| /* |
| * Licensed to the Apache Software Foundation (ASF) under one or more |
| * contributor license agreements. See the NOTICE file distributed with |
| * this work for additional information regarding copyright ownership. |
| * The ASF licenses this file to You under the Apache License, Version 2.0 |
| * (the "License"); you may not use this file except in compliance with |
| * the License. You may obtain a copy of the License at |
| * |
| * http://www.apache.org/licenses/LICENSE-2.0 |
| * |
| * Unless required by applicable law or agreed to in writing, software |
| * distributed under the License is distributed on an "AS IS" BASIS, |
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
| * See the License for the specific language governing permissions and |
| * limitations under the License. |
| */ |
| package org.apache.solr.common.util; |
| |
| import java.io.IOException; |
| import java.io.StringReader; |
| import java.lang.ref.WeakReference; |
| import java.util.Arrays; |
| import java.util.Collections; |
| import java.util.List; |
| import java.util.Map; |
| import java.util.concurrent.atomic.AtomicReference; |
| |
| import org.apache.commons.lang3.StringUtils; |
| import org.apache.solr.SolrTestCaseJ4; |
| import org.apache.solr.util.RecordingJSONParser; |
| |
| |
| public class TestJsonRecordReader extends SolrTestCaseJ4 { |
| |
| public void testOneLevelSplit() throws IOException { |
| String json = "{\n" + |
| " \"a\":\"A\" ,\n" + |
| " \"b\":[\n" + |
| " {\"c\":\"C\",\"d\":\"D\" ,\"e\": {\n" + |
| " \"s\":\"S\",\n" + |
| " \"t\":3}},\n" + |
| " {\"c\":\"C1\",\"d\":\"D1\"},\n" + |
| " {\"c\":\"C2\",\"d\":\"D2\"}\n" + |
| " ]\n" + |
| "}"; |
| JsonRecordReader streamer = JsonRecordReader.getInst("/b", Arrays.asList( |
| "a_s:/a", |
| "c_s:/b/c", |
| "d_s:/b/d", |
| "e_s:/b/e/s", |
| "e_i:/b/e/t" |
| )); |
| |
| List<Map<String, Object>> records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(3, records.size()); |
| assertEquals(3l, ((Map) records.get(0)).get("e_i")); |
| assertEquals("D2", ((Map) records.get(2)).get("d_s")); |
| assertNull(((Map) records.get(1)).get("e_s")); |
| assertNull(((Map) records.get(2)).get("e_s")); |
| assertNull(((Map) records.get(1)).get("e_i")); |
| assertNull(((Map) records.get(2)).get("e_i")); |
| |
| // All parameters but /b/c is omitted |
| streamer = JsonRecordReader.getInst("/b", Arrays.asList( |
| "a:/a", |
| "d:/b/d", |
| "s:/b/e/s", |
| "t:/b/e/t" |
| )); |
| records = streamer.getAllRecords(new StringReader(json)); |
| for (Map<String, Object> record : records) { |
| assertNull(record.get("c")); |
| |
| } |
| |
| //one nested /b/e/* object is completely ignored |
| streamer = JsonRecordReader.getInst("/b", Arrays.asList( |
| "a:/a", |
| "c:/b/c", |
| "d:/b/d" |
| )); |
| records = streamer.getAllRecords(new StringReader(json)); |
| for (Map<String, Object> record : records) { |
| assertNull(record.get("s")); |
| assertNull(record.get("t")); |
| } |
| |
| //nested /b/e/* object is completely ignored even though /b/e is mapped |
| streamer = JsonRecordReader.getInst("/b", Arrays.asList( |
| "a_s:/a", |
| "c_s:/b/c", |
| "d_s:/b/d", |
| "e:/b/e" |
| |
| )); |
| records = streamer.getAllRecords(new StringReader(json)); |
| for (Map<String, Object> record : records) { |
| assertNull(record.get("s")); |
| assertNull(record.get("t")); |
| assertNull(record.get("e")); |
| } |
| |
| |
| streamer = JsonRecordReader.getInst("/b", Arrays.asList( |
| "a_s:/a", |
| "c_s:/b/c", |
| "d_s:/b/d", |
| "/b/e/*" |
| )); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(3, records.size()); |
| assertEquals(3l, ((Map) records.get(0)).get("t")); |
| assertEquals("S", ((Map) records.get(0)).get("s")); |
| assertNull(((Map) records.get(1)).get("s")); |
| assertNull(((Map) records.get(2)).get("s")); |
| |
| |
| } |
| |
| public void testSrcField() throws Exception { |
| String json = "{\n" + |
| " \"id\" : \"123\",\n" + |
| " \"description\": \"Testing /json/docs srcField 1\",\n" + |
| "\n" + |
| " \"nested_data\" : {\n" + |
| " \"nested_inside\" : \"check check check 1\"\n" + |
| " }\n" + |
| "}"; |
| |
| String json2 = |
| " {\n" + |
| " \"id\" : \"345\",\n" + |
| " \"payload\": \""+ StringUtils.repeat("0123456789", 819) + |
| "\",\n" + |
| " \"description\": \"Testing /json/docs srcField 2\",\n" + |
| "\n" + |
| " \"nested_data\" : {\n" + |
| " \"nested_inside\" : \"check check check 2\"\n" + |
| " }\n" + |
| "}"; |
| |
| String json3 = |
| " {\n" + |
| " \"id\" : \"678\",\n" + |
| " \"description\": \"Testing /json/docs srcField 3\",\n" + |
| "\n" + |
| " \"nested_data\" : {\n" + |
| " \"nested_inside\" : \"check check check 3\"\n" + |
| " }\n" + |
| "}"; |
| |
| |
| JsonRecordReader streamer = JsonRecordReader.getInst("/", Arrays.asList("id:/id")); |
| RecordingJSONParser parser = new RecordingJSONParser(new StringReader(json + json2 + json3)); |
| |
| streamer.streamRecords(parser, new JsonRecordReader.Handler() { |
| int count = 0; |
| |
| @Override |
| public void handle(Map<String, Object> record, String path) { |
| count++; |
| String buf = parser.getBuf(); |
| parser.resetBuf(); |
| |
| @SuppressWarnings({"rawtypes"}) |
| Map m = (Map) Utils.fromJSONString(buf); |
| if (count == 1) { |
| assertEquals(m.get("id"), "123"); |
| assertEquals(m.get("description"), "Testing /json/docs srcField 1"); |
| assertEquals(((Map) m.get("nested_data")).get("nested_inside"), "check check check 1"); |
| } |
| if (count++ == 2) { |
| assertEquals(m.get("id"), "345"); |
| assertEquals(m.get("description"), "Testing /json/docs srcField 2"); |
| assertEquals(((Map) m.get("nested_data")).get("nested_inside"), "check check check 2"); |
| } |
| if (count++ == 3) { |
| assertEquals(m.get("id"), "678"); |
| assertEquals(m.get("description"), "Testing /json/docs srcField 3"); |
| assertEquals(((Map) m.get("nested_data")).get("nested_inside"), "check check check 3"); |
| } |
| |
| } |
| }); |
| |
| } |
| |
| public void testRecursiveWildCard() throws IOException { |
| String json = "{\n" + |
| " \"a\":\"A\" ,\n" + |
| " \"b\":[\n" + |
| " {\"c\":\"C\",\"d\":\"D\" ,\"e\": {\n" + |
| " \"s\":\"S\",\n" + |
| " \"t\":3 ,\"u\":{\"v\":3.1234,\"w\":false}}},\n" + |
| " {\"c\":\"C1\",\"d\":\"D1\"},\n" + |
| " {\"c\":\"C2\",\"d\":\"D2\"}\n" + |
| " ]\n" + |
| "}"; |
| JsonRecordReader streamer; |
| List<Map<String, Object>> records; |
| |
| streamer = JsonRecordReader.getInst("/b", Collections.singletonList("/b/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(3, records.size()); |
| assertEquals("records " + records, 3l, ((Map) records.get(0)).get("t")); |
| assertEquals("records " + records, "S", ((Map) records.get(0)).get("s")); |
| assertEquals("records " + records, 3.1234, ((Map) records.get(0)).get("v")); |
| assertEquals("records " + records, false, ((Map) records.get(0)).get("w")); |
| for (Map<String, Object> record : records) { |
| assertNotNull("records " + records, record.get("c")); |
| assertNotNull("records " + records, record.get("d")); |
| } |
| |
| streamer = JsonRecordReader.getInst("/", Collections.singletonList("/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(1, records.size()); |
| assertEquals(3, ((List) ((Map) records.get(0)).get("c")).size()); |
| assertEquals(3, ((List) ((Map) records.get(0)).get("d")).size()); |
| assertEquals("records " + records, 3l, ((Map) records.get(0)).get("t")); |
| assertEquals("records " + records, "S", ((Map) records.get(0)).get("s")); |
| assertEquals("records " + records, "A", ((Map) records.get(0)).get("a")); |
| assertEquals("records " + records, false, ((Map) records.get(0)).get("w")); |
| |
| } |
| |
| public void testRecursiveWildcard2() throws Exception { |
| String json = "{\n" + |
| " \"first\": \"John\",\n" + |
| " \"last\": \"Doe\",\n" + |
| " \"grade\": 8,\n" + |
| " \"exams\": [\n" + |
| " {\n" + |
| " \"subject\": \"Maths\",\n" + |
| " \"test\" : \"term1\",\n" + |
| " \"marks\":90},\n" + |
| " {\n" + |
| " \"subject\": \"Biology\",\n" + |
| " \"test\" : \"term1\",\n" + |
| " \"marks\":86}\n" + |
| " ]\n" + |
| "}"; |
| |
| JsonRecordReader streamer; |
| List<Map<String, Object>> records; |
| |
| streamer = JsonRecordReader.getInst("/exams", Collections.singletonList("/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(2, records.size()); |
| for (Map<String, Object> record : records) { |
| assertEquals(6, record.size()); |
| assertTrue(record.containsKey("subject")); |
| assertTrue(record.containsKey("test")); |
| assertTrue(record.containsKey("marks")); |
| } |
| |
| streamer = JsonRecordReader.getInst("/exams", Collections.singletonList("$FQN:/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(2, records.size()); |
| for (Map<String, Object> record : records) { |
| assertEquals(6, record.size()); |
| assertTrue(record.containsKey("exams.subject")); |
| assertTrue(record.containsKey("exams.test")); |
| assertTrue(record.containsKey("exams.marks")); |
| } |
| |
| streamer = JsonRecordReader.getInst("/", Collections.singletonList("txt:/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(1, records.size()); |
| assertEquals(9, ((List) records.get(0).get("txt")).size()); |
| |
| } |
| |
| public void testNestedDocs() throws Exception { |
| String json = "{a:{" + |
| "b:{c:d}," + |
| "x:y" + |
| "}}"; |
| JsonRecordReader streamer = JsonRecordReader.getInst("/|/a/b", Arrays.asList("/a/x", "/a/b/*")); |
| streamer.streamRecords(new StringReader(json), (record, path) -> { |
| assertEquals(record.get("x"), "y"); |
| assertEquals(((Map) record.get("b")).get("c"), "d"); |
| }); |
| json = "{a:{" + |
| "b:[{c:c1, e:e1},{c:c2, e :e2, d:{p:q}}]," + |
| "x:y" + |
| "}}"; |
| streamer.streamRecords(new StringReader(json), (record, path) -> { |
| assertEquals(record.get("x"), "y"); |
| @SuppressWarnings({"rawtypes"}) |
| List l = (List) record.get("b"); |
| @SuppressWarnings({"rawtypes"}) |
| Map m = (Map) l.get(0); |
| assertEquals(m.get("c"), "c1"); |
| assertEquals(m.get("e"), "e1"); |
| m = (Map) l.get(1); |
| assertEquals(m.get("c"), "c2"); |
| assertEquals(m.get("e"), "e2"); |
| }); |
| streamer = JsonRecordReader.getInst("/|/a/b", Arrays.asList("$FQN:/**")); |
| streamer.streamRecords(new StringReader(json), (record, path) -> { |
| assertEquals(record.get("a.x"), "y"); |
| @SuppressWarnings({"rawtypes"}) |
| List l = (List) record.get("b"); |
| @SuppressWarnings({"rawtypes"}) |
| Map m = (Map) l.get(0); |
| assertEquals(m.get("c"), "c1"); |
| assertEquals(m.get("e"), "e1"); |
| m = (Map) l.get(1); |
| assertEquals(m.get("c"), "c2"); |
| assertEquals(m.get("e"), "e2"); |
| assertEquals(m.get("d.p"), "q"); |
| }); |
| } |
| |
| public void testNestedJsonWithFloats() throws Exception { |
| |
| String json = "{\n" + |
| " \"a_string\" : \"abc\",\n" + |
| " \"a_num\" : 2.0,\n" + |
| " \"a\" : {\n" + |
| " \"b\" : [\n" + |
| " {\"id\":\"1\", \"title\" : \"test1\"},\n" + |
| " {\"id\":\"2\", \"title\" : \"test2\"}\n" + |
| " ]\n" + |
| " }\n" + |
| "}\n"; |
| |
| JsonRecordReader streamer; |
| List<Map<String, Object>> records; |
| |
| streamer = JsonRecordReader.getInst("/a/b", Collections.singletonList("title_s:/a/b/title")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(2, records.size()); |
| } |
| |
| public void testClearPreviousRecordFields() throws Exception { |
| String json = "{\n" + |
| "'first': 'John',\n" + |
| "'exams': [\n" + |
| "{'subject': 'Maths', 'test' : 'term1', 'marks':90},\n" + |
| "{'subject': 'Biology', 'test' : 'term1', 'marks':86}\n" + |
| "]\n" + |
| "}\n" + |
| "{\n" + |
| "'first': 'Bob',\n" + |
| "'exams': [\n" + |
| "{'subject': 'Maths', 'test': 'term1', 'marks': 95\n" + |
| "}\n" + |
| ",\n" + |
| "{\n" + |
| "'subject': 'Biology', 'test' : 'term1', 'marks': 92}\n" + |
| "]\n" + |
| "}"; |
| |
| |
| JsonRecordReader streamer; |
| List<Map<String, Object>> records; |
| |
| streamer = JsonRecordReader.getInst("/exams", Collections.singletonList("/**")); |
| records = streamer.getAllRecords(new StringReader(json)); |
| assertEquals(4, records.size()); |
| |
| for (Map<String, Object> record : records) { |
| for (Map.Entry<String, Object> e : record.entrySet()) { |
| assertFalse(e.getValue() instanceof List); |
| } |
| } |
| } |
| |
| public void testArrayOfRootObjects() throws Exception { |
| String json = "[{'fieldA':'A1'}, {'fieldB':'B2'}]"; |
| JsonRecordReader streamer; |
| List<Map<String, Object>> records; |
| |
| final AtomicReference<WeakReference<String>> ref = new AtomicReference<>(); |
| streamer = JsonRecordReader.getInst("/", Collections.singletonList("$FQN:/**")); |
| streamer.streamRecords(new StringReader(json), (record, path) -> { |
| System.gc(); |
| if (ref.get() != null) { |
| assertNull("This reference is still intact :" + ref.get().get(), ref.get().get()); |
| } |
| String fName = record.keySet().iterator().next(); |
| ref.set(new WeakReference<>(fName)); |
| }); |
| |
| |
| } |
| |
| public void testAIOOBE() throws IOException { |
| String json = "[ {\n" + |
| " \"taxon_group\" : {\n" + |
| " \"identifiers\" : {\n" + |
| " \"bioentry_id\" : 1876284,\n" + |
| " \"namespace\" : \"NCBI\",\n" + |
| " \"primary_id\" : \"AAAAA_ID_19303\",\n" + |
| " \"version\" : null,\n" + |
| " \"name\" : \"AAAAA_ID_19303\",\n" + |
| " \"description\" : \"Taxon group for NCBI taxon 1286265\",\n" + |
| " \"accession\" : \"AAAAA_ID_19303\"\n" + |
| " },\n" + |
| " \"source\" : [\n" + |
| " {\n" + |
| " \"ID\" : \"AAAAA_ID_19303_0\",\n" + |
| " \"segment_group_serotype\" : \"H3\",\n" + |
| " \"primary_key\" : 11877892,\n" + |
| " \"name\" : \"segment_group\",\n" + |
| " \"segment_group_NA_subtype\" : \"\",\n" + |
| " \"segmentgroup_sequence_count\" : \"1\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"segment_group_submitter_lab\" : \"Microbiology, Faculty of Medicine Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Jawa Tengah 57126, Indonesia\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"segment_group_submission_date\" : \"22-JAN-2013\",\n" + |
| " \"segment_group_HA_subtype\" : \"H3\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"taxon_group_serotype\" : \"H3\",\n" + |
| " \"taxon_group_sequence_count\" : \"1\",\n" + |
| " \"ID\" : \"AAAAA_ID_19303\",\n" + |
| " \"primary_key\" : 11877893,\n" + |
| " \"name\" : \"source\",\n" + |
| " \"db_xref\" : [\n" + |
| " \"taxon:1286265\"\n" + |
| " ],\n" + |
| " \"taxon_group_HA_subtype\" : \"H3\",\n" + |
| " \"taxon_group_segment_group_count\" : \"1\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"taxon_group_NA_subtype\" : \"\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " }\n" + |
| " ],\n" + |
| " \"segment_groups\" : [\n" + |
| " {\n" + |
| " \"identifiers\" : {\n" + |
| " \"bioentry_id\" : 1876283,\n" + |
| " \"namespace\" : \"NCBI\",\n" + |
| " \"primary_id\" : \"AAAAA_ID_19303_0\",\n" + |
| " \"version\" : null,\n" + |
| " \"name\" : \"AAAAA_ID_19303_0\",\n" + |
| " \"description\" : \"Segment group 0 for AAAAA_ID_19303 (NCBI taxon 1286265)\",\n" + |
| " \"accession\" : \"AAAAA_ID_19303_0\"\n" + |
| " },\n" + |
| " \"source\" : [\n" + |
| " {\n" + |
| " \"ID\" : \"KC513508\",\n" + |
| " \"primary_key\" : 22483564,\n" + |
| " \"nucleotide_gi\" : \"451898947\",\n" + |
| " \"name\" : \"gene\",\n" + |
| " \"HA_subtype\" : \"H3\",\n" + |
| " \"segment\" : \"4\",\n" + |
| " \"collection_date\" : \"22-Mar-2010\",\n" + |
| " \"NA_subtype\" : \"N2\",\n" + |
| " \"subtype\" : \"H3\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"standardized_collection_date\" : \"2010-03-22T00:00:00Z\",\n" + |
| " \"segment_name\" : \"HA\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"serotype\" : \"H3N2\",\n" + |
| " \"ncbi_accession\" : \"KC513508\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"mol_type\" : \"viral cRNA\",\n" + |
| " \"taxonomy_strain\" : \"A/Surakarta/1/2010\",\n" + |
| " \"identified_by\" : \"Afiono Agung Prasetyo\",\n" + |
| " \"HA_subtype\" : \"H3\",\n" + |
| " \"collection_date\" : \"22-Mar-2010\",\n" + |
| " \"standardized_collection_date\" : \"2010-03-22T00:00:00Z\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"serotype\" : \"H3N2\",\n" + |
| " \"organism\" : \"Influenza A virus (A/Surakarta/1/2010(H3N2))\",\n" + |
| " \"country\" : \"Indonesia\",\n" + |
| " \"primary_key\" : 22483566,\n" + |
| " \"isolation_source\" : \"nasal and throat swab\",\n" + |
| " \"collected_by\" : \"Afiono Agung Prasetyo\",\n" + |
| " \"name\" : \"source\",\n" + |
| " \"flu_type\" : \"A\",\n" + |
| " \"host\" : \"Homo sapiens\",\n" + |
| " \"db_xref\" : [\n" + |
| " \"taxon:1286265\"\n" + |
| " ],\n" + |
| " \"NA_subtype\" : \"N2\",\n" + |
| " \"strain\" : \"A/Surakarta/1/2010\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22483572,\n" + |
| " \"name\" : \"standard_host\",\n" + |
| " \"Host_NCBI_taxon_id\" : \"9605\",\n" + |
| " \"curation_status_code\" : \"150\",\n" + |
| " \"curation_date\" : \"2015-01-12\",\n" + |
| " \"program_version\" : \"v1.1.7\",\n" + |
| " \"source_tag\" : \"parse_host_v1\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"curation_status_message\" : \"success, archive and add on next major program revision\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22483576,\n" + |
| " \"Location_Lat_Long\" : \"-0.7892749906,113.9213256836\",\n" + |
| " \"name\" : \"standardized_location\",\n" + |
| " \"Location_Country_Alpha2\" : \"ID\",\n" + |
| " \"curation_status_code\" : \"150\",\n" + |
| " \"curation_date\" : \"2015-01-15\",\n" + |
| " \"program_version\" : \"v0.1\",\n" + |
| " \"source_tag\" : \"xxxxx_parse_location_v0\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"curation_status_message\" : \"success, archive and add on next major program revision\",\n" + |
| " \"start-end\" : 1,\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " }\n" + |
| " ],\n" + |
| " \"sequence\" : {\n" + |
| " \"string\" : \"CCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAGTGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACC\"\n" + |
| " },\n" + |
| " \"references\" : [\n" + |
| " {\n" + |
| " \"authors\" : \"Prasetyo,A.A.\",\n" + |
| " \"location\" : \"Unpublished\",\n" + |
| " \"title\" : \"Molecular Epidemiology Study of Human Respiratory Virus in Surakarta Indonesia\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"authors\" : \"Prasetyo,A.A.\",\n" + |
| " \"location\" : \"Submitted (22-JAN-2013) Microbiology, Faculty of Medicine Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Jawa Tengah 57126, Indonesia\",\n" + |
| " \"title\" : \"Direct Submission\"\n" + |
| " }\n" + |
| " ],\n" + |
| " \"name\" : \"AAAAA_ID_19303_0\",\n" + |
| " \"segments\" : [\n" + |
| " {\n" + |
| " \"identifiers\" : {\n" + |
| " \"bioentry_id\" : 1588885,\n" + |
| " \"namespace\" : \"NCBI\",\n" + |
| " \"primary_id\" : \"KC513508\",\n" + |
| " \"version\" : 1,\n" + |
| " \"name\" : \"KC513508\",\n" + |
| " \"description\" : \"Influenza A virus (A/Surakarta/1/2010(H3N2)) segment 4 hemagglutinin (HA) gene, partial cds.\",\n" + |
| " \"accession\" : \"KC513508\"\n" + |
| " },\n" + |
| " \"source\" : [\n" + |
| " {\n" + |
| " \"mol_type\" : \"viral cRNA\",\n" + |
| " \"identified_by\" : \"Afiono Agung Prasetyo\",\n" + |
| " \"HA_subtype\" : \"H3\",\n" + |
| " \"segment\" : \"4\",\n" + |
| " \"collection_date\" : \"22-Mar-2010\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"serotype\" : \"H3N2\",\n" + |
| " \"organism\" : \"Influenza A virus (A/Surakarta/1/2010(H3N2))\",\n" + |
| " \"country\" : \"Indonesia\",\n" + |
| " \"primary_key\" : 22511042,\n" + |
| " \"isolation_source\" : \"nasal and throat swab\",\n" + |
| " \"collected_by\" : \"Afiono Agung Prasetyo\",\n" + |
| " \"name\" : \"source\",\n" + |
| " \"host\" : \"Homo sapiens\",\n" + |
| " \"NA_subtype\" : \"N2\",\n" + |
| " \"db_xref\" : [\n" + |
| " \"taxon:1286265\"\n" + |
| " ],\n" + |
| " \"strain\" : \"A/Surakarta/1/2010\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511045,\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"gene\" : \"HA\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"name\" : \"gene\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511046,\n" + |
| " \"protein_id\" : \"AGF80141.1\",\n" + |
| " \"gene\" : \"HA\",\n" + |
| " \"name\" : \"CDS\",\n" + |
| " \"db_xref\" : [\n" + |
| " \"GI:451898948\"\n" + |
| " ],\n" + |
| " \"codon_start\" : \"2\",\n" + |
| " \"source_tag\" : \"EMBL/GenBank/SwissProt\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"translation\" : \"PYDVPDYASLRSLVASSGTLEFNSESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHH\",\n" + |
| " \"product\" : \"hemagglutinin\",\n" + |
| " \"start-end\" : \"1..260\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511053,\n" + |
| " \"name\" : \"asdf_typing\",\n" + |
| " \"segment\" : \"4\",\n" + |
| " \"flu_type\" : \"A\",\n" + |
| " \"bitscore\" : \"277.3\",\n" + |
| " \"full_lineage\" : \"X_XX_XX_XxxxxXxxxx\",\n" + |
| " \"lineage\" : \"AAAAAAAAAA\",\n" + |
| " \"curation_date\" : \"2015-01-07\",\n" + |
| " \"subtype\" : \"H3\",\n" + |
| " \"program_version\" : \"v2.8.2\",\n" + |
| " \"source_tag\" : \"some_text_some\",\n" + |
| " \"Evalue\" : \"4.6e-85\",\n" + |
| " \"segment_name\" : \"HA\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"bitscore\" : \"464\",\n" + |
| " \"subj_location\" : \"342..601\",\n" + |
| " \"slen\" : \"1701\",\n" + |
| " \"sseqid\" : \"someID_someID_some\",\n" + |
| " \"mismatch\" : \"3\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"qcovs\" : \"100\",\n" + |
| " \"qlen\" : \"260\",\n" + |
| " \"qcovhsp\" : \"100\",\n" + |
| " \"primary_key\" : 22511048,\n" + |
| " \"pident\" : \"98.85\",\n" + |
| " \"name\" : \"segtypeAlign\",\n" + |
| " \"qseqid\" : \"KC513508\",\n" + |
| " \"gaps\" : \"0\",\n" + |
| " \"curation_date\" : \"2015-01-15\",\n" + |
| " \"typing\" : \"A_HA_H3\",\n" + |
| " \"length\" : \"260\",\n" + |
| " \"evalue\" : \"2e-132\",\n" + |
| " \"source_tag\" : \"asdf_asdf_asdfv1\",\n" + |
| " \"program_version\" : \"v1.1.2\",\n" + |
| " \"curation_status\" : \"true\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"gapopen\" : \"0\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511060,\n" + |
| " \"name\" : \"standard_host\",\n" + |
| " \"Host_NCBI_taxon_id\" : \"9605\",\n" + |
| " \"curation_status_code\" : \"150\",\n" + |
| " \"curation_date\" : \"2015-01-12\",\n" + |
| " \"program_version\" : \"v1.1.7\",\n" + |
| " \"source_tag\" : \"parse_host_v1\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"curation_status_message\" : \"success, archive and add on next major program revision\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511052,\n" + |
| " \"name\" : \"flu_segtype\",\n" + |
| " \"flu_type\" : \"A\",\n" + |
| " \"curation_date\" : \"2015-01-15\",\n" + |
| " \"subtype\" : \"H3\",\n" + |
| " \"program_version\" : \"v1.1.2\",\n" + |
| " \"source_tag\" : \"asdf_asdf_asd_v1\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"segtype\" : \"HA\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511056,\n" + |
| " \"prot_coord\" : \"115..87\",\n" + |
| " \"name\" : \"exon\",\n" + |
| " \"curation_date\" : \"2015-01-07\",\n" + |
| " \"source_tag\" : \"asdf_asdfas_v2\",\n" + |
| " \"program_version\" : \"v2.8.2\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"start-end\" : \"2..259\",\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"nstart\" : \"2\",\n" + |
| " \"primary_key\" : 22511058,\n" + |
| " \"pend\" : \"200\",\n" + |
| " \"aaseq\" : \"PYDVPDYASLRSLVASSGTLEFNSESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHH\",\n" + |
| " \"p_pc_coverage\" : \"15.19\",\n" + |
| " \"name\" : \"CDS\",\n" + |
| " \"score\" : \"461\",\n" + |
| " \"nend\" : \"259\",\n" + |
| " \"curation_date\" : \"2015-01-07\",\n" + |
| " \"program_version\" : \"v2.8.2\",\n" + |
| " \"source_tag\" : \"asdf_asdfas_v2\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"product\" : \"A_HA_H3\",\n" + |
| " \"ntlength\" : \"258\",\n" + |
| " \"start-end\" : \"1..260\",\n" + |
| " \"curation_status\" : \"true\",\n" + |
| " \"pstart\" : \"115\"\n" + |
| " },\n" + |
| " {\n" + |
| " \"primary_key\" : 22511062,\n" + |
| " \"Location_Lat_Long\" : \"-0.7892749906,113.9213256836\",\n" + |
| " \"name\" : \"standardized_location\",\n" + |
| " \"Location_Country_Alpha2\" : \"ID\",\n" + |
| " \"curation_status_code\" : \"150\",\n" + |
| " \"curation_date\" : \"2015-01-15\",\n" + |
| " \"program_version\" : \"v0.1\",\n" + |
| " \"source_tag\" : \"asdf_asdf_asdf_asdfn_v0\",\n" + |
| " \"strand\" : \"1\",\n" + |
| " \"curation_status_message\" : \"success, archive and add on next major program revision\",\n" + |
| " \"start-end\" : 1,\n" + |
| " \"curation_status\" : \"true\"\n" + |
| " }\n" + |
| " ],\n" + |
| " \"sequence\" : {\n" + |
| " \"length\" : 260,\n" + |
| " \"string\" : \"CCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAGTGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACC\"\n" + |
| " },\n" + |
| " \"name\" : \"KC513508\",\n" + |
| " \"annotations\" : {\n" + |
| " \"keyword\" : \"\",\n" + |
| " \"curation_date\" : \"2015-01-03\",\n" + |
| " \"comment\" : [\n" + |
| " \"##Assembly-Data-START## Assembly Method :: CLC Main Workbench v. 6.8 Sequencing Technology :: Sanger dideoxy1 sequencing ##Assembly-Data-END## \"\n" + |
| " ],\n" + |
| " \"date_changed\" : \"25-FEB-2013\",\n" + |
| " \"curation_status\" : \"false\"\n" + |
| " }\n" + |
| " }\n" + |
| " ],\n" + |
| " \"annotations\" : {\n" + |
| " \"keyword\" : \"\",\n" + |
| " \"curation_date\" : \"2015-01-05\",\n" + |
| " \"comment\" : [\n" + |
| " \"##Assembly-Data-START## Assembly Method :: CLC Main Workbench v. 6.8 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END## \"\n" + |
| " ]\n" + |
| " }}]}}]"; |
| |
| RecordingJSONParser parser = new RecordingJSONParser(new StringReader(json)); |
| JsonRecordReader recordReader = JsonRecordReader.getInst("/",Collections.singletonList("/**")); |
| try { |
| recordReader.streamRecords(parser, (record, path) -> { |
| }); /*don't care*/ |
| } catch (RuntimeException e) { |
| parser.error("").printStackTrace(); |
| throw e; |
| } |
| } |
| } |
