Merge pull request #1685 from sbesson/2591_cli_flake8

Run flake8 on all the CLI plugins

.travis.yml

@@ -1,9 +1,9 @@
 language: java
 
 env:
-    - BUILD="build-all" TEST="-p"
-    - BUILD="build-default test-compile" TEST="-py test -Dtest.with.fail=true"
-    - BUILD="build-all test-compile-all" TEST="-cpp test -Dtest.with.fail=true"
+    - BUILD=all BUILD_TARGET="build-all" TEST_TARGET="-p"
+    - BUILD=py BUILD_TARGET="build-default test-compile" TEST_TARGET="-py test -Dtest.with.fail=true"
+    - BUILD=cpp BUILD_TARGET="build-all test-compile-all" TEST_TARGET="-cpp test -Dtest.with.fail=true"
 
 jdk:
   - openjdk7
@@ -18,9 +18,11 @@ before_install:
     - git config --global user.name 'Snoopy Crime Cop'
     - sudo pip install scc --use-mirrors
     - scc travis-merge
+    - if [[ $BUILD == 'py' ]]; then sudo pip install flake8 --use-mirrors; fi
 
-install: python build.py $BUILD
+install: python build.py $BUILD_TARGET
 
 # Running python tests as script, since there's no compile step.
 script:
-    - python build.py $TEST
+    - if [[ $BUILD == 'py' ]]; then flake8 -v components/tools/OmeroPy/src/omero/plugins;  fi
+    - python build.py $TEST_TARGET

components/tools/OmeroPy/src/omero/plugins/basics.py

@@ -30,7 +30,7 @@
 class QuitControl(BaseControl):
 
     def __call__(self, args):
-        self.ctx.exit("", newline = False)
+        self.ctx.exit("", newline=False)
 
 
 class VersionControl(BaseControl):
@@ -42,7 +42,8 @@ def __call__(self, args):
 class LoadControl(BaseControl):
 
     def _configure(self, parser):
-        parser.add_argument("infile", nargs="*", type=FileType("r"), default=[sys.stdin])
+        parser.add_argument("infile", nargs="*", type=FileType("r"),
+                            default=[sys.stdin])
         parser.set_defaults(func=self.__call__)
 
     def __call__(self, args):
@@ -55,7 +56,9 @@ def __call__(self, args):
 class ShellControl(BaseControl):
 
     def _configure(self, parser):
-        parser.add_argument("--login", action="store_true", help="Logins in and sets the 'client' variable")
+        parser.add_argument(
+            "--login", action="store_true",
+            help="Logins in and sets the 'client' variable")
         parser.add_argument("arg", nargs="*", help="Arguments for IPython.")
         parser.set_defaults(func=self.__call__)
 
@@ -75,13 +78,13 @@ def __call__(self, args):
         if args.login:
             import omero
             client = self.ctx.conn(args)
-            ns = {"client": client, "omero":omero}
+            ns = {"client": client, "omero": omero}
 
         try:
             # IPython 0.11 (see #7112)
             from IPython import embed
             embed(user_ns=ns)
-        except ImportError, ie:
+        except ImportError:
             from IPython.Shell import IPShellEmbed
             ipshell = IPShellEmbed(args.arg)
             ipshell(local_ns=ns)
@@ -94,10 +97,12 @@ class HelpControl(BaseControl):
     """
 
     def _configure(self, parser):
-        self.__parser__ = parser # For formatting later
+        self.__parser__ = parser  # For formatting later
         parser.set_defaults(func=self.__call__)
-        parser.add_argument("--all", action="store_true", help="Print help for all topics")
-        parser.add_argument("topic", nargs="?", help="Topic for more information")
+        parser.add_argument(
+            "--all", action="store_true", help="Print help for all topics")
+        parser.add_argument(
+            "topic", nargs="?", help="Topic for more information")
 
     def _complete(self, text, line, begidx, endidx):
         """
@@ -110,9 +115,12 @@ def _complete(self, text, line, begidx, endidx):
     def __call__(self, args):
 
         self.ctx.waitForPlugins()
-        #commands = "\n".join([" %s" % name for name in sorted(self.ctx.controls)])
+        #commands = "\n".join([" %s" % name for name in
+        #sorted(self.ctx.controls)])
         #topics = "\n".join([" %s" % topic for topic in self.ctx.topics])
-        commands, topics = [self.__parser__._format_list(x) for x in [sorted(self.ctx.controls), sorted(self.ctx.topics)]]
+        commands, topics = [
+            self.__parser__._format_list(x) for x in
+            [sorted(self.ctx.controls), sorted(self.ctx.topics)]]
 
         if args.all:
             for control in sorted(self.ctx.controls):
@@ -129,6 +137,8 @@ def __call__(self, args):
                 self.ctx.out("\n")
         elif not args.topic:
             #self.ctx.invoke("-h")
+            key_list = {"program_name": sys.argv[0], "version": VERSION,
+                        "commands": commands, "topics": topics}
             print """usage: %(program_name)s <command> [options] args
 See 'help <command>' or '<command> -h' for more information on syntax
 Type 'quit' to exit
@@ -139,15 +149,18 @@ def __call__(self, args):
 Other help topics:
 %(topics)s
 
-For additional information, see http://trac.openmicroscopy.org.uk/ome/wiki/OmeroCli
+For additional information, see:
+http://www.openmicroscopy.org/site/support/omero4/users/\
+command-line-interface.html
 Report bugs to <ome-users@lists.openmicroscopy.org.uk>
-""" % {"program_name":sys.argv[0],"version":VERSION, "commands":commands, "topics":topics}
+""" % key_list
 
         else:
             try:
-                c = self.ctx.controls[args.topic]
+                print 1
+                self.ctx.controls[args.topic]
                 self.ctx.invoke("%s -h" % args.topic)
-            except KeyError, ke:
+            except KeyError:
                 try:
                     self.ctx.out(self.ctx.topics[args.topic])
                 except KeyError:

components/tools/OmeroPy/src/omero/plugins/cecog.py

@@ -12,21 +12,19 @@
 import re
 import sys
 
-from omero.cli import BaseControl, CLI, OMERODIR
-from omero_ext.argparse import FileType
+from omero.cli import BaseControl, CLI
 
 import omero
 import omero.constants
 
-from omero.rtypes import *
+from omero.rtypes import rstring
 
 
 class CecogControl(BaseControl):
     """CeCog integration plugin.
 
-Provides actions for prepairing data and otherwise
-integrating with Cecog. See the Run_Cecog_4.1.py
-script.
+Provides actions for prepairing data and otherwise integrating with Cecog. See
+the Run_Cecog_4.1.py script.
     """
 
     # [MetaMorph_PlateScanPackage]
@@ -45,8 +43,11 @@ def _configure(self, parser):
         merge.add_argument("path", help="Path to image files")
 
         rois = parser.add(sub, self.rois, self.rois.__doc__)
-        rois.add_argument("-f", "--file", required=True, help="Details file to be parsed")
-        rois.add_argument("-i", "--image", required=True, help="Image id which should have ids attached")
+        rois.add_argument(
+            "-f", "--file", required=True, help="Details file to be parsed")
+        rois.add_argument(
+            "-i", "--image", required=True,
+            help="Image id which should have ids attached")
 
         for x in (merge, rois):
             x.add_login_arguments()
@@ -57,28 +58,36 @@ def _configure(self, parser):
     def merge(self, args):
         """Uses PIL to read multiple planes from a local folder.
 
-Planes are combined and uploaded to OMERO as new images with additional T, C, Z dimensions.
+Planes are combined and uploaded to OMERO as new images with additional T, C,
+Z dimensions.
 
-It should be run as a local script (not via scripting service) in order that it has
-access to the local users file system. Therefore need EMAN2 or PIL installed locally.
+It should be run as a local script (not via scripting service) in order that
+it has access to the local users file system. Therefore need EMAN2 or PIL
+installed locally.
 
 Example usage:
-will$ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/0037/
+    $ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/0037/
 
-Since this dir does not contain folders, this will upload images in '0037' into a Dataset called Demo_data
-in a Project called 'Data'.
+    Since this dir does not contain folders, this will upload images in '0037'
+    into a Dataset called Demo_data in a Project called 'Data'.
 
-will$ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/
+    $ bin/omero cecog merge /Applications/CecogPackage/Data/Demo_data/
 
-Since this dir does contain folders, this will look for images in all subdirectories of 'Demo_data' and
-upload images into a Dataset called Demo_data in a Project called 'Data'.
+    Since this dir does contain folders, this will look for images in all
+    subdirectories of 'Demo_data' and upload images into a Dataset called
+    Demo_data in a Project called 'Data'.
 
-Images will be combined in Z, C and T according to the MetaMorph_PlateScanPackage naming convention.
-E.g. tubulin_P0037_T00005_Cgfp_Z1_S1.tiff is Point 37, Timepoint 5, Channel gfp, Z 1. S?
-see /Applications/CecogPackage/CecogAnalyzer.app/Contents/Resources/resources/naming_schemes.conf
+Images will be combined in Z, C and T according to the \
+MetaMorph_PlateScanPackage naming convention.
+E.g. tubulin_P0037_T00005_Cgfp_Z1_S1.tiff is Point 37, Timepoint 5, Channel \
+gfp, Z 1. S?
+see \
+/Applications/CecogPackage/CecogAnalyzer.app/Contents/Resources/resources/\
+naming_schemes.conf
 """
         """
-        Processes the command args, makes project and dataset then calls uploadDirAsImages() to process and
+        Processes the command args, makes project and dataset then calls
+        uploadDirAsImages() to process and
         upload the images to OMERO.
         """
         from omero.rtypes import unwrap
@@ -90,7 +99,8 @@ def merge(self, args):
         updateService = client.sf.getUpdateService()
         pixelsService = client.sf.getPixelsService()
 
-        # if we don't have any folders in the 'dir' E.g. CecogPackage/Data/Demo_data/0037/
+        # if we don't have any folders in the 'dir' E.g.
+        # CecogPackage/Data/Demo_data/0037/
         # then 'Demo_data' becomes a dataset
         subDirs = []
         for f in os.listdir(path):
@@ -111,7 +121,8 @@ def merge(self, args):
         p = p[:-1]
         p = os.path.dirname(p)
         projectName = os.path.basename(p)   # e.g. Data
-        self.ctx.err("Putting images in Project: %s  Dataset: %s" % (projectName, datasetName))
+        self.ctx.err("Putting images in Project: %s  Dataset: %s"
+                     % (projectName, datasetName))
 
         # create dataset
         dataset = omero.model.DatasetI()
@@ -130,35 +141,42 @@ def merge(self, args):
         if len(subDirs) > 0:
             for subDir in subDirs:
                 self.ctx.err("Processing images in %s" % subDir)
-                rv = uploadDirAsImages(client.sf, queryService, updateService, pixelsService, subDir, dataset)
+                rv = uploadDirAsImages(client.sf, queryService, updateService,
+                                       pixelsService, subDir, dataset)
                 self.ctx.out("%s" % unwrap(rv))
 
         # if there are no sub-directories, just put all the images in the dir
         else:
             self.ctx.err("Processing images in %s" % path)
-            rv = uploadDirAsImages(client.sf, queryService, updateService, pixelsService, path, dataset)
+            rv = uploadDirAsImages(client.sf, queryService, updateService,
+                                   pixelsService, path, dataset)
             self.ctx.out("%s" % unwrap(rv))
 
     def rois(self, args):
-        """Parses an object_details text file, as generated by CeCog Analyzer and saves the data as ROIs on an Image in OMERO.
+        """Parses an object_details text file, as generated by CeCog Analyzer
+and saves the data as ROIs on an Image in OMERO.
 
 Text file is of the form:
 
 frame	objID	classLabel	className	centerX	centerY	mean	        sd
-1	    10  	6       	lateana	    1119	41	    76.8253796095	54.9305640673
+1	    10  	6       	lateana	    1119	41	    76.8253796095 \
+54.9305640673
 
 
 Example usage:
-bin/omero cecog rois -f Data/Demo_output/analyzed/0037/statistics/P0037__object_details.txt -i 502
+bin/omero cecog rois -f \
+Data/Demo_output/analyzed/0037/statistics/P0037__object_details.txt -i 502
 """
         """
-        Processes the command args, parses the object_details.txt file and creates ROIs on the image specified in OMERO
+        Processes the command args, parses the object_details.txt file and
+        creates ROIs on the image specified in OMERO
         """
         from omero.util.script_utils import uploadCecogObjectDetails
         filePath = args.file
         imageId = args.image
         if not os.path.exists(filePath):
-            self.ctx.die(654, "Could find the object_details file at %s" % filePath)
+            self.ctx.die(654, "Could find the object_details file at %s"
+                         % filePath)
 
         client = self.ctx.conn(args)
         updateService = client.sf.getUpdateService()

components/tools/OmeroPy/src/omero/plugins/chgrp.py

@@ -13,29 +13,37 @@
    defined here will be added to the Cli class for later use.
 """
 
-from omero.cli import BaseControl, CLI, GraphControl, ExperimenterGroupArg
+from omero.cli import CLI, GraphControl, ExperimenterGroupArg
 import sys
 
-HELP="""Move data between groups
+HELP = """Move data between groups
 
 Example Usage:
 
-  omero chgrp 101 /Image:1                     # Move all of Image 1 to group 101
-  omero chgrp Group:101 /Image:1               # Move all of Image 1 to group 101
-  omero chgrp ExperimenterGroup:101 /Image:1   # Move all of Image 1 to group 101
-  omero chgrp "My Lab" /Image:1                # Move all of Image 1 to group "myLab"
-
-  omero chgrp --edit 101 /Image:1              # Open an editor with all the chgrp
-                                               # options filled out with defaults.
-
-  omero chgrp --opt /Image:KEEP /Plate:1       # Calls chgrp on Plate, leaving all
+  omero chgrp 101 /Image:1                     # Move all of Image 1 to \
+group 101
+  omero chgrp Group:101 /Image:1               # Move all of Image 1 to \
+group 101
+  omero chgrp ExperimenterGroup:101 /Image:1   # Move all of Image 1 to \
+group 101
+  omero chgrp "My Lab" /Image:1                # Move all of Image 1 to \
+group "myLab"
+
+  omero chgrp --edit 101 /Image:1              # Open an editor with all \
+the chgrp
+                                               # options filled out with \
+defaults.
+
+  omero chgrp --opt /Image:KEEP /Plate:1       # Calls chgrp on Plate, \
+leaving all
                                                # images in the previous group.
 
   What data is moved is the same as that which would be deleted by a similar
   call to "omero delete /Image:1"
 
 """
 
+
 class ChgrpControl(GraphControl):
 
     def cmd_type(self):
@@ -44,7 +52,9 @@ def cmd_type(self):
         return omero.cmd.Chgrp
 
     def _pre_objects(self, parser):
-        parser.add_argument("grp", nargs="?", type=ExperimenterGroupArg, help="""Group to move objects to""")
+        parser.add_argument(
+            "grp", nargs="?", type=ExperimenterGroupArg,
+            help="""Group to move objects to""")
 
     def _process_request(self, req, args, client):
         req.grp = args.grp.lookup(client)
@@ -57,7 +67,9 @@ def create_error_report(self, rsp):
         if isinstance(rsp, omero.cmd.GraphConstraintERR):
             if "Fileset" in rsp.constraints:
                 fileset = rsp.constraints.get("Fileset")
-                return "You cannot move part of fileset %s; only complete filesets can be moved to another group.\n" % ", ".join(str(x) for x in fileset)
+                return "You cannot move part of fileset %s; only complete" \
+                    " filesets can be moved to another group.\n" % \
+                    ", ".join(str(x) for x in fileset)
             else:
                 return super(ChgrpControl, self).create_error_report(rsp)
         else: