Merge pull request #23 from joshmoore/53compatible

test omero53 in travis

.gitignore

@@ -1,2 +1,4 @@
 *.pyc
-.DS_Store
+.*un~
+.omero
+.DS_Store

.omeroci/app-config

@@ -0,0 +1,6 @@
+set -e
+set -u
+OMERO_VENV=${OMERO_VENT:-/opt/omero/web/venv}
+OMERO_DIST=${OMERO_DIST:-/opt/omero/web/OMERO.web}
+${OMERO_VENV}/bin/python \
+    $OMERO_DIST/bin/omero config append omero.web.apps '"omero_mapr"'

.travis.yml

@@ -8,23 +8,8 @@ python:
 services:
   - docker
 
-env:
-  - OMEROBUILD=OMERO-DEV-merge-build
-
 before_install:
-  - docker --version
-  - pip install docker-compose
-  - docker-compose -v
-
-before_script:
-  - pip install flake8 pycodestyle pep8-naming
-  - flake8 --version
-  - flake8 -v .
-  - python setup.py sdist install
+  - git clone git://github.com/openmicroscopy/omero-test-infra .omero
 
 script:
-  - echo 'Tested in CI'
-#  - docker-compose -f docker/docker-compose.yml up --build --abort-on-container-exit
-#  - exitcode=$(docker inspect -f '{{.State.ExitCode}}' docker_maprtest_1)
-#  - docker-compose -f docker/docker-compose.yml rm -fv
-#  - exit $exitcode
+  - .omero/app-docker

omero_mapr/__init__.py

@@ -26,7 +26,7 @@
 from omero_mapr.utils.version import get_version
 
 
-VERSION = (0, 1, 14)
+VERSION = (0, 2, 0)
 
 __version__ = get_version(VERSION)
 

omero_mapr/show.py

@@ -88,7 +88,7 @@ def _find_first_selected(self):
                 self.conn.SERVICE_OPTS.setOmeroGroup('-1')
                 first_selected = self._load_first_selected(
                     first_obj, attributes)
-            except:
+            except Exception:
                 pass
             if first_obj not in self.TOP_LEVEL_PREFIXES:
                 # Need to see if first item has parents
@@ -268,7 +268,7 @@ def mapr_paths_to_object(conn, mapann_value,
         # Experimenter is always present
         try:
             experimenter_id = e[0]["owner"]
-        except:
+        except Exception:
             experimenter_id = -1
         path.append({
             'type': 'experimenter',
@@ -281,7 +281,7 @@ def mapr_paths_to_object(conn, mapann_value,
                 'type': 'map',
                 'id': map_value,
             })
-        except:
+        except Exception:
             pass
 
         try:
@@ -290,7 +290,7 @@ def mapr_paths_to_object(conn, mapann_value,
                     'type': 'screen',
                     'id': e[0]["screen_id"]
                 })
-        except:
+        except Exception:
             pass
 
         try:
@@ -300,7 +300,7 @@ def mapr_paths_to_object(conn, mapann_value,
                     'type': 'plate',
                     'id': plate_id,
                 })
-        except:
+        except Exception:
             pass
 
         try:
@@ -309,7 +309,7 @@ def mapr_paths_to_object(conn, mapann_value,
                     'type': 'project',
                     'id': e[0]["project_id"]
                 })
-        except:
+        except Exception:
             pass
 
         try:
@@ -318,7 +318,7 @@ def mapr_paths_to_object(conn, mapann_value,
                     'type': 'dataset',
                     'id': e[0]["dataset_id"],
                 })
-        except:
+        except Exception:
             pass
 
         # Image is always present
@@ -327,7 +327,7 @@ def mapr_paths_to_object(conn, mapann_value,
                 'type': 'image',
                 'id': e[0]["image_id"]
             })
-        except:
+        except Exception:
             pass
         paths.append(path)
     return paths

omero_mapr/testlib/__init__.py

@@ -28,7 +28,6 @@
 from omero.constants.namespaces import NSBULKANNOTATIONS
 from omero.util.populate_metadata import BulkToMapAnnotationContext
 from omero.util.populate_metadata import ParsingContext
-from omero.util.temp_files import create_path
 
 from omeroweb.testlib import IWebTest
 
@@ -39,22 +38,6 @@ class IMaprTest(IWebTest):
     Extends IWebTest (ITest)
     """
 
-    def create_csv(
-        self,
-        col_names="Well,Well Type,Concentration",
-        row_data=("A1,Control,0", "A2,Treatment,10")
-    ):
-
-        csv_file_name = create_path("test", ".csv")
-        csv_file = open(csv_file_name, 'w')
-        try:
-            csv_file.write(col_names)
-            csv_file.write("\n")
-            csv_file.write("\n".join(row_data))
-        finally:
-            csv_file.close()
-        return str(csv_file_name)
-
     def set_name(self, obj, name):
         q = self.client.sf.getQueryService()
         up = self.client.sf.getUpdateService()
@@ -68,8 +51,8 @@ def create_screen(self, row_count, col_count):
             plate = self.importPlates(plateRows=row_count,
                                       plateCols=col_count)[0]
         except AttributeError:
-            plate = self.import_plates(plateRows=row_count,
-                                       plateCols=col_count)[0]
+            plate = self.import_plates(plate_rows=row_count,
+                                       plate_cols=col_count)[0]
         plate = self.set_name(plate, "Plate001")
         screen = ScreenI()
         screen.name = rstring("Screen001")
@@ -125,6 +108,6 @@ def populate_data(self, csv, cfg):
         fileid = table_file_ann.file.id.val
 
         ctx = BulkToMapAnnotationContext(
-         self.client, self.screen.proxy(), fileid=fileid, cfg=cfg)
+            self.client, self.screen.proxy(), fileid=fileid, cfg=cfg)
         ctx.parse()
         ctx.write_to_omero()

omero_mapr/views.py

@@ -71,7 +71,7 @@
 except ImportError:
     try:
         import Image  # see ticket:2597
-    except:
+    except ImportError:
         logger.error(
             "You need to install the Python Imaging Library. Get it at"
             " http://www.pythonware.com/products/pil/")

tests/conftest.py

@@ -48,7 +48,7 @@ def pytest_configure():
                 "config": {
                     "default": ["Gene Symbol"],
                     "all": ["Gene Symbol", "Gene Identifier"],
-                    "ns": ["openmicroscopy.org/omero/bulk_annotations"],
+                    "ns": ["openmicroscopy.org/mapr/gene"],
                     "label": "Gene",
                     "case_sensitive": True,
                 }
@@ -58,7 +58,7 @@ def pytest_configure():
                 "config": {
                     "default": ["Phenotype"],
                     "all": ["Phenotype", "Phenotype Term Accession"],
-                    "ns": ["openmicroscopy.org/omero/bulk_annotations"],
+                    "ns": ["openmicroscopy.org/mapr/phenotype"],
                     "label": "Phenotype",
                 }
             },
@@ -67,7 +67,7 @@ def pytest_configure():
                 "config": {
                     "default": ["Organism"],
                     "all": ["Organism"],
-                    "ns": ["openmicroscopy.org/omero/bulk_annotations"],
+                    "ns": ["openmicroscopy.org/mapr/organism"],
                     "label": "Organism",
                 }
             },

tests/integration/bulk_to_map_annotation_context.yml

@@ -1,6 +1,6 @@
 ---
 name: Screen001
-version: 1
+version: 2
 
 defaults:
     # Should the column be processed when creating bulk-annotations (yes/no)
@@ -21,19 +21,39 @@ defaults:
 
 columns:
 
-  - name: Organism
+  - name: Channels
     include: yes
 
-  - name: Gene Identifier
-    include: yes
-  - name: Gene Identifier
-    clientname: Gene Identifier URL
-    clientvalue: http://www.ebi.ac.uk/cmpo/{{ value|urlencode }}
-    include: yes
-  - name: Gene Symbol
-    include: yes
+  - group:
+      namespace: openmicroscopy.org/mapr/gene
+      columns:
+      - name: Gene Identifier
+        include: yes
+      - name: Gene Identifier
+        clientname: Gene Identifier URL
+        clientvalue: http://www.pombase.org/spombe/result/{{ value|urlencode }}
+        include: yes
+      - name: Gene Symbol
+        include: yes
+
+  - group:
+      namespace: openmicroscopy.org/mapr/organism
+      columns:
+      - name: Organism
+        include: yes
 
 advanced:
     # If a map-annotation is attached to a well also attach it to all images
     # in the well
-    well_to_images: yes
+    well_to_images: yes
+
+    # TODO: Primary key config should be in a global config
+    ignore_missing_primary_key: yes
+    primary_group_keys:
+    - namespace: openmicroscopy.org/mapr/gene
+      keys:
+      - Gene Identifier
+      - Gene Symbol
+    - namespace: openmicroscopy.org/mapr/organism
+      keys:
+      - Organism