Skip to content

Blitz Gateway flake8 fixes #4982

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jburel merged 3 commits into from
Dec 6, 2016
Merged

Blitz Gateway flake8 fixes #4982

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
d0f8d93
Lots of flake8 fixes in Blitz Gateway
will-moore Nov 17, 2016
7e8f77d
Fix merge conflicts
will-moore Dec 5, 2016
e14a0cd
Add space after #
will-moore Dec 5, 2016
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
153 changes: 78 additions & 75 deletions components/tools/OmeroPy/src/omero/gateway/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#!/usr/bin/env python

# !/usr/bin/env python
# -*- coding: utf-8 -*-
#
# blitz_gateway - python bindings and wrappers to access an OMERO blitz server
Expand All @@ -13,7 +14,6 @@

# Set up the python include paths
import os
THISPATH = os.path.dirname(os.path.abspath(__file__))

import warnings
from collections import defaultdict
Expand Down Expand Up @@ -44,7 +44,13 @@
from gettext import gettext as _

import logging
from math import sqrt

from omero.rtypes import rstring, rint, rlong, rbool
from omero.rtypes import rtime, rlist, rdouble, unwrap

logger = logging.getLogger(__name__)
THISPATH = os.path.dirname(os.path.abspath(__file__))

try:
from PIL import Image, ImageDraw, ImageFont # see ticket:2597
Expand All @@ -57,10 +63,6 @@
except:
logger.error(
'No Pillow installed, line plots and split channel will fail!')
from math import sqrt

from omero.rtypes import rstring, rint, rlong, rbool
from omero.rtypes import rtime, rlist, rdouble, unwrap


def omero_type(val):
Expand Down Expand Up @@ -211,9 +213,9 @@ def __eq__(self, a):
:return: True if objects are same - see above
:rtype: Boolean
"""
return (type(a) == type(self)
and self._obj.id == a._obj.id
and self.getName() == a.getName())
return (type(a) == type(self) and
self._obj.id == a._obj.id and
self.getName() == a.getName())

def __bstrap__(self):
"""
Expand Down Expand Up @@ -334,8 +336,8 @@ def _getParentWrappers(self):
# self.__class__.PARENT_WRAPPER_CLASS \
# = self.PARENT_WRAPPER_CLASS = g[self.PARENT_WRAPPER_CLASS]
# return self.PARENT_WRAPPER_CLASS
if (pwc != self.PARENT_WRAPPER_CLASS
or pwc != self.__class__.PARENT_WRAPPER_CLASS):
if (pwc != self.PARENT_WRAPPER_CLASS or
pwc != self.__class__.PARENT_WRAPPER_CLASS):
self.__class__.PARENT_WRAPPER_CLASS \
= self.PARENT_WRAPPER_CLASS = pwc
return self.PARENT_WRAPPER_CLASS
Expand Down Expand Up @@ -394,9 +396,9 @@ def findChildByName(self, name, description=None):
"""
for c in self.listChildren():
if c.getName() == name:
if (description is None
or omero_type(description)
== omero_type(c.getDescription())):
if (description is None or
omero_type(description) ==
omero_type(c.getDescription())):
return c
return None

Expand All @@ -422,8 +424,8 @@ def getDate(self):
"""

try:
if (self._obj.acquisitionDate.val is not None
and self._obj.acquisitionDate.val > 0):
if (self._obj.acquisitionDate.val is not None and
self._obj.acquisitionDate.val > 0):
t = self._obj.acquisitionDate.val
return datetime.fromtimestamp(t/1000)
except:
Expand Down Expand Up @@ -460,9 +462,9 @@ def saveAs(self, details):
"""
if self._conn.isAdmin():
d = self.getDetails()
if (d.getOwner()
and d.getOwner().omeName == details.getOwner().omeName
and d.getGroup().name == details.getGroup().name):
if (d.getOwner() and
d.getOwner().omeName == details.getOwner().omeName and
d.getGroup().name == details.getGroup().name):
return self.save()
else:
newConn = self._conn.suConn(
Expand Down Expand Up @@ -863,8 +865,8 @@ def _getAnnotationLinks(self, ns=None):
rv = self.copyAnnotationLinks()
if ns is not None:
rv = filter(
lambda x: x.getChild().getNs()
and x.getChild().getNs().val == ns, rv)
lambda x: x.getChild().getNs() and
x.getChild().getNs().val == ns, rv)
return rv

def unlinkAnnotations(self, ns):
Expand Down Expand Up @@ -1019,12 +1021,12 @@ def linkAnnotation(self, ann, sameOwner=False):
if sameOwner:
d = self.getDetails()
ad = ann.getDetails()
if (self._conn.isAdmin()
and self._conn.getUserId() != d.getOwner().id):
if (self._conn.isAdmin() and
self._conn.getUserId() != d.getOwner().id):
# Keep the annotation owner the same as the linked of object's
if (ad.getOwner()
and d.getOwner().omeName == ad.getOwner().omeName
and d.getGroup().name == ad.getGroup().name):
if (ad.getOwner() and
d.getOwner().omeName == ad.getOwner().omeName and
d.getGroup().name == ad.getGroup().name):
newConn = ann._conn
else:
# p = omero.sys.Principal()
Expand Down Expand Up @@ -1174,9 +1176,9 @@ def __getattr__(self, attr):

# handle lookup of 'get' methods, using '_attrs' dict to define how we
# wrap returned objects.
if (attr != 'get'
and attr.startswith('get')
and hasattr(self, '_attrs')):
if (attr != 'get' and
attr.startswith('get') and
hasattr(self, '_attrs')):
tattr = attr[3].lower() + attr[4:] # 'getName' -> 'name'
# find attr with 'name'
attrs = filter(lambda x: tattr in x, self._attrs)
Expand Down Expand Up @@ -1229,8 +1231,8 @@ def wrap():
# If this is a _unit, then we ignore val
# since it's not an rtype to unwrap.
if not hasattr(rv, "_unit"):
return (isinstance(rv.val, StringType)
and rv.val.decode('utf8') or rv.val)
return (isinstance(rv.val, StringType) and
rv.val.decode('utf8') or rv.val)
return rv
raise AttributeError(
"'%s' object has no attribute '%s'"
Expand Down Expand Up @@ -2055,8 +2057,8 @@ def connect(self, sUuid=None):
return self.connect()
else: # pragma: no cover
logger.debug(
"BlitzGateway.connect().createSession(): "
+ traceback.format_exc())
"BlitzGateway.connect().createSession(): " +
traceback.format_exc())
logger.info(
"first create session threw SecurityViolation, "
"retry (but only once)")
Expand All @@ -2078,8 +2080,8 @@ def connect(self, sUuid=None):
except:
logger.info("Failed to create session.")
logger.debug(
"BlitzGateway.connect().createSession(): "
+ traceback.format_exc())
"BlitzGateway.connect().createSession(): " +
traceback.format_exc())
# time.sleep(10)
self._createSession()

Expand Down Expand Up @@ -2235,9 +2237,9 @@ def canWrite(self, obj):
:return: Boolean
"""

return (self.isAdmin()
or (self.getUserId() == obj.getDetails().getOwner().getId()
and obj.getDetails().getPermissions().isUserWrite()))
return (self.isAdmin() or
(self.getUserId() == obj.getDetails().getOwner().getId() and
obj.getDetails().getPermissions().isUserWrite()))

def canOwnerWrite(self, obj):
"""
Expand Down Expand Up @@ -2285,8 +2287,8 @@ def setGroupForSession(self, groupid):
"""
if self.getEventContext().groupId == groupid:
return None
if (groupid not in self._ctx.memberOfGroups
and 0 not in self._ctx.memberOfGroups):
if (groupid not in self._ctx.memberOfGroups and
0 not in self._ctx.memberOfGroups):
return False
self._lastGroupId = self._ctx.groupId
self._ctx = None
Expand Down Expand Up @@ -2715,8 +2717,8 @@ def createGroup(self, name, owner_Ids=None, member_Ids=None, perms=None,
group = omero.model.ExperimenterGroupI()
group.name = rstring(str(name))
group.description = (
(description != "" and description is not None)
and rstring(str(description)) or None)
(description != "" and description is not None) and
rstring(str(description)) or None)
if perms is not None:
group.details.permissions = omero.model.PermissionsI(perms)
group.ldap = rbool(ldap)
Expand Down Expand Up @@ -3092,10 +3094,10 @@ def buildQuery(self, obj_type, ids=None, params=None, attributes=None):
params.map["ids"] = rlist([rlong(a) for a in ids])

# support filtering by owner (not for some object types)
if (params.theFilter
and params.theFilter.ownerId
and obj_type.lower()
not in ["experimentergroup", "experimenter"]):
if (params.theFilter and
params.theFilter.ownerId and
obj_type.lower() not in
["experimentergroup", "experimenter"]):
clauses.append("owner.id = (:eid)")
params.map["eid"] = params.theFilter.ownerId

Expand Down Expand Up @@ -4155,9 +4157,9 @@ def parse_time(c, i):

d_from = parse_time(created, 0)
d_to = parse_time(created, 1)
d_type = (useAcquisitionDate
and "acquisitionDate"
or "details.creationEvent.time")
d_type = (useAcquisitionDate and
"acquisitionDate" or
"details.creationEvent.time")

try:
rv = []
Expand Down Expand Up @@ -4507,9 +4509,9 @@ def __eq__(self, a):
:return: True if annotations are the same - see above
:rtype: Boolean
"""
return (type(a) == type(self) and self._obj.id == a._obj.id
and self.getValue() == a.getValue()
and self.getNs() == a.getNs())
return (type(a) == type(self) and self._obj.id == a._obj.id and
self.getValue() == a.getValue() and
self.getNs() == a.getNs())

def _getQueryString(self):
"""
Expand Down Expand Up @@ -4718,11 +4720,11 @@ def isOriginalMetadata(self):
"""

try:
if (self._obj.ns is not None
and self._obj.ns.val
== omero.constants.namespaces.NSCOMPANIONFILE
and self.getFile().getName()
== omero.constants.annotation.file.ORIGINALMETADATA):
if (self._obj.ns is not None and
self._obj.ns.val ==
omero.constants.namespaces.NSCOMPANIONFILE and
self.getFile().getName() ==
omero.constants.annotation.file.ORIGINALMETADATA):
return True
except:
logger.info(traceback.format_exc())
Expand Down Expand Up @@ -5485,8 +5487,8 @@ def groupSummary(self, exclude_self=False):
userId = self._conn.getUserId()
colleagues = []
leaders = []
if (not self.isPrivate() or self._conn.isLeader(self.id)
or self._conn.isAdmin()):
if (not self.isPrivate() or self._conn.isLeader(self.id) or
self._conn.isAdmin()):
for d in self.copyGroupExperimenterMap():
if d is None or d.child.id.val == userId:
continue
Expand Down Expand Up @@ -5761,8 +5763,8 @@ def getColumnLabels(self):
Returns a list of labels for the columns on this plate.
E.g. [1, 2, 3...] or ['A', 'B', 'C'...] etc
"""
if (self.columnNamingConvention
and self.columnNamingConvention.lower() == 'letter'):
if (self.columnNamingConvention and
self.columnNamingConvention.lower() == 'letter'):
# this should simply be precalculated!
return [_letterGridLabel(x)
for x in range(self.getGridSize()['columns'])]
Expand All @@ -5774,8 +5776,8 @@ def getRowLabels(self):
Returns a list of labels for the rows on this plate.
E.g. [1, 2, 3...] or ['A', 'B', 'C'...] etc
"""
if (self.rowNamingConvention
and self.rowNamingConvention.lower() == 'number'):
if (self.rowNamingConvention and
self.rowNamingConvention.lower() == 'number'):
return range(1, self.getGridSize()['rows']+1)
else:
# this should simply be precalculated!
Expand Down Expand Up @@ -7167,8 +7169,9 @@ def simpleMarshal(self, xtra=None, parents=False):
'height': self.getSizeY(),
}
if rv['size']['height'] and rv['size']['width']:
rv['tiled'] = ((rv['size']['height'] * rv['size']['width'])
> (maxplanesize[0] * maxplanesize[1]))
rv['tiled'] = ((rv['size']['height'] *
rv['size']['width']) >
(maxplanesize[0] * maxplanesize[1]))
else:
rv['tiled'] = False

Expand Down Expand Up @@ -7724,9 +7727,9 @@ def setActiveChannels(self, channels, windows=None, colors=None,
if (reverseMaps is not None and
reverseMaps[idx] is not None):
self.setReverseIntensity(c, reverseMaps[idx])
if (windows is not None
and windows[idx][0] is not None
and windows[idx][1] is not None):
if (windows is not None and
windows[idx][0] is not None and
windows[idx][1] is not None):
self._re.setChannelWindow(
c, float(windows[idx][0]), float(windows[idx][1]),
self._conn.SERVICE_OPTS)
Expand Down Expand Up @@ -7896,11 +7899,11 @@ def getPixelLine(self, z, t, pos, axis, channels=None, range=None):
(bw, rp.isFloat(), rp.isSigned()), None)
if key is None:
logger.error(
"Unknown data type: "
+ str((bw, rp.isFloat(), rp.isSigned())))
plot = array.array(key, (axis == 'h'
and rp.getRow(pos, z, c, t)
or rp.getCol(pos, z, c, t)))
"Unknown data type: " +
str((bw, rp.isFloat(), rp.isSigned())))
plot = array.array(key, (axis == 'h' and
rp.getRow(pos, z, c, t) or
rp.getCol(pos, z, c, t)))
plot.byteswap() # TODO: Assuming ours is a little endian
# system now move data into the windowMin..windowMax range
offset = -chw[c][0]
Expand Down Expand Up @@ -8285,8 +8288,8 @@ def _wordwrap(self, width, text, font):
while len(tokens) > 1:
p1 = 0
p2 = 1
while (p2 <= len(tokens)
and font.getsize(' '.join(tokens[p1:p2]))[0] < width):
while (p2 <= len(tokens) and
font.getsize(' '.join(tokens[p1:p2]))[0] < width):
p2 += 1
rv.append(' '.join(tokens[p1:p2-1]))
tokens = tokens[p2-1:]
Expand Down