def load(self, filename):
self.tabptr = 0
self.tabdata = []
self.tasks = []
self.track = []
self.keyref = {}
with ZipFile(filename, "r") as wtab:
workflowFile = wtab.open("workflow.cwl", "r")
self.workflow = yamler(io.TextIOWrapper(workflowFile))
templateFile = wtab.open("template.yml", "r")
self.template = yamler(io.TextIOWrapper(templateFile))
for cwlfile in wtab.namelist():
if ".cwl" in cwlfile and cwlfile != "workflow.cwl":
taskfile = wtab.open(cwlfile, "r")
self.tasks.append(
[cwlfile, yamler(io.TextIOWrapper(taskfile))])
header = 0
for line in wtab.open("table.txt", "r"):
line = line.decode("utf8")
line = line.strip()
if line[0] == '#':
continue
if header == 2:
self.tabdata.append(re.split(' ', line))
self.keyref[(self.tabdata[-1])[1]] = len(self.tabdata) - 1
self.track.append(TR_COMPLETE)
continue
if header == 0:
self.fieldnames = re.split(' ', line)
header = 1
else:
self.fieldtypes = re.split(' ', line)
header = 2
self.lastfilename = filename
def makeyml(pathname, command):
"""
Generates a yml file to guide execution, based on the specific->general hierarchy
Run specific parameters override batch specific parameters override global parameters
:param pathname: The path of the project of interest
"""
if ".wtx" in command:
wt = Worktable(command)
cmdDict = wt.template
else:
cmdyml = (re.split(".cwl", command)[0]).strip() + ".yml"
cmdDict = yamler(open(scriptFolder + "/" + cmdyml, "r"))
globalDict = yamler(open(coreFolder + "/stoa.yml", "r"))
if not os.path.exists("stoa.yml"):
open("stoa.yml", "a").close()
batchDict = yamler(open("stoa.yml", "r"))
if not os.path.exists(pathname + "/stoa.yml"):
open(pathname + "/stoa.yml", "a").close()
specDict = yamler(open(pathname + "/stoa.yml", "r"))
for key in cmdDict:
globalDict[key] = cmdDict[key]
for key in batchDict:
globalDict[key] = batchDict[key]
for key in specDict:
globalDict[key] = specDict[key]
writeyaml(globalDict, pathname + "/runraw.yml")
ymlvars(pathname + "/runraw.yml", pathname + "/run.yml",
coreFolder + "/" + pathname)
def ExecCWL(cmdFile, pathname):
result = {}
success = 0
if ".wtx" in cmdFile:
wt = Worktable(cmdFile)
wtFile = cmdFile
cmdFile = wt.unpack()
else:
wt = False
cmdFile = scriptFolder + "/" + cmdFile
try:
result = cwlinvoke(
pathname, cmdFile,
yamler(open(pathname + "/run.yml", "r"), convert=True))
writeyaml(result, pathname + "/.pipelog.txt")
except WorkflowException as werr:
success = 1
log = open(pathname + "/.pipelog.txt", "a")
log.write("Workflow Exception: {}\n".format(werr.args))
log.close()
#writeyaml(result, pathname+"/stoa_out.yml")
if wt:
wt.repack(cmdFile) # Needs a more efficient indexing method here
index = wt.byref(pathname)
wt.update(index, parsecwloutput(pathname, result))
wt.save(wtFile)
return success
def parseAction(filename):
"""
Parses a script file to extract directives
:param filename: The name of the script file
:return: A list of directives
"""
properties = {}
tree = yamler(filename)
if 'stoa' in tree:
for item in tree['stoa']:
properties[item] = tree['stoa'][item]
return properties
def addtask(self, filename):
newfile = re.split("/", filename)[-1]
self.tasks.append([newfile, yamler(open(filename, "r"))])
def addtask(self, filename):
self.task.append([filename, yamler(open(filename, "r"))])
def addfile(self, filename):
if ".cwl" in filename:
self.workflow = yamler(open(filename, "r"))
if ".yml" in filename:
self.template = yamler(open(filename, "r"))
started = False
targetFolder = ""
currentFolder = {}
userspace = {}
session = {}
runStatus = "Nothing"
tasklist = {}
siteroot = "http://127.0.0.1:8888"
scriptPath = os.path.realpath(__file__)
webPath = os.path.split(scriptPath)[0] + "/"
config = yamler(open("stoa.yml", "r"))
projectname = config['stoa-info']['project-name']
handlerpath = config['stoa-info']['filehandler']['script']
handlerpattern = config['stoa-info']['filehandler']['pattern']
handler_name, fext = os.path.splitext(os.path.split(handlerpath)[-1])
filehandler = load_source(handler_name, handlerpath)
reftables = {}
if 'reftable' in config['stoa-info']:
reftables[config['stoa-info']['reftable']
['name']] = config['stoa-info']['reftable']['coords']
obsfile = "" #TODO: Link this value to config file
stopCommand = "<a href=\"javascript:getPath('r')\">Click here to stop batch</a>"