@toxplanet/pegasus-sdk 1.2.4 → 1.2.6

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Files changed (3) hide show
  1. package/lib/chemicals.js +140 -106
  2. package/lib/search.js +6 -3
  3. package/package.json +1 -1
package/lib/chemicals.js CHANGED
@@ -734,7 +734,7 @@ class ChemicalsService {
734
734
  */
735
735
  async searchByName(searchTerm, limit = 10) {
736
736
  if (!searchTerm) {
737
- return { results: [] };
737
+ return { results: [], total: { value: 0, relation: 'eq' } };
738
738
  }
739
739
 
740
740
  try {
@@ -771,7 +771,10 @@ class ChemicalsService {
771
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  score: hit._score
772
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  }));
773
773
 
774
- return { results };
774
+ return {
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+ results,
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+ total: result?.hits?.total ?? { value: results.length, relation: 'eq' }
777
+ };
775
778
  } catch (error) {
776
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  logError('pegasus-sdk', 'ChemicalsService', 'searchByName', error);
777
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  throw error;
@@ -786,7 +789,7 @@ class ChemicalsService {
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  */
787
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  async searchBySynonym(synonymTerm, limit = 10) {
788
791
  if (!synonymTerm) {
789
- return { results: [] };
792
+ return { results: [], total: { value: 0, relation: 'eq' } };
790
793
  }
791
794
 
792
795
  try {
@@ -823,7 +826,10 @@ class ChemicalsService {
823
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  score: hit._score
824
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  }));
825
828
 
826
- return { results };
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+ return {
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+ results,
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+ total: result?.hits?.total ?? { value: results.length, relation: 'eq' }
832
+ };
827
833
  } catch (error) {
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  logError('pegasus-sdk', 'ChemicalsService', 'searchBySynonym', error);
829
835
  throw error;
@@ -896,13 +902,16 @@ class ChemicalsService {
896
902
  index: async (params) => {
897
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  const chemical = params.body;
898
904
  const result = await this.createChemical(chemical);
899
-
905
+
900
906
  return {
901
- _index: params.index,
902
- _id: result.chemicalId,
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- _version: 1,
904
- result: 'created',
905
- _source: result
907
+ body: {
908
+ _index: params.index,
909
+ _id: result.chemicalId,
910
+ _version: 1,
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+ result: 'created',
912
+ _source: result
913
+ },
914
+ statusCode: 200
906
915
  };
907
916
  },
908
917
 
@@ -958,7 +967,10 @@ class ChemicalsService {
958
967
 
959
968
  if (cdiDocuments.length === 0) {
960
969
  logInfo('pegasus-sdk', `[ChemicalsService.bulk] No CDI documents to index, returning empty no-op response`);
961
- return { took: 0, errors: false, items: [] };
970
+ return {
971
+ body: { took: 0, errors: false, items: [] },
972
+ statusCode: 200
973
+ };
962
974
  }
963
975
 
964
976
  logInfo('pegasus-sdk', `[ChemicalsService.bulk] Calling bulkIndexFielded with ${cdiDocuments.length} CDI documents`);
@@ -972,17 +984,20 @@ class ChemicalsService {
972
984
  }
973
985
 
974
986
  return {
975
- took: 1,
976
- errors: result.errors.length > 0,
977
- items: result.results.map((res, idx) => ({
978
- index: {
979
- _index: 'chemical_data_index',
980
- _id: cdiDocuments[idx].source_id,
981
- status: res.success ? 200 : 400,
982
- result: res.success ? 'created' : 'error',
983
- ...(res.success ? {} : { error: { type: 'mapper_parsing_exception', reason: res.error } })
984
- }
985
- }))
987
+ body: {
988
+ took: 1,
989
+ errors: result.errors.length > 0,
990
+ items: result.results.map((res, idx) => ({
991
+ index: {
992
+ _index: 'chemical_data_index',
993
+ _id: cdiDocuments[idx].source_id,
994
+ status: res.success ? 200 : 400,
995
+ result: res.success ? 'created' : 'error',
996
+ ...(res.success ? {} : { error: { type: 'mapper_parsing_exception', reason: res.error } })
997
+ }
998
+ }))
999
+ },
1000
+ statusCode: 200
986
1001
  };
987
1002
  } catch (error) {
988
1003
  logError('pegasus-sdk', 'ChemicalsService.bulk', 'Fatal error during bulk indexing', error);
@@ -992,46 +1007,61 @@ class ChemicalsService {
992
1007
 
993
1008
  get: async (params) => {
994
1009
  const result = await this.getChemicalBySourceId(params.id);
995
-
1010
+
996
1011
  if (!result) {
997
1012
  return {
998
- _index: params.index,
999
- _id: params.id,
1000
- found: false
1013
+ body: {
1014
+ _index: params.index,
1015
+ _id: params.id,
1016
+ found: false
1017
+ },
1018
+ statusCode: 200
1001
1019
  };
1002
1020
  }
1003
-
1021
+
1004
1022
  return {
1005
- _index: params.index,
1006
- _id: params.id,
1007
- _version: 1,
1008
- found: true,
1009
- _source: result
1023
+ body: {
1024
+ _index: params.index,
1025
+ _id: params.id,
1026
+ _version: 1,
1027
+ found: true,
1028
+ _source: result
1029
+ },
1030
+ statusCode: 200
1010
1031
  };
1011
1032
  },
1012
1033
 
1013
1034
  update: async (params) => {
1014
1035
  const result = await this.updateChemical(params.id, params.body);
1015
-
1036
+
1016
1037
  return {
1017
- _index: params.index,
1018
- _id: params.id,
1019
- _version: 2,
1020
- result: result ? 'updated' : 'noop',
1021
- _source: result
1038
+ body: {
1039
+ _index: params.index,
1040
+ _id: params.id,
1041
+ _version: 2,
1042
+ result: result ? 'updated' : 'noop',
1043
+ _source: result
1044
+ },
1045
+ statusCode: 200
1022
1046
  };
1023
1047
  },
1024
1048
 
1025
1049
  delete: async (params) => {
1026
1050
  if (params.index === 'synonym_lookup_index') {
1027
- return { _index: params.index, _id: params.id, result: 'not_found' };
1051
+ return {
1052
+ body: { _index: params.index, _id: params.id, result: 'not_found' },
1053
+ statusCode: 200
1054
+ };
1028
1055
  }
1029
1056
  const result = await this.deleteBySourceId(params.id);
1030
-
1057
+
1031
1058
  return {
1032
- _index: params.index,
1033
- _id: params.id,
1034
- result: result ? 'deleted' : 'not_found'
1059
+ body: {
1060
+ _index: params.index,
1061
+ _id: params.id,
1062
+ result: result ? 'deleted' : 'not_found'
1063
+ },
1064
+ statusCode: 200
1035
1065
  };
1036
1066
  },
1037
1067
 
@@ -1039,12 +1069,18 @@ class ChemicalsService {
1039
1069
  const sourceId = params.body?.query?.term?.chemical_set_identifier
1040
1070
  || params.body?.query?.term?.source_id;
1041
1071
  if (!sourceId) {
1042
- return { deleted: 0, failures: [] };
1072
+ return {
1073
+ body: { deleted: 0, failures: [] },
1074
+ statusCode: 200
1075
+ };
1043
1076
  }
1044
1077
  const result = await this.deleteBySourceId(sourceId);
1045
1078
  return {
1046
- deleted: result ? 1 : 0,
1047
- failures: []
1079
+ body: {
1080
+ deleted: result ? 1 : 0,
1081
+ failures: []
1082
+ },
1083
+ statusCode: 200
1048
1084
  };
1049
1085
  },
1050
1086
 
@@ -1052,86 +1088,84 @@ class ChemicalsService {
1052
1088
  let searchTerm = '';
1053
1089
  let limit = params.body?.size || 10;
1054
1090
 
1091
+ const toLegacySource = (r) => ({
1092
+ chemical_name: r.name,
1093
+ chemical_name_sensitive: r.name,
1094
+ chemical_name_sort: (r.name || '').toLowerCase(),
1095
+ chemical_identifier: [...(r.cas || []), ...(r.identifiers || [])],
1096
+ chemical_set_identifier: (r.cas && r.cas[0]) || r.id || ''
1097
+ });
1098
+
1055
1099
  if (params.index === 'synonym_lookup_index') {
1056
1100
  const query = params.body?.query;
1057
- searchTerm = query?.match?.chemical_name ||
1058
- query?.term?.chemical_name ||
1101
+ searchTerm = query?.match?.chemical_name ||
1102
+ query?.term?.chemical_name ||
1059
1103
  query?.query_string?.query || '';
1060
1104
  const searchResults = await this.searchBySynonym(searchTerm, limit);
1061
-
1105
+
1062
1106
  return {
1063
- took: 1,
1064
- timed_out: false,
1065
- _shards: {
1066
- total: 1,
1067
- successful: 1,
1068
- skipped: 0,
1069
- failed: 0
1070
- },
1071
- hits: {
1072
- total: {
1073
- value: searchResults.results.length,
1074
- relation: 'eq'
1107
+ body: {
1108
+ took: 1,
1109
+ timed_out: false,
1110
+ _shards: {
1111
+ total: 1,
1112
+ successful: 1,
1113
+ skipped: 0,
1114
+ failed: 0
1075
1115
  },
1076
- max_score: searchResults.results[0]?.score || 0,
1077
- hits: searchResults.results.map(result => ({
1078
- _index: params.index,
1079
- _id: result.id,
1080
- _score: result.score,
1081
- _source: {
1082
- postgres_id: result.id,
1083
- chemical_name: result.name,
1084
- cas_numbers: result.cas,
1085
- identifier_values: result.identifiers,
1086
- synonyms: result.synonyms
1087
- }
1088
- }))
1089
- }
1116
+ hits: {
1117
+ total: searchResults.total ?? { value: searchResults.results.length, relation: 'eq' },
1118
+ max_score: searchResults.results[0]?.score || 0,
1119
+ hits: searchResults.results.map(result => ({
1120
+ _index: params.index,
1121
+ _id: result.id,
1122
+ _score: result.score,
1123
+ _source: toLegacySource(result)
1124
+ }))
1125
+ }
1126
+ },
1127
+ statusCode: 200
1090
1128
  };
1091
1129
  } else {
1092
1130
  const query = params.body?.query;
1093
- searchTerm = query?.match?.chemical_name ||
1094
- query?.term?.chemical_name ||
1131
+ searchTerm = query?.match?.chemical_name ||
1132
+ query?.term?.chemical_name ||
1095
1133
  query?.query_string?.query || '';
1096
1134
  const searchResults = await this.searchByName(searchTerm, limit);
1097
-
1135
+
1098
1136
  return {
1099
- took: 1,
1100
- timed_out: false,
1101
- _shards: {
1102
- total: 1,
1103
- successful: 1,
1104
- skipped: 0,
1105
- failed: 0
1106
- },
1107
- hits: {
1108
- total: {
1109
- value: searchResults.results.length,
1110
- relation: 'eq'
1137
+ body: {
1138
+ took: 1,
1139
+ timed_out: false,
1140
+ _shards: {
1141
+ total: 1,
1142
+ successful: 1,
1143
+ skipped: 0,
1144
+ failed: 0
1111
1145
  },
1112
- max_score: searchResults.results[0]?.score || 0,
1113
- hits: searchResults.results.map(result => ({
1114
- _index: params.index,
1115
- _id: result.id,
1116
- _score: result.score,
1117
- _source: {
1118
- postgres_id: result.id,
1119
- chemical_name: result.name,
1120
- cas_numbers: result.cas,
1121
- identifier_values: result.identifiers,
1122
- synonyms: result.synonyms
1123
- }
1124
- }))
1125
- }
1146
+ hits: {
1147
+ total: searchResults.total ?? { value: searchResults.results.length, relation: 'eq' },
1148
+ max_score: searchResults.results[0]?.score || 0,
1149
+ hits: searchResults.results.map(result => ({
1150
+ _index: params.index,
1151
+ _id: result.id,
1152
+ _score: result.score,
1153
+ _source: toLegacySource(result)
1154
+ }))
1155
+ }
1156
+ },
1157
+ statusCode: 200
1126
1158
  };
1127
1159
  }
1128
1160
  },
1129
1161
 
1130
1162
  count: async (params) => {
1131
1163
  if (params.index === 'synonym_lookup_index') {
1132
- return await this.getTotalSynonymCount();
1164
+ const result = await this.getTotalSynonymCount();
1165
+ return { body: result, statusCode: 200 };
1133
1166
  }
1134
- return await this.countAll();
1167
+ const result = await this.countAll();
1168
+ return { body: result, statusCode: 200 };
1135
1169
  }
1136
1170
  };
1137
1171
  }
package/lib/search.js CHANGED
@@ -94,7 +94,7 @@ class SearchService {
94
94
  */
95
95
  async searchChemicals(query, options = {}) {
96
96
  if (!query) {
97
- return { results: [] };
97
+ return { results: [], total: { value: 0, relation: 'eq' } };
98
98
  }
99
99
 
100
100
  // Extract options with defaults
@@ -165,7 +165,10 @@ class SearchService {
165
165
  score: hit._score
166
166
  }));
167
167
 
168
- return { results };
168
+ return {
169
+ results,
170
+ total: result?.hits?.total ?? { value: results.length, relation: 'eq' }
171
+ };
169
172
  } catch (error) {
170
173
  logError('pegasus-sdk', 'SearchService', 'searchChemicals', error);
171
174
  throw error;
@@ -356,7 +359,7 @@ class SearchService {
356
359
  chemical_set_identifier: (r.cas && r.cas[0]) || r.id || '',
357
360
  }
358
361
  })),
359
- total: { value: pegasusResults.results.length, relation: 'eq' }
362
+ total: pegasusResults.total ?? { value: pegasusResults.results.length, relation: 'eq' }
360
363
  },
361
364
  timed_out: false,
362
365
  _shards: { total: 1, successful: 1, failed: 0 }
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@toxplanet/pegasus-sdk",
3
- "version": "1.2.4",
3
+ "version": "1.2.6",
4
4
  "description": "SDK for migrating chemical data to Pegasus PostgreSQL + OpenSearch architecture with Elasticsearch client compatibility",
5
5
  "main": "index.js",
6
6
  "type": "commonjs",