def __init__(self, parent):
"""
Load from userhome/.xnat.cfg
:param parent:
"""
super(OPEXUploaderGUI, self).__init__(parent)
self.Bind(wx.EVT_CLOSE, self.OnExit)
self.SetTitle("OPEX Uploader App")
self.SetPosition(wx.Point(100, 100))
self.SetSize((700, 700))
self.configfile = join(expanduser('~'), '.xnat.cfg')
self.resource_dir = findResourceDir()
self.configdb = join(self.resource_dir, 'opexconfig.db')
self.loaded = self.__loadConfig()
self.runoptions = self.__loadOptions()
self.opexid = False
self.subjectchars = 6
if self.loaded:
self.chOptions.SetItems(sorted(self.runoptions.keys()))
self.dbedit.AppendItems(self.config.keys())
# # DISPLAY OUTPUT IN WINDOW as stdout
sys.stdout = LogOutput(self.tcResults)
# Update status bar from Thread
EVT_RESULT(self, self.__statusoutput)
self.m_statusBar1.SetStatusText(
'Welcome to the Uploader! Help is available from the Menu')
self.Show()
def OnHelp(self, e):
"""
Show the User Help Guide
:param e:
:return:
"""
resource_dir = findResourceDir()
projdir = dirname(resource_dir)
local_readme_url = join(projdir, 'README.md')
readme_url = 'https://raw.githubusercontent.com/QBI-Software/OPEXUploader/master/README.md'
http = urllib3.PoolManager(cert_reqs='CERT_REQUIRED',
ca_certs=certifi.where())
mdfile = http.request('GET', readme_url)
# Write locally
if sys.platform == 'win32':
flag = 'wb'
else:
flag = 'w'
with open(local_readme_url, flag) as output:
output.write(mdfile.data)
help_page = join(resource_dir, 'HELP.html')
md = markdown.Markdown()
md.convertFile(local_readme_url, help_page)
# Load to dialog
dlg = dlgHelp(self)
dlg.m_htmlWin1.LoadPage(help_page)
dlg.Show()
def __loadopexfile(self):
"""
Load experiment info from opex.csv
:return:
"""
try:
self.resource_dir = findResourceDir()
opexfile = join(self.resource_dir, 'opex.csv')
opex = pandas.read_csv(opexfile)
msg = 'OPEX Resources loaded: %s from %s' % (not opex.empty,
opexfile)
logging.info(msg)
return opex
except Exception as e:
msg = 'OPEX Resources NOT loaded: %s' % (e.args[0])
logging.error(msg)
raise IOError(e)
def __init__(self, subjects=None):
"""
List of subjects from XNAT as collection
:param subjects:
:param csvfile: spreadsheet export from OPEX subjects tab (with counts)
"""
self.subjects = subjects
self.subjectids = None
self.data = None
self.minmth = 0
self.maxmth = 12
configdb = join(findResourceDir(), 'opexconfig.db')
if not access(configdb, R_OK):
raise IOError('Cannot find config database')
self.dbi = DBI(configdb)
self.expts = self.dbi.getExpts()
self.xnat = None
self.__loaddata()
def __init__(self,
datafile=None,
sheet=0,
skiplines=0,
header=None,
etype=None):
msg = 'DataParser: datafile=%s sheet=%s skiplines=%s header=%s etype=%s' % (
datafile, str(sheet), str(skiplines), str(header), str(etype))
print(msg)
logging.info(msg)
self.datafile = datafile # full pathname to data file
self.resource_dir = findResourceDir()
configdb = join(self.resource_dir, 'opexconfig.db')
if not access(configdb, R_OK):
print(configdb)
raise IOError('Cannot find config database {}'.format(configdb))
try:
self.dbi = DBI(configdb)
self.etype = etype
if etype is not None:
self.info = self.dbi.getInfo(etype)
self.fields = self.dbi.getFields(etype)
else:
self.info = None
self.fields = None
self.subjects = None
self.incorrect = self.dbi.getIDs()
if self.datafile is not None and len(self.datafile) > 0:
(bname, extn) = splitext(basename(self.datafile))
self.ftype = extn # extension - xlsx or csv
self.sheet = sheet
self.skiplines = skiplines
self.header = header
self._loadData()
except Exception as e:
raise e
def __init__(self, parent):
super(IdsDialog, self).__init__(parent)
self.resource_dir = findResourceDir()
self.idfile = join(self.resource_dir, 'incorrectIds.csv')
self.iddb = join(self.resource_dir, 'opexconfig.db')
self.__loadData()
def test_FieldsDir(self):
resourcedir = findResourceDir()
expected = os.path.join(resourcedir, 'fields')
print('Testing: ', expected)
self.assertTrue(os.path.exists(expected))
def test_ResourceDir(self):
resourcedir = findResourceDir()
print('Resource dir: ', resourcedir)
expected = 'resources'
self.assertEqual(os.path.basename(resourcedir), expected)
def setUp(self):
self.resourcedir = findResourceDir()
configdb = join(self.resourcedir, 'opexconfig_test.db')
self.dbi = DBI(configdb)
self.dbi.getconn()