X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fthreedbeacons%2FTDBeaconsFTSRestClient.java;h=73939c32ed4c167be900581aaa4579c36ff61ba8;hb=bb3748fd2cc3ee8e8e0409599569e24e88974a17;hp=9c6f45a2df3c6af21969770861d72a57c1f75eb1;hpb=a848ed8eb380e5f9d915b0d7a062feec4f9d3dad;p=jalview.git diff --git a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java index 9c6f45a..73939c3 100644 --- a/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java +++ b/src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java @@ -21,25 +21,26 @@ 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.FTSRestClient; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; +import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource; 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; - + private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/"; + + public static FTSRestClientI instance = null; + protected TDBeaconsFTSRestClient() - { + { } - @SuppressWarnings("unchecked") @Override public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest) @@ -47,8 +48,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient { try { - String query = tdbRestRequest.getFieldToSearchBy() - + tdbRestRequest.getSearchTerm(); + String query = tdbRestRequest.getSearchTerm(); Client client; Class clientResponseClass; if (Platform.isJS()) @@ -60,6 +60,7 @@ public class TDBeaconsFTSRestClient extends FTSRestClient else /** * Java only + * * @j2sIgnore */ { @@ -71,18 +72,25 @@ public class TDBeaconsFTSRestClient extends FTSRestClient .path(query); URI uri = webResource.getURI(); System.out.println(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; - + // Check the response status and report exception if one occurs - int responseStatus = clientResponse.getStatus(); + int responseStatus = isMocked() ? (mockQuery.equals(query) ? 200 : 404) : clientResponse.getStatus(); switch (responseStatus) { // if success @@ -93,17 +101,20 @@ public class TDBeaconsFTSRestClient extends FTSRestClient } else { - responseString = clientResponse.getEntity(String.class); + responseString = isMocked() ? mockResponse: 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(); @@ -124,58 +135,70 @@ public class TDBeaconsFTSRestClient extends FTSRestClient throw e; } } - + } - - public String setSearchTerm(String term) { + + /** + * 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(); List result = null; - + try { if (jsonObj == null) { - jsonObj = (Map) JSONUtils.parse(tdbJsonResponseString); + jsonObj = (Map) JSONUtils + .parse(tdbJsonResponseString); } - - Object uniprot_entry = jsonObj.get("uniprot_entry"); - Long seqLength = (Long) ((Map) jsonObj.get("uniprot_entry")).get("sequence_length"); - //System.out.println(uniprot_entry); - //System.out.println(jsonObj); - //System.out.println("seqLenght :" + seqLength); - - //Map tdbResponse = (Map) jsonObj.get("structures"); + + 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();) + for (Iterator strucIter = structures.iterator(); strucIter + .hasNext();) { - Map structure = (Map) strucIter.next(); + Map structure = (Map) strucIter + .next(); result.add(getFTSData(structure, tdbRestRequest)); numFound++; - //System.out.println(structure); } - - //System.out.println("1 : " + structures.get(1)); - searchResult.setNumberOfItemsFound(numFound); + + searchResult.setNumberOfItemsFound(numFound); searchResult.setSearchSummary(result); - searchResult.setSequenceLength(seqLength); - + } catch (ParseException e) { e.printStackTrace(); @@ -183,30 +206,45 @@ public class TDBeaconsFTSRestClient extends FTSRestClient return searchResult; } -private static FTSData getFTSData(Map tdbJsonStructure, + private static FTSData getFTSData(Map tdbJsonStructure, FTSRestRequest tdbRequest) { - // TODO Auto-generated method stub + // TODO: consider reusing PDBFTSRestClient.getFTSData ? + 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; + } + + for (FTSDataColumnI field : displayFields) + { + String fieldData = (tdbJsonStructure.get(field.getCode()) == null) + ? " " : tdbJsonStructure.get(field.getCode()).toString(); - System.out.println("Field : " + field + " Data : " + fieldData); + // System.out.println("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 { @@ -219,14 +257,14 @@ private static FTSData getFTSData(Map tdbJsonStructure, : fieldData; } catch (Exception e) { - //e.printStackTrace(); + // e.printStackTrace(); System.out.println("offending value:" + fieldData + fieldData); } } } final String primaryKey1 = primaryKey; final Object[] summaryRowData1 = summaryRowData; - + return new FTSData() { @@ -241,7 +279,7 @@ private static FTSData getFTSData(Map tdbJsonStructure, { return primaryKey1; } - + /** * Returns a string representation of this object; */ @@ -257,7 +295,7 @@ private static FTSData getFTSData(Map tdbJsonStructure, } return summaryFieldValues.toString(); } - + /** * Returns hash code value for this object */ @@ -275,19 +313,20 @@ private static FTSData getFTSData(Map tdbJsonStructure, }; } -// 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) { @@ -300,7 +339,7 @@ private static FTSData getFTSData(Map tdbJsonStructure, { return "/fts/tdbeacons_data_columns.txt"; } - + public static FTSRestClientI getInstance() { if (instance == null) @@ -309,7 +348,7 @@ private static FTSData getFTSData(Map tdbJsonStructure, } return instance; } - + private Collection allDefaultDisplayedStructureDataColumns; public Collection getAllDefaultDisplayedStructureDataColumns() @@ -323,5 +362,26 @@ 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; + } }