Merge branch 'master' of github.com:bst-mug/trec-pm

src/main/java/at/medunigraz/imi/bst/lexigram/Lexigram.java

@@ -1,6 +1,7 @@
 package at.medunigraz.imi.bst.lexigram;
 
 import at.medunigraz.imi.bst.config.TrecConfig;
+import at.medunigraz.imi.bst.trec.expansion.CachedWebRequester;
 import at.medunigraz.imi.bst.trec.model.Topic;
 import at.medunigraz.imi.bst.trec.model.TopicSet;
 import at.medunigraz.imi.bst.trec.stats.CSVStatsWriter;
@@ -28,6 +29,8 @@ public class Lexigram {
 
     private static final String ENDPOINT = "https://api.lexigram.io/v1/lexigraph/";
 
+    private static final CachedWebRequester REQUESTER = new CachedWebRequester("cache/lexigramV2.ser");
+
     private static final List<String> NOISE = new ArrayList<>();
     static {
         NOISE.add("classification");
@@ -39,37 +42,6 @@ public class Lexigram {
         NOISE.add("ca - ");
     }
 
-    private static class Cache {
-        private static final String FILENAME = "cache/lexigram.ser";
-        private static HashMap<String, String> CALLS = new HashMap<>();
-        static {
-            if (Files.exists(Paths.get(FILENAME))) {
-                load();
-            }
-        }
-
-        private static void load() {
-            try {
-                ObjectInputStream ois = new ObjectInputStream(new FileInputStream(FILENAME));
-                CALLS = (HashMap) ois.readObject();
-                ois.close();
-            } catch (Exception e) {
-                throw new RuntimeException(e);
-            }
-        }
-
-        private static void save() {
-            try
-            {
-                ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(FILENAME));
-                oos.writeObject(CALLS);
-                oos.close();
-            } catch(IOException e) {
-                throw new RuntimeException(e);
-            }
-        }
-    }
-
     public static boolean isAPIKeyLoaded() {
         final int MIN_API_KEY_LENGTH = 20;
         return TrecConfig.LEXIGRAM_APIKEY.length() > MIN_API_KEY_LENGTH;
@@ -231,39 +203,7 @@ private static String cleanUpString(String label) {
     }
 
     private static JSONObject get(String url) {
-        if (!Cache.CALLS.containsKey(url)) {
-            HttpResponse<JsonNode> response = null;
-            try {
-                response = Unirest.get(url)
-                        .header("authorization", "Bearer " + TrecConfig.LEXIGRAM_APIKEY)
-                        .asJson();
-            } catch (UnirestException e) {
-                throw new RuntimeException(e);
-            }
-
-            if (response.getStatus() == 401) {
-                throw new RuntimeException("Unauthorized access to Lexigram API. Place your key in the file trec-pm.properties.");
-            }
-
-            if (response.getStatus() != 200) {
-                throw new RuntimeException("Got status code " + response.getStatus() + " from Lexigram API with body " + response.getBody());
-            }
-
-            JSONObject body = new JSONObject(response.getBody());
-
-            String firstArrayObject = "";
-            try {
-                firstArrayObject = body.getJSONObject("object").toString();
-            } catch (JSONException e) {
-                LOG.error("Unexpected response from Lexigram API: " + body);
-                throw e;
-            }
-
-            Cache.CALLS.put(url, firstArrayObject);
-            Cache.save();
-        }
-
-        return new JSONObject(Cache.CALLS.get(url));
+        return new JSONObject(REQUESTER.get(url, TrecConfig.LEXIGRAM_APIKEY));
     }
 
     /**

src/main/java/at/medunigraz/imi/bst/trec/expansion/CachedWebRequester.java

@@ -0,0 +1,117 @@
+package at.medunigraz.imi.bst.trec.expansion;
+
+import com.mashape.unirest.http.HttpResponse;
+import com.mashape.unirest.http.JsonNode;
+import com.mashape.unirest.http.Unirest;
+import com.mashape.unirest.http.exceptions.UnirestException;
+
+import java.io.*;
+import java.util.HashMap;
+
+public class CachedWebRequester {
+
+    private File cacheFile;
+
+    private HashMap<String, String> cache = new HashMap<>();
+
+    public CachedWebRequester(String filename) {
+        this.cacheFile = new File(filename);
+
+        if (cacheFile.exists()) {
+            try {
+                cache = load(cacheFile);
+            } catch (IOException | ClassNotFoundException e) {
+                throw new RuntimeException(e);
+            }
+        }
+    }
+
+    /**
+     * Make a web request to a given url and cache results.
+     *
+     * @param url
+     * @return
+     */
+    public String get(String url) {
+        if (!cache.containsKey(url)) {
+            String data = getResource(url);
+            put(url, data);
+        }
+        return cache.get(url);
+    }
+
+    /**
+     * Make a web request to a given restricted url and cache results.
+     *
+     * @param url
+     * @param bearer The bearer token.
+     * @return
+     */
+    public String get(String url, String bearer) {
+        if (!cache.containsKey(url)) {
+            String data = getRestrictedResource(url, bearer);
+            put(url, data);
+        }
+        return cache.get(url);
+    }
+
+    private HashMap<String, String> load(File file) throws IOException, ClassNotFoundException {
+        ObjectInputStream ois = new ObjectInputStream(new FileInputStream(file));
+        HashMap<String, String> ret = (HashMap) ois.readObject();
+        ois.close();
+        return ret;
+    }
+
+    private void save(Object object, File file) throws IOException {
+        ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(file));
+        oos.writeObject(object);
+        oos.close();
+    }
+
+    private void put(String url, String data) {
+        cache.put(url, data);
+
+        // Try to persist cache on disk
+        try {
+            save(cache, cacheFile);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    private String getRestrictedResource(String url, String bearer) {
+        HttpResponse<JsonNode> response = null;
+        try {
+            response = Unirest.get(url)
+                    .header("authorization", String.format("Bearer %s", bearer))
+                    .asJson();
+        } catch (UnirestException e) {
+            throw new RuntimeException(e);
+        }
+
+        return parseResponse(response);
+    }
+
+    private String getResource(String url) {
+        HttpResponse<JsonNode> response = null;
+        try {
+            response = Unirest.get(url).asJson();
+        } catch (UnirestException e) {
+            throw new RuntimeException(e);
+        }
+
+        return parseResponse(response);
+    }
+
+    private String parseResponse(HttpResponse<JsonNode> response) {
+        if (response.getStatus() == 401) {
+            throw new RuntimeException("Unauthorized access to API. Check your keys in the file trec-pm.properties.");
+        }
+
+        if (response.getStatus() != 200) {
+            throw new RuntimeException("Got status code " + response.getStatus() + " from API with body " + response.getBody());
+        }
+
+        return response.getBody().toString();
+    }
+}

src/main/java/at/medunigraz/imi/bst/trec/expansion/DGIdb.java

@@ -0,0 +1,122 @@
+package at.medunigraz.imi.bst.trec.expansion;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.json.JSONArray;
+import org.json.JSONObject;
+
+import java.util.*;
+
+public class DGIdb {
+
+    private static final Logger LOG = LogManager.getLogger();
+
+    private static final String ENDPOINT = "http://dgidb.org/api/v2/interactions.json";
+
+    private static final int DEFAULT_MINIMAL_SCORE = 0;
+
+    private static final boolean DEFAULT_EXPERT_CURATED_ONLY = false;
+
+    private static final CachedWebRequester REQUESTER = new CachedWebRequester("cache/dgidb.ser");
+
+    public Set<String> getDrugInteractions(String gene) {
+        return getDrugInteractions(gene, DEFAULT_EXPERT_CURATED_ONLY, DEFAULT_MINIMAL_SCORE);
+    }
+
+    public Set<String> getDrugInteractions(String gene, boolean expertCuratedOnly) {
+        return getDrugInteractions(gene, expertCuratedOnly, DEFAULT_MINIMAL_SCORE);
+    }
+
+    /**
+     * Get a list of known drug interactions for a given gene.
+     *
+     * @param gene The gene to query.
+     * @param expertCuratedOnly Whether the results should be restricted by `source_trust_levels`.
+     * @param minimalScore A minimal score, as given by the DGIdb.
+     * @return A set of drug interactions, sorted by decreasing score.
+     */
+    public Set<String> getDrugInteractions(String gene, boolean expertCuratedOnly, int minimalScore) {
+        Map<Integer, Map<String, Set<String>>> data = getData(gene, expertCuratedOnly);
+
+        Set<String> ret = new LinkedHashSet<>();
+        data.entrySet().stream()
+                .filter(e -> e.getKey() >= minimalScore)
+                .sorted(Map.Entry.comparingByKey(Comparator.reverseOrder()))
+                .forEach(e -> ret.addAll(e.getValue().keySet()));
+
+        return ret;
+    }
+
+    public Set<String> getPublications(String gene) {
+        return getPublications(gene, DEFAULT_EXPERT_CURATED_ONLY, DEFAULT_MINIMAL_SCORE);
+    }
+
+    public Set<String> getPublications(String gene, boolean expertCuratedOnly) {
+        return getPublications(gene, expertCuratedOnly, DEFAULT_MINIMAL_SCORE);
+    }
+
+    /**
+     * Get a list of PubMed IDs backing drug interaction claims.
+     *
+     * @param gene The gene to query.
+     * @param expertCuratedOnly Whether the results should be restricted by `source_trust_levels`.
+     * @param minimalScore A minimal score, as given by the DGIdb.
+     * @return A set of PubMed IDs, sorted by score.
+     */
+    public Set<String> getPublications(String gene, boolean expertCuratedOnly, int minimalScore) {
+        Map<Integer, Map<String, Set<String>>> data = getData(gene, expertCuratedOnly);
+
+        Set<String> ret = new LinkedHashSet<>();
+        data.entrySet().stream()
+                .filter(e -> e.getKey() >= minimalScore)
+                .sorted(Map.Entry.comparingByKey(Comparator.reverseOrder()))
+                .forEach(e -> e.getValue().forEach((k, v) -> ret.addAll(v)));
+
+        return ret;
+    }
+
+    /**
+     *
+     * @param gene
+     * @param expertCuratedOnly
+     * @return A two-level map `score -> (drugName -> pmids)`
+     */
+    private Map<Integer, Map<String, Set<String>>> getData(String gene, boolean expertCuratedOnly) {
+        // TODO EML4-ALK must split
+        // TODO check any unwanted gene (e.g. coming from prepositions)
+
+        String url = String.format(ENDPOINT + "?genes=%s", gene);
+        url = expertCuratedOnly ? url + "&source_trust_levels=Expert%20curated" : url;
+
+        JSONObject data = new JSONObject(REQUESTER.get(url));
+
+        Map<Integer, Map<String, Set<String>>> ret = new TreeMap<>();
+
+        JSONArray matchedTerms = data.getJSONArray("matchedTerms");
+        for (Object term : matchedTerms) {
+            JSONArray interactions = ((JSONObject) term).getJSONArray("interactions");
+            for (int i = 0; i < interactions.length(); i++) {
+                JSONObject interaction = (JSONObject) interactions.get(i);
+
+                int score = interaction.getInt("score");
+                String drugName = interaction.getString("drugName").toLowerCase();
+
+                Set<String> pmids = new LinkedHashSet<>();
+                interaction.getJSONArray("pmids").forEach(e -> pmids.add(e.toString()));
+
+                if (!ret.containsKey(score)) {
+                    ret.put(score, new TreeMap<>());
+                }
+
+                // The map might already contain an interaction for a given gene if there are multiple matched terms.
+                Map<String, Set<String>> interactionsByScore = ret.get(score);
+                if (!interactionsByScore.containsKey(drugName)) {
+                    interactionsByScore.put(drugName, new LinkedHashSet<>());
+                }
+                interactionsByScore.get(drugName).addAll(pmids);
+            }
+        }
+
+        return ret;
+    }
+}

src/main/java/at/medunigraz/imi/bst/trec/experiment/ExperimentsBuilder.java

@@ -123,6 +123,12 @@ public ExperimentsBuilder withGeneFamily() {
 		return this;
 	}
 
+	public ExperimentsBuilder withDrugInteraction() {
+		Query previousDecorator = buildingExp.getDecorator();
+		buildingExp.setDecorator(new DrugInteractionQueryDecorator(previousDecorator));
+		return this;
+	}
+
 	public ExperimentsBuilder withGoldStandard(Experiment.GoldStandard gold) {
 		buildingExp.setGoldStandard(gold);
 		return this;

src/main/java/at/medunigraz/imi/bst/trec/model/Topic.java

@@ -35,6 +35,8 @@ public class Topic {
 	// MUST be public to be accessed via Reflection on SubTemplateQueryDecorator
 	public List<String> geneHypernyms = new ArrayList<>();
 
+	public List<String> drugInteractions = new ArrayList<>();
+
 	public Topic() {
 
 	}
@@ -153,6 +155,11 @@ public Topic withGeneHypernym(String hypernym) {
 		this.geneHypernyms.add(hypernym);
 		return this;
 	}
+
+	public Topic withDrugInteraction(String interaction) {
+		this.drugInteractions.add(interaction);
+		return this;
+	}
 
 	private static boolean hasElement(Element element, String name) {
 		return element.getElementsByTagName(name).getLength() > 0 ? true : false;
@@ -240,6 +247,10 @@ public Map<String, String> getAttributes() {
 		for (int i = 0; i < geneHypernyms.size(); i++) {
 			ret.put("geneHypernyms" + i, geneHypernyms.get(i));
 		}
+
+		for (int i = 0; i < drugInteractions.size(); i++) {
+			ret.put("drugInteractions" + i, drugInteractions.get(i));
+		}
 
 		return ret;
 	}