merging develop into issue-497-fix

.github/workflows/buildandtestpython.yml

@@ -13,9 +13,9 @@ jobs:
         python-version: [3.8, 3.9, '3.10', '3.11']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Download Test Data

.github/workflows/pythonpublish.yml

@@ -8,9 +8,9 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

isatools/isatab/dump/write.py

@@ -62,8 +62,9 @@ def flatten(current_list):
         log.warning(s_graph.nodes())
 
         sample_in_path_count = 0
+        protocol_in_path_count = 0
         longest_path = _longest_path_and_attrs(paths, s_graph.indexes)
-
+        
         for node_index in longest_path:
             node = s_graph.indexes[node_index]
             if isinstance(node, Source):
@@ -76,8 +77,9 @@ def flatten(current_list):
                     map(lambda x: get_comment_column(
                         olabel, x), node.comments))
             elif isinstance(node, Process):
-                olabel = "Protocol REF.{}".format(node.executes_protocol.name)
+                olabel = "Protocol REF.{}".format(protocol_in_path_count)
                 columns.append(olabel)
+                protocol_in_path_count += 1
                 if node.executes_protocol.name not in protnames.keys():
                     protnames[node.executes_protocol.name] = protrefcount
                     protrefcount += 1
@@ -104,6 +106,7 @@ def flatten(current_list):
                 columns += flatten(map(lambda x: get_fv_columns(olabel, x),
                                        node.factor_values))
 
+
         omap = get_object_column_map(columns, columns)
         # load into dictionary
         df_dict = dict(map(lambda k: (k, []), flatten(omap)))
@@ -113,6 +116,7 @@ def flatten(current_list):
                 df_dict[k].extend([""])
 
             sample_in_path_count = 0
+            protocol_in_path_count = 0
             for node_index in path_:
                 node = s_graph.indexes[node_index]
                 if isinstance(node, Source):
@@ -129,8 +133,8 @@ def flatten(current_list):
                         df_dict[colabel][-1] = co.value
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                    protocol_in_path_count += 1
                     df_dict[olabel][-1] = node.executes_protocol.name
                     for pv in node.parameter_values:
                         pvlabel = "{0}.Parameter Value[{1}]".format(
@@ -263,6 +267,8 @@ def flatten(current_list):
             if _longest_path_and_attrs(paths, a_graph.indexes) is None:
                 raise IOError(
                     "Could not find any valid end-to-end paths in assay graph")
+
+            protocol_in_path_count = 0
             for node_index in _longest_path_and_attrs(paths, a_graph.indexes):
                 node = a_graph.indexes[node_index]
                 if isinstance(node, Sample):
@@ -279,9 +285,9 @@ def flatten(current_list):
                                 node.factor_values))
 
                 elif isinstance(node, Process):
-                    olabel = "Protocol REF.{}".format(
-                        node.executes_protocol.name)
+                    olabel = "Protocol REF.{}".format(protocol_in_path_count)
                     columns.append(olabel)
+                    protocol_in_path_count += 1
                     if node.executes_protocol.name not in protnames.keys():
                         protnames[node.executes_protocol.name] = protrefcount
                         protrefcount += 1
@@ -338,12 +344,12 @@ def pbar(x):
                 for k in df_dict.keys():  # add a row per path
                     df_dict[k].extend([""])
 
+                protocol_in_path_count = 0
                 for node_index in path_:
                     node = a_graph.indexes[node_index]
                     if isinstance(node, Process):
-                        olabel = "Protocol REF.{}".format(
-                            node.executes_protocol.name
-                        )
+                        olabel = "Protocol REF.{}".format(protocol_in_path_count)
+                        protocol_in_path_count += 1
                         df_dict[olabel][-1] = node.executes_protocol.name
                         if node.executes_protocol.protocol_type:
                             oname_label = get_column_header(

isatools/model/context.py

@@ -1,6 +1,10 @@
+from __future__ import annotations
+
 from os import path
 from re import sub
 from abc import ABCMeta
+import requests
+from json import loads
 
 from isatools.model.identifiable import Identifiable
 
@@ -12,32 +16,53 @@
 EXCEPTIONS = {
     'OntologySource': 'OntologySourceReference',
     'Characteristic': 'MaterialAttributeValueNumber',
-    'StudyFactor': 'Factor'
+    'StudyFactor': 'Factor',
+    'DataFile': "Data",
+    'RawDataFile': "RawData"
 }
 
 
-def get_name(name):
+def get_name(name: str) -> str:
+    """ Get the name of the class to include in the context name.
+    :param name: the name of the class.
+    :return: the name of the class to include in the context name.
+    """
     if name in EXCEPTIONS:
         return EXCEPTIONS[name]
     return name
 
 
 def camelcase2snakecase(camelcase: str) -> str:
+    """ Convert a camelcase string to snakecase.
+    :param camelcase: the camelcase string to convert
+    :return: the snakecase string
+    """
     return sub(r'(?<!^)(?=[A-Z])', '_', camelcase).lower()
 
 
 def gen_id(classname: str) -> str:
+    """ Generate an identifier based on the class name
+    :param classname: the name of the class
+    :return: the identifier
+    """
     from uuid import uuid4
     prefix = '#' + camelcase2snakecase(classname) + '/'
     return prefix + str(uuid4())
 
 
 class ContextPath:
+    """
+    A class to manage the context of the JSON-LD serialization. This should not be used directly. Use the `context`
+    object and `set_context()` function instead.
+    """
 
-    def __init__(self):
+    def __init__(self) -> None:
+        """ Initialize the context path. """
         self.__context = 'obo'
         self.all_in_one = True
         self.local = True
+        self.include_contexts = False
+        self.contexts = {}
         self.get_context()
         self.prepend_url = None
 
@@ -46,14 +71,17 @@ def context(self) -> str:
         return self.__context
 
     @context.setter
-
     def context(self, val: str) -> None:
         allowed_context = ['obo', 'sdo', 'wd', 'sio']
         if val not in allowed_context:
             raise ValueError('Context name must be one in %s but got %s' % (allowed_context, val))
         self.__context = val
 
-    def get_context(self, classname: str = 'allinone'):
+    def get_context(self, classname: str = 'allinone') -> str | dict:
+        """ Get the context needed to serialize ISA to JSON-LD. Will either return a URL to the context of resolve the
+        context and include it in the instance.
+        :param classname: the name of the class to get the context for.
+        """
         classname = get_name(classname)
         classname = camelcase2snakecase(classname)
         name = self.__context
@@ -62,12 +90,25 @@ def get_context(self, classname: str = 'allinone'):
         if self.all_in_one:
             filename = 'isa_allinone_%s_context.jsonld' % name
 
-        return path.join(path_source, name, filename) if self.local else path_source + filename
-
-    def __repr__(self):
+        context_path = path.join(path_source, filename) if self.local else path_source + filename
+        return context_path if not self.include_contexts else self.load_context(context_path)
+
+    def load_context(self, context_path: str) -> dict:
+        """
+        Load the context from the given path or URL. If the context is already loaded, return it.
+        :param context_path: the path or URL to the context.
+        """
+        if context_path in self.contexts:
+            return self.contexts[context_path]
+        if self.local:
+            with open(context_path, 'r') as f:
+                return loads(f.read())
+        return requests.get(context_path).json()
+
+    def __repr__(self) -> str:
         return self.__context
 
-    def __str__(self):
+    def __str__(self) -> str:
         return self.__context
 
 
@@ -96,7 +137,9 @@ def set_context(
 
 
 class LDSerializable(metaclass=ABCMeta):
-    def __init__(self):
+    """ A mixin used by ISA objects to provide utility methods for JSON-LD serialization. """
+
+    def __init__(self) -> None:
         self.context = context
 
     def gen_id(self) -> str:
@@ -107,17 +150,24 @@ def gen_id(self) -> str:
             return self.id if self.id.startswith('http') else prepend + self.id
         return prepend + gen_id(self.__class__.__name__)
 
-    def get_context(self):
+    def get_context(self) -> str | dict:
+        """ Get the context for the object. """
         return self.context.get_context(classname=self.__class__.__name__)
 
-    def get_ld_attributes(self):
+    def get_ld_attributes(self) -> dict:
+        """ Generate and return the LD attributes for the object. """
         return {
             '@type': get_name(self.__class__.__name__).replace('Number', ''),
             '@context': self.get_context(),
             '@id': self.gen_id()
         }
 
-    def update_isa_object(self, isa_object, ld=False):
+    def update_isa_object(self, isa_object, ld=False) -> object:
+        """ Update the ISA object with the LD attributes if necessary. Needs to be called
+        after serialization the object.
+        :param isa_object: the ISA object to update.
+        :param ld: if True, update the object with the LD attributes, else return the object before injection
+        """
         if not ld:
             return isa_object
         isa_object.update(self.get_ld_attributes())

isatools/resources/schemas/isa_model_version_1_0_schemas/core/assay_schema.json

@@ -6,8 +6,8 @@
   "description": "JSON Schema describing an ISA model Assay object",
   "type": "object",
   "properties": {
-    "@id": { "type": "string", "format": "uri" },
-    "@context": { "type": "string", "format": "uri"},
+    "@id": { "type": "string", "format": "uri-reference" },
+    "@context": { "type": "string", "format": "uri-reference"},
     "@type" : { "type": "string", "enum": ["Assay"] },
     "filename" : { "type" : "string" },
     "measurementType" : {

isatools/resources/schemas/isa_model_version_1_0_schemas/core/comment_schema.json

@@ -6,8 +6,8 @@
     "description": "JSON-schema representing an ISA model Comment object",
     "type": "object",
     "properties": {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["Comment"] },
         "name": {
             "type": "string"

isatools/resources/schemas/isa_model_version_1_0_schemas/core/data_schema.json

@@ -6,8 +6,8 @@
     "description": "JSON-schema representing an ISA model Data object",
     "type": "object",
     "properties": {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["Data"] },
         "name": {
             "type": "string"

isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_schema.json

@@ -6,8 +6,8 @@
     "description": "JSON-schema representing an ISA model Factor object",
     "type": "object",
     "properties": {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["Factor"] },
         "factorName": {
             "type": "string"

isatools/resources/schemas/isa_model_version_1_0_schemas/core/factor_value_schema.json

@@ -6,9 +6,9 @@
     "description": "JSON-schema representing an ISA model Factor Value object",
     "type": "object",
     "properties": {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
-        "@type" : { "type": "string", "enum": ["FactorValue"] },
+         "@id": { "type": "string", "format": "uri-reference" },
+         "@context": { "type": "string", "format": "uri-reference"},
+         "@type" : { "type": "string", "enum": ["FactorValue"] },
          "category" : {
              "$ref": "factor_schema.json#"
         },

isatools/resources/schemas/isa_model_version_1_0_schemas/core/investigation_schema.json

@@ -6,8 +6,8 @@
     "description" : "JSON-schema representing an ISA mode Investigation object",
     "type" : "object",
     "properties" : {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["Investigation"] },
         "filename": { "type" : "string"},
         "identifier" : { "type" : "string" },

isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_schema.json

@@ -6,8 +6,8 @@
     "description" : "JSON-schema representing a characteristics category (what appears between the brackets in Characteristics[]) in the ISA model",
     "type" : "object",
     "properties" : {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["MaterialAttribute"] },
         "characteristicType": {
             "$ref": "ontology_annotation_schema.json#"

isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_attribute_value_schema.json

@@ -6,8 +6,8 @@
     "description" : "JSON-schema representing an ISA model material attribute (or characteristic) value object",
     "type" : "object",
     "properties" : {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["MaterialAttributeValue"] },
         "category" : {
              "$ref": "material_attribute_schema.json#"

isatools/resources/schemas/isa_model_version_1_0_schemas/core/material_schema.json

@@ -6,8 +6,8 @@
   "description" : "JSON-schema representing an ISA model material object, which is not a source or a sample (as they have specific schemas) - this will correspond to 'Extract Name', 'Labeled Extract Name'",
   "type" : "object",
   "properties" : {
-    "@id": { "type": "string", "format": "uri" },
-    "@context": { "type": "string", "format": "uri"},
+    "@id": { "type": "string", "format": "uri-reference" },
+    "@context": { "type": "string", "format": "uri-reference"},
     "@type" : { "type": "string", "enum": ["Material"] },
     "name" : { "type" : "string" },
     "type": {

isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json

@@ -6,8 +6,8 @@
     "description" : "JSON-schema representing an ISA model Ontology Reference or annotation (for fields that are required to be ontology annotations)",
     "type" : "object",
     "properties" : {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference" },
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["OntologyAnnotation"] },
         "annotationValue": {
             "anyOf": [

isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_source_reference_schema.json

@@ -6,8 +6,8 @@
     "description" : "JSON-schema representing an ISA model ontology reference object",
     "type" : "object",
     "properties" : {
-        "@id": { "type": "string", "format": "uri" },
-        "@context": { "type": "string", "format": "uri"},
+        "@id": { "type": "string", "format": "uri-reference"},
+        "@context": { "type": "string", "format": "uri-reference"},
         "@type" : { "type": "string", "enum": ["OntologySourceReference"] },
         "comments": {
             "type": "array",