From 2cbc2e45a74eb8cf8040f9a71636289ca2db5241 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Thu, 19 Mar 2015 14:50:29 +0000 Subject: [PATCH] JAL-1668 finally clean up --- src/jalview/ws/dbsources/PDBRestClient.java | 106 ++++++++++++++++----------- src/jalview/ws/uimodel/PDBRestRequest.java | 5 ++ src/jalview/ws/uimodel/PDBRestResponse.java | 22 ++++-- 3 files changed, 82 insertions(+), 51 deletions(-) diff --git a/src/jalview/ws/dbsources/PDBRestClient.java b/src/jalview/ws/dbsources/PDBRestClient.java index 039d23f..1ab6125 100644 --- a/src/jalview/ws/dbsources/PDBRestClient.java +++ b/src/jalview/ws/dbsources/PDBRestClient.java @@ -23,16 +23,24 @@ import com.sun.jersey.api.client.config.ClientConfig; import com.sun.jersey.api.client.config.DefaultClientConfig; import com.sun.jersey.api.json.JSONConfiguration; +/** + * A rest client for querying the Search endpoing of the PDB REST API + * + * @author tcnofoegbu + * + */ public class PDBRestClient { - private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?"; + private static String PDB_SEARCH_ENDPOINT = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?"; + + private static int DEFAULT_RESPONSE_SIZE = 200; /** * Takes a PDBRestRequest object and returns a response upon execution * * @param pdbRestRequest - * the pdbRequest to be sent - * @return the pdbResponse object for the given pdbRequest + * the PDBRestRequest instance to be processed + * @return the pdbResponse object for the given request */ public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest) { @@ -41,45 +49,52 @@ public class PDBRestClient Boolean.TRUE); Client client = Client.create(clientConfig); - String query = pdbRestRequest.getFieldToSearchBy() - + pdbRestRequest.getSearchTerm() - + ((pdbRestRequest.isAllowEmptySeq()) ? "" - : " AND molecule_sequence:['' TO *]"); - String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest .getWantedFields()); - - String responseSize = (pdbRestRequest.getResponseSize() == 0) ? "200" - : String.valueOf(pdbRestRequest.getResponseSize()); + int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE + : pdbRestRequest.getResponseSize(); String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest - .getFieldToSortBy().trim().isEmpty()) ? "" - : (pdbRestRequest + .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc" : " desc")); - WebResource webResource = client.resource(pdbSearchEndpoint) + // Build request parameters for the REST Request + WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT) .queryParam("wt", "json").queryParam("fl", wantedFields) - .queryParam("rows", responseSize) - .queryParam("q", query) + .queryParam("rows", String.valueOf(responseSize)) + .queryParam("q", pdbRestRequest.getQuery()) .queryParam("sort", sortParam); + + // Execute the REST request ClientResponse clientResponse = webResource.accept( MediaType.APPLICATION_JSON).get(ClientResponse.class); + // Get the JSON string from the response object String responseString = clientResponse.getEntity(String.class); + + // Check the response status and report exception if one occurs if (clientResponse.getStatus() != 200) { + String errorMessage = ""; if (clientResponse.getStatus() == 400) { - throw new RuntimeException(parseJsonExceptionString(responseString)); + errorMessage = parseJsonExceptionString(responseString); + throw new RuntimeException(errorMessage); } else { - throw new RuntimeException("Failed : HTTP error code : " - + clientResponse.getStatus()); + errorMessage = "Failed : HTTP error code : " + + clientResponse.getStatus(); + throw new RuntimeException(errorMessage); } } + + // Make redundant objects eligible for garbage collection to conserve + // memory clientResponse = null; client = null; + + // Process the response and return the result to the caller. return parsePDBJsonResponse(responseString, pdbRestRequest); } @@ -87,8 +102,8 @@ public class PDBRestClient * Process error response from PDB server if/when one occurs. * * @param jsonResponse - * the json string containing error message from the server - * @return the processed error message from the json string + * the JSON string containing error message from the server + * @return the processed error message from the JSON string */ public static String parseJsonExceptionString(String jsonErrorResponse) { @@ -111,21 +126,20 @@ public class PDBRestClient } /** - * Parses json response string from PDB REST API to a PDBRestResponse - * instance. The parsed response is dynamic and based upon some of the request - * parameters. + * Parses the JSON response string from PDB REST API. The response is dynamic + * hence, only fields specifically requested for in the 'wantedFields' + * parameter is fetched/processed * * @param pdbJsonResponseString - * the json string to be parsed + * the JSON string to be parsed * @param pdbRestRequest * the request object which contains parameters used to process the - * json string + * JSON string * @return */ @SuppressWarnings("unchecked") public static PDBRestResponse parsePDBJsonResponse( - String pdbJsonResponseString, - PDBRestRequest pdbRestRequest) + String pdbJsonResponseString, PDBRestRequest pdbRestRequest) { PDBRestResponse searchResult = new PDBRestResponse(); List result = null; @@ -148,7 +162,8 @@ public class PDBRestClient .hasNext();) { JSONObject doc = docIter.next(); - result.add(searchResult.new PDBResponseSummary(doc, pdbRestRequest)); + result.add(searchResult.new PDBResponseSummary(doc, + pdbRestRequest)); } searchResult.setNumberOfItemsFound(numFound); searchResult.setResponseTime(queryTime); @@ -162,11 +177,12 @@ public class PDBRestClient } /** - * Takes a collection of PDBDocField and converts its code values into a comma - * delimited string. + * Takes a collection of PDBDocField and converts its 'code' Field values into + * a comma delimited string. * * @param pdbDocfields - * @return + * the collection of PDBDocField to process + * @return the comma delimited string from the pdbDocFields collection */ public static String getPDBDocFieldsAsCommaDelimitedString( Collection pdbDocfields) @@ -179,7 +195,7 @@ public class PDBRestClient { returnedFields.append(",").append(field.getCode()); } - returnedFields.deleteCharAt(0); + returnedFields.deleteCharAt(0); result = returnedFields.toString(); } return result; @@ -197,14 +213,16 @@ public class PDBRestClient public static int getPDBIdColumIndex( Collection wantedFeilds, boolean hasRefSeq) { - int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; // If a reference sequence is - // attached then start counting from - // 1 else start from zero + + // If a reference sequence is attached then start counting from 1 else + // start from zero + int pdbFeildIndexCounter = hasRefSeq ? 1 : 0; + for (PDBDocField feild : wantedFeilds) { if (feild.equals(PDBDocField.PDB_ID)) { - break; // once PDB Id index is determined exit iteration + break; // Once PDB Id index is determined exit iteration } ++pdbFeildIndexCounter; } @@ -212,7 +230,7 @@ public class PDBRestClient } /** - * Represents the fields retrievable from a PDB Document response + * This enum represents the fields available in the PDB JSON response * */ public enum PDBDocField @@ -252,14 +270,14 @@ public class PDBRestClient "Max observed residues", "max_observed_residues"), ORG_SCI_NAME( "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM( "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH( - "Crystallisation Ph", "crystallisation_ph"), BIO_FUNCTION( - "Biological Function", "biological_function"), BIO_PROCESS( - "Biological Process", "biological_process"), BIO_CELL_COMP( + "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION( + "Biological Function", "biological_function"), BIOLOGICAL_PROCESS( + "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT( "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME( "Compound Name", "compound_name"), COMPOUND_ID("Compound Id", "compound_id"), COMPOUND_WEIGHT("Compound Weight", - "compound_weight"), COMP_SYS_NAME("Compound Systematic Name", - "compound_systematic_name"), INTERACTING_LIG( + "compound_weight"), COMPOUND_SYSTEMATIC_NAME( + "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG( "Interacting Ligands", "interacting_ligands"), JOURNAL( "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE( "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL( @@ -317,4 +335,4 @@ public class PDBRestClient return name; } } -} +} \ No newline at end of file diff --git a/src/jalview/ws/uimodel/PDBRestRequest.java b/src/jalview/ws/uimodel/PDBRestRequest.java index 2b9a7f3..70dae0b 100644 --- a/src/jalview/ws/uimodel/PDBRestRequest.java +++ b/src/jalview/ws/uimodel/PDBRestRequest.java @@ -127,4 +127,9 @@ public class PDBRestRequest this.associatedSequence = associatedSequence; } + public String getQuery() + { + return fieldToSearchBy + searchTerm + + (isAllowEmptySeq() ? "" : " AND molecule_sequence:['' TO *]"); + } } diff --git a/src/jalview/ws/uimodel/PDBRestResponse.java b/src/jalview/ws/uimodel/PDBRestResponse.java index fb227ee..7f570a4 100644 --- a/src/jalview/ws/uimodel/PDBRestResponse.java +++ b/src/jalview/ws/uimodel/PDBRestResponse.java @@ -77,8 +77,8 @@ public class PDBRestResponse /** - * Convenience method to obtain a Table model for a given summary List and - * request + * Convenience method to obtain a Table model for a given summary List based + * on the request parameters * * @param request * the PDBRestRequest object which holds useful information for @@ -115,8 +115,6 @@ public class PDBRestResponse /** * Model for a unique response summary * - * @author tcnofoegbu - * */ public class PDBResponseSummary { @@ -126,7 +124,7 @@ public class PDBRestResponse private String associatedSequence; - public PDBResponseSummary(JSONObject doc, PDBRestRequest request) + public PDBResponseSummary(JSONObject pdbJsonDoc, PDBRestRequest request) { Collection diplayFields = request.getWantedFields(); String associatedSeq = request.getAssociatedSequence(); @@ -143,10 +141,11 @@ public class PDBRestResponse for (PDBDocField field : diplayFields) { - String fieldData = (doc.get(field.getCode()) == null) ? "" : doc + String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? "" + : pdbJsonDoc .get(field.getCode()).toString(); if (field.equals(PDBDocField.PDB_ID) - && doc.get(PDBDocField.PDB_ID.getCode()) != null) + && pdbJsonDoc.get(PDBDocField.PDB_ID.getCode()) != null) { this.pdbId = fieldData; summaryRowData[colCounter++] = this.pdbId; @@ -178,6 +177,9 @@ public class PDBRestResponse this.summaryRowData = summaryData; } + /** + * Returns a string representation of this object; + */ @Override public String toString() { @@ -189,12 +191,18 @@ public class PDBRestResponse return summaryFieldValues.toString(); } + /** + * Returns hash code value for this object + */ @Override public int hashCode() { return Objects.hash(this.pdbId, this.toString()); } + /** + * Indicates whether some object is equal to this one + */ @Override public boolean equals(Object that) { -- 1.7.10.2