@GET
@Path ("{subscription}/peek")
@RequiresPermissions ("databus|poll|{subscription}")
@Timed (name = "bv.emodb.databus.DatabusResource1.peek", absolute = true)
@ApiOperation (value = "Peek operation.",
        notes = "Returns an List of Events.",
        response = Event.class
)
public Response peek(@QueryParam ("partitioned") BooleanParam partitioned,
                     @PathParam ("subscription") String subscription,
                     @QueryParam ("limit") @DefaultValue ("10") IntParam limit,
                     @QueryParam ("includeTags") @DefaultValue ("false") BooleanParam includeTags,
                     @Authenticated Subject subject) {
    // For backwards compatibility with older clients only include tags if explicitly requested
    // (default is false).
    PeekOrPollResponseHelper helper = getPeekOrPollResponseHelper(includeTags.get());
    Iterator<Event> events = getClient(partitioned).peek(subject, subscription, limit.get());
    return Response.ok().entity(helper.asEntity(events)).build();
}
 

@GET
@Path ("{subscription}/poll")
@RequiresPermissions ("databus|poll|{subscription}")
@ApiOperation (value = "poll operation.",
        notes = "Returns a Response.",
        response = Response.class
)
public Response poll(@QueryParam ("partitioned") BooleanParam partitioned,
                     @PathParam ("subscription") String subscription,
                     @QueryParam ("ttl") @DefaultValue ("30") SecondsParam claimTtl,
                     @QueryParam ("limit") @DefaultValue ("10") IntParam limit,
                     @QueryParam ("ignoreLongPoll") @DefaultValue ("false") BooleanParam ignoreLongPoll,
                     @QueryParam ("includeTags") @DefaultValue ("false") BooleanParam includeTags,
                     @Context HttpServletRequest request,
                     @Authenticated Subject subject) {
    // For backwards compatibility with older clients only include tags if explicitly requested
    // (default is false).
    PeekOrPollResponseHelper helper = getPeekOrPollResponseHelper(includeTags.get());
    return _poller.poll(subject, getClient(partitioned), subscription, claimTtl.get(), limit.get(), request,
            ignoreLongPoll.get(), helper);
}
 

@GET
@Path("/suggestions/{term}")
@ApiOperation(value = "Suggest terms",
notes = "Suggests terms based on a mispelled or mistyped term.",
response = String.class,
responseContainer = "List")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Object suggestFromTerm(
    @ApiParam( value = "Mispelled term", required = true )
    @PathParam("term") String term,
    @ApiParam( value = DocumentationStrings.RESULT_LIMIT_DOC, required = false )
    @QueryParam("limit") @DefaultValue("1") IntParam limit) {
  List<String> suggestions = newArrayList(Iterables.limit(vocabulary.getSuggestions(term), limit.get()));
  return suggestions;
}
 

@GET
@Path("/{id}")
@ApiOperation(value = "Get all properties of a node", response = Graph.class)
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
@Produces({MediaType.APPLICATION_JSON, CustomMediaTypes.APPLICATION_GRAPHSON,
    MediaType.APPLICATION_XML, CustomMediaTypes.APPLICATION_GRAPHML,
    CustomMediaTypes.APPLICATION_XGMML, CustomMediaTypes.TEXT_GML, CustomMediaTypes.TEXT_CSV,
    CustomMediaTypes.TEXT_TSV, CustomMediaTypes.IMAGE_JPEG, CustomMediaTypes.IMAGE_PNG})
public Object getNode(
    @ApiParam(value = DocumentationStrings.GRAPH_ID_DOC,
        required = true) @PathParam("id") String id,
    @ApiParam(value = DocumentationStrings.PROJECTION_DOC,
        required = false) @QueryParam("project") @DefaultValue("*") Set<String> projection,
    @ApiParam(value = DocumentationStrings.JSONP_DOC,
        required = false) @QueryParam("callback") String callback) {
  return getNeighbors(id, new IntParam("0"), new BooleanParam("false"), new HashSet<String>(),
      "BOTH", new BooleanParam("false"), projection, callback);
}
 

@GET
@Path("/{id}")
public BlogPost getPost(@PathParam("id") IntParam id, @Context DSLContext create) {
    final Record4<Integer, String, OffsetDateTime, String[]> record = create
            .select(BLOG_POST.ID, BLOG_POST.BODY, BLOG_POST.CREATED_AT, arrayAgg(POST_TAG.TAG_NAME))
            .from(BLOG_POST)
            .leftOuterJoin(POST_TAG)
            .on(BLOG_POST.ID.equal(POST_TAG.POST_ID))
            .where(BLOG_POST.ID.equal(id.get()))
            .groupBy(BLOG_POST.ID, BLOG_POST.BODY, BLOG_POST.CREATED_AT)
            .fetchOne();

    if (record == null) {
        throw new WebApplicationException(Response.Status.NOT_FOUND);
    }

    final Integer postId = record.value1();
    final String text = record.value2();
    final OffsetDateTime createdAt = record.value3();
    final List<String> tags = Arrays.asList(record.value4());

    return BlogPost.create(postId, text, createdAt, tags);
}
 

/**
 * Get one or more IDs as a Google Protocol Buffer response
 *
 * @param agent
 *            User Agent
 * @param count
 *            Number of IDs to return
 * @return generated IDs
 */
@GET
@Timed
@Produces(ProtocolBufferMediaType.APPLICATION_PROTOBUF)
@CacheControl(mustRevalidate = true, noCache = true, noStore = true)
public SnowizardResponse getIdAsProtobuf(
        @HeaderParam(HttpHeaders.USER_AGENT) final String agent,
        @QueryParam("count") final Optional<IntParam> count) {

    final List<Long> ids = Lists.newArrayList();
    if (count.isPresent()) {
        for (int i = 0; i < count.get().get(); i++) {
            ids.add(getId(agent));
        }
    } else {
        ids.add(getId(agent));
    }
    return SnowizardResponse.newBuilder().addAllId(ids).build();
}
 

@GET
@Path("{channel}")
@RequiresPermissions("system|replicate_databus")
@Timed(name = "bv.emodb.databus.ReplicationResource1.get", absolute = true)
public List<ReplicationEvent> get(@PathParam("channel") String channel,
                                  @QueryParam("limit") @DefaultValue("100") IntParam limit) {
    return _replicationSource.get(channel, limit.get());
}
 

@GET
@Path("{subscription}/peek")
public List<Event> peek(@PathParam("subscription") String subscription,
                        @QueryParam("limit") @DefaultValue("10") IntParam limit) {
    checkLegalSubscriptionName(subscription);
    return fromInternal(_eventStore.peek(subscription, limit.get()));
}
 

@GET
@Path("{subscription}/poll")
public List<Event> poll(@PathParam("subscription") String subscription,
                        @QueryParam("ttl") @DefaultValue("30") SecondsParam claimTtl,
                        @QueryParam("limit") @DefaultValue("10") IntParam limit) {
    checkLegalSubscriptionName(subscription);
    return fromInternal(_eventStore.poll(subscription, claimTtl.get(), limit.get()));
}
 

@GET
@Path("{queue}/peek")
@RequiresPermissions("queue|poll|{queue}")
@Timed(name = "bv.emodb.queue.QueueResource1.peek", absolute = true)
@ApiOperation (value = "Peek operation.",
        notes = "Returns a List of Messages",
        response = Message.class
)
public List<Message> peek(@PathParam("queue") String queue,
                          @QueryParam("limit") @DefaultValue("10") IntParam limit) {
    // Not partitioned.  Peeking ignores claims.
    return _queueService.peek(queue, limit.get());
}
 

@GET
@Path("{queue}/poll")
@RequiresPermissions("queue|poll|{queue}")
@Timed(name = "bv.emodb.queue.QueueResource1.poll", absolute = true)
@ApiOperation (value = "Poll operation",
        notes = "Returns a List of Messages.",
        response = Message.class
)
public List<Message> poll(@QueryParam("partitioned") BooleanParam partitioned,
                          @PathParam("queue") String queue,
                          @QueryParam("ttl") @DefaultValue("30") SecondsParam claimTtl,
                          @QueryParam("limit") @DefaultValue("10") IntParam limit,
                          @Authenticated Subject subject) {
    return getService(partitioned, subject.getAuthenticationId()).poll(queue, claimTtl.get(), limit.get());
}
 

@GET
@Path("{queue}/peek")
@RequiresPermissions("queue|poll|{queue}")
@Timed(name = "bv.emodb.dedupq.DedupQueueResource1.peek", absolute = true)
@ApiOperation (value = "Peek operation.",
        notes = "Returns a List of Messages.",
        response = Message.class
)
public List<Message> peek(@QueryParam("partitioned") BooleanParam partitioned,
                          @PathParam("queue") String queue,
                          @QueryParam("limit") @DefaultValue("10") IntParam limit,
                          @Authenticated Subject subject) {
    // Not partitioned.  Peeking ignores claims.
    return getService(partitioned, subject.getAuthenticationId()).peek(queue, limit.get());
}
 

@GET
@Path("{queue}/poll")
@RequiresPermissions("queue|poll|{queue}")
@Timed(name = "bv.emodb.dedupq.DedupQueueResource1.poll", absolute = true)
@ApiOperation (value = "Poll operation.",
        notes = "Returns a List of Messages",
        response = Message.class
)
public List<Message> poll(@QueryParam("partitioned") BooleanParam partitioned,
                          @PathParam("queue") String queue,
                          @QueryParam("ttl") @DefaultValue("30") SecondsParam claimTtl,
                          @QueryParam("limit") @DefaultValue("10") IntParam limit,
                          @Authenticated Subject subject) {
    return getService(partitioned, subject.getAuthenticationId()).poll(queue, claimTtl.get(), limit.get());
}
 

@GET
@Path ("_table/{table}/size")
@RequiresPermissions ("sor|read|{table}")
@Timed (name = "bv.emodb.sor.DataStoreResource1.getTableSize", absolute = true)
@ApiOperation (value = "Returns Table Size",
        notes = "Returns a long",
        response = long.class
)
public long getTableSize(@PathParam ("table") String table, @QueryParam ("limit") @Nullable IntParam limit) {
    return limit == null ?
            _dataStore.getTableApproximateSize(table) :
            _dataStore.getTableApproximateSize(table, limit.get());
}
 

/**
 * Retrieves a list split identifiers for the specified table.
 */
@GET
@Path ("_split/{table}")
@RequiresPermissions ("sor|read|{table}")
@Timed (name = "bv.emodb.sor.DataStoreResource1.getSplits", absolute = true)
@ApiOperation (value = "Retrieves a list split identifiers for the specified table.",
        notes = "Retrieves a list split identifiers for the specified table.",
        response = Collection.class
)
public Collection<String> getSplits(@PathParam ("table") String table,
                                    @QueryParam ("size") @DefaultValue ("10000") IntParam desiredRecordsPerSplit) {
    return _dataStore.getSplits(table, desiredRecordsPerSplit.get());
}
 

@GET
@Path("/neighbors/{id}")
@ApiOperation(value = "Get neighbors", response = Graph.class)
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
@Produces({MediaType.APPLICATION_JSON, CustomMediaTypes.APPLICATION_GRAPHSON,
    MediaType.APPLICATION_XML, CustomMediaTypes.APPLICATION_GRAPHML,
    CustomMediaTypes.APPLICATION_XGMML, CustomMediaTypes.TEXT_GML, CustomMediaTypes.TEXT_CSV,
    CustomMediaTypes.TEXT_TSV, CustomMediaTypes.IMAGE_JPEG, CustomMediaTypes.IMAGE_PNG})
public Object getNeighbors(
    @ApiParam(value = DocumentationStrings.GRAPH_ID_DOC,
        required = true) @PathParam("id") String id,
    @ApiParam(value = "How far to traverse neighbors",
        required = false) @QueryParam("depth") @DefaultValue("1") IntParam depth,
    @ApiParam(value = "Traverse blank nodes",
        required = false) @QueryParam("blankNodes") @DefaultValue("false") BooleanParam traverseBlankNodes,
    @ApiParam(value = "Which relationship to traverse",
        required = false) @QueryParam("relationshipType") Set<String> relationshipTypes,
    @ApiParam(value = DocumentationStrings.DIRECTION_DOC, required = false,
        allowableValues = DocumentationStrings.DIRECTION_ALLOWED) @QueryParam("direction") @DefaultValue("BOTH") String direction,
    @ApiParam(value = "Should subproperties and equivalent properties be included",
        required = false) @QueryParam("entail") @DefaultValue("false") BooleanParam entail,
    @ApiParam(value = DocumentationStrings.PROJECTION_DOC,
        required = false) @QueryParam("project") @DefaultValue("*") Set<String> projection,
    @ApiParam(value = DocumentationStrings.JSONP_DOC,
        required = false) @QueryParam("callback") String callback) {
  return getNeighborsFromMultipleRoots(newHashSet(id), depth, traverseBlankNodes,
      relationshipTypes, direction, entail, projection, callback);
}
 

@POST
@Path("/entities")
@Consumes("application/x-www-form-urlencoded")
@ApiOperation(value = "Get entities from text", 
response = EntityAnnotation.class, 
responseContainer = "List",
notes = "Get the entities from content without embedding them in the source - only the entities are returned. " +
    DocumentationStrings.REST_ABUSE_DOC)
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Object postEntities(
    @ApiParam( value = DocumentationStrings.CONTENT_DOC, required = true)
    final @FormParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @FormParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @FormParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @FormParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @FormParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @FormParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers) {
  return getEntities(content, includeCategories, excludeCategories, minLength, 
      longestOnly, includeAbbrev, includeAcronym, includeNumbers);
}
 

/***
 * A convenience call for retrieving both a list of entities and annotated content
 * 
 * @param content The content to annotate
 * @param includeCategories A set of categories to include
 * @param excludeCategories A set of categories to exclude
 * @param minLength The minimum length of annotated entities
 * @param longestOnly Should only the longest entity be returned for an overlapping group
 * @param includeAbbrev Should abbreviations be included
 * @param includeAcronym Should acronyms be included
 * @param includeNumbers Should numbers be included
 * @return A list of entities and the annotated content
 * @throws IOException 
 */
@POST
@Path("/complete")
@Consumes("application/x-www-form-urlencoded")
@ApiOperation(value = "Get embedded annotations as well as a separate list", 
response = Annotations.class, 
notes="A convenience resource for retrieving both a list of entities and annotated content. " + DocumentationStrings.REST_ABUSE_DOC)
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Annotations postEntitiesAndContent(
    @ApiParam( value = DocumentationStrings.CONTENT_DOC, required = true)
    final @FormParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @FormParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @FormParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @FormParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @FormParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @FormParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers) throws IOException {
  return this.getEntitiesAndContent(content, includeCategories, excludeCategories, minLength, longestOnly, includeAbbrev, includeAcronym, includeNumbers);
}
 

@POST
@Timed
public Response put(@QueryParam("summary") @DefaultValue("false") BooleanFlag summary,
                    @QueryParam("details") @DefaultValue("false") BooleanFlag details,
                    @QueryParam("sync") @DefaultValue("false") BooleanFlag sync,
                    @QueryParam("sync_timeout") @DefaultValue("120000") IntParam sync_timeout,
                    JsonNode body) throws Exception {
  LOG.trace("put; summary: {}, details: {}, sync: {}, sync_timeout: {}, body: {}",
            summary, details, sync, sync_timeout, body);

  WriteBatch batch = ts.writeBatch();
  try {
    batch.setFlushMode(SessionConfiguration.FlushMode.AUTO_FLUSH_BACKGROUND);
    if (sync_timeout.get() > 0) batch.setTimeoutMillis(sync_timeout.get());

    int datapoints = 0;
    List<Error> errors = new ArrayList<>();
    Iterator<JsonNode> nodes;
    if (body.isArray()) {
      nodes = body.elements();
    } else {
      nodes = Iterators.singletonIterator(body);
    }

    while (nodes.hasNext()) {
      datapoints++;
      JsonNode node = nodes.next();
      try {
        Datapoint datapoint = mapper.treeToValue(node, Datapoint.class);
        batch.writeDatapoint(datapoint.getMetric(),
                             datapoint.getTags(),
                             datapoint.getTimestamp(),
                             datapoint.getValue());
      } catch (JsonProcessingException e) {
        errors.add(new Error(node, e.getMessage()));
      }
    }

    batch.flush();
    RowErrorsAndOverflowStatus batchErrors = batch.getPendingErrors();
    for (RowError rowError : batchErrors.getRowErrors()) {
      errors.add(new Error(null, rowError.getErrorStatus().toString()
       + " (op " + rowError.getOperation().toString() + ")"));
    }

    if (errors.isEmpty()) {
      LOG.debug("put {} datapoints: {}", datapoints, body);
      return Response.noContent().build();
    } else {
      LOG.error("failed to write {} of {} body: {}", errors.size(), datapoints, errors);
      if (details.get()) {
        Detail detail = new Detail(errors, errors.size(), datapoints - errors.size());
        return Response.status(Response.Status.BAD_REQUEST).entity(detail).build();
      } else if (summary.get()) {
        Summary s = new Summary(errors.size(), datapoints - errors.size());
        return Response.status(Response.Status.BAD_REQUEST).entity(s).build();
      } else {
        return Response.status(Response.Status.BAD_REQUEST).build();
      }
    }

  } finally {
    batch.close();
  }
}
 

@GET
@Path("/autocomplete/{term}")
@ApiOperation(value = "Find a concept by its prefix",
notes = "This resource is designed for autocomplete services.",
response = Completion.class,
responseContainer = "List")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public List<Completion> findByPrefix(
    @ApiParam( value = "Term prefix to find", required = true )
    @PathParam("term") String termPrefix,
    @ApiParam( value = DocumentationStrings.RESULT_LIMIT_DOC, required = false )
    @QueryParam("limit") @DefaultValue("20") IntParam limit,
    @ApiParam( value = DocumentationStrings.SEARCH_SYNONYMS, required = false )
    @QueryParam("searchSynonyms") @DefaultValue("true") BooleanParam searchSynonyms,
    @ApiParam( value = DocumentationStrings.SEARCH_ABBREVIATIONS, required = false )
    @QueryParam("searchAbbreviations") @DefaultValue("false") BooleanParam searchAbbreviations,
    @ApiParam( value = DocumentationStrings.SEARCH_ACRONYMS, required = false )
    @QueryParam("searchAcronyms") @DefaultValue("false") BooleanParam searchAcronyms,
    @ApiParam( value = DocumentationStrings.INCLUDE_DEPRECATED_CLASSES, required = false )
    @QueryParam("includeDeprecated") @DefaultValue("false") BooleanParam includeDeprecated,
    @ApiParam( value = "Categories to search (defaults to all)", required = false )
    @QueryParam("category") List<String> categories,
    @ApiParam( value = "CURIE prefixes to search (defaults to all)", required = false )
    @QueryParam("prefix") List<String> prefixes) {
  Vocabulary.Query.Builder builder = new Vocabulary.Query.Builder(termPrefix).
      categories(categories).
      prefixes(prefixes).
      includeDeprecated(includeDeprecated.get()).
      includeSynonyms(searchSynonyms.get()).
      includeAbbreviations(searchAbbreviations.get()).
      includeAcronyms(searchAcronyms.get()).
      limit(1000);
  List<Concept> concepts = vocabulary.getConceptsFromPrefix(builder.build());
  List<Completion> completions = getCompletions(builder.build(), concepts);
  // TODO: Move completions to scigraph-core for #51
  sort(completions);
  int endIndex = limit.get() > completions.size() ? completions.size() : limit.get();
  completions = completions.subList(0, endIndex);
  return completions;
}
 

@GET
@Path("/term/{term}")
@ApiOperation(value = "Find a concept from a term",
notes = "Makes a best effort to provide \"exactish\" matching. " +
    "Individual tokens within multi-token labels are not matched" + 
    " (ie: \"foo bar\" would not be returned by a search for \"bar\")."
    + " Results are not guaranteed to be unique.",
    response = Concept.class,
    responseContainer="List")
@ApiResponses({
  @ApiResponse(code = 404, message = "Concept with term could not be found")
})
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public List<ConceptDTO> findByTerm(
    @ApiParam( value = "Term to find", required = true )
    @PathParam("term") String term,
    @ApiParam( value = DocumentationStrings.RESULT_LIMIT_DOC, required = false )
    @QueryParam("limit") @DefaultValue("20") IntParam limit,
    @ApiParam( value = DocumentationStrings.SEARCH_SYNONYMS, required = false )
    @QueryParam("searchSynonyms") @DefaultValue("true") BooleanParam searchSynonyms,
    @ApiParam( value = DocumentationStrings.SEARCH_ABBREVIATIONS, required = false )
    @QueryParam("searchAbbreviations") @DefaultValue("false") BooleanParam searchAbbreviations,
    @ApiParam( value = DocumentationStrings.SEARCH_ACRONYMS, required = false )
    @QueryParam("searchAcronyms") @DefaultValue("false") BooleanParam searchAcronyms,
    @ApiParam( value = "Categories to search (defaults to all)", required = false )
    @QueryParam("category") List<String> categories,
    @ApiParam( value = "CURIE prefixes to search (defaults to all)", required = false )
    @QueryParam("prefix") List<String> prefixes) {
  Vocabulary.Query.Builder builder = new Vocabulary.Query.Builder(term).
      categories(categories).
      prefixes(prefixes).
      includeSynonyms(searchSynonyms.get()).
      includeAbbreviations(searchAbbreviations.get()).
      includeAcronyms(searchAcronyms.get()).
      limit(limit.get());
  List<Concept> concepts = vocabulary.getConceptsFromTerm(builder.build());
  if (concepts.isEmpty()) {
    throw new WebApplicationException(404);
  } else {
    List<ConceptDTO> dtos = transform(concepts, conceptDtoTransformer);
    return dtos;
  }
}
 

@GET
@Path("/search/{term}")
@ApiOperation(value = "Find a concept from a term fragment",
notes = "Searches the complete text of the term. "
    + "Individual tokens within multi-token labels are matched" + 
    " (ie: \"foo bar\" would be returned by a search for \"bar\"). Results are not guaranteed to be unique.",
    response = ConceptDTO.class,
    responseContainer= "List")
@ApiResponses({
  @ApiResponse(code = 404, message = "Concept with term could not be found")
})
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public List<ConceptDTO> searchByTerm(
    @ApiParam( value = "Term to find", required = true )
    @PathParam("term") String term,
    @ApiParam( value = DocumentationStrings.RESULT_LIMIT_DOC, required = false )
    @QueryParam("limit") @DefaultValue("20") IntParam limit,
    @ApiParam( value = DocumentationStrings.SEARCH_SYNONYMS, required = false )
    @QueryParam("searchSynonyms") @DefaultValue("true") BooleanParam searchSynonyms,
    @ApiParam( value = DocumentationStrings.SEARCH_ABBREVIATIONS, required = false )
    @QueryParam("searchAbbreviations") @DefaultValue("false") BooleanParam searchAbbreviations,
    @ApiParam( value = DocumentationStrings.SEARCH_ACRONYMS, required = false )
    @QueryParam("searchAcronyms") @DefaultValue("false") BooleanParam searchAcronyms,
    @ApiParam( value = "Categories to search (defaults to all)", required = false )
    @QueryParam("category") List<String> categories,
    @ApiParam( value = "CURIE prefixes to search (defaults to all)", required = false )
    @QueryParam("prefix") List<String> prefixes) {
  Vocabulary.Query.Builder builder = new Vocabulary.Query.Builder(term).
      categories(categories).
      prefixes(prefixes).
      includeSynonyms(searchSynonyms.get()).
      includeAbbreviations(searchAbbreviations.get()).
      includeAcronyms(searchAcronyms.get()).
      limit(limit.get());
  List<Concept> concepts = vocabulary.searchConcepts(builder.build());
  if (concepts.isEmpty()) {
    throw new WebApplicationException(404);
  } else {
    List<ConceptDTO> dtos = transform(concepts, conceptDtoTransformer);
    return dtos;
  }
}
 

@GET
@Produces("text/plain; charset=utf-8")
@ApiOperation(value = "Annotate text", response = String.class,
notes="This service is designed to annotate shorter fragments of text. Use the POST version if your content is too long.")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Response annotate(
    @ApiParam( value = DocumentationStrings.CONTENT_DOC, required = true)
    final @QueryParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @QueryParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @QueryParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @QueryParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @QueryParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @QueryParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers) {
  StreamingOutput stream = new StreamingOutput() {
    @Override
    public void write(OutputStream os) throws IOException,
    WebApplicationException {
      Writer writer = new BufferedWriter(new OutputStreamWriter(os));

      EntityFormatConfiguration.Builder configBuilder = new EntityFormatConfiguration.Builder(new StringReader(content)).writeTo(writer);
      configBuilder.includeCategories(includeCategories);
      configBuilder.excludeCategories(excludeCategories);
      configBuilder.longestOnly(longestOnly.get());
      configBuilder.includeAbbreviations(includeAbbrev.get());
      configBuilder.includeAncronyms(includeAcronym.get());
      configBuilder.includeNumbers(includeNumbers.get());
      configBuilder.minLength(minLength.get());

      try {
        processor.annotateEntities(configBuilder.get());
      } catch (Exception e) {
        logger.log(Level.WARNING, e.getMessage(), e);
        throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
      }
      writer.flush();
    }
  };
  return Response.ok(stream).build();
}
 

@GET
@Path("/url")
@Produces(MediaType.TEXT_HTML)
@ApiOperation(value = "Annotate a URL", response = String.class, 
notes="Annotate the content of a URL (presumably an HTML page). <em>NOTE:</em> this method will add a &lt;base&gt; element to the head.")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Response annotateUrl(
    @ApiParam( value = "", required = true)
    final @QueryParam("url") @DefaultValue("") String url,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @QueryParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @QueryParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @QueryParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @QueryParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @QueryParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers,
    @ApiParam( value = DocumentationStrings.IGNORE_TAGS_DOC, required = false)
    final @QueryParam("ignoreTag") Set<String> ignoreTags,
    @ApiParam( value = DocumentationStrings.STYLESHEETS_DOC, required = false)
    final @QueryParam("stylesheet") List<String> stylesheets,
    @ApiParam( value = DocumentationStrings.SCRIPTS_DOC, required = false)
    final @QueryParam("scripts") List<String> scripts,
    @ApiParam( value = DocumentationStrings.TARGET_IDS_DOC, required = false)
    final @QueryParam("targetId") Set<String> targetIds,
    @ApiParam( value = DocumentationStrings.CSS_CLASS_DOCS, required = false)
    final @QueryParam("targetClass") Set<String> targetClasses) {
  StreamingOutput stream = new StreamingOutput() {
    @Override
    public void write(OutputStream os) throws IOException,
    WebApplicationException {
      Writer writer = new BufferedWriter(new OutputStreamWriter(os, Charsets.UTF_8));

      URL source = new URL(url);
      try (Reader reader = new BufferedReader(new InputStreamReader(source.openStream(), Charsets.UTF_8))) {
        EntityFormatConfiguration.Builder configBuilder = new EntityFormatConfiguration.Builder(reader).writeTo(writer);
        configBuilder.includeCategories(includeCategories);
        configBuilder.excludeCategories(excludeCategories);
        configBuilder.longestOnly(longestOnly.get());
        configBuilder.includeAbbreviations(includeAbbrev.get());
        configBuilder.includeAncronyms(includeAcronym.get());
        configBuilder.includeNumbers(includeNumbers.get());
        configBuilder.minLength(minLength.get());
        if (!ignoreTags.isEmpty()) {
          configBuilder.ignoreTags(ignoreTags);
        }
        configBuilder.stylesheets(stylesheets);
        configBuilder.scripts(scripts);
        configBuilder.url(source);
        configBuilder.targetIds(targetIds);
        configBuilder.targetClasses(targetClasses);

        try {
          processor.annotateEntities(configBuilder.get());
          reader.close();
        } catch (Exception e) {
          logger.log(Level.WARNING, e.getMessage(), e);
          throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
        }
        writer.flush();
      }
    }
  };
  return Response.ok(stream).build();
}
 

@POST
@Consumes("application/x-www-form-urlencoded")
@ApiOperation(value = "Annotate text", response = String.class, 
notes = "A POST resource for API clients wishing to annotate longer content. This is most likely the method of choice for most clients. "
    + DocumentationStrings.REST_ABUSE_DOC
    )
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Response annotatePost(
    @ApiParam(value = DocumentationStrings.CONTENT_DOC, required = true)
    final @FormParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @FormParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @FormParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @FormParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @FormParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @FormParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @FormParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers,
    @ApiParam( value = DocumentationStrings.IGNORE_TAGS_DOC, required = false)
    final @FormParam("ignoreTag") Set<String> ignoreTags,
    @ApiParam( value = DocumentationStrings.STYLESHEETS_DOC, required = false)
    final @FormParam("stylesheet") List<String> stylesheets,
    @ApiParam( value = DocumentationStrings.SCRIPTS_DOC, required = false)
    final @FormParam("scripts") List<String> scripts,
    @ApiParam( value = DocumentationStrings.TARGET_IDS_DOC, required = false)
    final @FormParam("targetId") Set<String> targetIds,
    @ApiParam( value = DocumentationStrings.CSS_CLASS_DOCS, required = false)
    final @FormParam("targetClass") Set<String> targetClasses) {
  StreamingOutput stream = new StreamingOutput() {
    @Override
    public void write(OutputStream os) throws IOException,
    WebApplicationException {
      Writer writer = new BufferedWriter(new OutputStreamWriter(os, Charsets.UTF_8));

      EntityFormatConfiguration.Builder configBuilder = new EntityFormatConfiguration.Builder(new StringReader(content)).writeTo(writer);
      configBuilder.includeCategories(includeCategories);
      configBuilder.excludeCategories(excludeCategories);
      configBuilder.longestOnly(longestOnly.get());
      configBuilder.includeAbbreviations(includeAbbrev.get());
      configBuilder.includeAncronyms(includeAcronym.get());
      configBuilder.includeNumbers(includeNumbers.get());
      configBuilder.minLength(minLength.get());
      if (!ignoreTags.isEmpty()) {
        configBuilder.ignoreTags(ignoreTags);
      }
      configBuilder.stylesheets(stylesheets);
      configBuilder.scripts(scripts);
      configBuilder.targetIds(targetIds);
      configBuilder.targetClasses(targetClasses);

      try {
        processor.annotateEntities(configBuilder.get());
      } catch (Exception e) {
        logger.log(Level.WARNING, e.getMessage(), e);
        throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
      }
      writer.flush();
    }
  };
  return Response.ok(stream).build();
}
 

@GET
@Path("/entities")
@ApiOperation(value = "Get entities from text",
response = EntityAnnotation.class,
responseContainer = "List",
notes="Get entities from content without embedding them in the source.")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public List<EntityAnnotation> getEntities(
    @ApiParam( value = DocumentationStrings.CONTENT_DOC, required = true)
    final @QueryParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @QueryParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @QueryParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @QueryParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @QueryParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @QueryParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers) {
  List<EntityAnnotation> entities = newArrayList();
  try {
    EntityFormatConfiguration.Builder configBuilder = new EntityFormatConfiguration.Builder(new StringReader(content));
    configBuilder.includeCategories(includeCategories);
    configBuilder.excludeCategories(excludeCategories);
    configBuilder.includeAbbreviations(includeAbbrev.get());
    configBuilder.includeAncronyms(includeAcronym.get());
    configBuilder.includeNumbers(includeNumbers.get());
    configBuilder.minLength(minLength.get());
    configBuilder.longestOnly(longestOnly.get());
    entities = processor.annotateEntities(configBuilder.get());
  } catch (Exception e) {
    logger.log(Level.WARNING, e.getMessage(), e);
    throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
  }
  return entities;
}
 

/*** 
 * @return A list of entities and the annotated content
 */
@GET
@Path("/complete")
@Consumes("application/x-www-form-urlencoded")
@ApiOperation(value = "Get embedded annotations as well as a separate list", 
response = Annotations.class, 
notes="A convenience resource for retrieving both a list of entities and annotated content")
@Timed
@CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
public Annotations getEntitiesAndContent(
    @ApiParam( value = DocumentationStrings.CONTENT_DOC, required = true)
    final @QueryParam("content") @DefaultValue("") String content,
    @ApiParam( value = DocumentationStrings.INCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("includeCat") Set<String> includeCategories,
    @ApiParam( value = DocumentationStrings.EXCLUDE_CATEGORIES_DOC, required = false)
    final @QueryParam("excludeCat") Set<String> excludeCategories,
    @ApiParam( value = DocumentationStrings.MINIMUM_LENGTH_DOC, required = false)
    final @QueryParam("minLength") @DefaultValue("4") IntParam minLength,
    @ApiParam( value = DocumentationStrings.LONGEST_ENTITY_DOC, required = false)
    final @QueryParam("longestOnly") @DefaultValue("false") BooleanParam longestOnly,
    @ApiParam( value = DocumentationStrings.INCLUDE_ABBREV_DOC, required = false)
    final @QueryParam("includeAbbrev") @DefaultValue("false") BooleanParam includeAbbrev,
    @ApiParam( value = DocumentationStrings.INCLUDE_ACRONYMS_DOC, required = false)
    final @QueryParam("includeAcronym") @DefaultValue("false") BooleanParam includeAcronym,
    @ApiParam( value = DocumentationStrings.INCLUDE_NUMBERS_DOC, required = false)
    final @QueryParam("includeNumbers") @DefaultValue("false") BooleanParam includeNumbers
    ) throws IOException {
  Annotations annotations = new Annotations();
  StringWriter writer = new StringWriter();
  EntityFormatConfiguration.Builder configBuilder = new EntityFormatConfiguration.Builder(new StringReader(content));
  configBuilder.includeCategories(includeCategories);
  configBuilder.excludeCategories(excludeCategories);
  configBuilder.includeAbbreviations(includeAbbrev.get());
  configBuilder.includeAncronyms(includeAcronym.get());
  configBuilder.includeNumbers(includeNumbers.get());
  configBuilder.minLength(minLength.get());
  configBuilder.longestOnly(longestOnly.get());
  configBuilder.writeTo(writer);
  annotations.delegate = processor.annotateEntities(configBuilder.get());
  annotations.content = writer.toString();

  return annotations;
}