X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;fp=src%2Fjalview%2Ffts%2Fservice%2Funiprot%2FUniProtFTSRestClient.java;h=182729314c88773d772e2c66b8aa59957ae00aca;hp=2606b628b01a694d7347c3a1d3144480c0cf0de0;hb=4469e6d2c6a0c05c6278b10b0a157522aaa98091;hpb=cd36659dd8a3855b3d1eb61cafbb0bbf604142be diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java index 2606b62..1827293 100644 --- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java +++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java @@ -21,6 +21,9 @@ package jalview.fts.service.uniprot; +import java.lang.invoke.MethodHandles; +import java.net.MalformedURLException; +import java.net.URL; import java.util.ArrayList; import java.util.Collection; import java.util.List; @@ -37,31 +40,63 @@ import jalview.bin.Cache; import jalview.bin.Console; 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.ChannelProperties; import jalview.util.MessageManager; import jalview.util.Platform; +/* + * 2022-07-20 bsoares + * See https://issues.jalview.org/browse/JAL-4036 + * The new Uniprot API is not dissimilar to the old one, but has some important changes. + * Some group names have changed slightly, some old groups have gone and there are quite a few new groups. + * + * Most changes are mappings of old column ids to new field ids. There are a handful of old + * columns not mapped to new fields, and new fields without an old column. + * [aside: not all possible columns were listed in the resources/fts/uniprot_data_columns.txt file. + * These were presumably additions after the file was created] + * For existing/mapped fields, the same preferences found in the resource file have been migrated to + * the new file with the new field name, id and group. + * + * The new mapped groups and files are stored and read from resources/fts/uniprot_data_columns-2022.txt. + * + * There is now no "sort" query string parameter. + * + * See https://www.uniprot.org/help/api_queries + * + * SIGNIFICANT CHANGE: Pagination is no longer performed using a record offset, but with a "cursor" + * query string parameter that is not really a cursor. The value is an opaque string that is passed (or + * rather a whole URL is passed) in the "Link" header of the HTTP response of the previous page. + * Where such a link is passed it is put into the cursors ArrayList. + * There are @Overridden methods in UniprotFTSPanel. + */ + public class UniProtFTSRestClient extends FTSRestClient { - private static final String DEFAULT_UNIPROT_DOMAIN = "https://legacy.uniprot.org"; + private static final String DEFAULT_UNIPROT_DOMAIN = "https://rest.uniprot.org"; + + private static final String USER_AGENT = ChannelProperties + .getProperty("app_name", "Jalview") + " " + + Cache.getDefault("VERSION", "Unknown") + " " + + MethodHandles.lookup().lookupClass() + " help@jalview.org"; static { Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN); } - private static FTSRestClientI instance = null; + private static UniProtFTSRestClient instance = null; public final String uniprotSearchEndpoint; public UniProtFTSRestClient() { super(); - uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN", - DEFAULT_UNIPROT_DOMAIN) + "/uniprot/"; + this.clearCursors(); + uniprotSearchEndpoint = Cache.getDefault("UNIPROT_2022_DOMAIN", + DEFAULT_UNIPROT_DOMAIN) + "/uniprotkb/search"; } @SuppressWarnings("unchecked") @@ -69,6 +104,12 @@ public class UniProtFTSRestClient extends FTSRestClient public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest) throws Exception { + return executeRequest(uniprotRestRequest, null); + } + + public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest, + String cursor) throws Exception + { try { String wantedFields = getDataColumnsFieldsAsCommaDelimitedString( @@ -85,11 +126,10 @@ public class UniProtFTSRestClient extends FTSRestClient } else { - query = uniprotRestRequest.getFieldToSearchBy() - .equalsIgnoreCase("Search All") - ? uniprotRestRequest.getSearchTerm() - + " or mnemonic:" - + uniprotRestRequest.getSearchTerm() + query = uniprotRestRequest.getFieldToSearchBy().equalsIgnoreCase( + "Search All") ? uniprotRestRequest.getSearchTerm() + // + " or mnemonic:" + // + uniprotRestRequest.getSearchTerm() : uniprotRestRequest.getFieldToSearchBy() + ":" + uniprotRestRequest.getSearchTerm(); } @@ -119,18 +159,62 @@ public class UniProtFTSRestClient extends FTSRestClient WebResource webResource = null; webResource = client.resource(uniprotSearchEndpoint) - .queryParam("format", "tab") - .queryParam("columns", wantedFields) - .queryParam("limit", String.valueOf(responseSize)) - .queryParam("offset", String.valueOf(offSet)) - .queryParam("sort", "score").queryParam("query", query); - if (Console.isDebugEnabled()) + .queryParam("format", "tsv") + .queryParam("fields", wantedFields) + .queryParam("size", String.valueOf(responseSize)) + /* 2022 new api has no "sort" + * .queryParam("sort", "score") + */ + .queryParam("query", query); + if (offSet != 0 && cursor != null && cursor.length() > 0) + // 2022 new api does not do pagination with an offset, it requires a + // "cursor" parameter with a key (given for the next page). + // (see https://www.uniprot.org/help/pagination) { - Console.debug("Uniprot FTS Request: " + webResource.toString()); + webResource = webResource.queryParam("cursor", cursor); } + Console.debug( + "Uniprot FTS Request: " + webResource.getURI().toString()); // Execute the REST request - ClientResponse clientResponse = webResource - .accept(MediaType.TEXT_PLAIN).get(clientResponseClass); + WebResource.Builder wrBuilder = webResource + .accept(MediaType.TEXT_PLAIN); + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + wrBuilder.header("User-Agent", USER_AGENT); + } + ClientResponse clientResponse = wrBuilder.get(clientResponseClass); + + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + if (clientResponse.getHeaders().containsKey("Link")) + { + // extract the URL from the 'Link: ; ref="stuff"' header + String linkHeader = clientResponse.getHeaders().get("Link") + .get(0); + if (linkHeader.indexOf("<") > -1) + { + String temp = linkHeader.substring(linkHeader.indexOf("<") + 1); + if (temp.indexOf(">") > -1) + { + String nextUrl = temp.substring(0, temp.indexOf(">")); + // then get the cursor value from the query string parameters + String nextCursor = getQueryParam("cursor", nextUrl); + setCursor(cursorPage + 1, nextCursor); + } + } + } + } + String uniProtTabDelimittedResponseString = clientResponse .getEntity(String.class); // Make redundant objects eligible for garbage collection to conserve @@ -144,15 +228,27 @@ public class UniProtFTSRestClient extends FTSRestClient throw new Exception(errorMessage); } - int xTotalResults = Platform.isJS() ? 1 - : Integer.valueOf(clientResponse.getHeaders() - .get("X-Total-Results").get(0)); + // new Uniprot API is not including a "X-Total-Results" header when there + // are 0 results + List resultsHeaders = clientResponse.getHeaders() + .get("X-Total-Results"); + int xTotalResults = 0; + if (Platform.isJS()) + { + xTotalResults = 1; + } + else if (resultsHeaders != null && resultsHeaders.size() >= 1) + { + xTotalResults = Integer.valueOf(resultsHeaders.get(0)); + } clientResponse = null; client = null; return parseUniprotResponse(uniProtTabDelimittedResponseString, uniprotRestRequest, xTotalResults); } catch (Exception e) { + Console.warn("Problem with the query: " + e.getMessage()); + Console.debug("Exception stacktrace:", e); String exceptionMsg = e.getMessage(); if (exceptionMsg.contains("SocketException")) { @@ -352,7 +448,7 @@ public class UniProtFTSRestClient extends FTSRestClient }; } - public static FTSRestClientI getInstance() + public static UniProtFTSRestClient getInstance() { if (instance == null) { @@ -364,7 +460,94 @@ public class UniProtFTSRestClient extends FTSRestClient @Override public String getColumnDataConfigFileName() { - return "/fts/uniprot_data_columns.txt"; + return "/fts/uniprot_data_columns-2022.txt"; + } + + /* 2022-07-20 bsoares + * used for the new API "cursor" pagination. See https://www.uniprot.org/help/pagination + */ + private ArrayList cursors; + + private int cursorPage = 0; + + protected int getCursorPage() + { + return cursorPage; + } + + protected void setCursorPage(int i) + { + cursorPage = i; + } + + protected void setPrevCursorPage() + { + if (cursorPage > 0) + cursorPage--; + } + + protected void setNextCursorPage() + { + cursorPage++; + } + + protected void clearCursors() + { + cursors = new ArrayList(10); } -} + protected String getCursor(int i) + { + return cursors.get(i); + } + + protected String getNextCursor() + { + if (cursors.size() < cursorPage + 2) + return null; + return cursors.get(cursorPage + 1); + } + + protected String getPrevCursor() + { + if (cursorPage == 0) + return null; + return cursors.get(cursorPage - 1); + } + + protected void setCursor(int i, String c) + { + cursors.ensureCapacity(i + 1); + while (cursors.size() <= i) + { + cursors.add(null); + } + cursors.set(i, c); + Console.debug( + "Set UniprotFRSRestClient cursors[" + i + "] to '" + c + "'"); + // cursors.add(c); + } + + public static String getQueryParam(String param, String u) + { + if (param == null || u == null) + return null; + try + { + URL url = new URL(u); + String[] kevs = url.getQuery().split("&"); + for (int j = 0; j < kevs.length; j++) + { + String[] kev = kevs[j].split("=", 2); + if (param.equals(kev[0])) + { + return kev[1]; + } + } + } catch (MalformedURLException e) + { + Console.warn("Could not obtain next page 'cursor' value from 'u"); + } + return null; + } +} \ No newline at end of file