Test in travis

.gitignore

@@ -1,4 +1,5 @@
 # Ignore .omero since it is automatically generated by the server
 .omero
 *.pyc
-.gitignore
+.gitignore
+*.DS_Store*

.travis.yml

@@ -1,6 +1,15 @@
 language: python
-python:
-  - "2.7"
-  - "2.7_with_system_site_packages"
-install: pip install flake8 pycodestyle pep8-naming
-script: flake8 -v .
+
+virtualenv:
+  system_site_packages: true
+
+sudo: required
+
+services:
+  - docker
+
+before_install:
+  - git clone --recurse-submodules git://github.com/openmicroscopy/omero-test-infra .omero
+
+script:
+  - .omero/scripts-docker

README.md → README.rst

@@ -2,13 +2,14 @@ OMERO Core Scripts
 ==================
 
 This directory contains OMERO scripts which use the
-OMERO.scripts API. All scripts (e.g. "*.py") present in the
+OMERO.scripts API. All scripts (e.g. ``*.py``) present in the
 directory will be automatically distributed with all binary
 builds. Which file-endings will be detected and how they
 will be launched are both configured centrally in the server.
-".py", ".jy", and ".m" (MATLAB) files should all be detected
+``.py``, ``.jy", and ``.m`` (MATLAB) files should all be detected
 by default starting with OMERO 5.
 
+
 Categories
 ----------
 

omero/export_scripts/Batch_Image_Export.py

@@ -57,7 +57,7 @@ def log(text):
     # Handle unicode
     try:
         text = text.encode('utf8')
-    except:
+    except UnicodeEncodeError:
         pass
     log_strings.append(str(text))
 
@@ -373,7 +373,7 @@ def get_t_range(size_t, script_params):
     exp_dir = os.path.join(curr_dir, folder_name)
     try:
         os.mkdir(exp_dir)
-    except:
+    except OSError:
         pass
     # max size (default 12kx12k)
     size = conn.getDownloadAsMaxSizeSetting()
@@ -602,7 +602,8 @@ def run_script():
         conn = BlitzGateway(client_obj=client)
 
         script_params = client.getInputs(unwrap=True)
-        log(script_params)
+        for key, value in script_params.iteritems():
+            log("%s:%s" % (key, value))
 
         # call the main script - returns a file annotation wrapper
         file_annotation, message = batch_image_export(conn, script_params)

omero/export_scripts/Make_Movie.py

@@ -333,7 +333,7 @@ def calculate_ranges(size_z, size_t, command_args):
     plane_map = {}
     if "Plane_Map" not in command_args:
         z_start = 0
-        z_end = size_z
+        z_end = size_z-1
         if "Z_Start" in command_args and command_args["Z_Start"] >= 0 and \
                 command_args["Z_Start"] < size_z:
             z_start = command_args["Z_Start"]
@@ -627,6 +627,7 @@ def write_movie(command_args, conn):
     output = "localfile.%s" % ext
     build_avi(mw, mh, filelist, frames_per_sec, output, format)
     mimetype = formatMimetypes[format]
+    omero_image._re.close()
 
     if not os.path.exists(output):
         return None, "Failed to create movie file: %s" % output

omero/figure_scripts/Movie_Figure.py

@@ -484,7 +484,7 @@ def get_tags(name, tags_list, pd_list):
                 scalebar = None
             else:
                 log("Scalebar is %d microns" % scalebar)
-        except:
+        except ValueError:
             log("Invalid value for scalebar: %s" % str(sb))
             scalebar = None
 

omero/figure_scripts/Movie_ROI_Figure.py

@@ -581,15 +581,15 @@ def get_tags(name, tags_list, pd_list):
         w = command_args["Width"]
         try:
             width = int(w)
-        except:
+        except ValueError:
             log("Invalid width: %s Using default value: %d" % (str(w), size_x))
 
     height = size_y
     if "Height" in command_args:
         h = command_args["Height"]
         try:
             height = int(h)
-        except:
+        except ValueError:
             log("Invalid height: %s Using default value" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
@@ -632,7 +632,7 @@ def get_tags(name, tags_list, pd_list):
                 scalebar = None
             else:
                 log("Scalebar is %d microns" % scalebar)
-        except:
+        except ValueError:
             log("Invalid value for scalebar: %s" % str(sb))
             scalebar = None
 

omero/figure_scripts/ROI_Split_Figure.py

@@ -651,15 +651,15 @@ def get_tags(name, tags_list, pd_list):
         w = command_args["Width"]
         try:
             width = int(w)
-        except:
+        except ValueError:
             log("Invalid width: %s Using default value: %d" % (str(w), size_x))
 
     height = size_y
     if "Height" in command_args:
         h = command_args["Height"]
         try:
             height = int(h)
-        except:
+        except ValueError:
             log("Invalid height: %s Using default value" % (str(h), size_y))
 
     log("Image dimensions for all panels (pixels): width: %d  height: %d"
@@ -735,7 +735,7 @@ def get_tags(name, tags_list, pd_list):
                 scalebar = None
             else:
                 log("Scalebar is %d microns" % scalebar)
-        except:
+        except ValueError:
             log("Invalid value for scalebar: %s" % str(sb))
             scalebar = None
 

omero/figure_scripts/Split_View_Figure.py

@@ -65,7 +65,7 @@ def log(text):
     # Handle unicode
     try:
         text = text.encode('utf8')
-    except:
+    except UnicodeEncodeError:
         pass
     log_strings.append(text)
 

omero/figure_scripts/Thumbnail_Figure.py

@@ -59,7 +59,7 @@ def log(text):
     """
     try:
         text = text.encode('utf8')
-    except:
+    except UnicodeEncodeError:
         pass
     log_lines.append(text)
 

omero/util_scripts/Channel_Offsets.py

@@ -142,7 +142,7 @@ def offset_plane_gen():
                 try:
                     plane = pixels.getPlane(*zct_list[i])
                     dt = plane.dtype
-                except:
+                except Exception:
                     # E.g. the Z-index is out of range - Simply supply an
                     # array of zeros.
                     if dt is None:

omero/util_scripts/Combine_Images.py

@@ -489,7 +489,7 @@ def combine_images(conn, parameter_map):
     for s in services:
         try:
             s.close()
-        except:
+        except Exception:
             pass
 
     if output_images:

omero/util_scripts/Dataset_To_Plate.py

@@ -59,7 +59,7 @@ def add_image_to_plate(conn, image, plate_id, column, row, remove_from=None):
         ws.well = well
         well.addWellSample(ws)
         update_service.saveObject(ws)
-    except:
+    except Exception:
         return False
 
     # remove from Datast

setup.py

@@ -0,0 +1,83 @@
+import os
+import sys
+
+from setuptools import setup
+from setuptools.command.test import test as test_command
+
+
+class PyTest(test_command):
+    user_options = [
+        ('test-path=', 't', "base dir for test collection"),
+        ('test-ice-config=', 'i',
+         "use specified 'ice config' file instead of default"),
+        ('test-pythonpath=', 'p', "prepend 'pythonpath' to PYTHONPATH"),
+        ('test-marker=', 'm', "only run tests including 'marker'"),
+        ('test-no-capture', 's', "don't suppress test output"),
+        ('test-failfast', 'x', "Exit on first error"),
+        ('test-verbose', 'v', "more verbose output"),
+        ('test-quiet', 'q', "less verbose output"),
+        ('junitxml=', None, "create junit-xml style report file at 'path'"),
+        ('pdb', None, "fallback to pdb on error"),
+        ]
+
+    def initialize_options(self):
+        test_command.initialize_options(self)
+        self.test_pythonpath = None
+        self.test_string = None
+        self.test_marker = None
+        self.test_path = 'test'
+        self.test_failfast = False
+        self.test_quiet = False
+        self.test_verbose = False
+        self.test_no_capture = False
+        self.junitxml = None
+        self.pdb = False
+        self.test_ice_config = None
+
+    def finalize_options(self):
+        test_command.finalize_options(self)
+        self.test_args = [self.test_path]
+        if self.test_string is not None:
+            self.test_args.extend(['-k', self.test_string])
+        if self.test_marker is not None:
+            self.test_args.extend(['-m', self.test_marker])
+        if self.test_failfast:
+            self.test_args.extend(['-x'])
+        if self.test_verbose:
+            self.test_args.extend(['-v'])
+        if self.test_quiet:
+            self.test_args.extend(['-q'])
+        if self.junitxml is not None:
+            self.test_args.extend(['--junitxml', self.junitxml])
+        if self.pdb:
+            self.test_args.extend(['--pdb'])
+        self.test_suite = True
+        if 'ICE_CONFIG' not in os.environ:
+            os.environ['ICE_CONFIG'] = self.test_ice_config
+
+    def run_tests(self):
+        if self.test_pythonpath is not None:
+            sys.path.insert(0, self.test_pythonpath)
+        # import here, cause outside the eggs aren't loaded
+        import pytest
+        errno = pytest.main(self.test_args)
+        sys.exit(errno)
+
+
+version = '0.1.0'
+url = "https://github.com/ome/omero-cli-render/"
+
+setup(
+    version=version,
+    name='omero-scripts',
+    description="OMERO scripts",
+    long_description="OMERO scripts",
+    author='The Open Microscopy Team',
+    author_email='ome-devel@lists.openmicroscopy.org.uk',
+    license='GPL-2.0+',
+    url='%s' % url,
+    zip_safe=False,
+    download_url='%s' % url,
+    cmdclass={'test': PyTest},
+    tests_require=['pytest'],
+)