fix to isa model to enable serialization of @id for key objects, fixing associated tests, tweaks to json-ld context files

Author: oerc0042

isa-cookbook/content/notebooks/isa-api-programmatic-rebuild-of-BII-S-3.ipynb

@@ -7,6 +7,15 @@
     "### Loading the ISA-API"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!pip install -e ."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

isa-cookbook/content/notebooks/isa-json-conversion-to-rdf-linked-data.ipynb

@@ -44,8 +44,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#!pip install -e .\n",
-    "!pwd"
+    "!pip install -e .\n"
    ]
   },
   {

isa-cookbook/content/notebooks/output/BII-S-3-synth/BII-S-3-isa.json

@@ -61,14 +61,14 @@ Study Factor Type	chemical substance	dose	time
 Study Factor Type Term Accession Number	http://purl.obolibrary.org/obo/CHEBI_59999	http://www.ebi.ac.uk/efo/EFO_0000428	http://purl.obolibrary.org/obo/PATO_0000165
 Study Factor Type Term Source REF	CHEBI	EFO	PATO
 STUDY ASSAYS
-Study Assay File Name	a_gilbert-assay-Gx.txt	a_gilbert-assay-Tx.txt	a_gilbert-assay-Gx.txt	a_gilbert-assay-Tx.txt
-Study Assay Measurement Type	metagenome sequencing	transcription profiling	metagenome sequencing	transcription profiling
-Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0002623	http://purl.obolibrary.org/obo/OBI_0000424	http://purl.obolibrary.org/obo/OBI_0002623	http://purl.obolibrary.org/obo/OBI_0000424
-Study Assay Measurement Type Term Source REF	OBI	OBI	OBI	OBI
-Study Assay Technology Type	nucleotide sequencing	nucleotide sequencing	nucleotide sequencing	nucleotide sequencing
-Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000626	http://purl.obolibrary.org/obo/OBI_0000626	http://purl.obolibrary.org/obo/OBI_0000626	http://purl.obolibrary.org/obo/OBI_0000626
-Study Assay Technology Type Term Source REF	OBI	OBI	OBI	OBI
-Study Assay Technology Platform				
+Study Assay File Name	a_gilbert-assay-Gx.txt	a_gilbert-assay-Tx.txt
+Study Assay Measurement Type	metagenome sequencing	transcription profiling
+Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0002623	http://purl.obolibrary.org/obo/OBI_0000424
+Study Assay Measurement Type Term Source REF	OBI	OBI
+Study Assay Technology Type	nucleotide sequencing	nucleotide sequencing
+Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000626	http://purl.obolibrary.org/obo/OBI_0000626
+Study Assay Technology Type Term Source REF	OBI	OBI
+Study Assay Technology Platform		
 STUDY PROTOCOLS
 Study Protocol Name	sample collection	aliquoting-0	nucleic acid extraction	mRNA extraction - standard procedure 3	genomic DNA extraction - standard procedure 4	reverse transcription - standard procedure 5	library construction	nucleic acid sequencing	sequence analysis - standard procedure 7
 Study Protocol Type	sample collection	sample collection	nucleic acid extraction	labeling	nucleic acid extraction	reverse transcription	library construction	nucleic acid sequencing	data transformation

isa-cookbook/content/notebooks/output/BII-S-3-synth/i_investigation.txt

@@ -1,6 +1,6 @@
 query introspection {
-    schemas: __schema {
-        types  {     ...FullType   }
+     schemas: __schema {
+        types {     ...FullType   }
     }
 }
 
@@ -16,7 +16,7 @@ fragment FullType on __Type {
             type { kind }
         }
     }
-    fields(includeDeprecated: true) {
+    fields(includeDeprecated: false) {
         name
         description
         args {...InputValue }
@@ -47,41 +47,41 @@ fragment TypeRef on __Type {
             kind
             name
             description
-            ofType {
-                name
-                inputFields {
-                    name
-                    description
-                    defaultValue
-                    type {
-                        kind
-                        name
-                        description
-                        ofType {name}
-                        inputFields {
-                            name
-                            description
-                            defaultValue
-                        }
-                    }
-                }
-            }
-            inputFields {
-                name
-                description
-                defaultValue
-                type {
-                    kind
-                    name
-                    description
-                    ofType {name}
-                    inputFields {
-                        name
-                        description
-                        defaultValue
-                    }
-                }
-            }
+#            ofType {
+#                name
+#                inputFields {
+#                    name
+#                    description
+#                    defaultValue
+#                    type {
+#                        kind
+#                        name
+#                        description
+#                        ofType {name}
+#                       inputFields {
+#                            name
+#                            description
+#                            defaultValue
+#                       }
+#                    }
+#                }
+#            }
+#            inputFields {
+#                name
+#                description
+#                defaultValue
+#                type {
+#                    kind
+#                    name
+#                    description
+#                    ofType {name}
+#                    inputFields {
+#                        name
+#                        description
+#                        defaultValue
+#                    }
+#                }
+#            }
         }
     }
 }

isatools/graphQL/queries/introspection.gql

@@ -27,7 +27,7 @@ def find_measurement(measurement_type, expected_value, operator):
 def find_exposure_value(sample, expected_value, target):
     """
     Tests if a given sample contains the given factor value
-    :param sample: the sample too look at
+    :param sample: the sample to look at
     :param expected_value: the value to look for
     :param target: the target of sample to look into
     :return: {Boolean}
@@ -49,7 +49,7 @@ def find_exposure_value(sample, expected_value, target):
 def find_characteristics(sample, expected_value):
     """
     Tests if a given sample contains the given characteristics
-    :param sample: the sample too look at
+    :param sample: the sample to look at
     :param expected_value: the value to look for
     :return: {Boolean}
     """

isatools/graphQL/utils/find.py

@@ -24,7 +24,7 @@ def validate_outputs(outputs):
 
 def validate_target(inputs, input_type):
     """
-    Validate the target depending of the input_type.
+    Validate the target depending on the input_type.
     :param inputs: the value to validate
     :param input_type: 'input' or 'output'
     :return: True or raise Exception

isatools/graphQL/utils/validate.py

@@ -252,6 +252,7 @@ def __ne__(self, other):
 
     def to_dict(self, ld=False):
         investigation = {
+            "@id": self.id,
             "identifier": self.identifier,
             "title": self.title,
             "description": self.description,
@@ -269,6 +270,7 @@ def to_ld(self):
         return self.to_dict(ld=True)
 
     def from_dict(self, investigation):
+        self.id = investigation.get("@id", "")
         self.identifier = investigation.get("identifier", "")
         self.title = investigation.get("title", "")
         self.public_release_date = investigation.get("publicReleaseDate", "")

isatools/model/investigation.py

@@ -204,6 +204,7 @@ def __ne__(self, other):
 
     def to_dict(self, ld=False):
         person = {
+            "@id": self.id,
             "address": self.address,
             "affiliation": self.affiliation,
             "comments": [comment.to_dict(ld=ld) for comment in self.comments],
@@ -218,6 +219,7 @@ def to_dict(self, ld=False):
         return self.update_isa_object(person, ld=ld)
 
     def from_dict(self, person):
+        self.id = person.get("@id", "")
         self.address = person["address"] if "address" in person else ""
         self.affiliation = person["affiliation"] if "affiliation" in person else ""
         self.email = person["email"] if "email" in person else ""

isatools/model/person.py

@@ -1,8 +1,9 @@
 from isatools.model.comments import Commentable
+from isatools.model.identifiable import Identifiable
 from isatools.model.ontology_annotation import OntologyAnnotation
 
 
-class Publication(Commentable):
+class Publication(Commentable, Identifiable):
     """A publication associated with an investigation or study.
 
     Attributes:
@@ -17,9 +18,10 @@ class Publication(Commentable):
         comments: Comments associated with instances of this class.
     """
 
-    def __init__(self, pubmed_id="", doi="", author_list="", title="", status=None, comments=None):
+    def __init__(self, id_="", pubmed_id="", doi="", author_list="", title="", status=None, comments=None):
         super().__init__(comments)
 
+        self.id = id_
         self.__pubmed_id = pubmed_id
         self.__doi = doi
         self.__author_list = author_list
@@ -127,6 +129,7 @@ def to_dict(self, ld=False):
         if isinstance(self.status, OntologyAnnotation):
             status = self.status.to_dict()
         publication = {
+            "@id": self.id,
             "authorList": self.author_list,
             "doi": self.doi,
             "pubMedID": self.pubmed_id,
@@ -137,12 +140,12 @@ def to_dict(self, ld=False):
         return self.update_isa_object(publication, ld=ld)
 
     def from_dict(self, publication):
+        self.id = publication.get("@id", "")
         self.author_list = publication["authorList"] if "authorList" in publication else ""
         self.doi = publication["doi"] if "doi" in publication else ""
         self.pubmed_id = publication["pubMedID"] if "pubMedID" in publication else ""
         self.title = publication["title"] if "title" in publication else ""
         self.load_comments(publication.get("comments", []))
-
         status = OntologyAnnotation()
         status.from_dict(publication.get("status", {}))
         self.status = status