feat(docs): improve documentation and configuration (#20)

* fix: refactoring oba main class

create multiples methods and comments

* Add relation configuration

* feat(docs): improve documentation

README.md

@@ -15,3 +15,25 @@ More information at [OpenAPI Specification | Swagger](https://swagger.io/specifi
 ### OWL
 
 The W3C Web Ontology Language (OWL) is a Semantic Web language designed to represent rich and complex knowledge about things, groups of things, and relations between things. OWL is a computational logic-based language such that knowledge expressed in **OWL can be exploited by computer programs**, e.g., to verify the consistency of that knowledge or to make implicit knowledge explicit. OWL documents, known as ontologies, can be published in the World Wide Web 
+
+## Features
+- [x] Generate an OpenAPI specification from multiple ontologies (OWL).
+    - [x] Convert to OWL Classes to OpenAPI schemas.
+    - [x] Create paths (GET, POST, DELETE, PUT) for each schema.
+    - [x] Read an OpenAPI base file with the description, documentation and servers of the API.
+- [x] Generate a Python server ready to use:
+    - [x] Use [OpenAPITools/openapi-generator](https://github.com/OpenAPITools/openapi-generator/) to generate the Python server.
+    - [x] Automatically, generate the controller code (methods) using [Mustache Template](https://github.com/OpenAPITools/openapi-generator/wiki/Mustache-Template-Variables)
+    - [x] Use authentication using Firebase. 
+       - The user can read any graph.
+       - The user can write his/her graph.
+    - [x] Run the queries (these are SPARQL queries are autogenerated):
+       - [x] Get a resource from any graph (e.g., `GET /models/id`)
+       - [x] Get all the resources with a specified type from any graph. (e.g., `GET /models`)
+       - [x] Delete a resource from his/her graph. (e.g., `DELETE /models/id`)
+       - [x] Create (POST) a resource from his/her graph. (e.g., `POST /models`)
+       - [x] Update (PUT) a resource from his/her graph. (e.g., `PUT /models/id`)
+       - [ ] Get a resource related to another resource from any graph (e.g., `GET /models/id/parameters`)
+     - [x] Obtain the results from the endpoint as JSON or JSON/LD.
+- [x] Selected the paths to be created
+

config.yaml

@@ -10,3 +10,21 @@ ontologies:
 name: modelcatalog
 output_dir: outputs
 openapi_base: modelcatalog_info.yaml
+
+endpoint:
+  url: http://endpoint.mint.isi.edu/modelCatalog-1.2.0
+  prefix: https://w3id.org/okn/i/mint/
+  graph_base: http://ontosoft.isi.edu:3030/modelCatalog-1.2.0/data/
+
+firebase:
+  key:
+
+relations:
+    ModelConfiguration:
+      - predicate: hasInput
+        path: inputs
+      - predicate: hasOutput
+        path: outputs
+    Setup:
+      - predicate: hasInput
+        path: inputs

src/main/java/edu/isi/oba/Mapper.java

@@ -1,14 +1,12 @@
 package edu.isi.oba;
 
+import edu.isi.oba.config.RelationConfig;
 import io.swagger.v3.oas.models.Paths;
 import io.swagger.v3.oas.models.media.Schema;
 import io.swagger.v3.oas.models.media.StringSchema;
 import io.swagger.v3.oas.models.media.XML;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.*;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
-import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory;
 import org.semanticweb.owlapi.util.DefaultPrefixManager;
 
 import java.io.IOException;
@@ -24,14 +22,18 @@ class Mapper {
   public String ont_prefix;
   List<String> selected_paths;
 
-  public Mapper(String ont_url, String ont_prefix, Map<String, String> prefixes, List<String> paths) throws OWLOntologyCreationException, IOException {
+  public Mapper(String ont_url, String ont_prefix, Map<String, String> prefixes,
+                List<String> paths, Map<String, List<RelationConfig>> relations)
+          throws OWLOntologyCreationException, IOException {
     OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
     OWLOntology ontology = manager.loadOntology(IRI.create(ont_url));
     OWLDocumentFormat format = manager.getOntologyFormat(ontology);
     this.selected_paths = paths;
     this.ont_prefix = ont_prefix;
     setPrefixes(format, prefixes);
-    schemas = this.createSchemas(ontology);
+    schemas = this.createSchemas(ontology, relations);
+
+
   }
 
   /**
@@ -56,9 +58,10 @@ private void setPrefixes(OWLDocumentFormat format, Map<String, String> prefixes)
    * The schemas includes the properties
    *
    * @param ontology  Represents an OWL 2 ontology
+   * @param relations
    * @return schemas
    */
-  private Map<String, Schema> createSchemas(OWLOntology ontology) {
+  private Map<String, Schema> createSchemas(OWLOntology ontology, Map<String, List<RelationConfig>> relations) {
     Set<OWLClass> classes;
     classes = ontology.   getClassesInSignature();
     Map<String, Schema> schemas = new HashMap<>();
@@ -92,6 +95,14 @@ private Map<String, Schema> createSchemas(OWLOntology ontology) {
           Schema schema = mapperSchema.getSchema();
           schemas.put(schema.getName(), schema);
 
+
+          //obtain the relations
+//          List<RelationConfig> model_relations = relations.get(mapperSchema.name);
+//          for (RelationConfig model_relation : model_relations){
+//              add_path_relation(pathGenerator, model_relation.getSubject(), model_relation.getPredicate(), model_relation.getPath());
+//          }
+
+
           if (this.selected_paths == null){
             add_path(pathGenerator, mapperSchema);
           } else {
@@ -134,4 +145,10 @@ private void add_path(Path pathGenerator, MapperSchema mapperSchema) {
     this.paths.addPathItem(singular_name, pathGenerator.generate_singular(mapperSchema.name));
   }
 
+  private void add_path_relation(Path pathGenerator, String schema_name, String predicate, String path) {
+    String relation = "/" + schema_name.toLowerCase() + "s/{id}/" + path;
+    this.paths.addPathItem(relation, pathGenerator.generate_plural(schema_name));
+
+  }
+
 }

src/main/java/edu/isi/oba/Oba.java

@@ -1,5 +1,8 @@
 package edu.isi.oba;
 
+import edu.isi.oba.config.OntologyConfig;
+import edu.isi.oba.config.RelationConfig;
+import edu.isi.oba.config.YamlConfig;
 import io.swagger.v3.oas.models.OpenAPI;
 import io.swagger.v3.parser.OpenAPIV3Parser;
 import org.apache.commons.io.FileUtils;
@@ -8,83 +11,102 @@
 import org.yaml.snakeyaml.constructor.Constructor;
 
 import java.io.*;
-import java.net.URI;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+
 import org.apache.commons.cli.*;
 
 class Oba {
 
   public static void main(String[] args) throws Exception {
-          Options options = new Options();
-          Option input = new Option("c", "config", true, "configuration file path");
-          input.setRequired(true);
-          options.addOption(input);
-
-
-          CommandLineParser parser = new DefaultParser();
-          HelpFormatter formatter = new HelpFormatter();
-          CommandLine cmd;
-          String config_yaml = null;
-
-
-          try {
-            cmd = parser.parse(options, args);
-            config_yaml = cmd.getOptionValue("config");
-          } catch (ParseException e) {
-            System.out.println(e.getMessage());
-            formatter.printHelp("utility-name", options);
-            System.exit(1);
-          }
-          Constructor constructor = new Constructor(YamlConfig.class);
-          Yaml yaml = new Yaml( constructor );
-
-          InputStream config_input = null;
-          try {
-            config_input = new FileInputStream(new File(config_yaml));
-          } catch (FileNotFoundException e) {
-            System.err.println("Configuration file not found: " + config_yaml);
-          }
-          YamlConfig data = yaml.loadAs( config_input, YamlConfig.class );
-
-          OpenAPI openapi_base = new OpenAPIV3Parser().read(data.getOpenapi_base());
-
+    //parse command line
+    String config_yaml = get_config_yaml(args);
+    //read the config yaml from command line
+    YamlConfig data = get_yaml_data(config_yaml);
+    //read ontologies and get schema and paths
+    List<Mapper> mappers = get_mappers(data);
+    //get base of openapi
+    OpenAPI openapi_base = new OpenAPIV3Parser().read(data.getOpenapi_base());
+    //obtain the output directory to write the openapi specification
+    String dir = data.getOutput_dir() + File.separator + data.getName();
+    //write the openapi specification
+    generate_openapi_spec(openapi_base, mappers, dir);
+  }
 
-          Map<String, OntologyConfig> ontologies = data.getOntologies();
-          List<Mapper> mappers = new ArrayList<>();
-          List<String> paths = data.getPaths();
-          String dir = data.getOutput_dir() + File.separator + data.getName() ;
+  private static List<Mapper> get_mappers(YamlConfig data) throws OWLOntologyCreationException, IOException {
+    Map<String, OntologyConfig> ontologies = data.getOntologies();
+    List<Mapper> mappers = new ArrayList<>();
+    List<String> paths = data.getPaths();
+    Map<String, List<RelationConfig>> relations = data.getRelations();
+    for (Map.Entry<String, OntologyConfig> entry : ontologies.entrySet()) {
+      OntologyConfig ontology = entry.getValue();
+      Mapper mapper = extract_info(ontology.getXmlUrl(), ontology.getPrefix(), ontology.getPrefixUri(), paths, relations);
+      mappers.add(mapper);
+    }
+    return mappers;
+  }
 
-          for (Map.Entry<String, OntologyConfig> entry : ontologies.entrySet()) {
-            OntologyConfig ontology = entry.getValue();
-            Mapper mapper = extract_info(ontology.getXmlUrl(), ontology.getPrefix(), ontology.getPrefixUri(), paths);
-            mappers.add(mapper);
-          }
-          String fileName = dir;
-          Path destinationProject = Paths.get(fileName);
-          Path baseProject = Paths.get("./tools/base_project/");
-          if (Files.exists(destinationProject)){
-            System.err.println("The destination project exists");
-          }
-          FileUtils.copyDirectory(baseProject.toFile(), destinationProject.toFile());
-          Serializer serializer = new Serializer(mappers, destinationProject, openapi_base);
+  private static void generate_openapi_spec(OpenAPI openapi_base, List<Mapper> mappers, String dir) throws IOException {
+    String fileName = dir;
+    Path destinationProject = Paths.get(fileName);
+    Path baseProject = Paths.get("./tools/base_project/");
+    if (Files.exists(destinationProject)) {
+      System.err.println("The destination project exists");
+    }
+    FileUtils.copyDirectory(baseProject.toFile(), destinationProject.toFile());
+    Serializer serializer = new Serializer(mappers, destinationProject, openapi_base);
+
+    Path destinationQueries = Paths.get(destinationProject + "/.openapi-generator/template/static_files/queries/");
+    Path sourceQueries = Paths.get("queries");
+    FileUtils.copyDirectory(sourceQueries.toFile(), destinationQueries.toFile());
+  }
 
-          Path destinationQueries = Paths.get(destinationProject + "/.openapi-generator/template/static_files/queries/");
-          Path sourceQueries = Paths.get("queries");
-          FileUtils.copyDirectory(sourceQueries.toFile(), destinationQueries.toFile());
+  private static YamlConfig get_yaml_data(String config_yaml) {
+    Constructor constructor = new Constructor(YamlConfig.class);
+    Yaml yaml = new Yaml(constructor);
+
+    InputStream config_input = null;
+    try {
+      config_input = new FileInputStream(new File(config_yaml));
+    } catch (FileNotFoundException e) {
+      System.err.println("Configuration file not found: " + config_yaml);
+    }
+    //Yaml config parse
+    return yaml.loadAs(config_input, YamlConfig.class);
+  }
 
+  private static String get_config_yaml(String[] args) {
+    //obtain the options to pass configuration
+    Options options = new Options();
+    Option input = new Option("c", "config", true, "configuration file path");
+    input.setRequired(true);
+    options.addOption(input);
+
+    CommandLineParser parser = new DefaultParser();
+    HelpFormatter formatter = new HelpFormatter();
+    CommandLine cmd;
+    String config_yaml = null;
+
+    try {
+      cmd = parser.parse(options, args);
+      config_yaml = cmd.getOptionValue("config");
+    } catch (ParseException e) {
+      System.out.println(e.getMessage());
+      formatter.printHelp("utility-name", options);
+      System.exit(1);
+    }
+    return config_yaml;
   }
 
 
-        public static Mapper extract_info(String ont_serialization_url, String ont_prefix, String ont_uri, List<String> paths) throws OWLOntologyCreationException, IOException {
-          Map<String, String> prefixes = new HashMap<>();
-          prefixes.put(ont_prefix, ont_uri);
-          return new Mapper(ont_serialization_url, ont_prefix, prefixes, paths);
-        }
+  public static Mapper extract_info(String ont_serialization_url, String ont_prefix, String ont_uri, List<String> paths, Map<String, List<RelationConfig>> relations) throws OWLOntologyCreationException, IOException {
+    Map<String, String> prefixes = new HashMap<>();
+    prefixes.put(ont_prefix, ont_uri);
+    return new Mapper(ont_serialization_url, ont_prefix, prefixes, paths, relations);
+  }
 }

src/main/java/edu/isi/oba/Path.java

@@ -40,6 +40,7 @@ public PathItem generate_plural(String schemaName){
 
   }
 
+
   public PathItem user_login() {
     List<Parameter> parameters = new ArrayList<>();
     ApiResponses apiResponses = new ApiResponses();

src/main/java/edu/isi/oba/config/EndpointConfig.java

@@ -0,0 +1,31 @@
+package edu.isi.oba.config;
+
+public class EndpointConfig {
+  public String url;
+  public String prefix;
+  public String graph_base;
+
+  public String getUrl() {
+    return url;
+  }
+
+  public void setUrl(String url) {
+    this.url = url;
+  }
+
+  public String getPrefix() {
+    return prefix;
+  }
+
+  public void setPrefix(String prefix) {
+    this.prefix = prefix;
+  }
+
+  public String getGraph_base() {
+    return graph_base;
+  }
+
+  public void setGraph_base(String graph_base) {
+    this.graph_base = graph_base;
+  }
+}

src/main/java/edu/isi/oba/config/FirebaseConfig.java

@@ -0,0 +1,14 @@
+package edu.isi.oba.config;
+
+public class FirebaseConfig {
+  private String key;
+
+  public String getKey() {
+    return key;
+  }
+
+  public void setKey(String key) {
+    this.key = key;
+  }
+}
+

src/main/java/edu/isi/oba/OntologyConfig.java → src/main/java/edu/isi/oba/config/OntologyConfig.java

@@ -1,7 +1,8 @@
-package edu.isi.oba;
+package edu.isi.oba.config;
 
 import java.util.List;
 
+
 public class OntologyConfig {
   private String xmlUrl;
   private String prefix;
@@ -32,3 +33,4 @@ public void setPrefixUri(String prefixUri) {
   }
 }
 
+

src/main/java/edu/isi/oba/config/RelationConfig.java

@@ -0,0 +1,33 @@
+package edu.isi.oba.config;
+
+public class RelationConfig {
+  public String getSubject() {
+    return subject;
+  }
+
+  public void setSubject(String subject) {
+    this.subject = subject;
+  }
+
+  public String getPath() {
+    return path;
+  }
+
+  public void setPath(String path) {
+    this.path = path;
+  }
+
+  public String getPredicate() {
+    return predicate;
+  }
+
+  public void setPredicate(String predicate) {
+    this.predicate = predicate;
+  }
+
+  private String subject;
+  private String path;
+  private String predicate;
+
+
+}