test omero53 in travis

.travis.yml

@@ -24,7 +24,7 @@ before_script:
 
 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 $exitcode
+  - docker-compose -f docker/docker-compose.yml up --build --abort-on-container-exit
+  - exitcode=$(docker inspect -f '{{.State.ExitCode}}' docker_maprtest_1)
+  - docker-compose -f docker/docker-compose.yml rm -fv
+  - exit $exitcode

omero_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/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()

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

tests/integration/bulk_to_map_annotation_context_ns.csv

@@ -1,7 +1,7 @@
-Plate,Well Number,Well,Gene Identifier,Gene Symbol,Organism
-Plate001,1,A1,cdc14,CG7134,Homo sapiens
-Plate001,1,A2,cdc14,FBgn0031952,Homo sapiens
-Plate001,2,A3,CDC14,YFR028C,Mouse
-Plate001,2,A4,Cdc14,YFR028C,Mouse
-Plate001,3,A5,beta'Cop,apostrophe,Human
-Plate001,4,A6,percent,123 (abc%def),Some organism
+Plate,Well Number,Well,Gene Identifier,Gene Symbol,Organism,Channels
+Plate001,1,A1,cdc14,CG7134,Homo sapiens,1a
+Plate001,1,A2,cdc14,FBgn0031952,Homo sapiens,1b
+Plate001,2,A3,CDC14,YFR028C,Mouse,2a
+Plate001,2,A4,Cdc14,YFR028C,Mouse,2b
+Plate001,3,A5,beta'Cop,apostrophe,Human,3
+Plate001,4,A6,percent,123 (abc%def),Some organism,4

tests/integration/test_config.py

@@ -69,7 +69,7 @@ def wildcard_settings(settings):
                 "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,
                 }
@@ -79,7 +79,7 @@ def wildcard_settings(settings):
                 "config": {
                     "default": ["Phenotype"],
                     "all": ["Phenotype", "Phenotype Term Accession"],
-                    "ns": ["openmicroscopy.org/omero/bulk_annotations"],
+                    "ns": ["openmicroscopy.org/mapr/phenotype"],
                     "label": "Phenotype",
                     "wildcard": {
                         "enabled": False
@@ -91,7 +91,7 @@ def wildcard_settings(settings):
                 "config": {
                     "default": ["Organism"],
                     "all": ["Organism"],
-                    "ns": ["openmicroscopy.org/omero/bulk_annotations"],
+                    "ns": ["openmicroscopy.org/mapr/organism"],
                     "label": "Organism",
                     "wildcard": {
                         "enabled": True