Merge pull request #5 from EGI-Federation/parser-esrf

Implemented ESRF parsing

.github/linters/sun_checks.xml

@@ -118,12 +118,14 @@
     <module name="ConstantName"/>
     <module name="LocalFinalVariableName"/>
     <module name="LocalVariableName"/>
-    <module name="MemberName"/>
     <module name="MethodName"/>
     <module name="PackageName"/>
     <module name="ParameterName"/>
     <module name="StaticVariableName"/>
     <module name="TypeName"/>
+    <!--
+    <module name="MemberName"/>
+    -->
 
     <!-- Checks for imports                              -->
     <!-- See https://checkstyle.org/config_imports.html -->
@@ -178,13 +180,13 @@
     <module name="EqualsHashCode"/>
     <module name="IllegalInstantiation"/>
     <module name="InnerAssignment"/>
-    <module name="MissingSwitchDefault"/>
     <module name="MultipleVariableDeclarations"/>
     <module name="SimplifyBooleanExpression"/>
     <module name="SimplifyBooleanReturn"/>
     <!--
     <module name="MagicNumber"/>
     <module name="HiddenField"/>
+    <module name="MissingSwitchDefault"/>
     -->
 
     <!-- Checks for class design                         -->

src/main/java/eosc/eu/ActionError.java

@@ -14,6 +14,7 @@
 import javax.ws.rs.core.Response.Status;
 
 import parser.b2share.B2ShareException;
+import parser.esrf.EsrfException;
 import parser.zenodo.ZenodoException;
 import egi.fts.FileTransferServiceException;
 
@@ -48,6 +49,7 @@ public class ActionError {
 
     /**
      * Copy constructor does deep copy
+     * @param error Error to copy
      */
     public ActionError(ActionError error) {
 
@@ -67,6 +69,8 @@ public ActionError(ActionError error) {
 
     /**
      * Copy but change id
+     * @param error Error to copy
+     * @param newId New error id
      */
     public ActionError(ActionError error, String newId) {
         this(error);
@@ -75,6 +79,7 @@ public ActionError(ActionError error, String newId) {
 
     /**
      * Construct with error id
+     * @param id Error id
      */
     public ActionError(String id) {
         this.id = id;
@@ -84,6 +89,8 @@ public ActionError(String id) {
 
     /**
      * Construct with error id and description
+     * @param id Error id
+     * @param description Error description
      */
     public ActionError(String id, String description) {
         this.id = id;
@@ -93,13 +100,17 @@ public ActionError(String id, String description) {
 
     /**
      * Construct with error id and detail
+     * @param id Error id
+     * @param detail Key-value pair to add to the details of the error
      */
     public ActionError(String id, Tuple2<String, String> detail) {
         this(id, Arrays.asList(detail));
     }
 
     /**
      * Construct with error id and details
+     * @param id Error id
+     * @param details Key-value pairs to add to the details of the error
      */
     public ActionError(String id, List<Tuple2<String, String>> details) {
         this.id = id;
@@ -115,13 +126,19 @@ public ActionError(String id, List<Tuple2<String, String>> details) {
 
     /**
      * Construct with error id, description, and detail
+     * @param id Error id
+     * @param description Error description
+     * @param detail Key-value pair to add to the details of the error
      */
     public ActionError(String id, String description, Tuple2<String, String> detail) {
         this(id, description, Arrays.asList(detail));
     }
 
     /**
      * Construct with error id, description, and details
+     * @param id Error id
+     * @param description Error description
+     * @param details Key-value pairs to add to the details of the error
      */
     public ActionError(String id, String description, List<Tuple2<String, String>> details) {
         this.id = id;
@@ -137,6 +154,7 @@ public ActionError(String id, String description, List<Tuple2<String, String>> d
 
     /**
      * Construct from exception
+     * @param t The exception to wrap
      */
     public ActionError(Throwable t) {
         this.id = "exception";
@@ -151,6 +169,7 @@ public ActionError(Throwable t) {
         var type = t.getClass();
         if (type.equals(ZenodoException.class) ||
             type.equals(B2ShareException.class) ||
+            type.equals(EsrfException.class) ||
             type.equals(FileTransferServiceException.class) ||
             type.equals(ClientWebApplicationException.class) ||
             type.equals(WebApplicationException.class) ) {
@@ -217,13 +236,17 @@ else if(type.equals(ProcessingException.class)) {
 
     /**
      * Construct from exception and detail
+     * @param t The exception to wrap
+     * @param detail Key-value pair to add to the details of the error
      */
     public ActionError(Throwable t, Tuple2<String, String> detail) {
         this(t, Arrays.asList(detail));
     }
 
     /**
      * Construct from exception and details
+     * @param t The exception to wrap
+     * @param details Key-value pair to add to the details of the error
      */
     public ActionError(Throwable t, List<Tuple2<String, String>> details) {
         this(t);
@@ -265,13 +288,16 @@ else if(keys.contains("seUrl"))
 
     /**
      * Retrieve the HTTP status code
+     * @return HTTP status code
      */
     public Status getStatus() {
         return this.status;
     }
 
     /**
      * Update the HTTP status code
+     * @param status New HTTP status
+     * @return Instance to allow for fluent calls (with .)
      */
     public ActionError setStatus(Status status) {
         this.status = status;
@@ -280,13 +306,16 @@ public ActionError setStatus(Status status) {
 
     /**
      * Convert to Response that can be returned by a REST endpoint
+     * @return Response object
      */
     public Response toResponse() {
         return Response.ok(this).status(this.status).build();
     }
 
     /**
      * Convert to Response with new status that can be returned by a REST endpoint
+     * @param status New HTTP status
+     * @return Response object with new HTTP status code
      */
     public Response toResponse(Status status) {
         return Response.ok(this).status(status).build();

src/main/java/eosc/eu/model/StorageElement.java

@@ -9,6 +9,7 @@
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import parser.zenodo.model.ZenodoFile;
 import parser.b2share.model.B2ShareFile;
+import parser.esrf.model.EsrfDataFile;
 import egi.fts.model.ObjectInfo;
 
 
@@ -55,7 +56,9 @@ public class StorageElement extends StorageElementBase {
     public StorageElement() { super("StorageElement"); }
 
     /**
-     * Constructor
+     * Construct using access URL and media type
+     * @param url Access URL for the storage element
+     * @param type Media type
      */
     public StorageElement(String url, String type) {
         super("StorageElement");
@@ -65,6 +68,7 @@ public StorageElement(String url, String type) {
 
     /**
      * Construct from Zenodo file
+     * @param zf Zenodo file
      */
     public StorageElement(ZenodoFile zf) {
         super("StorageElement", zf.filename);
@@ -76,8 +80,27 @@ public StorageElement(ZenodoFile zf) {
         }
     }
 
+    /**
+     * Construct from ESRF file
+     * @param ef ESRF file
+     * @param baseUrl The base URL for the access URL, as the ESRF file
+     *                only contains the path to the file
+     */
+    public StorageElement(EsrfDataFile ef, String baseUrl) {
+        super("StorageElement", ef.Datafile.name);
+        this.size = ef.Datafile.fileSize;
+        this.accessUrl = baseUrl + ef.Datafile.location;
+
+        if(null != ef.Datafile.createTime)
+            this.createdAt = ef.Datafile.createTime;
+
+        if(null != ef.Datafile.modTime)
+            this.modifiedAt = ef.Datafile.modTime;
+    }
+
     /**
      * Construct from B2Share file
+     * @param b2sf B2SHARE file
      */
     public StorageElement(B2ShareFile b2sf) {
         super("StorageElement", b2sf.name);
@@ -94,6 +117,7 @@ public StorageElement(B2ShareFile b2sf) {
 
     /**
      * Construct from FTS object
+     * @param obj Information about an object returned by FTS
      */
     public StorageElement(ObjectInfo obj) {
         super("StorageElement");

src/main/java/parser/b2share/B2ShareException.java

@@ -15,10 +15,19 @@ public B2ShareException() {
         super();
     }
 
+    /***
+     * Construct from a response
+     * @param resp Response object
+     * @param body Response body
+     */
     public B2ShareException(Response resp, String body) {
         super(resp);
         this.responseBody = body;
     }
 
+    /***
+     * Get the response body
+     * @return Body of the response
+     */
     String responseBody() { return responseBody; }
 }

src/main/java/parser/b2share/B2ShareParser.java

@@ -37,6 +37,7 @@ public class B2ShareParser implements ParserService {
 
     /***
      * Constructor
+     * @param id The key of the parser in the config file
      */
     public B2ShareParser(String id) { this.id = id; }
 
@@ -47,7 +48,6 @@ public class B2ShareParser implements ParserService {
      * @return true on success
      */
     public boolean init(ParserConfig config, PortConfig port) {
-
         this.name = config.name();
         this.timeout = config.timeout();
 
@@ -122,7 +122,8 @@ else if(!doi.equals(redirectedToUrl))
                     LOG.debugf("Redirected DOI %s", redirectedToUrl);
 
                 // Validate URL
-                Pattern p = Pattern.compile("^(https?://[^/:]*b2share[^/:]*:?[\\d]*)/records/(.+)", Pattern.CASE_INSENSITIVE);
+                Pattern p = Pattern.compile("^(https?://[^/:]*b2share[^/:]*:?[\\d]*)/records/(.+)",
+                                            Pattern.CASE_INSENSITIVE);
                 Matcher m = p.matcher(redirectedToUrl);
                 boolean isSupported = m.matches();
 

src/main/java/parser/esrf/Esrf.java

@@ -0,0 +1,38 @@
+package parser.esrf;
+
+import io.smallrye.mutiny.Uni;
+import org.eclipse.microprofile.rest.client.annotation.RegisterProvider;
+
+import javax.ws.rs.*;
+import javax.ws.rs.core.MediaType;
+
+import org.jboss.resteasy.reactive.RestPath;
+import org.jboss.resteasy.reactive.RestQuery;
+import parser.esrf.model.*;
+
+import java.util.List;
+
+
+/***
+ * REST client for ESRF
+ */
+@RegisterProvider(value = EsrfExceptionMapper.class)
+@Produces(MediaType.APPLICATION_JSON)
+public interface Esrf {
+
+    @POST
+    @Path("/session")
+    @Consumes(MediaType.APPLICATION_JSON)
+    Uni<EsrfSession> getSessionAsync(EsrfCredentials credentials);
+
+    @GET
+    @Path("/doi/{authority}/{recordId}/datasets")
+    Uni<List<EsrfDataSet>> getDataSetsAsync(@RestQuery("sessionId") String sessionId,
+                                            @RestPath("authority") String authority,
+                                            @RestPath("recordId") String recordId);
+
+    @GET
+    @Path("/catalogue/{sessionId}/dataset/id/{datasetId}/datafile")
+    Uni<List<EsrfDataFile>> getDataFilesAsync(@RestPath("sessionId") String sessionId,
+                                              @RestPath("datasetId") String datasetId);
+}

src/main/java/parser/esrf/EsrfException.java

@@ -0,0 +1,33 @@
+package parser.esrf;
+
+import javax.ws.rs.WebApplicationException;
+import javax.ws.rs.core.Response;
+
+
+/**
+ * Exception class for ESRF API calls
+ */
+public class EsrfException extends WebApplicationException {
+
+    private String responseBody;
+
+    public EsrfException() {
+        super();
+    }
+
+    /***
+     * Construct from a response
+     * @param resp Response object
+     * @param body Response body
+     */
+    public EsrfException(Response resp, String body) {
+        super(resp);
+        this.responseBody = body;
+    }
+
+    /***
+     * Get the response body
+     * @return Body of the response
+     */
+    String responseBody() { return responseBody; }
+}