X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Fpdb%2FPDBFTSRestClient.java;h=b4e56606fb9a48f906e7b521b4493b5977c9fb7a;hb=8e7cf85a7f61f425e808cac53ead7bc27e402242;hp=a03cf147adab6878c951600d9c4765a2cb30a03c;hpb=5a256ef0ca648a8f4722da20475cbd01655d9de4;p=jalview.git diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java index a03cf14..b4e5660 100644 --- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java +++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java @@ -20,6 +20,7 @@ */ package jalview.fts.service.pdb; +import jalview.bin.Jalview; import jalview.datamodel.SequenceI; import jalview.fts.api.FTSData; import jalview.fts.api.FTSDataColumnI; @@ -27,6 +28,7 @@ import jalview.fts.api.FTSRestClientI; import jalview.fts.core.FTSRestClient; import jalview.fts.core.FTSRestRequest; import jalview.fts.core.FTSRestResponse; +import jalview.util.JSONUtils; import jalview.util.MessageManager; import java.net.URI; @@ -34,35 +36,22 @@ 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 jalview.javascript.web.Client; -//import jalview.javascript.web.ClientResponse; -//import jalview.javascript.web.WebResource; - import com.sun.jersey.api.client.Client; import com.sun.jersey.api.client.ClientResponse; import com.sun.jersey.api.client.WebResource; - -import com.sun.jersey.api.client.config.ClientConfig; import com.sun.jersey.api.client.config.DefaultClientConfig; /** * A rest client for querying the Search endpoint of the PDB API * - * BH 2018: just a tiny tweak here - for SwingJS, we coerce the classes to be - * from jalview.javascript.web instead of com.sun.jersey.api.client - * - * * @author tcnofoegbu - * */ public class PDBFTSRestClient extends FTSRestClient { @@ -83,16 +72,13 @@ public class PDBFTSRestClient extends FTSRestClient * @return the pdbResponse object for the given request * @throws Exception */ - @SuppressWarnings("unused") + @SuppressWarnings({ "unused", "unchecked" }) @Override public FTSRestResponse executeRequest(FTSRestRequest pdbRestRequest) throws Exception { try { - Client client; - WebResource webResource; - String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( pdbRestRequest.getWantedFields()); int responseSize = (pdbRestRequest.getResponseSize() == 0) @@ -133,18 +119,26 @@ public class PDBFTSRestClient extends FTSRestClient + (pdbRestRequest.isAllowUnpublishedEntries() ? "" : " AND status:REL"); - if (/** @j2sNative true || */ - false) + // 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 + Client client; + Class clientResponseClass; + if (Jalview.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 { - // Build request parameters for the REST Request - ClientConfig clientConfig = new DefaultClientConfig(); - client = Client.create(clientConfig); + // Java only + client = Client.create(new DefaultClientConfig()); + clientResponseClass = ClientResponse.class; } + WebResource webResource; if (pdbRestRequest.isFacet()) { webResource = client.resource(PDB_SEARCH_ENDPOINT) @@ -169,7 +163,7 @@ public class PDBFTSRestClient extends FTSRestClient // Execute the REST request ClientResponse clientResponse = webResource - .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class); + .accept(MediaType.APPLICATION_JSON).get(clientResponseClass ); // Get the JSON string from the response object String responseString = clientResponse.getEntity(String.class); @@ -228,7 +222,8 @@ public class PDBFTSRestClient extends FTSRestClient * the JSON string containing error message from the server * @return the processed error message from the JSON string */ - public static String parseJsonExceptionString(String jsonErrorResponse) + @SuppressWarnings("unchecked") +public static String parseJsonExceptionString(String jsonErrorResponse) { StringBuilder errorMessage = new StringBuilder( "\n============= PDB Rest Client RunTime error =============\n"); @@ -255,13 +250,12 @@ public class PDBFTSRestClient extends FTSRestClient // 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(); @@ -299,23 +293,20 @@ public class PDBFTSRestClient extends FTSRestClient 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")) + Map 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()); if (numFound > 0) { result = new ArrayList(); - JSONArray docs = (JSONArray) pdbResponse.get("docs"); - for (Iterator docIter = docs.iterator(); docIter + List docs = (List) pdbResponse.get("docs"); + for (Iterator docIter = docs.iterator(); docIter .hasNext();) { - JSONObject doc = docIter.next(); + Map doc = (Map) docIter.next(); result.add(getFTSData(doc, pdbRestRequest)); } searchResult.setNumberOfItemsFound(numFound); @@ -329,7 +320,7 @@ public class PDBFTSRestClient extends FTSRestClient return searchResult; } - public static FTSData getFTSData(JSONObject pdbJsonDoc, + public static FTSData getFTSData(Map pdbJsonDoc, FTSRestRequest request) { @@ -470,4 +461,33 @@ public class PDBFTSRestClient extends FTSRestClient } return allDefaultDisplayedStructureDataColumns; } + + @SuppressWarnings("unchecked") +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"); + try + { + Map jsonObj = (Map) JSONUtils.parse("{\"a\":3}"); + System.out.println(jsonObj); + } catch (ParseException e) + { + e.printStackTrace(); + } + + } + + }