X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Furls%2FIdentifiersUrlProvider.java;h=45d3863fd19ef61a4e65566d379b2a3b59eeef2c;hb=e63a4d52c27252dfb83efeeee1bda6c89b6dddec;hp=3501169ada665b9ea75647166aeb9856901b6fbd;hpb=44fc22cf950ff114ce3a5a07600e7a7eb5fd1216;p=jalview.git diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java index 3501169..45d3863 100644 --- a/src/jalview/urls/IdentifiersUrlProvider.java +++ b/src/jalview/urls/IdentifiersUrlProvider.java @@ -25,19 +25,16 @@ import static jalview.util.UrlConstants.DB_ACCESSION; import static jalview.util.UrlConstants.DELIM; import static jalview.util.UrlConstants.SEP; -import java.io.BufferedInputStream; -import java.io.File; +import jalview.util.UrlLink; + import java.io.FileNotFoundException; -import java.io.FileOutputStream; import java.io.FileReader; import java.io.IOException; -import java.io.InputStream; -import java.net.URL; import java.util.ArrayList; import java.util.HashMap; import java.util.Iterator; import java.util.List; -import java.util.Map.Entry; +import java.util.StringTokenizer; import java.util.Vector; import org.json.simple.JSONArray; @@ -57,62 +54,37 @@ public class IdentifiersUrlProvider extends UrlProviderImpl { // map of string ids to urls - private HashMap> urls; + private HashMap urls; // list of selected urls private ArrayList selectedUrls; - /* - * Location of file for identifiers.org download - */ - public static final String ID_ORG_FILE = System.getProperty("user.home") - + File.separatorChar + ".jalview_identifiers"; - - public IdentifiersUrlProvider(String cachedUrlList, String idFileName) - { - try - { - // File idFile = getIdentifiers(); - urls = readIdentifiers(new FileReader(idFileName)); - selectedUrls = new ArrayList(); - checkSelectionMatchesUrls(cachedUrlList); - - } catch (IOException e) - { - System.out.println("Exception reading URLs from identifiers.org"); - System.out.println(e.getMessage()); - } - } - - private File getIdentifiers() throws IOException + public IdentifiersUrlProvider(String cachedUrlList) { - String identifiersorgUrl = "http://identifiers.org/rest/collections/"; - String outfile = "identifiers.json"; - int BUFFER_SIZE = 4096; - - URL url = new URL(identifiersorgUrl); - InputStream is = new BufferedInputStream(url.openStream()); - FileOutputStream os = new FileOutputStream(outfile); - byte[] buffer = new byte[BUFFER_SIZE]; - int bytesRead = -1; - while ((bytesRead = is.read(buffer)) != -1) - { - os.write(buffer, 0, bytesRead); - } - os.close(); - is.close(); - - return new File(outfile); + urls = readIdentifiers(IdOrgSettings.getDownloadLocation()); + selectedUrls = new ArrayList(); + checkSelectionMatchesUrls(cachedUrlList); } - private HashMap> readIdentifiers( - FileReader reader) + /** + * Read data from an identifiers.org download file + * + * @param idFileName + * name of identifiers.org download file + * @return hashmap of identifiers.org data, keyed by MIRIAM id + */ + private HashMap readIdentifiers( + String idFileName) { JSONParser parser = new JSONParser(); - HashMap> idData = new HashMap>(); + + // identifiers.org data + HashMap idData = new HashMap(); try { + FileReader reader = new FileReader(idFileName); + JSONArray jsonarray = (JSONArray) parser.parse(reader); // loop over each entry in JSON array and build HashMap entry @@ -120,10 +92,10 @@ public class IdentifiersUrlProvider extends UrlProviderImpl { JSONObject item = (JSONObject) jsonarray.get(i); - HashMap idEntry = new HashMap(); - idEntry.put("name", (String) item.get("name")); - idEntry.put("url", (String) item.get("url")); - idData.put((String) item.get("id"), idEntry); + String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION + + DELIM; + UrlLink link = new UrlLink((String) item.get("name") + SEP + url); + idData.put((String) item.get("id"), link); } } catch (FileNotFoundException e) { @@ -140,29 +112,18 @@ public class IdentifiersUrlProvider extends UrlProviderImpl private void checkSelectionMatchesUrls(String cachedUrlList) { - - String[] prevSelected = cachedUrlList.split("\\" + SEP); - for (String id : prevSelected) + StringTokenizer st = new StringTokenizer(cachedUrlList, SEP); + while (st.hasMoreElements()) { - if (urls.containsKey(id)) - { - selectedUrls.add(id); - } - } - - // reset defaultUrl in case it is no longer selected - setDefaultUrl(defaultUrl); - } + String id = st.nextToken(); - private void checkSelectionMatchesUrls(Vector idList) - { - String[] prevSelected = new String[idList.size()]; - idList.toArray(prevSelected); - for (String id : prevSelected) - { - if (urls.containsKey(id)) + if (isMiriamId(id)) { - selectedUrls.add(id); + // this is an identifiers.org MIRIAM id + if (urls.containsKey(id)) + { + selectedUrls.add(id); + } } } @@ -185,11 +146,16 @@ public class IdentifiersUrlProvider extends UrlProviderImpl } @Override - public String writeUrlsAsString() + public String writeUrlsAsString(boolean selected) { + if (!selected) + { + return ""; // we don't cache unselected identifiers.org urls + } + + StringBuffer links = new StringBuffer(); if (!selectedUrls.isEmpty()) { - StringBuffer links = new StringBuffer(); for (String k : selectedUrls) { links.append(k); @@ -197,9 +163,8 @@ public class IdentifiersUrlProvider extends UrlProviderImpl } // remove last SEP links.setLength(links.length() - 1); - return links.toString(); } - return ""; + return links.toString(); } @Override @@ -208,9 +173,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl Vector links = new Vector(); for (String key : selectedUrls) { - links.add(urls.get(key).get("name") + SEP + urls.get(key).get("url") - + "/" + DELIM - + DB_ACCESSION + DELIM); + links.add(urls.get(key).toString()); } return links; } @@ -218,18 +181,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl @Override public List getLinksForTable() { - ArrayList displayLinks = new ArrayList(); - for (Entry> entry : urls.entrySet()) - { - String key = entry.getKey(); - boolean isDefault = (key == defaultUrl); - boolean isSelected = (selectedUrls.contains(key)); - displayLinks.add(new UrlLinkDisplay(key, - entry.getValue().get("name"), - entry.getValue().get("url") - + "/" + DELIM + DB_ACCESSION + DELIM, isSelected, isDefault)); - } - return displayLinks; + return super.getLinksForTable(urls, selectedUrls, false); } @Override @@ -243,7 +195,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl UrlLinkDisplay link = it.next(); // Handle links with MIRIAM ids only - if (isMiriamId(link.getId())) // TODO separate use of name and id + if (isMiriamId(link.getId())) { // select/deselect links accordingly and set default url @@ -267,18 +219,13 @@ public class IdentifiersUrlProvider extends UrlProviderImpl @Override public String getDefaultUrl(String seqid) { - if (seqid.length() < MIN_SUBST_LENGTH) - { - return null; - } - else if (defaultUrl == null) - { - return null; - } - else - { - return urls.get(defaultUrl).get("url") + "/" + seqid; - } + return super.getDefaultUrl(seqid, urls); + } + + @Override + public String getDefaultUrlId() + { + return defaultUrl; } @Override