X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSRestClient.java;h=cbeaff157a9bf66f38e67e15b5400614180089dc;hb=1a34e43f7fb8e6d4f559026c6f0a207893124c6d;hp=8e634632a85cfd83555f4ef86d55c930b5f7a2ec;hpb=24fb77e77301499aa9e4e12d40d2ab42e06f56ca;p=jalview.git diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java index 8e63463..cbeaff1 100644 --- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java +++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java @@ -59,7 +59,7 @@ public class PDBFTSRestClient extends FTSRestClient private static FTSRestClientI instance = null; - public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?"; + public static final String PDB_SEARCH_ENDPOINT = "https://www.ebi.ac.uk/pdbe/search/pdb/select?"; protected PDBFTSRestClient() { @@ -82,10 +82,12 @@ public class PDBFTSRestClient extends FTSRestClient ClientConfig clientConfig = new DefaultClientConfig(); Client client = Client.create(clientConfig); - String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(pdbRestRequest - .getWantedFields()); - int responseSize = (pdbRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize() + String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( + pdbRestRequest.getWantedFields()); + int responseSize = (pdbRestRequest.getResponseSize() == 0) + ? getDefaultResponsePageSize() : pdbRestRequest.getResponseSize(); + int offSet = pdbRestRequest.getOffSet(); String sortParam = null; if (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest.getFieldToSortBy().trim().isEmpty()) @@ -107,11 +109,11 @@ public class PDBFTSRestClient extends FTSRestClient } } - String facetPivot = (pdbRestRequest.getFacetPivot() == null || pdbRestRequest - .getFacetPivot().isEmpty()) ? "" : pdbRestRequest - .getFacetPivot(); - String facetPivotMinCount = String.valueOf(pdbRestRequest - .getFacetPivotMinCount()); + String facetPivot = (pdbRestRequest.getFacetPivot() == null + || pdbRestRequest.getFacetPivot().isEmpty()) ? "" + : pdbRestRequest.getFacetPivot(); + String facetPivotMinCount = String + .valueOf(pdbRestRequest.getFacetPivotMinCount()); String query = pdbRestRequest.getFieldToSearchBy() + pdbRestRequest.getSearchTerm() @@ -128,6 +130,7 @@ public class PDBFTSRestClient extends FTSRestClient .queryParam("wt", "json").queryParam("fl", wantedFields) .queryParam("rows", String.valueOf(responseSize)) .queryParam("q", query) + .queryParam("start", String.valueOf(offSet)) .queryParam("sort", sortParam).queryParam("facet", "true") .queryParam("facet.pivot", facetPivot) .queryParam("facet.pivot.mincount", facetPivotMinCount); @@ -137,12 +140,12 @@ public class PDBFTSRestClient extends FTSRestClient webResource = client.resource(PDB_SEARCH_ENDPOINT) .queryParam("wt", "json").queryParam("fl", wantedFields) .queryParam("rows", String.valueOf(responseSize)) - .queryParam("q", query) - .queryParam("sort", sortParam); + .queryParam("start", String.valueOf(offSet)) + .queryParam("q", query).queryParam("sort", sortParam); } // Execute the REST request - ClientResponse clientResponse = webResource.accept( - MediaType.APPLICATION_JSON).get(ClientResponse.class); + ClientResponse clientResponse = webResource + .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class); // Get the JSON string from the response object String responseString = clientResponse.getEntity(String.class); @@ -159,8 +162,8 @@ public class PDBFTSRestClient extends FTSRestClient } else { - errorMessage = getMessageByHTTPStatusCode(clientResponse - .getStatus()); + errorMessage = getMessageByHTTPStatusCode( + clientResponse.getStatus(), "PDB"); throw new Exception(errorMessage); } } @@ -178,16 +181,14 @@ public class PDBFTSRestClient extends FTSRestClient if (exceptionMsg.contains("SocketException")) { // No internet connection - throw new Exception( - MessageManager - .getString("exception.unable_to_detect_internet_connection")); + throw new Exception(MessageManager.getString( + "exception.unable_to_detect_internet_connection")); } else if (exceptionMsg.contains("UnknownHostException")) { // The server 'www.ebi.ac.uk' is unreachable - throw new Exception( - MessageManager - .getString("exception.pdb_server_unreachable")); + throw new Exception(MessageManager.formatMessage( + "exception.fts_server_unreachable", "PDB Solr")); } else { @@ -196,36 +197,6 @@ public class PDBFTSRestClient extends FTSRestClient } } - public String getMessageByHTTPStatusCode(int code) - { - String message = ""; - switch (code) - { - case 410: - message = MessageManager - .getString("exception.pdb_rest_service_no_longer_available"); - break; - case 403: - case 404: - message = MessageManager.getString("exception.resource_not_be_found"); - break; - case 408: - case 409: - case 500: - case 501: - case 502: - case 503: - case 504: - case 505: - message = MessageManager.getString("exception.pdb_server_error"); - break; - - default: - break; - } - return message; - } - /** * Process error response from PDB server if/when one occurs. * @@ -289,8 +260,8 @@ public class PDBFTSRestClient extends FTSRestClient .parse(pdbJsonResponseString); JSONObject pdbResponse = (JSONObject) jsonObj.get("response"); - String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get( - "QTime").toString(); + String queryTime = ((JSONObject) jsonObj.get("responseHeader")) + .get("QTime").toString(); int numFound = Integer .valueOf(pdbResponse.get("numFound").toString()); if (numFound > 0) @@ -327,8 +298,9 @@ public class PDBFTSRestClient extends FTSRestClient Collection diplayFields = request.getWantedFields(); SequenceI associatedSeq = request.getAssociatedSequence(); int colCounter = 0; - summaryRowData = new Object[(associatedSeq != null) ? diplayFields - .size() + 1 : diplayFields.size()]; + summaryRowData = new Object[(associatedSeq != null) + ? diplayFields.size() + 1 + : diplayFields.size()]; if (associatedSeq != null) { associatedSequence = associatedSeq; @@ -353,15 +325,17 @@ public class PDBFTSRestClient extends FTSRestClient { try { - summaryRowData[colCounter++] = (field.getDataColumnClass() == Integer.class) ? Integer - .valueOf(fieldData) - : (field.getDataColumnClass() == Double.class) ? Double - .valueOf(fieldData) - : fieldData; + summaryRowData[colCounter++] = (field.getDataType() + .getDataTypeClass() == Integer.class) + ? Integer.valueOf(fieldData) + : (field.getDataType() + .getDataTypeClass() == Double.class) + ? Double.valueOf(fieldData) + : sanitiseData(fieldData); } catch (Exception e) { e.printStackTrace(); - System.out.println("offending value:" + fieldData); + System.out.println("offending value:" + fieldData); } } } @@ -407,16 +381,29 @@ public class PDBFTSRestClient extends FTSRestClient { return Objects.hash(primaryKey1, this.toString()); } + + @Override + public boolean equals(Object that) + { + return this.toString().equals(that.toString()); + } }; } + private static String sanitiseData(String data) + { + String cleanData = data.replaceAll("\\[\"", "").replaceAll("\\]\"", "") + .replaceAll("\\[", "").replaceAll("\\]", "") + .replaceAll("\",\"", ", ").replaceAll("\"", ""); + return cleanData; + } + @Override public String getColumnDataConfigFileName() { - return getResourceFile("/fts/pdb_data_columns.conf"); + return "/fts/pdb_data_columns.txt"; } - public static FTSRestClientI getInstance() { if (instance == null) @@ -425,4 +412,18 @@ public class PDBFTSRestClient extends FTSRestClient } return instance; } + + private Collection allDefaultDisplayedStructureDataColumns; + + public Collection getAllDefaultDisplayedStructureDataColumns() + { + if (allDefaultDisplayedStructureDataColumns == null + || allDefaultDisplayedStructureDataColumns.isEmpty()) + { + allDefaultDisplayedStructureDataColumns = new ArrayList(); + allDefaultDisplayedStructureDataColumns + .addAll(super.getAllDefaultDisplayedFTSDataColumns()); + } + return allDefaultDisplayedStructureDataColumns; + } }