/*
* 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.invoke.MethodHandles;
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.lang.StringUtils;
import org.apache.solr.SolrTestCaseJ4;
import org.apache.solr.util.RecordingJSONParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class TestJsonRecordReader extends SolrTestCaseJ4 {
private static final Logger log = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
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();
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("$FQN:/**"));
records = streamer.getAllRecords(new StringReader(json));
assertEquals(2, records.size());
for (Map<String, Object> record : records) {
assertEquals(6, record.size());
assertTrue(record.containsKey("exams.subject"));
assertTrue(record.containsKey("exams.test"));
assertTrue(record.containsKey("exams.marks"));
}
streamer = JsonRecordReader.getInst("/", Collections.singletonList("txt:/**"));
records = streamer.getAllRecords(new StringReader(json));
assertEquals(1, records.size());
assertEquals(9, ((List) records.get(0).get("txt")).size());
}
public void testNestedDocs() throws Exception {
String json = "{a:{" +
"b:{c:d}," +
"x:y" +
"}}";
JsonRecordReader streamer = JsonRecordReader.getInst("/|/a/b", Arrays.asList("/a/x", "/a/b/*"));
streamer.streamRecords(new StringReader(json), (record, path) -> {
assertEquals(record.get("x"), "y");
assertEquals(((Map) record.get(null)).get("c"), "d");
});
json = "{a:{" +
"b:[{c:c1, e:e1},{c:c2, e :e2, d:{p:q}}]," +
"x:y" +
"}}";
streamer.streamRecords(new StringReader(json), (record, path) -> {
assertEquals(record.get("x"), "y");
List l = (List) record.get(null);
Map m = (Map) l.get(0);
assertEquals(m.get("c"), "c1");
assertEquals(m.get("e"), "e1");
m = (Map) l.get(1);
assertEquals(m.get("c"), "c2");
assertEquals(m.get("e"), "e2");
});
streamer = JsonRecordReader.getInst("/|/a/b", Arrays.asList("$FQN:/**"));
streamer.streamRecords(new StringReader(json), (record, path) -> {
assertEquals(record.get("a.x"), "y");
List l = (List) record.get(null);
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;
}
}
}