X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fthreedbeacons%2FTDBeaconsFTSRestClient.java;h=c275bda4ab0f2c6285db3cc07c9298aea5a44e8f;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=e6d45e5a07de9d65b5967413ba111d1421229175;hpb=f640efee12150d1ae174c64c936f4630716cb7c4;p=jalview.git diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java index e6d45e5..c275bda 100644 --- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java +++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.fts.service.threedbeacons; import java.net.URI; @@ -6,7 +26,6 @@ import java.util.Collection; import java.util.Iterator; import java.util.List; import java.util.Map; -import java.util.Objects; import javax.ws.rs.core.MediaType; @@ -21,25 +40,36 @@ import jalview.datamodel.SequenceI; import jalview.fts.api.FTSData; import jalview.fts.api.FTSDataColumnI; import jalview.fts.api.FTSRestClientI; +import jalview.fts.api.StructureFTSRestClientI; +import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; import jalview.fts.core.FTSRestClient; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; -import jalview.fts.service.pdb.PDBFTSRestClient; import jalview.util.JSONUtils; import jalview.util.MessageManager; import jalview.util.Platform; public class TDBeaconsFTSRestClient extends FTSRestClient + implements StructureFTSRestClientI { - private static final String DEFAULT_THREEDBEACONS_DOMAIN = - "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/"; - - private static FTSRestClientI instance = null; - + /** + * production server URI + */ + private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/"; + + /** + * dev server URI + */ + private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/"; + + private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API; + + public static FTSRestClientI instance = null; + protected TDBeaconsFTSRestClient() - { + { } - + @SuppressWarnings("unchecked") @Override public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest) @@ -47,16 +77,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient { try { - // Removed wantedFields, sortParam & facetPivot from PDBFTSRClient - String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( - tdbRestRequest.getWantedFields()); - int responseSize = (tdbRestRequest.getResponseSize() == 0) - ? getDefaultResponsePageSize() - : tdbRestRequest.getResponseSize(); - //int offSet = pdbRestRequest.getOffSet(); - - String query = tdbRestRequest.getFieldToSearchBy() - + tdbRestRequest.getSearchTerm(); + String query = tdbRestRequest.getSearchTerm(); Client client; Class clientResponseClass; if (Platform.isJS()) @@ -68,37 +89,44 @@ public class TDBeaconsFTSRestClient extends FTSRestClient else /** * Java only + * * @j2sIgnore */ { client = Client.create(new DefaultClientConfig()); clientResponseClass = ClientResponse.class; } + WebResource webResource; - webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN) - .queryParam("ac", query); -// .queryParam("rows", String.valueOf(responseSize)) -// .queryParam("P",query); + webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query); + URI uri = webResource.getURI(); - - System.out.println(uri); - + jalview.bin.Console.outPrintln(uri.toString()); + // Execute the REST request - ClientResponse clientResponse = webResource - .accept(MediaType.APPLICATION_JSON).get(clientResponseClass); - + ClientResponse clientResponse; + if (isMocked()) + { + clientResponse = null; + } + else + { + clientResponse = webResource.accept(MediaType.APPLICATION_JSON) + .get(clientResponseClass); + } + // Get the JSON string from the response object or directly from the // client (JavaScript) Map jsonObj = null; String responseString = null; - - System.out.println("query >>>>>>> " + tdbRestRequest.toString()); - + // Check the response status and report exception if one occurs - int responseStatus = clientResponse.getStatus(); + int responseStatus = isMocked() + ? (mockQueries.containsKey(query) ? 200 : 404) + : clientResponse.getStatus(); switch (responseStatus) { - // if succesful + // if success case 200: if (Platform.isJS()) { @@ -106,84 +134,106 @@ public class TDBeaconsFTSRestClient extends FTSRestClient } else { - responseString = clientResponse.getEntity(String.class); + responseString = isMocked() ? mockQueries.get(query) + : clientResponse.getEntity(String.class); } break; case 400: throw new Exception(parseJsonExceptionString(responseString)); + case 404: + return emptyTDBeaconsJsonResponse(); default: throw new Exception( getMessageByHTTPStatusCode(responseStatus, "3DBeacons")); } // Process the response and return the result to the caller. - return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest); + return parseTDBeaconsJsonResponse(responseString, jsonObj, + tdbRestRequest); } catch (Exception e) { String exceptionMsg = e.getMessage(); - if (exceptionMsg.contains("SocketException")) - { - // No internet connection - throw new Exception(MessageManager.getString( - "exception.unable_to_detect_internet_connection")); - } - else if (exceptionMsg.contains("UnknownHostException")) - { - // The server is unreachable - throw new Exception(MessageManager.formatMessage( - "exception.fts_server_unreachable", "3DB Hub")); - } - else + if (exceptionMsg != null) { - throw e; + if (exceptionMsg.contains("SocketException")) + { + // No internet connection + throw new Exception(MessageManager.getString( + "exception.unable_to_detect_internet_connection")); + } + else if (exceptionMsg.contains("UnknownHostException")) + { + // The server is unreachable + throw new Exception(MessageManager.formatMessage( + "exception.fts_server_unreachable", "3DB Hub")); + } } + throw e; + } - + } - - public String setSearchTerm() { + + /** + * returns response for when the 3D-Beacons service doesn't have a record for + * the given query - in 2.11.2 this triggers a failover to the PDBe FTS + * + * @return null + */ + private FTSRestResponse emptyTDBeaconsJsonResponse() + { return null; } - + + public String setSearchTerm(String term) + { + return term; + } + public static FTSRestResponse parseTDBeaconsJsonResponse( String tdbJsonResponseString, FTSRestRequest tdbRestRequest) { return parseTDBeaconsJsonResponse(tdbJsonResponseString, (Map) null, tdbRestRequest); } - + @SuppressWarnings("unchecked") - public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString, - Map jsonObj, FTSRestRequest tdbRestRequest) + public static FTSRestResponse parseTDBeaconsJsonResponse( + String tdbJsonResponseString, Map jsonObj, + FTSRestRequest tdbRestRequest) { FTSRestResponse searchResult = new FTSRestResponse(); - //searchResult.setNumberOfItemsFound(1); List result = null; - + try { if (jsonObj == null) { - jsonObj = (Map) JSONUtils.parse(tdbJsonResponseString); + jsonObj = (Map) JSONUtils + .parse(tdbJsonResponseString); } - //Map tdbResponse = (Map) jsonObj.get("structures"); - //String seqLength = tdbEntry.get("sequence_length").toString(); - //int seqLength = Integer.valueOf(tdbEntry.get("sequence_length").toString()); - - int seqLength = (int) ((Map) jsonObj.get("uniprot_entry")).get("sequence_length"); - result = new ArrayList<>(); + + Object uniprot_entry = jsonObj.get("uniprot_entry"); + // TODO: decide if anything from uniprot_entry needs to be reported via + // the FTSRestResponse object + // Arnaud added seqLength = (Long) ((Map) + // jsonObj.get("uniprot_entry")).get("sequence_length"); + List structures = (List) jsonObj.get("structures"); + result = new ArrayList<>(); + int numFound = 0; for (Iterator strucIter = structures.iterator(); strucIter .hasNext();) { - Map structure = (Map) strucIter.next(); + Map structure = (Map) strucIter + .next(); result.add(getFTSData(structure, tdbRestRequest)); numFound++; } - searchResult.setNumberOfItemsFound(numFound); - searchResult.setSearchSummary(result); - searchResult.setSequenceLength(seqLength); - + + searchResult.setNumberOfItemsFound(numFound); + searchResult.setSearchSummary(result); + } catch (ParseException e) { e.printStackTrace(); @@ -191,28 +241,45 @@ public class TDBeaconsFTSRestClient extends FTSRestClient return searchResult; } -private static FTSData getFTSData(Map tdbJsonStructure, + private static FTSData getFTSData( + Map tdbJsonStructureSummary, FTSRestRequest tdbRequest) { - // TODO Auto-generated method stub String primaryKey = null; Object[] summaryRowData; + + SequenceI associatedSequence; + Collection displayFields = tdbRequest.getWantedFields(); + SequenceI associatedSeq = tdbRequest.getAssociatedSequence(); int colCounter = 0; - summaryRowData = new Object[displayFields.size()]; - for (FTSDataColumnI field : displayFields) { - String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " " + summaryRowData = new Object[(associatedSeq != null) + ? displayFields.size() + 1 + : displayFields.size()]; + if (associatedSeq != null) + { + associatedSequence = associatedSeq; + summaryRowData[0] = associatedSequence; + colCounter = 1; + } + Map tdbJsonStructure = (Map) tdbJsonStructureSummary + .get("summary"); + for (FTSDataColumnI field : displayFields) + { + String fieldData = (tdbJsonStructure.get(field.getCode()) == null) + ? " " : tdbJsonStructure.get(field.getCode()).toString(); + // jalview.bin.Console.outPrintln("Field : " + field + " Data : " + fieldData); if (field.isPrimaryKeyColumn()) { primaryKey = fieldData; summaryRowData[colCounter++] = primaryKey; } - else if (fieldData == null || fieldData.isEmpty()) + else if (fieldData == null || fieldData.trim().isEmpty()) { summaryRowData[colCounter++] = null; } - else + else { try { @@ -225,75 +292,31 @@ private static FTSData getFTSData(Map tdbJsonStructure, : fieldData; } catch (Exception e) { - e.printStackTrace(); - System.out.println("offending value:" + fieldData); + // e.printStackTrace(); + jalview.bin.Console.outPrintln("offending value:" + fieldData + fieldData); } } } final String primaryKey1 = primaryKey; final Object[] summaryRowData1 = summaryRowData; - - return new FTSData() - { - - @Override - public Object[] getSummaryData() - { - return summaryRowData1; - } - - @Override - public Object getPrimaryKey() - { - return primaryKey1; - } - - /** - * Returns a string representation of this object; - */ - @Override - public String toString() - { - StringBuilder summaryFieldValues = new StringBuilder(); - for (Object summaryField : summaryRowData1) - { - summaryFieldValues.append( - summaryField == null ? " " : summaryField.toString()) - .append("\t"); - } - return summaryFieldValues.toString(); - } - - /** - * Returns hash code value for this object - */ - @Override - public int hashCode() - { - return Objects.hash(primaryKey1, this.toString()); - } - @Override - public boolean equals(Object that) - { - return this.toString().equals(that.toString()); - } - }; + return new TDB_FTSData(primaryKey, tdbJsonStructure, summaryRowData1); } -// private static FTSData getFTSData(Map doc, -// FTSRestRequest tdbRestRequest) -// { -// String primaryKey = null; -// -// Object[] summaryRowData; -// -// Collection displayFields = tdbRestRequest.getWantedFields(); -// int colCounter = 0; -// summaryRowData = new Object[displayFields.size() + 1]; -// -// return null; -// } + // private static FTSData getFTSData(Map doc, + // FTSRestRequest tdbRestRequest) + // { + // String primaryKey = null; + // + // Object[] summaryRowData; + // + // Collection displayFields = + // tdbRestRequest.getWantedFields(); + // int colCounter = 0; + // summaryRowData = new Object[displayFields.size() + 1]; + // + // return null; + // } private String parseJsonExceptionString(String jsonErrorString) { @@ -304,10 +327,9 @@ private static FTSData getFTSData(Map tdbJsonStructure, @Override public String getColumnDataConfigFileName() { - // TODO Auto-generated method stub - return null; + return "/fts/tdbeacons_data_columns.txt"; } - + public static FTSRestClientI getInstance() { if (instance == null) @@ -316,9 +338,10 @@ private static FTSData getFTSData(Map tdbJsonStructure, } return instance; } - + private Collection allDefaultDisplayedStructureDataColumns; + @Override public Collection getAllDefaultDisplayedStructureDataColumns() { if (allDefaultDisplayedStructureDataColumns == null @@ -330,5 +353,26 @@ private static FTSData getFTSData(Map tdbJsonStructure, } return allDefaultDisplayedStructureDataColumns; } - + + @Override + public String[] getPreferencesColumnsFor(PreferenceSource source) + { + String[] columnNames = null; + switch (source) + { + case SEARCH_SUMMARY: + columnNames = new String[] { "", "Display", "Group" }; + break; + case STRUCTURE_CHOOSER: + columnNames = new String[] { "", "Display", "Group" }; + break; + case PREFERENCES: + columnNames = new String[] { "3DB Beacons Field", + "Show in search summary", "Show in structure summary" }; + break; + default: + break; + } + return columnNames; + } }