X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSRestClient.java;h=5619075dfb43d3d30cd59b75d18cb09751491931;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=c0ca3a5f8aa9fc95fa7fdfe33084a7c180fabba0;hpb=e58d21a916e1beda1091e286723afb494ab62cc3;p=jalview.git diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java index c0ca3a5..5619075 100644 --- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java +++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java @@ -20,28 +20,20 @@ */ package jalview.fts.service.pdb; -import jalview.bin.Jalview; -import jalview.datamodel.SequenceI; -import jalview.fts.api.FTSData; -import jalview.fts.api.FTSDataColumnI; -import jalview.fts.api.FTSRestClientI; -import jalview.fts.core.FTSRestClient; -import jalview.fts.core.FTSRestRequest; -import jalview.fts.core.FTSRestResponse; -import jalview.util.MessageManager; - +import java.io.File; +import java.io.FileInputStream; +import java.io.FileReader; import java.net.URI; +import java.nio.CharBuffer; import java.util.ArrayList; 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; -import org.json.simple.JSONArray; -import org.json.simple.JSONObject; -import org.json.simple.parser.JSONParser; import org.json.simple.parser.ParseException; import com.sun.jersey.api.client.Client; @@ -49,12 +41,28 @@ import com.sun.jersey.api.client.ClientResponse; import com.sun.jersey.api.client.WebResource; import com.sun.jersey.api.client.config.DefaultClientConfig; +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; +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.alphafold.AlphafoldRestClient; +import jalview.util.JSONUtils; +import jalview.util.MessageManager; +import jalview.util.Platform; + /** * A rest client for querying the Search endpoint of the PDB API * * @author tcnofoegbu */ public class PDBFTSRestClient extends FTSRestClient + implements StructureFTSRestClientI { private static FTSRestClientI instance = null; @@ -122,19 +130,24 @@ public class PDBFTSRestClient extends FTSRestClient // Build request parameters for the REST Request - // BH 2018 the trick here is to coerce the classes in Javascript to be - // different from the ones in Java yet still allow this to be correct for Java + // BH 2018 the trick here is to coerce the classes in Javascript to be + // different from the ones in Java yet still allow this to be correct for + // Java Client client; Class clientResponseClass; - if (Jalview.isJS()) + if (Platform.isJS()) { // JavaScript only -- coerce types to Java types for Java client = (Client) (Object) new jalview.javascript.web.Client(); clientResponseClass = (Class) (Object) jalview.javascript.web.ClientResponse.class; } else + /** + * Java only + * + * @j2sIgnore + */ { - // Java only client = Client.create(new DefaultClientConfig()); clientResponseClass = ClientResponse.class; } @@ -162,40 +175,74 @@ public class PDBFTSRestClient extends FTSRestClient URI uri = webResource.getURI(); - // Execute the REST request - ClientResponse clientResponse = webResource - .accept(MediaType.APPLICATION_JSON).get(clientResponseClass ); + jalview.bin.Console.outPrintln(uri); + ClientResponse clientResponse = null; + int responseStatus = -1; + // Get the JSON string from the response object or directly from the + // client (JavaScript) + Map jsonObj = null; + String responseString = null; - // Get the JSON string from the response object - String responseString = clientResponse.getEntity(String.class); - // System.out.println("query >>>>>>> " + pdbRestRequest.toString()); + jalview.bin.Console.outPrintln("query >>>>>>> " + pdbRestRequest.toString()); - // Check the response status and report exception if one occurs - if (clientResponse.getStatus() != 200) + if (!isMocked()) { - String errorMessage = ""; - if (clientResponse.getStatus() == 400) + // Execute the REST request + clientResponse = webResource.accept(MediaType.APPLICATION_JSON) + .get(clientResponseClass); + responseStatus = clientResponse.getStatus(); + } + else + { + // mock response + if (mockQueries.containsKey(uri.toString())) { - errorMessage = parseJsonExceptionString(responseString); - throw new Exception(errorMessage); + responseStatus = 200; } else { - errorMessage = getMessageByHTTPStatusCode( - clientResponse.getStatus(), "PDB"); - throw new Exception(errorMessage); + // FIXME - may cause unexpected exceptions for callers when mocked + responseStatus = 400; } } - // Make redundant objects eligible for garbage collection to conserve - // memory - clientResponse = null; - client = null; + // Check the response status and report exception if one occurs + switch (responseStatus) + { + case 200: + + if (isMocked()) + { + responseString = mockQueries.get(uri.toString()); + } + else + { + if (Platform.isJS()) + { + jsonObj = clientResponse.getEntity(Map.class); + } + else + { + responseString = clientResponse.getEntity(String.class); + } + } + break; + case 400: + throw new Exception(isMocked() ? "400 response (Mocked)" + : parseJsonExceptionString(responseString)); + default: + throw new Exception( + getMessageByHTTPStatusCode(responseStatus, "PDB")); + } // Process the response and return the result to the caller. - return parsePDBJsonResponse(responseString, pdbRestRequest); + return parsePDBJsonResponse(responseString, jsonObj, pdbRestRequest); } catch (Exception e) { + if (e.getMessage() == null) + { + throw (e); + } String exceptionMsg = e.getMessage(); if (exceptionMsg.contains("SocketException")) { @@ -223,40 +270,43 @@ public class PDBFTSRestClient extends FTSRestClient * the JSON string containing error message from the server * @return the processed error message from the JSON string */ + @SuppressWarnings("unchecked") public static String parseJsonExceptionString(String jsonErrorResponse) { StringBuilder errorMessage = new StringBuilder( "\n============= PDB Rest Client RunTime error =============\n"); - -// { -// "responseHeader":{ -// "status":0, -// "QTime":0, -// "params":{ -// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL", -// "fl":"pdb_id,title,experimental_method,resolution", -// "start":"0", -// "sort":"overall_quality desc", -// "rows":"500", -// "wt":"json"}}, -// "response":{"numFound":1,"start":0,"docs":[ -// { -// "experimental_method":["X-ray diffraction"], -// "pdb_id":"4zhp", -// "resolution":2.46, -// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}] -// }} -// + // { + // "responseHeader":{ + // "status":0, + // "QTime":0, + // "params":{ + // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL", + // "fl":"pdb_id,title,experimental_method,resolution", + // "start":"0", + // "sort":"overall_quality desc", + // "rows":"500", + // "wt":"json"}}, + // "response":{"numFound":1,"start":0,"docs":[ + // { + // "experimental_method":["X-ray diffraction"], + // "pdb_id":"4zhp", + // "resolution":2.46, + // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S + // cluster"}] + // }} + // try { - JSONParser jsonParser = new JSONParser(); - JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonErrorResponse); - JSONObject errorResponse = (JSONObject) jsonObj.get("error"); + Map jsonObj = (Map) JSONUtils + .parse(jsonErrorResponse); + Map errorResponse = (Map) jsonObj + .get("error"); - JSONObject responseHeader = (JSONObject) jsonObj + Map responseHeader = (Map) jsonObj .get("responseHeader"); - JSONObject paramsObj = (JSONObject) responseHeader.get("params"); + Map paramsObj = (Map) responseHeader + .get("params"); String status = responseHeader.get("status").toString(); String message = errorResponse.get("msg").toString(); String query = paramsObj.get("q").toString(); @@ -286,37 +336,51 @@ public class PDBFTSRestClient extends FTSRestClient * JSON string * @return */ - @SuppressWarnings("unchecked") public static FTSRestResponse parsePDBJsonResponse( String pdbJsonResponseString, FTSRestRequest pdbRestRequest) { + return parsePDBJsonResponse(pdbJsonResponseString, + (Map) null, pdbRestRequest); + } + + @SuppressWarnings("unchecked") + public static FTSRestResponse parsePDBJsonResponse( + String pdbJsonResponseString, Map jsonObj, + FTSRestRequest pdbRestRequest) + { FTSRestResponse searchResult = new FTSRestResponse(); List result = null; try { - JSONParser jsonParser = new JSONParser(); - JSONObject jsonObj = (JSONObject) jsonParser - .parse(pdbJsonResponseString); - - JSONObject pdbResponse = (JSONObject) jsonObj.get("response"); - String queryTime = ((JSONObject) jsonObj.get("responseHeader")) - .get("QTime").toString(); + if (jsonObj == null) + { + jsonObj = (Map) JSONUtils + .parse(pdbJsonResponseString); + } + Map pdbResponse = (Map) jsonObj + .get("response"); + String queryTime = ((Map) jsonObj + .get("responseHeader")).get("QTime").toString(); int numFound = Integer .valueOf(pdbResponse.get("numFound").toString()); + List docs = (List) pdbResponse.get("docs"); + + result = new ArrayList(); if (numFound > 0) { - result = new ArrayList(); - JSONArray docs = (JSONArray) pdbResponse.get("docs"); - for (Iterator docIter = docs.iterator(); docIter - .hasNext();) + + for (Iterator docIter = docs.iterator(); docIter.hasNext();) { - JSONObject doc = docIter.next(); + Map doc = (Map) docIter.next(); result.add(getFTSData(doc, pdbRestRequest)); } - searchResult.setNumberOfItemsFound(numFound); - searchResult.setResponseTime(queryTime); - searchResult.setSearchSummary(result); } + // this is the total number found by the query, + // rather than the set returned in SearchSummary + searchResult.setNumberOfItemsFound(numFound); + searchResult.setResponseTime(queryTime); + searchResult.setSearchSummary(result); + } catch (ParseException e) { e.printStackTrace(); @@ -324,7 +388,7 @@ public class PDBFTSRestClient extends FTSRestClient return searchResult; } - public static FTSData getFTSData(JSONObject pdbJsonDoc, + public static FTSData getFTSData(Map pdbJsonDoc, FTSRestRequest request) { @@ -349,8 +413,10 @@ public class PDBFTSRestClient extends FTSRestClient for (FTSDataColumnI field : diplayFields) { + // jalview.bin.Console.outPrintln("Field " + field); String fieldData = (pdbJsonDoc.get(field.getCode()) == null) ? "" : pdbJsonDoc.get(field.getCode()).toString(); + // jalview.bin.Console.outPrintln("Field Data : " + fieldData); if (field.isPrimaryKeyColumn()) { primaryKey = fieldData; @@ -374,7 +440,7 @@ public class PDBFTSRestClient extends FTSRestClient } catch (Exception e) { e.printStackTrace(); - System.out.println("offending value:" + fieldData); + jalview.bin.Console.outPrintln("offending value:" + fieldData); } } } @@ -454,44 +520,38 @@ public class PDBFTSRestClient extends FTSRestClient private Collection allDefaultDisplayedStructureDataColumns; + @Override public Collection getAllDefaultDisplayedStructureDataColumns() { if (allDefaultDisplayedStructureDataColumns == null || allDefaultDisplayedStructureDataColumns.isEmpty()) { - allDefaultDisplayedStructureDataColumns = new ArrayList(); + allDefaultDisplayedStructureDataColumns = new ArrayList<>(); allDefaultDisplayedStructureDataColumns .addAll(super.getAllDefaultDisplayedFTSDataColumns()); } return allDefaultDisplayedStructureDataColumns; } - - public static void main(String[] args) { - - - // check for transpiler fix associated with JSONParser yylex.java use of charAt() - // instead of codePointAt() - - String s = "e"; - char c = 'c'; - char f = 'f'; - s += c | f; - int x = c&f; - int y = 2 & c; - int z = c ^ 5; - String result = s +x + y + z; - assert (result == "e103982102"); - JSONParser jsonParser = new JSONParser(); - try - { - JSONObject jsonObj = (JSONObject) jsonParser.parse("{\"a\":3}"); - System.out.println(jsonObj); - } catch (ParseException e) + + @Override + public String[] getPreferencesColumnsFor(PreferenceSource source) + { + String[] columnNames = null; + switch (source) { - e.printStackTrace(); + case SEARCH_SUMMARY: + columnNames = new String[] { "", "Display", "Group" }; + break; + case STRUCTURE_CHOOSER: + columnNames = new String[] { "", "Display", "Group" }; + break; + case PREFERENCES: + columnNames = new String[] { "PDB Field", "Show in search summary", + "Show in structure summary" }; + break; + default: + break; } - + return columnNames; } - - }