname_embedded, fname_embedded)
response += deltamessage
return response
response = response_success
response += response_directory % (shname, webresultdir + mydir + "/" +
aname, aname, fname)
response += response_embedded % (webresultdir + mydir + "/" +
fname_embedded, fname_embedded)
response += response_rpbs % (rpbs_website, mydir, fname_embedded)
response += deltamessage
return response