def onNotes(self):
notes_program = pw.Config.SCIPION_NOTES_PROGRAM
notes_args = pw.Config.SCIPION_NOTES_ARGS
args = []
notes_file = self.project.getPath('Logs', pw.Config.SCIPION_NOTES_FILE)
# If notesFile does not exist, it is created and an explanation/documentation comment is added at the top.
if not os.path.exists(notes_file):
f = open(notes_file, 'a')
f.write(pw.genNotesHeading())
f.close()
# Then, it will be opened as specified in the conf
if notes_program:
args.append(notes_program)
# Custom arguments
if notes_args:
args.append(notes_args)
args.append(notes_file)
subprocess.Popen(args) # nonblocking
else:
# if no program has been selected
# xdg-open will try to guess but
# if the file does not exist it
# will return an error so If the file does
# not exist I will create an empty one
# 'a' will avoid accidental truncation
openTextFileEditor(notes_file)
def visualize(self, obj, **kwargs):
# The sequence object is visualized in a tmp file;
# To build this tmp file we use a method (saveFile) from the class
# SequenceHandler that requires a Biopython sequence (Bio.Seq.Seq
# object);
# Step 1: transformation of the sequence of our Scipion Sequence
# object (obj.getSequence()) in a Biopython Sequence:
# Let keep the SequenceHandler import here to avoid a default BioPython
# import
seqHandler = emconv.SequenceHandler(obj.getSequence(),
isAminoacid=obj.getIsAminoacids())
seqBio = seqHandler._sequence # Bio.Seq.Seq object
# Step 2: retrieving of the other args needed in the saveFile method
seqID = obj.getId()
seqName = obj.getSeqName()
seqDescription = obj.getDescription()
seqFileName = os.path.abspath(
self.protocol._getExtraPath(seqName + ".fasta"))
# Step 3: Sequence saved in the extra file
seqHandler.saveFile(seqFileName,
seqID,
sequence=seqBio,
name=seqName,
seqDescription=seqDescription,
type="fasta")
# Step 4: Visualization of extra file
openTextFileEditor(seqFileName)
def onExportTreeGraph(self):
runsGraph = self.project.getRunsGraph(refresh=True)
useId = not pwutils.envVarOn('SCIPION_TREE_NAME')
dotStr = runsGraph.printDot(useId=useId)
with tempfile.NamedTemporaryFile(suffix='.gv', mode="w") as dotFile:
dotFile.write(dotStr)
dotFile.flush()
openTextFileEditor(dotFile.name)
if useId:
print("\nexport SCIPION_TREE_NAME=1 # to use names instead of ids")
else:
print("\nexport SCIPION_TREE_NAME=0 # to use ids instead of names")
def onExportTreeGraph(self):
runsGraph = self.project.getRunsGraph(refresh=True)
useId = not pwutils.envVarOn('SCIPION_TREE_NAME')
dotStr = runsGraph.printDot(useId=useId)
with tempfile.NamedTemporaryFile(suffix='.gv') as dotFile:
dotFile.write(dotStr)
dotFile.flush()
openTextFileEditor(dotFile.name)
if useId:
print "\nexport SCIPION_TREE_NAME=1 # to use names instead of ids"
else:
print "\nexport SCIPION_TREE_NAME=0 # to use ids instead of names"
def onNotes(self):
if not all(var in os.environ for var in ['SCIPION_NOTES_PROGRAM',
'SCIPION_NOTES_FILE',
'SCIPION_NOTES_ARGS']):
return self.showError("Missing variables SCIPION_NOTES_* under\n"
"[VARIABLES] section in the configuration file\n"
"~/.config/scipion/scipion.conf")
args = []
# Program name
program = os.environ.get('SCIPION_NOTES_PROGRAM', None)
notesFile = self.project.getPath('Logs', os.environ['SCIPION_NOTES_FILE'])
if program:
args.append(program)
# Custom arguments
if os.environ.get('SCIPION_NOTES_ARGS', None):
args.append(os.environ['SCIPION_NOTES_ARGS'])
args.append(notesFile)
subprocess.Popen(args) #nonblocking
else:
openTextFileEditor(notesFile)
def onNotes(self):
if not all(var in os.environ for var in [
'SCIPION_NOTES_PROGRAM', 'SCIPION_NOTES_FILE',
'SCIPION_NOTES_ARGS'
]):
return self.showError(
"Missing variables SCIPION_NOTES_* under\n"
"[VARIABLES] section in the configuration file\n"
"~/.config/scipion/scipion.conf")
args = []
# Program name
program = os.environ.get('SCIPION_NOTES_PROGRAM', None)
notesFile = self.project.getPath('Logs',
os.environ['SCIPION_NOTES_FILE'])
if program:
args.append(program)
# Custom arguments
if os.environ.get('SCIPION_NOTES_ARGS', None):
args.append(os.environ['SCIPION_NOTES_ARGS'])
args.append(notesFile)
subprocess.Popen(args) #nonblocking
else:
openTextFileEditor(notesFile)
def visualize(self, obj, **kwargs):
prot = obj
fnPlot = prot._getPath('plot.png')
if os.path.exists(fnPlot):
openTextFileEditor(fnPlot)
def visualize(self, obj, **kwargs):
fnStatistics = self.protocol._getPath("statistics.txt")
if exists(fnStatistics):
openTextFileEditor(fnStatistics)
def visualize(self, obj, **kwargs):
fnAnalysis = obj.fnAnalysis.get()
if exists(fnAnalysis):
openTextFileEditor(fnAnalysis)
def visualize(self, obj, **kwargs):
fnCSV = self.protocol.getFilenameOut()
if exists(fnCSV):
openTextFileEditor(fnCSV)
def visualize(self, obj, **kwargs):
fnStatistics = self.protocol._getPath("statistics.txt")
if exists(fnStatistics):
openTextFileEditor(fnStatistics)
def visualize(self, obj, **kwargs):
fnAnalysis = obj.fnAnalysis.get()
if exists(fnAnalysis):
openTextFileEditor(fnAnalysis)
def visualize(self, obj, **kwargs):
fnCSV = self.protocol.getFilenameOut()
if exists(fnCSV):
openTextFileEditor(fnCSV)