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Merge pull request #178 from cweedall/feature/option-flags-from-confi…
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…g-file

Refactor configuration/option flags from config file.  Add placeholder flags for (property) array generation and PATCH path
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@dgarijo
dgarijo authored May 6, 2024
2 parents 8b2e833 + 8b0da60 commit a69d201
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Showing 11 changed files with 184 additions and 143 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<packaging>jar</packaging>
<groupId>edu.isi.oba</groupId>
<artifactId>oba</artifactId>
<version>3.8.0</version>
<version>3.8.1</version>
<name>core</name>
<url>https://github.com/KnowledgeCaptureAndDiscovery/OBA</url>

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31 changes: 10 additions & 21 deletions src/main/java/edu/isi/oba/Mapper.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package edu.isi.oba;

import edu.isi.oba.config.CONFIG_FLAG;
import edu.isi.oba.config.YamlConfig;
import static edu.isi.oba.Oba.logger;

Expand Down Expand Up @@ -33,17 +34,11 @@ class Mapper {
YamlConfig config_data;

public OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
private Boolean follow_references;
private Boolean default_descriptions;
private Boolean default_properties;

public Mapper(YamlConfig config_data) throws OWLOntologyCreationException, IOException {
this.config_data = config_data;
this.selected_paths = config_data.getPaths();
this.mappedClasses = new ArrayList<>();
this.follow_references = config_data.getFollow_references();
this.default_descriptions = config_data.getDefault_descriptions();
this.default_properties = config_data.getDefault_properties();

List<String> config_ontologies = config_data.getOntologies();
String destination_dir = config_data.getOutput_dir() + File.separator + config_data.getName();
Expand Down Expand Up @@ -106,14 +101,10 @@ private void download_ontologies(List<String> config_ontologies, String destinat
* The schemas includes the properties
*
* @param destination_dir directory to write the final results
* @param config_data yaml configuration
*/
public void createSchemas(String destination_dir) {
Query query = new Query(destination_dir);
Path pathGenerator = new Path(this.config_data.getEnable_get_paths(),
this.config_data.getEnable_post_paths(),
this.config_data.getEnable_put_paths(),
this.config_data.getEnable_delete_paths(),
PathGenerator pathGenerator = new PathGenerator(this.config_data.getConfigFlags(),
this.config_data.getAuth().getEnable()
);

Expand Down Expand Up @@ -148,7 +139,7 @@ public void createSchemas(String destination_dir) {
}
}

private void add_user_path(Path pathGenerator) {
private void add_user_path(PathGenerator pathGenerator) {
//User schema
Map<String, Schema> userProperties = new HashMap<>();
StringSchema username = new StringSchema();
Expand All @@ -165,7 +156,7 @@ private void add_user_path(Path pathGenerator) {
this.paths.addPathItem("/user/login", pathGenerator.user_login(userSchema.getName()));
}

private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator, OWLOntology ontology,
private List<OWLClass> add_owlclass_to_openapi(Query query, PathGenerator pathGenerator, OWLOntology ontology,
String defaultOntologyPrefixIRI, OWLClass cls, Boolean topLevel) {
List<OWLClass> ref = new ArrayList<>();
String classPrefixIRI = cls.getIRI().getNamespace();
Expand All @@ -182,7 +173,7 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,
if(ontology.containsClassInSignature(clsToCheck.getIRI())) {
System.out.println("ADD "+ clsToCheck);
for (OWLOntology temp_ontology : this.ontologies) {
if (follow_references) {
if (this.config_data.getConfigFlagValue(CONFIG_FLAG.FOLLOW_REFERENCES)) {
this.mappedClasses.add(clsToCheck);
getMapperSchema(query, temp_ontology, clsToCheck, this.schemaDescriptions.get(clsToCheck.getIRI()));
add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, clsToCheck, false);
Expand All @@ -197,11 +188,9 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,
logger.info("The class " + ref_class + " exists ");
} else {
for (OWLOntology temp_ontology : this.ontologies) {
if ( follow_references ) {
if (this.config_data.getConfigFlagValue(CONFIG_FLAG.FOLLOW_REFERENCES)) {
this.mappedClasses.add(ref_class);
getMapperSchema(query, temp_ontology, ref_class,this.schemaDescriptions.get(ref_class.getIRI()));
// OWLDocumentFormat format = ontology.getFormat();
// String temp_defaultOntologyPrefixIRI = format.asPrefixOWLDocumentFormat().getDefaultPrefix();
add_owlclass_to_openapi(query, pathGenerator, temp_ontology, classPrefixIRI, ref_class, false);
}
}
Expand All @@ -219,7 +208,7 @@ private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator,

private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass cls, String cls_description) {
//Convert from OWL Class to OpenAPI Schema.
MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, cls_description, schemaNames, ontology, this.follow_references, this.default_descriptions, this.default_properties);
MapperSchema mapperSchema = new MapperSchema(this.ontologies, cls, cls_description, schemaNames, ontology, this.config_data.getConfigFlags());
//Write queries
query.write_readme(mapperSchema.name);
//Create the OpenAPI schema
Expand All @@ -228,7 +217,7 @@ private MapperSchema getMapperSchema(Query query, OWLOntology ontology, OWLClass
return mapperSchema;
}

private void addOpenAPIPaths(Path pathGenerator, MapperSchema mapperSchema, OWLClass cls) {
private void addOpenAPIPaths(PathGenerator pathGenerator, MapperSchema mapperSchema, OWLClass cls) {
if (selected_classes != null && !selected_classes.contains(cls)) {
logger.info("Ignoring class " + cls.toString());
} else {
Expand All @@ -251,11 +240,11 @@ private void setSchemaNames(Set<OWLClass> classes) {
private void setSchemaDrescriptions(Set<OWLClass> classes, OWLOntology ontology){
for (OWLClass cls: classes) {
System.out.println(cls);
schemaDescriptions.put(cls.getIRI(), ObaUtils.getDescription(cls, ontology, this.default_descriptions));
schemaDescriptions.put(cls.getIRI(), ObaUtils.getDescription(cls, ontology, this.config_data.getConfigFlagValue(CONFIG_FLAG.DEFAULT_DESCRIPTIONS)));
}
}

private void add_path(Path pathGenerator, MapperSchema mapperSchema) {
private void add_path(PathGenerator pathGenerator, MapperSchema mapperSchema) {
String singular_name = "/" + mapperSchema.name.toLowerCase() + "s/{id}";
String plural_name = "/" + mapperSchema.name.toLowerCase() + "s";
//Create the plural paths: for example: /models/
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45 changes: 21 additions & 24 deletions src/main/java/edu/isi/oba/MapperOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@

import io.swagger.models.Method;
import io.swagger.v3.oas.models.Operation;
import io.swagger.v3.oas.models.headers.Header;
import io.swagger.v3.oas.models.media.*;
import io.swagger.v3.oas.models.parameters.Parameter;
import io.swagger.v3.oas.models.parameters.PathParameter;
Expand Down Expand Up @@ -30,14 +29,12 @@ class MapperOperation {
private final ApiResponses apiResponses = new ApiResponses();
private final Cardinality cardinality;
private final Schema schema;
private final Operation operation;

public Operation getOperation() {
return operation;
}

private final Operation operation;


public MapperOperation(String schemaName, String schemaURI, Method method, Cardinality cardinality, Boolean auth) {
this.auth = auth;
this.cardinality = cardinality;
Expand All @@ -50,6 +47,9 @@ public MapperOperation(String schemaName, String schemaURI, Method method, Cardi
case GET:
setOperationGet();
break;
case PATCH:
setOperationPatch();
break;
case PUT:
setOperationPut();
break;
Expand All @@ -59,7 +59,8 @@ public MapperOperation(String schemaName, String schemaURI, Method method, Cardi
case DELETE:
setOperationDelete();
break;

default:
break;
}

if (cardinality == Cardinality.SINGULAR){
Expand All @@ -70,32 +71,30 @@ public MapperOperation(String schemaName, String schemaURI, Method method, Cardi
.schema(new StringSchema()));
}

if (auth && (method == Method.PUT || method == Method.POST || method == Method.DELETE )) {
if (auth && Set.of(Method.PATCH, Method.PUT, Method.POST, Method.DELETE).contains(method)) {
parameters.add(new QueryParameter()
.description("Username")
.name("user")
.required(false)
.schema(new StringSchema()));
}

operation = new Operation()
.description(description)
.summary(summary)
.addTagsItem(schemaName)
.parameters(parameters)
.responses(apiResponses);


if (method == Method.PUT || method == Method.POST ){
if (Set.of(Method.PATCH, Method.PUT, Method.POST).contains(method)) {
operation.setRequestBody(requestBody);
}


if (method == Method.PUT || method == Method.POST || method == Method.DELETE ){
if (Set.of(Method.PATCH, Method.PUT, Method.POST, Method.DELETE).contains(method)) {
SecurityRequirement securityRequirement = new SecurityRequirement();
securityRequirement.addList("BearerAuth");
operation.addSecurityItem(securityRequirement);
}

}

private void setOperationGet() {
Expand All @@ -113,7 +112,7 @@ private void setOperationGet() {
case PLURAL:
summary = "List all instances of " + this.schemaName;
description = "Gets a list of all instances of " + this.schemaName +
" (more information in " +this.schemaURI+")";
" (more information in " + this.schemaURI + ")";
responseDescriptionOk = "Successful response - returns an array with the instances of " + schemaName + ".";

//Set response
Expand All @@ -140,9 +139,9 @@ private void setOperationGet() {
.schema(new IntegerSchema()._default(100).maximum(BigDecimal.valueOf(200)).minimum(BigDecimal.valueOf(1))));
break;
case SINGULAR:
summary = "Get a single " + this.schemaName +" by its id";
description = "Gets the details of a given " + this.schemaName+
" (more information in " +this.schemaURI+")";
summary = "Get a single " + this.schemaName + " by its id";
description = "Gets the details of a given " + this.schemaName +
" (more information in " + this.schemaURI + ")";
responseDescriptionOk = "Gets the details of a given " + schemaName;

//Set request
Expand All @@ -153,7 +152,10 @@ private void setOperationGet() {
break;

}
}

private void setOperationPatch() {
// TODO: implement
}

private void setOperationPost() {
Expand All @@ -177,13 +179,12 @@ private void setOperationPost() {
);
}


private void setOperationPut() {
String requestDescription = "An old " + this.schemaName + "to be updated";

summary = "Update an existing " + this.schemaName;
description = "Updates an existing " + this.schemaName+
" (more information in " +this.schemaURI+")";
description = "Updates an existing " + this.schemaName +
" (more information in " + this.schemaURI + ")";

//Set request
MediaType mediaType = new MediaType().schema(schema);
Expand All @@ -199,22 +200,18 @@ private void setOperationPut() {
)
.addApiResponse("404", new ApiResponse()
.description("Not Found"));

}


private void setOperationDelete() {
summary = "Delete an existing " + this.schemaName;
description = "Delete an existing " + this.schemaName+
" (more information in " +this.schemaURI+")";
description = "Delete an existing " + this.schemaName +
" (more information in " + this.schemaURI + ")";

//Set the response
apiResponses
.addApiResponse("202", new ApiResponse()
.description("Deleted"))
.addApiResponse("404", new ApiResponse()
.description("Not Found"));

}

}
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