Integration tests update

semDiff/mergeEntities.py

@@ -266,13 +266,17 @@ def modify_references(self):
 
                             for reference in look_for:
                                 if reference in field['items']:
+
                                     sub_item_iterator = 0
                                     for sub_item in field['items'][reference]:
                                         if '$ref' in sub_item:
-                                            field_ref = sub_item['$ref']
+                                            field_ref = sub_item['$ref'].replace('#', '')
+
                                             if field_ref in self.name_mapping:
+                                                print(field_ref)
+                                                print(self.output['schemas'][schema]['properties'])
                                                 self.output['schemas'][schema]['properties'][
-                                                    reference]['items'][
+                                                    item]['items'][reference][
                                                     sub_item_iterator]['$ref'] = \
                                                     self.name_mapping[field_ref] + "#"
                                         sub_item_iterator += 1

source/API/apiClient.rst

@@ -7,13 +7,22 @@ The JSONLDschema package offers and API client that provides most of the library
 Here we include the documentation of each of the Python classes and properties for the API client.
 
 
+API client
+-------------------------------------------
+
+
+.. image:: ../_static/classes_api_client.png
+
 .. automodule:: client
     :members:
     :noindex:
 
 
----------------
+API utilities
+-------------------------------------------
+
 
+.. image:: ../_static/classes_api_utility.png
 
 .. automodule:: utility
     :members:

source/cedar/cedarIndex.rst

@@ -5,6 +5,7 @@ CEDAR Templating Tools
 
 Cedar utilities
 -------------------------------------------
+
 .. toctree::
    cedarUtilities
 

source/cedar/cedarUtilities.rst

@@ -3,16 +3,22 @@ Code documentation for the CEDAR utilities
 =============================================
 
 
-The CEDAR client will provide all the links the the CEDAR API functionality such as get, post and updates on templates,
-template elements, folders, instances ect ...
+The CEDAR client provides all the links the the CEDAR API functionality such as GET, POST and updates on templates,
+template elements, folders, instances, and so on.
 
 
+
+.. image:: ../_static/classes_cedar_client.png
+
 .. automodule:: client
     :members:
 
 ---------------
 
-The schema2cedar classes will help you transform your JSON schemas draft 04 into compatible CEDAR schemas
+
+The schema2cedar classes will help you transform your JSON schemas draft-04 into compatible CEDAR schemas, which can be visualised on the CEDAR Workbench tool.
+
+.. image:: ../_static/classes_cedar_schema2cedar.png
 
 .. automodule:: schema2cedar
     :members:

source/index.rst

@@ -6,7 +6,7 @@
 Welcome to jsonldschema's documentation!
 ========================================
 
-The JSONLDschema python package offers functionality to support the creation and use of machine-actionable and FAIR (Findable, Accessible, Interoperable and Reusable) metadata models expressed as `JSON-schemas <https://json-schema.org/>`_ for `JSON-LD <http://json-ld.org/>`_ data.
+The JSONLDschema python package offers functionality to support the creation and use of machine-actionable and FAIR (Findable, Accessible, Interoperable and Reusable) metadata models expressed as `JSON-schemas <https://json-schema.org/>`_ to generate `JSON-LD <http://json-ld.org/>`_ data.
 
 The approach relies on representing the metadata models as JSON-schemas with additional JSON-LD context files to provide semantic annotations to the model.
 

source/semDiff/semanticComparator.rst

@@ -2,13 +2,22 @@
 How to compare and merge set of JSON-LD-schemas: code documentation
 ====================================================================
 
+
+Compare entities
+-------------------------------------------
+
 .. image:: ../_static/classes_semDiff_compareEntities.png
 
 .. automodule:: compareEntities
     :members:
     :private-members:
     :special-members:
 
+
+Compare network
+-------------------------------------------
+
+
 .. image:: ../_static/classes_semDiff_compareNetwork.png
 
 .. automodule:: compareNetwork
@@ -17,13 +26,21 @@ How to compare and merge set of JSON-LD-schemas: code documentation
     :special-members:
 
 
+Full difference
+-------------------------------------------
+
+
 .. image:: ../_static/classes_semDiff_fullDiff.png
 
 .. automodule:: fullDiff
     :members:
     :private-members:
     :special-members:
 
+
+Merge entities
+-------------------------------------------
+
 .. image:: ../_static/classes_semDiff_mergeEntities.png
 
 .. automodule:: mergeEntities

source/validation/validationUtilities.rst

@@ -8,5 +8,8 @@ How to validate JSON-schemas and instances: code documentation
 .. automodule:: miflowcyt_validate
     :members:
 
+
+.. image:: ../_static/classes_validate_miflowcyt_validate.png
+
 .. autoclass:: FlowRepoClient
     :members:

tests/fullDiffOutput/merges/example_merge.json

@@ -42,7 +42,7 @@
                     "items": {
                         "anyOf": [
                             {
-                                "$ref": "test1_second_schema.json#"
+                                "$ref": "test1_second_test2_second_merged_schema.json#"
                             },
                             {
                                 "$ref": "test1_third_schema.json#"
@@ -67,10 +67,10 @@
                     "items": {
                         "anyOf": [
                             {
-                                "$ref": "test2_second_schema.json#"
+                                "$ref": "test1_second_test2_second_merged_schema.json#"
                             },
                             {
-                                "$ref": "third_schema.json#"
+                                "$ref": "third_merged_schema.json#"
                             }
                         ]
                     }

tests/integration/make_fulldiff.py

@@ -1,6 +1,7 @@
 import json
 import os
 from semDiff.fullDiff import FullDiffGenerator
+import multiprocessing
 
 
 output_base_path = os.path.join(os.path.dirname(__file__), "../fullDiffOutput/")
@@ -25,9 +26,9 @@ def make_diff(network1, network2):
     MIACA_schema_url = "https://w3id.org/mircat/miaca/schema/miaca_schema.json"
     MyFlowCyt_schema_url = "https://w3id.org/mircat/miflowcyt/schema/miflowcyt_schema.json"
     MIACA_MIACME_merge_schema_url = \
-        "https://w3id.org/mircat/miaca_miacme_merge/schema/miaca_schema.json"
+        "https://w3id.org/mircat/miaca_miacme_merge/schema/miaca_miacme_merged_schema.json"
     MIACME_MIACA_merge_schem_url = \
-        "https://w3id.org/mircat/miacme_miaca_merge/schema/miacme_schema.json"
+        "https://w3id.org/mircat/miacme_miaca_merge/schema/miacme_miaca_merged_schema.json"
 
     regex = {
         "/schema": "/context/obo",
@@ -55,24 +56,31 @@ def make_diff(network1, network2):
         "regex": regex,
         "url": MyFlowCyt_schema_url
     }
-
     MIACA_MIACME_merge_network = {
         "name": "MIACA_MIACME_merge",
         "regex": regex2,
         "url": MIACA_MIACME_merge_schema_url
     }
 
-    make_diff(MIACA_network, MIACA_network)
-    make_diff(MIACA_network, MyFlowCyt_network)
-    make_diff(MIACA_network, MIACME_network)
+    processes = [
+        (MIACA_network, MIACME_network),
+        (MIACA_network, MyFlowCyt_network),
+        (MIACA_network, MIACA_network),
+
+        (MIACME_network, MIACME_network),
+        (MIACME_network, MyFlowCyt_network),
+        (MIACME_network, MIACA_network),
+
+        (MyFlowCyt_network, MIACME_network),
+        (MyFlowCyt_network, MyFlowCyt_network),
+        (MyFlowCyt_network, MIACA_network)
+    ]
 
-    make_diff(MIACME_network, MIACME_network)
-    make_diff(MIACME_network, MyFlowCyt_network)
-    make_diff(MIACME_network, MIACA_network)
+    cpu_count = multiprocessing.cpu_count()
+    p = multiprocessing.Pool(processes=cpu_count)
+    result = [p.apply_async(make_diff, args=(x, y)) for (x, y) in processes]
 
-    make_diff(MyFlowCyt_network, MyFlowCyt_network)
-    make_diff(MyFlowCyt_network, MIACME_network)
-    make_diff(MyFlowCyt_network, MIACA_network)
+    output = [pp.get() for pp in result]
 
     make_diff(MIACA_MIACME_merge_network, MIACA_network)
     make_diff(MIACA_network, MIACA_MIACME_merge_network)

tests/integration/test_schema2context.py

@@ -5,22 +5,22 @@
     prepare_input,
     create_and_save_contexts,
     generate_context_mapping_dict,
+    generate_labels_from_contexts,
     json
 )
 
 
 class TestSchema2Context(unittest.TestCase):
-
     input = dict({
-      "MIACME": {
-        "schema_url": "https://w3id.org/mircat/miacme/schema/miacme_schema.json"
-      },
-      "MIACA": {
-        "schema_url": "https://w3id.org/mircat/miaca/schema/miaca_schema.json"
-      },
-      "MIFlowCyt": {
-        "schema_url": "https://w3id.org/mircat/miflowcyt/schema/miflowcyt_schema.json"
-      }
+        "MIACME": {
+            "schema_url": "https://w3id.org/mircat/miacme/schema/miacme_schema.json"
+        },
+        "MIACA": {
+            "schema_url": "https://w3id.org/mircat/miaca/schema/miaca_schema.json"
+        },
+        "MIFlowCyt": {
+            "schema_url": "https://w3id.org/mircat/miflowcyt/schema/miflowcyt_schema.json"
+        }
     })
 
     base = {
@@ -49,8 +49,52 @@ def test_create_and_save_contexts(self):
     def test_generate_mapping_dict(self):
         for key in self.input:
             mapping, errors = generate_context_mapping_dict(
-                        self.input[key]["schema_url"],
-                        self.regexes, key)
+                self.input[key]["schema_url"],
+                self.regexes, key)
             print(json.dumps(mapping, indent=4))
             print(errors)
             self.assertTrue(mapping["networkName"] == key)
+
+    def test_generate_labels_from_contexts_1(self):
+        labels = {}
+        contexts = {
+            "cell_line_obo_context.jsonld": {
+                "@context": {
+                    "obo": "http://purl.obolibrary.org/obo/",
+                    "CellLine": "obo:CLO_0000031",
+                    "@language": "en",
+                    "ID": "obo:IAO_0000578",
+                    "lineQC": "obo:ERO_0001219",
+                    "validation": "obo:ERO_0002025",
+                    "cellLineName": "obo:IAO_0000590",
+                    "modifications": "obo:CLO_0000004",
+                    "passageNo": "obo:EFO_0007061",
+                    "cellSource": "obo:CL_0000000"
+                }
+            }
+        }
+        generate_labels_from_contexts(contexts, labels)
+        print(labels)
+
+    def test_generate_labels_from_contexts_2(self):
+        labels = {}
+        contexts = {
+            "@context": {
+                "obo": "http://purl.obolibrary.org/obo/",
+                "bao": "http://www.bioassayontology.org/bao#",
+                "ImagingCondition": "obo:FBbi_root_00000000",
+                "@language": "en",
+                "timeSeriesInterval": "obo:IAO_0000584",
+                "imageSequenceType": "obo:NCIT_C69268",
+                "pixels": "obo:NCIT_C48367",
+                "observationPeriod": "obo:NCIT_C25616",
+                "numericalAperture": "obo:NCIT_C44175",
+                "observationPeriodUnit": "obo:UO_0000003",
+                "objectiveLens": "obo:ERO_0000453",
+                "modality": "obo:FBbi_00000222",
+                "channelDefinition": "bao:BAO_0000184",
+                "timeSeriesIntervalUnit": "obo:UO_0000003"
+            }
+        }
+        generate_labels_from_contexts(contexts, labels)
+        print(labels)