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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,9 @@ | ||
| language: java | ||
| jdk: | ||
| - oraclejdk8 | ||
| - oraclejdk9 | ||
| - oraclejdk10 | ||
| - oraclejdk11 | ||
| - openjdk8 | ||
| - openjdk9 | ||
| - openjdk10 | ||
| - openjdk11 | ||
| script: mvn test -Delastic.hostname=$ELASTIC_HOSTNAME -Dlexigram.apikey=$LEXIGRAM_APIKEY -B | ||
| after_success: | ||
| - mvn -Delastic.hostname=$ELASTIC_HOSTNAME -Dlexigram.apikey=$LEXIGRAM_APIKEY clean test jacoco:report coveralls:report |
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117 changes: 117 additions & 0 deletions
117
src/main/java/at/medunigraz/imi/bst/trec/expansion/CachedWebRequester.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| package at.medunigraz.imi.bst.trec.expansion; | ||
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| 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; | ||
|
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| import java.io.*; | ||
| import java.util.HashMap; | ||
|
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| public class CachedWebRequester { | ||
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| private File cacheFile; | ||
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| private HashMap<String, String> cache = new HashMap<>(); | ||
|
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| public CachedWebRequester(String filename) { | ||
| this.cacheFile = new File(filename); | ||
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| if (cacheFile.exists()) { | ||
| try { | ||
| cache = load(cacheFile); | ||
| } catch (IOException | ClassNotFoundException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
| } | ||
|
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| /** | ||
| * 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); | ||
| } | ||
|
|
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| /** | ||
| * 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); | ||
| } | ||
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| 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; | ||
| } | ||
|
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| private void save(Object object, File file) throws IOException { | ||
| ObjectOutputStream oos = new ObjectOutputStream(new FileOutputStream(file)); | ||
| oos.writeObject(object); | ||
| oos.close(); | ||
| } | ||
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| private void put(String url, String data) { | ||
| cache.put(url, data); | ||
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| // Try to persist cache on disk | ||
| try { | ||
| save(cache, cacheFile); | ||
| } catch (IOException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
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| 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); | ||
| } | ||
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| return parseResponse(response); | ||
| } | ||
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| private String getResource(String url) { | ||
| HttpResponse<JsonNode> response = null; | ||
| try { | ||
| response = Unirest.get(url).asJson(); | ||
| } catch (UnirestException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
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| return parseResponse(response); | ||
| } | ||
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| 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."); | ||
| } | ||
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| if (response.getStatus() != 200) { | ||
| throw new RuntimeException("Got status code " + response.getStatus() + " from API with body " + response.getBody()); | ||
| } | ||
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| return response.getBody().toString(); | ||
| } | ||
| } |
122 changes: 122 additions & 0 deletions
122
src/main/java/at/medunigraz/imi/bst/trec/expansion/DGIdb.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| package at.medunigraz.imi.bst.trec.expansion; | ||
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| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.json.JSONArray; | ||
| import org.json.JSONObject; | ||
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| import java.util.*; | ||
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| public class DGIdb { | ||
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| private static final Logger LOG = LogManager.getLogger(); | ||
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| private static final String ENDPOINT = "http://dgidb.org/api/v2/interactions.json"; | ||
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| private static final int DEFAULT_MINIMAL_SCORE = 0; | ||
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| private static final boolean DEFAULT_EXPERT_CURATED_ONLY = false; | ||
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| private static final CachedWebRequester REQUESTER = new CachedWebRequester("cache/dgidb.ser"); | ||
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| public Set<String> getDrugInteractions(String gene) { | ||
| return getDrugInteractions(gene, DEFAULT_EXPERT_CURATED_ONLY, DEFAULT_MINIMAL_SCORE); | ||
| } | ||
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| public Set<String> getDrugInteractions(String gene, boolean expertCuratedOnly) { | ||
| return getDrugInteractions(gene, expertCuratedOnly, DEFAULT_MINIMAL_SCORE); | ||
| } | ||
|
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| /** | ||
| * 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); | ||
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| 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())); | ||
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| return ret; | ||
| } | ||
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| public Set<String> getPublications(String gene) { | ||
| return getPublications(gene, DEFAULT_EXPERT_CURATED_ONLY, DEFAULT_MINIMAL_SCORE); | ||
| } | ||
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| public Set<String> getPublications(String gene, boolean expertCuratedOnly) { | ||
| return getPublications(gene, expertCuratedOnly, DEFAULT_MINIMAL_SCORE); | ||
| } | ||
|
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| /** | ||
| * 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); | ||
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| 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))); | ||
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| return ret; | ||
| } | ||
|
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| /** | ||
| * | ||
| * @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) | ||
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| String url = String.format(ENDPOINT + "?genes=%s", gene); | ||
| url = expertCuratedOnly ? url + "&source_trust_levels=Expert%20curated" : url; | ||
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| JSONObject data = new JSONObject(REQUESTER.get(url)); | ||
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| Map<Integer, Map<String, Set<String>>> ret = new TreeMap<>(); | ||
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| 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); | ||
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| int score = interaction.getInt("score"); | ||
| String drugName = interaction.getString("drugName").toLowerCase(); | ||
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| Set<String> pmids = new LinkedHashSet<>(); | ||
| interaction.getJSONArray("pmids").forEach(e -> pmids.add(e.toString())); | ||
|
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| if (!ret.containsKey(score)) { | ||
| ret.put(score, new TreeMap<>()); | ||
| } | ||
|
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| // 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); | ||
| } | ||
| } | ||
|
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| return ret; | ||
| } | ||
| } |
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