diff --git a/CHANGELOG.md b/CHANGELOG.md index dddc320bc..db285d5c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,7 @@ Note: version releases in the 0.x.y range may introduce breaking changes. ### Added - Add spotless plugin, Add codestyle check to workflows ([#368](https://github.com/ehrbase/openEHR_SDK/pull/368)) - Add new Tool to interpret AQL against a template ([#379](https://github.com/ehrbase/openEHR_SDK/pull/379)) +- Add new Matrix serialisation format ([#381](https://github.com/ehrbase/openEHR_SDK/pull/381)) ### Fixed - Skip archetype slots not used by the template in example generator ([#369](https://github.com/ehrbase/openEHR_SDK/pull/369)) - enhance sdk aql parser to handle more cases ([#376](https://github.com/ehrbase/openEHR_SDK/pull/376)) diff --git a/aql/src/test/resources/newaql.sql b/aql/src/test/resources/newaql.sql new file mode 100644 index 000000000..9fa3aa0a4 --- /dev/null +++ b/aql/src/test/resources/newaql.sql @@ -0,0 +1,381 @@ +drop table if exists ehr.entry2; +create table ehr.entry2 +( + ehr_id uuid, + comp_id uuid, + num INTEGER, + entity_concept Text, + rm_entity text, + entity_path Text, + entity_idx INTEGER[], + field_idx INTEGER[], + field_idx_len INTEGER, + fields jsonb, + PRIMARY KEY (comp_id, num) +); + + +create index archetype_idx on ehr.entry2 (entity_concept, field_idx_len,ehr_id); + +create index type_idx on ehr.entry2 (rm_entity, field_idx_len,ehr_id); +-- composer +-- should be partial on where rm_entity = 'COMPOSITION' +create index composer_idx on ehr.entry2 (rm_entity, field_idx_len, (fields ->> '/composer/name'),ehr_id); +-- custom index for a cross patient query +-- should be partial on entity_concept = 'openEHR-EHR-EVALUATION.problem_diagnosis.v1' +create index diagnosis_idx on ehr.entry2 (entity_concept, field_idx_len, + (fields ->> '/data[at0001]/items[at0002]/value/value'), ehr_id); + + +DO +$$ + DECLARE + comp_size INTEGER := 100; + cid uuid; + eid uuid; + BEGIN + FOR e IN 0..5 BY 1 + LOOP + eid := uuid_generate_v4(); + FOR counter IN 1..comp_size BY 2 + LOOP + cid := uuid_generate_v4(); + insert into ehr.entry2 (ehr_id, comp_id,num, entity_concept,rm_entity, entity_path, entity_idx, field_idx, field_idx_len, fields) + + + values (eid,cid,0, 'openEHR-EHR-COMPOSITION.health_summary.v1', 'COMPOSITION', '/', '{}', '{}', 0, 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waren","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/_type":"CLUSTER","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/_type":"CLUSTER","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/items[at0046]/_type":"ELEMENT","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/items[at0046]/value/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/items[at0046]/value/value":"Norditalien","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/archetype_details/archetype_id/value":"openEHR-EHR-CLUSTER.location.v1","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/archetype_details/rm_version":"1.0.4","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/archetype_details/_type":"ARCHETYPED","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/archetype_node_id":"openEHR-EHR-CLUSTER.location.v1","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/items[openEHR-EHR-CLUSTER.location.v1]/name/value":"Standort","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/archetype_node_id":"at0134","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0134]/name/value":"Ortsbeschreibung","/data[at0001]/events[at0002]/data[at0003]/archetype_node_id":"at0003","/data[at0001]/events[at0002]/data[at0003]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/name/value":"Tree","/data[at0001]/events[at0002]/archetype_node_id":"at0002","/data[at0001]/events[at0002]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/name/value":"Jedes Ereignis","/data[at0001]/events[at0002]/time/_type":"DV_DATE_TIME","/data[at0001]/events[at0002]/time/value":"2020-05-11T22:53:12.039139+02:00","/data[at0001]/events[at0002]/time/magnitude":63724827192,"/archetype_node_id":"openEHR-EHR-OBSERVATION.travel_history.v0","/language/_type":"CODE_PHRASE","/language/terminology_id/_type":"TERMINOLOGY_ID","/language/terminology_id/value":"ISO_639-1","/language/code_string":"de","/encoding/_type":"CODE_PHRASE","/encoding/terminology_id/_type":"TERMINOLOGY_ID","/encoding/terminology_id/value":"IANA_character-sets","/encoding/code_string":"UTF-8","/archetype_details/archetype_id/value":"openEHR-EHR-OBSERVATION.travel_history.v0","/archetype_details/rm_version":"1.0.4","/archetype_details/_type":"ARCHETYPED","/name/_type":"DV_TEXT","/name/value":"Historie der Reise","/subject/_type":"PARTY_SELF"}'), + (eid,cid,13, 'openEHR-EHR-OBSERVATION.travel_event.v0', 'OBSERVATION', '/content[openEHR-EHR-SECTION.adhoc.v1,''Risikogebiet'']/items[openEHR-EHR-OBSERVATION.travel_event.v0]', '{0}', '{}', 0, '{"/_type":"OBSERVATION","/data[at0001]/_type":"HISTORY","/data[at0001]/archetype_node_id":"at0001","/data[at0001]/origin/_type":"DV_DATE_TIME","/data[at0001]/origin/value":"2020-05-11T22:53:12.039139+02:00","/data[at0001]/origin/magnitude":63724827192,"/data[at0001]/name/_type":"DV_TEXT","/data[at0001]/name/value":"History","/archetype_node_id":"openEHR-EHR-OBSERVATION.travel_event.v0","/language/_type":"CODE_PHRASE","/language/terminology_id/_type":"TERMINOLOGY_ID","/language/terminology_id/value":"ISO_639-1","/language/code_string":"de","/encoding/_type":"CODE_PHRASE","/encoding/terminology_id/_type":"TERMINOLOGY_ID","/encoding/terminology_id/value":"IANA_character-sets","/encoding/code_string":"UTF-8","/archetype_details/archetype_id/value":"openEHR-EHR-OBSERVATION.travel_event.v0","/archetype_details/rm_version":"1.0.4","/archetype_details/_type":"ARCHETYPED","/name/_type":"DV_TEXT","/name/value":"Reisefall","/subject/_type":"PARTY_SELF"}'), + (eid,cid,14, 'openEHR-EHR-OBSERVATION.travel_event.v0', 'OBSERVATION', '/content[openEHR-EHR-SECTION.adhoc.v1,''Risikogebiet'']/items[openEHR-EHR-OBSERVATION.travel_event.v0]', '{0}', '{0}', 1, '{"/data[at0001]/events[at0002]/_type":"INTERVAL_EVENT","/data[at0001]/events[at0002]/data[at0003]/_type":"ITEM_TREE","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/_type":"ELEMENT","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/_type":"DV_CODED_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/value":"Ja - national","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/defining_code/_type":"CODE_PHRASE","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/defining_code/terminology_id/_type":"TERMINOLOGY_ID","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/defining_code/terminology_id/value":"local","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/value/defining_code/code_string":"at0006","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0004,''Letzte Reise?'']/name/value":"Letzte Reise?","/data[at0001]/events[at0002]/data[at0003]/archetype_node_id":"at0003","/data[at0001]/events[at0002]/data[at0003]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/name/value":"Tree","/data[at0001]/events[at0002]/archetype_node_id":"at0002","/data[at0001]/events[at0002]/math_function/_type":"DV_CODED_TEXT","/data[at0001]/events[at0002]/math_function/value":"mean","/data[at0001]/events[at0002]/math_function/defining_code/_type":"CODE_PHRASE","/data[at0001]/events[at0002]/math_function/defining_code/terminology_id/_type":"TERMINOLOGY_ID","/data[at0001]/events[at0002]/math_function/defining_code/terminology_id/value":"openehr","/data[at0001]/events[at0002]/math_function/defining_code/code_string":"146","/data[at0001]/events[at0002]/width/_type":"DV_DURATION","/data[at0001]/events[at0002]/width/value":"P0D","/data[at0001]/events[at0002]/width/magnitude":0.0,"/data[at0001]/events[at0002]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/name/value":"Beliebiges Intervallereignis","/data[at0001]/events[at0002]/time/_type":"DV_DATE_TIME","/data[at0001]/events[at0002]/time/value":"2020-05-11T22:53:12.039139+02:00","/data[at0001]/events[at0002]/time/magnitude":63724827192}'), + (eid,cid,15, 'openEHR-EHR-OBSERVATION.travel_event.v0', 'OBSERVATION', '/content[openEHR-EHR-SECTION.adhoc.v1,''Risikogebiet'']/items[openEHR-EHR-OBSERVATION.travel_event.v0]', '{0}', '{0,0}', 2, '{"/data[at0001]/events[at0002]/data[at0003]/items[at0008]/_type":"CLUSTER","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/archetype_node_id":"at0008","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/name/value":"Bestimmte Reise"}'), + (eid,cid,16, 'openEHR-EHR-OBSERVATION.travel_event.v0', 'OBSERVATION', '/content[openEHR-EHR-SECTION.adhoc.v1,''Risikogebiet'']/items[openEHR-EHR-OBSERVATION.travel_event.v0]', '{0}', '{0,0,0}', 3, '{"/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/_type":"CLUSTER","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0011]/_type":"ELEMENT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0011]/value/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0011]/value/value":"Deutschland","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0012]/_type":"ELEMENT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0012]/value/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0012]/value/value":"Baden-Württemberg","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0013]/_type":"ELEMENT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0013]/value/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0013]/value/value":"Mannheim","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/archetype_node_id":"at0010","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/name/_type":"DV_TEXT","/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/name/value":"Bestimmtes Reiseziel"}'); + END LOOP; + END LOOP; + END; +$$; + +commit; + +set yb_enable_expression_pushdown = on; + +-- select example ehrId; +select distinct ehr_id +from ehr.entry2 +where (rm_entity = 'COMPOSITION') + and field_idx_len = 0 +limit 2; + +-- set example ehrId +SET ehr.id = '159dcd5f-a2cb-4c1a-9a55-626f823baa44'; +-- SET ehr.id = '0119934e-b2d9-447a-ad38-67dfb47b5d01'; + +-- get patient count +select count(distinct ehr_id) +from ehr.entry2 +where (rm_entity = 'COMPOSITION') + and field_idx_len = 0; + +-- get document count +select count(comp_id) +from ehr.entry2 +where (rm_entity = 'COMPOSITION') + and field_idx_len = 0; + + +-- Get second page of measurements with page size 10 which indicated high temperature and their time +set enable_hashjoin = on; +set enable_nestloop = on; +explain analyse +select "array_599434088_1".*, "array_599434088_2".* +from (select e2.ehr_id, e2.comp_id, fields ->> '/context/start_time/value'::text as "time",(fields -> '/context/start_time/magnitude')::numeric as "time_magnitude" + from ehr.entry2 e2 + where (rm_entity = 'COMPOSITION') + and field_idx_len = 0 + and ehr_id = current_setting('ehr.id')::uuid) as "array_599434088_1" + join lateral ( select (fields -> '/data[at0002]/events[at0003]/data[at0001]/items[at0004]/value/magnitude')::numeric + from ehr.entry2 e3 + where (entity_concept = 'openEHR-EHR-OBSERVATION.body_temperature.v2') + and field_idx_len = 0 + and ehr_id = current_setting('ehr.id')::uuid + and (fields -> + '/data[at0002]/events[at0003]/data[at0001]/items[at0004]/value/magnitude')::numeric > + 37.5 + and array_599434088_1.comp_id = e3.comp_id ) as "array_599434088_2" on true +order by "array_599434088_1"."time_magnitude" +limit 10 offset 10 +; +-- Get latest 'Corona_Anamnese' document for a specific patient +set enable_hashjoin = on; +set enable_nestloop = on; +explain analyse +select array_599434088_2.* +from (select e2.comp_id, fields ->> '/archetype_details/template_id/value' + from ehr.entry2 e2 + where (rm_entity = 'COMPOSITION') + and field_idx_len = 0 + and fields ->> '/archetype_details/template_id/value' = 'Corona_Anamnese' + and ehr_id = current_setting('ehr.id')::uuid + limit 1) as "array_599434088_1" + join lateral ( select * from ehr.entry2 e3 where e3.comp_id = array_599434088_1.comp_id ) as "array_599434088_2" + on true; + + + +--Get all patients which have a specific diagnosis for a specific health care facility +-- To big for hash join +set enable_hashjoin = off; +set enable_nestloop = on; +explain analyse +select distinct array_599434088_2.ehr_id +from (select e2.comp_id, e2.entity_concept, fields ->> '/composer/name' as "composer" + from ehr.entry2 e2 + where (rm_entity = 'COMPOSITION') + and field_idx_len = 0 + and fields ->> '/composer/name' = 'Silvia Blake' + ) as "array_599434088_1" + join lateral ( select ehr_id + from ehr.entry2 e3 + where entity_concept = 'openEHR-EHR-EVALUATION.problem_diagnosis.v1' + and field_idx_len = 0 + and fields ->> '/data[at0001]/items[at0002]/value/value' = 'Problem/Diagnosis name 10' + and e3.comp_id = array_599434088_1.comp_id ) as "array_599434088_2" on true; + + + +-- deep select + +-- the default just uses hash on the first join +set enable_nestloop = off; +set enable_hashjoin = on; + +explain analyse +select array_599434088_1.comp_id, + array_599434088_1.composer, + array_599434088_2.subject, + array_599434088_3.time, + array_599434088_4.art, + array_599434088_5.ziel +from (select e2.comp_id, e2.entity_concept, fields ->> '/composer/name' as "composer" + from ehr.entry2 e2 + where (rm_entity = 'COMPOSITION') + and field_idx_len = 0 + and ehr_id = current_setting('ehr.id')::uuid) as "array_599434088_1" + join lateral ( select e3.comp_id, fields ->> '/subject/_type' as "subject" + from ehr.entry2 e3 + where entity_concept = 'openEHR-EHR-OBSERVATION.travel_event.v0' + and field_idx_len = 0 + and ehr_id = current_setting('ehr.id')::uuid + and e3.comp_id = array_599434088_1.comp_id ) as "array_599434088_2" on true + join lateral ( select e4.comp_id, + e4.field_idx[1] as "R0", + fields ->> '/data[at0001]/events[at0002]/time/value' as "time" + from ehr.entry2 e4 + where entity_concept = 'openEHR-EHR-OBSERVATION.travel_event.v0' + and field_idx_len = 1 + and ehr_id = current_setting('ehr.id')::uuid + and e4.comp_id = array_599434088_2.comp_id ) as "array_599434088_3" on true + join lateral ( select e5.comp_id, + e5.field_idx[1] as "R0", + e5.field_idx[2] as "R1", + fields ->> '/data[at0001]/events[at0002]/data[at0003]/items[at0008]/name/value' as "art" + from ehr.entry2 e5 + where entity_concept = 'openEHR-EHR-OBSERVATION.travel_event.v0' + and field_idx_len = 2 + and ehr_id = current_setting('ehr.id')::uuid + and e5.comp_id = array_599434088_3.comp_id + and e5.field_idx[1] = array_599434088_3."R0") as "array_599434088_4" on true + join lateral ( select fields ->> + '/data[at0001]/events[at0002]/data[at0003]/items[at0008]/items[at0010]/items[at0011]/value/value' as "ziel" + from ehr.entry2 e6 + where entity_concept = 'openEHR-EHR-OBSERVATION.travel_event.v0' + and field_idx_len = 3 + and ehr_id = current_setting('ehr.id')::uuid + and e6.comp_id = array_599434088_3.comp_id + and e6.field_idx[1] = array_599434088_4."R0" + and e6.field_idx[2] = array_599434088_4."R1") as "array_599434088_5" on true; + + + + + + diff --git a/bom/pom.xml b/bom/pom.xml index 2d7e870e2..bd563be9e 100644 --- a/bom/pom.xml +++ b/bom/pom.xml @@ -228,6 +228,11 @@ commons-io ${commons-io.version} + + org.apache.commons + commons-csv + 1.9.0 + org.apache.commons commons-text diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/jsonencoding/CanonicalJson.java b/serialisation/src/main/java/org/ehrbase/serialisation/jsonencoding/CanonicalJson.java index 8595ebc4c..1d30fd32f 100644 --- a/serialisation/src/main/java/org/ehrbase/serialisation/jsonencoding/CanonicalJson.java +++ b/serialisation/src/main/java/org/ehrbase/serialisation/jsonencoding/CanonicalJson.java @@ -58,7 +58,7 @@ public class CanonicalJson implements RMDataFormat { - private static final ObjectMapper MARSHAL_OM = + public static final ObjectMapper MARSHAL_OM = ArchieObjectMapperProvider.getObjectMapper().copy(); static { diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CodeGenerator.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CodeGenerator.java new file mode 100644 index 000000000..25f4e490b --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CodeGenerator.java @@ -0,0 +1,55 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.Arrays; +import java.util.List; +import java.util.stream.Collectors; +import org.apache.commons.lang3.ArrayUtils; + +/** + * @author Stefan Spiska + */ +public class CodeGenerator { + + private static List code = List.of( + "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "y", "z", "1", + "2", "3", "4", "5", "6", "7", "8", "9", "0"); + + int current = 0; + + public String next() { + + String collect = Arrays.stream(split(current)).map(code::get).collect(Collectors.joining()); + current++; + return collect; + } + + private Integer[] split(int i) { + + Integer[] result = new Integer[1]; + + result[0] = i % code.size(); + + if (i / code.size() > 0) { + return ArrayUtils.addAll(split(i / code.size()), result); + } + + return result; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CompositionToMatrixWalker.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CompositionToMatrixWalker.java new file mode 100644 index 000000000..750bbcb96 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/CompositionToMatrixWalker.java @@ -0,0 +1,305 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.ehrbase.serialisation.jsonencoding.CanonicalJson.MARSHAL_OM; +import static org.ehrbase.serialisation.matrixencoding.MatrixUtil.addMissingChildren; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.node.ArrayNode; +import com.fasterxml.jackson.databind.node.BooleanNode; +import com.fasterxml.jackson.databind.node.NumericNode; +import com.fasterxml.jackson.databind.node.ObjectNode; +import com.fasterxml.jackson.databind.node.POJONode; +import com.fasterxml.jackson.databind.node.ValueNode; +import com.nedap.archie.rm.RMObject; +import com.nedap.archie.rm.archetyped.Archetyped; +import com.nedap.archie.rm.archetyped.Locatable; +import com.nedap.archie.rm.composition.Activity; +import com.nedap.archie.rm.composition.EventContext; +import com.nedap.archie.rm.datastructures.Element; +import com.nedap.archie.rm.datastructures.IntervalEvent; +import com.nedap.archie.rm.datavalues.quantity.DvInterval; +import com.nedap.archie.rm.datavalues.quantity.datetime.DvDate; +import com.nedap.archie.rm.datavalues.quantity.datetime.DvDateTime; +import com.nedap.archie.rm.datavalues.quantity.datetime.DvDuration; +import com.nedap.archie.rm.datavalues.quantity.datetime.DvTime; +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import org.apache.commons.lang3.StringUtils; +import org.ehrbase.aql.dto.path.AqlPath; +import org.ehrbase.serialisation.walker.Context; +import org.ehrbase.serialisation.walker.FromCompositionWalker; +import org.ehrbase.serialisation.walker.RmPrimitive; +import org.ehrbase.util.exception.SdkException; +import org.ehrbase.webtemplate.model.WebTemplateNode; + +/** + * @author Stefan Spiska + */ +public class CompositionToMatrixWalker extends FromCompositionWalker { + + public static final String MAGNITUDE = "/magnitude"; + private List resolveTo = List.of("OBSERVATION", "EVALUATION", "INSTRUCTION", "ACTION", "ADMIN_ENTRY"); + + @Override + protected FromWalkerDto extract( + Context context, WebTemplateNode child, boolean isChoice, Integer i) { + + FromWalkerDto next = new FromWalkerDto(context.getObjectDeque().peek()); + + // this belongs to composition thus COMPOSITION is the root + if (List.of("context", "links", "feeder_audit").contains(child.getId()) + && context.getNodeDeque().peek().getRmType().equals("COMPOSITION")) { + next.setRootFound(true); + } + + // Is this a RM type to which we resolve to, then add a new Entity + if (child.getNodeId() != null + && findTypeName(child.getNodeId()) != null + && resolveTo.contains(findTypeName(child.getNodeId()))) { + + Entity nextEntity = new Entity(next.getCurrentEntity()); + nextEntity.setArchetypeId(child.getNodeId()); + nextEntity.setPathFromRoot( + child.getAqlPathDto().removeStart(next.getCurrentEntity().getPathFromRoot())); + if (i != null) { + nextEntity.getEntityIdx().add(child.getAqlPath(), i); + } + next.updateEntity(nextEntity); + next.setRootFound(true); + // increment index + } else { + + if (i != null) { + + if (next.isRootFound()) { + next.getCurrentFieldIndex().add(child.getAqlPath(), i); + next.getMatrix() + .get(next.getCurrentEntity()) + .put(next.getCurrentFieldIndex(), new LinkedHashMap<>()); + } else { + next.getCurrentEntity().getEntityIdx().add(child.getAqlPath(), i); + if (!next.getMatrix().containsKey(next.getCurrentEntity())) { + next.getMatrix().put(next.getCurrentEntity(), new LinkedHashMap<>()); + } + next.getMatrix() + .get(next.getCurrentEntity()) + .put(next.getCurrentFieldIndex(), new LinkedHashMap<>()); + } + } + } + + addMissingChildren(child); + + return next; + } + + @Override + protected void preHandle(Context context) { + + WebTemplateNode node = context.getNodeDeque().peek(); + FromWalkerDto fromWalkerDto = context.getObjectDeque().peek(); + RMObject rmObject = context.getRmObjectDeque().peek(); + AqlPath relativ = node.getAqlPathDto() + .removeStart(fromWalkerDto.getCurrentEntity().getPathFromRoot()); + if (!visitChildren(node)) { + + if (rmObject instanceof RmPrimitive) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ, ((RmPrimitive) rmObject).getValue()); + } else { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .putAll(flatten(relativ, MARSHAL_OM.valueToTree(rmObject))); + } + + if (rmObject instanceof Archetyped) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd("/_type"), "ARCHETYPED"); + } + + addMagnitude(fromWalkerDto, rmObject, relativ); + + } else { + // add the type + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd("/_type"), node.getRmType()); + } + } + + /** + * Add the magnitude field to be used for comparison in the db. + * @param fromWalkerDto + * @param rmObject + * @param relativ + */ + private static void addMagnitude(FromWalkerDto fromWalkerDto, RMObject rmObject, AqlPath relativ) { + if (rmObject instanceof DvTime) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd(MAGNITUDE), ((DvTime) rmObject).getMagnitude()); + } + if (rmObject instanceof DvDate) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd(MAGNITUDE), ((DvDate) rmObject).getMagnitude()); + } + if (rmObject instanceof DvDateTime) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd(MAGNITUDE), ((DvDateTime) rmObject).getMagnitude()); + } + if (rmObject instanceof DvDuration) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .put(relativ.addEnd(MAGNITUDE), ((DvDuration) rmObject).getMagnitude()); + } + } + + /** + * Transform a {@link JsonNode} representing a subtree in a flat map; + * @param prefix + * @param node + * @return + */ + private Map flatten(AqlPath prefix, JsonNode node) { + + LinkedHashMap result = new LinkedHashMap<>(); + if (node instanceof ObjectNode) { + + for (Iterator> it = node.fields(); it.hasNext(); ) { + Map.Entry child = it.next(); + + result.putAll(flatten(prefix.addEnd("/" + child.getKey()), child.getValue())); + } + + } else if (node instanceof POJONode) { + try { + result.putAll(flatten(prefix, MARSHAL_OM.readTree((node).toString()))); + } catch (JsonProcessingException e) { + throw new SdkException(e.getMessage()); + } + } else if (node instanceof ValueNode) { + if (node instanceof NumericNode) { + result.put(prefix, node.numberValue()); + } else if (node instanceof BooleanNode) { + result.put(prefix, node.booleanValue()); + } else { + result.put(prefix, node.asText()); + } + } else if (node instanceof ArrayNode) { + try { + result.put(prefix, MARSHAL_OM.writeValueAsString(node)); + } catch (JsonProcessingException e) { + throw new SdkException(e.getMessage()); + } + } + + return result; + } + + @Override + protected void postHandle(Context context) { + + WebTemplateNode node = context.getNodeDeque().peek(); + FromWalkerDto fromWalkerDto = context.getObjectDeque().peek(); + RMObject rmObject = context.getRmObjectDeque().peek(); + AqlPath relativ = node.getAqlPathDto() + .removeStart(fromWalkerDto.getCurrentEntity().getPathFromRoot()); + + // missing in the webtemplate and thus have to be handled manually + if (rmObject instanceof Locatable) { + + add(fromWalkerDto, relativ.addEnd("/uid"), ((Locatable) rmObject).getUid()); + } + + if (rmObject instanceof Element) { + + add(fromWalkerDto, relativ.addEnd("/null_reason"), ((Element) rmObject).getNullReason()); + } + + if (rmObject instanceof IntervalEvent) { + + add(fromWalkerDto, relativ.addEnd("/sample_count"), ((IntervalEvent) rmObject).getSampleCount()); + } + + if (rmObject instanceof EventContext) { + + add(fromWalkerDto, relativ.addEnd("/location"), ((EventContext) rmObject).getLocation()); + } + + if (rmObject instanceof Activity) { + + add(fromWalkerDto, relativ.addEnd("/action_archetype_id"), ((Activity) rmObject).getActionArchetypeId()); + } + + if (rmObject instanceof DvInterval) { + add(fromWalkerDto, relativ.addEnd("/lower_included"), ((DvInterval) rmObject).isLowerIncluded()); + add(fromWalkerDto, relativ.addEnd("/upper_included"), ((DvInterval) rmObject).isUpperIncluded()); + add(fromWalkerDto, relativ.addEnd("/lower_unbounded"), ((DvInterval) rmObject).isLowerUnbounded()); + add(fromWalkerDto, relativ.addEnd("/upper_unbounded"), ((DvInterval) rmObject).isUpperUnbounded()); + } + } + + private void add(FromWalkerDto fromWalkerDto, AqlPath relativ, Object o) { + if (o != null) { + fromWalkerDto + .getMatrix() + .get(fromWalkerDto.getCurrentEntity()) + .get(fromWalkerDto.getCurrentFieldIndex()) + .putAll(flatten(relativ, MARSHAL_OM.valueToTree(o))); + } + } + + static String findTypeName(String atCode) { + String typeName = null; + + if (atCode.contains("openEHR-EHR-")) { + + typeName = StringUtils.substringBetween(atCode, "openEHR-EHR-", "."); + } else if (atCode.startsWith("at")) { + typeName = null; + } else { + typeName = atCode; + } + return typeName; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Encoder.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Encoder.java new file mode 100644 index 000000000..48f3069b8 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Encoder.java @@ -0,0 +1,29 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * @author Stefan Spiska + */ +public interface Encoder { + AqlPath encode(AqlPath path); + + AqlPath decode(AqlPath path); +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/EncoderTool.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/EncoderTool.java new file mode 100644 index 000000000..6ee5c3ad8 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/EncoderTool.java @@ -0,0 +1,90 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.ehrbase.aql.dto.path.predicate.PredicateHelper.NAME_VALUE; + +import java.util.Comparator; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * Helper class to build the encoding csv for {@link FixedCodeSetEncoder} + * @author Stefan Spiska + */ +class EncoderTool { + + private final CodeGenerator totalHelper = new CodeGenerator(); + private final CodeGenerator pathHelper = new CodeGenerator(); + + Map buildTotalEncodingMap(List seed) { + + Map encodingMap = new LinkedHashMap<>(); + + Comparator> comparator = Map.Entry.comparingByValue(); + + seed.stream() + .flatMap(r -> Stream.concat(Stream.of(r.getEntityPath()), r.getFields().keySet().stream())) + .filter(p -> isSimple(p.getNodes())) + .filter(p -> !p.getPath().equals("/")) + .collect(Collectors.groupingBy(Function.identity(), Collectors.counting())) + .entrySet() + .stream() + .sorted(comparator.reversed()) + .map(Map.Entry::getKey) + .forEach(p -> encodingMap.computeIfAbsent(p.getPath(), k -> "!" + totalHelper.next())); + + return encodingMap; + } + + Map buildPathEncodingMap(List seed) { + + Map encodingMap = new LinkedHashMap<>(); + + Comparator> comparator = Map.Entry.comparingByValue(); + + seed.stream() + .flatMap(r -> Stream.concat(Stream.of(r.getEntityPath()), r.getFields().keySet().stream())) + .filter(p -> !p.getPath().equals("/")) + .filter(p -> !isSimple(p.getNodes())) + .flatMap(p -> p.getNodes().stream()) + .map(AqlPath.AqlNode::getName) + .collect(Collectors.groupingBy(Function.identity(), Collectors.counting())) + .entrySet() + .stream() + .sorted(comparator.reversed()) + .map(Map.Entry::getKey) + .forEach(n -> encodingMap.computeIfAbsent(n, k -> pathHelper.next())); + + return encodingMap; + } + + private boolean isSimple(List nodes) { + return nodes.stream().allMatch(this::isSimple); + } + + private boolean isSimple(AqlPath.AqlNode node) { + + return node.getAtCode() == null && node.findOtherPredicate(NAME_VALUE) == null; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Entity.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Entity.java new file mode 100644 index 000000000..9dfc9fda6 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Entity.java @@ -0,0 +1,91 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.Objects; +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * @author Stefan Spiska + */ +class Entity { + + private AqlPath pathFromRoot; + private String archetypeId; + + private Index entityIdx = new Index(); + + public Entity() {} + + public Entity(Entity other) { + this.pathFromRoot = AqlPath.parse(other.pathFromRoot.getPath()); + this.archetypeId = other.archetypeId; + this.entityIdx = new Index(other.entityIdx); + } + + public AqlPath getPathFromRoot() { + return pathFromRoot; + } + + public void setPathFromRoot(AqlPath pathFromRoot) { + this.pathFromRoot = pathFromRoot; + } + + public String getArchetypeId() { + return archetypeId; + } + + public void setArchetypeId(String archetypeId) { + this.archetypeId = archetypeId; + } + + public Index getEntityIdx() { + return entityIdx; + } + + public void setEntityIdx(Index entityIdx) { + this.entityIdx = entityIdx; + } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + Entity entity = (Entity) o; + return Objects.equals(pathFromRoot, entity.pathFromRoot) + && Objects.equals(archetypeId, entity.archetypeId) + && Objects.equals(entityIdx, entity.entityIdx); + } + + @Override + public int hashCode() { + return Objects.hash(pathFromRoot, archetypeId, entityIdx); + } + + @Override + public String toString() { + return "Resolve{" + "pathFromRoot=" + + pathFromRoot + ", archetypeId='" + + archetypeId + '\'' + ", count=" + + entityIdx + '}'; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FixedCodeSetEncoder.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FixedCodeSetEncoder.java new file mode 100644 index 000000000..9fee9e0b6 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FixedCodeSetEncoder.java @@ -0,0 +1,113 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import com.google.common.collect.BiMap; +import com.google.common.collect.HashBiMap; +import java.io.IOException; +import java.io.InputStreamReader; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVParser; +import org.apache.commons.lang3.StringUtils; +import org.ehrbase.aql.dto.path.AqlPath; +import org.ehrbase.util.exception.SdkException; + +/** + * @author Stefan Spiska + */ +public class FixedCodeSetEncoder implements Encoder { + + private final BiMap totalEncoding = HashBiMap.create(); + private final BiMap pathEncoding = HashBiMap.create(); + + public FixedCodeSetEncoder() { + + try (CSVParser csv = new CSVParser( + new InputStreamReader(FixedCodeSetEncoder.class.getResourceAsStream("/encoder/totalpathencoding.csv")), + CSVFormat.DEFAULT.builder().setHeader("path", "code").build())) { + csv.stream().forEach(c -> totalEncoding.put(c.get(0), c.get(1))); + } catch (IOException e) { + throw new SdkException(e.getMessage(), e); + } + + try (CSVParser csv = new CSVParser( + new InputStreamReader(FixedCodeSetEncoder.class.getResourceAsStream("/encoder/pathencoding.csv")), + CSVFormat.DEFAULT.builder().setHeader("path", "code").build())) { + csv.stream().forEach(c -> pathEncoding.put(c.get(0), c.get(1))); + } catch (IOException e) { + throw new SdkException(e.getMessage(), e); + } + } + + @Override + public AqlPath encode(AqlPath path) { + + if (totalEncoding.containsKey(path.getPath())) { + return AqlPath.parse(totalEncoding.get(path.getPath())); + } + + AqlPath rootPath = AqlPath.ROOT_PATH; + + for (AqlPath.AqlNode aqlNode : path.getNodes()) { + AqlPath.AqlNode n = encode(aqlNode); + rootPath = rootPath.addEnd(n); + } + + return rootPath; + } + + private AqlPath.AqlNode encode(AqlPath.AqlNode node) { + + if (pathEncoding.containsKey(node.getName())) { + + return new AqlPath.AqlNode(pathEncoding.get(node.getName()), node.getAtCode(), node.getOtherPredicate()); + } + + return node; + } + + @Override + public AqlPath decode(AqlPath path) { + + String key = StringUtils.removeStart(path.getPath(), "/"); + + if (totalEncoding.containsValue(key)) { + return AqlPath.parse(totalEncoding.inverse().get(key)); + } + + AqlPath rootPath = AqlPath.ROOT_PATH; + + for (AqlPath.AqlNode aqlNode : path.getNodes()) { + AqlPath.AqlNode n = decode(aqlNode); + rootPath = rootPath.addEnd(n); + } + + return rootPath; + } + + private AqlPath.AqlNode decode(AqlPath.AqlNode node) { + + if (pathEncoding.containsValue(node.getName())) { + + return new AqlPath.AqlNode( + pathEncoding.inverse().get(node.getName()), node.getAtCode(), node.getOtherPredicate()); + } + + return node; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FromWalkerDto.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FromWalkerDto.java new file mode 100644 index 000000000..16cfb84e7 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/FromWalkerDto.java @@ -0,0 +1,79 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.LinkedHashMap; +import java.util.Map; +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * @author Stefan Spiska + */ +class FromWalkerDto { + + private final Map>> matrix; + + private Entity currentEntity; + private Index currentFieldIndex; + + private boolean rootFound = false; + + public FromWalkerDto() { + + this.matrix = new LinkedHashMap<>(); + } + + public FromWalkerDto(FromWalkerDto other) { + this.currentEntity = new Entity(other.currentEntity); + this.currentFieldIndex = new Index(other.currentFieldIndex); + this.matrix = other.matrix; + this.rootFound = other.rootFound; + } + + public boolean isRootFound() { + return rootFound; + } + + public void setRootFound(boolean rootFound) { + this.rootFound = rootFound; + } + + public Map>> getMatrix() { + return matrix; + } + + public Entity getCurrentEntity() { + return currentEntity; + } + + public void updateEntity(Entity currentEntity) { + this.currentEntity = currentEntity; + matrix.put(currentEntity, new LinkedHashMap<>()); + Index key = new Index(); + matrix.get(currentEntity).put(key, new LinkedHashMap<>()); + currentFieldIndex = key; + } + + public Index getCurrentFieldIndex() { + return currentFieldIndex; + } + + public void setCurrentFieldIndex(Index currentFieldIndex) { + this.currentFieldIndex = currentFieldIndex; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Index.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Index.java new file mode 100644 index 000000000..544c1ad65 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Index.java @@ -0,0 +1,67 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.LinkedHashMap; +import java.util.Objects; + +/** + * @author Stefan Spiska + */ +class Index { + + private final LinkedHashMap indexMap = new LinkedHashMap<>(); + + public Index() {} + + public Index(Index other) { + + indexMap.putAll(other.indexMap); + } + + public void add(String key, Integer value) { + indexMap.put(key, value); + } + + Integer[] getRepetitions() { + + return indexMap.values().toArray(new Integer[0]); + } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + Index index = (Index) o; + return Objects.equals(indexMap, index.indexMap); + } + + @Override + public int hashCode() { + return Objects.hash(indexMap); + } + + @Override + public String toString() { + return "Index{" + "indexMap=" + indexMap + '}'; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixFormat.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixFormat.java new file mode 100644 index 000000000..223fa590a --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixFormat.java @@ -0,0 +1,325 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.ehrbase.serialisation.matrixencoding.CompositionToMatrixWalker.findTypeName; + +import com.fasterxml.jackson.core.JsonGenerator; +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.databind.SerializerProvider; +import com.fasterxml.jackson.databind.module.SimpleModule; +import com.fasterxml.jackson.databind.ser.std.StdSerializer; +import com.nedap.archie.rm.RMObject; +import com.nedap.archie.rm.composition.Composition; +import java.io.IOException; +import java.io.StringReader; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collection; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.stream.Collectors; +import java.util.stream.IntStream; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.apache.commons.csv.CSVRecord; +import org.apache.commons.lang3.ArrayUtils; +import org.apache.commons.lang3.StringUtils; +import org.ehrbase.aql.dto.path.AqlPath; +import org.ehrbase.serialisation.RMDataFormat; +import org.ehrbase.util.exception.SdkException; +import org.ehrbase.webtemplate.templateprovider.TemplateProvider; + +/** + * @author Stefan Spiska + */ +public class MatrixFormat implements RMDataFormat { + + private enum HEADERS { + NUM, + ENTITY_CONCEPT, + RM_ENTITY, + ENTITY_PATH, + ENTITY_IDX, + FIELD_IDX, + FIELD_IDX_LEN, + FIELDS + } + + public static final CSVFormat CSV_FORMAT = + CSVFormat.DEFAULT.builder().setHeader(HEADERS.class).build(); + + public static final ObjectMapper MAPPER; + + static { + MAPPER = new ObjectMapper(); + SimpleModule module = new SimpleModule(); + module.addKeySerializer(AqlPath.class, new AqlPathKeyStdSerializer()); + + MAPPER.registerModule(module); + } + + private final Encoder encoder; + private final TemplateProvider templateProvider; + + public MatrixFormat(TemplateProvider templateProvider) { + this.templateProvider = templateProvider; + + encoder = null; + } + + public MatrixFormat(TemplateProvider templateProvider, Encoder encoder) { + this.templateProvider = templateProvider; + this.encoder = encoder; + } + + public Encoder getEncoder() { + return encoder; + } + + Map>> toMatrix(Composition composition) { + String templateId = composition.getArchetypeDetails().getTemplateId().getValue(); + Entity currentEntity = new Entity(); + currentEntity.setPathFromRoot(AqlPath.ROOT_PATH); + currentEntity.setArchetypeId(composition.getArchetypeNodeId()); + FromWalkerDto fromWalkerDto = new FromWalkerDto(); + fromWalkerDto.updateEntity(currentEntity); + new CompositionToMatrixWalker() + .walk( + composition, + fromWalkerDto, + templateProvider + .buildIntrospect(templateId) + .orElseThrow(() -> new SdkException(String.format("Unknown template %s", templateId))) + .getTree(), + templateId); + + return fromWalkerDto.getMatrix(); + } + + public List toTable(Composition composition) { + + List flatten = flatten(toMatrix(composition)); + + if (encoder != null) { + flatten.forEach(this::encode); + } + + return flatten; + } + + private List flatten(Map>> map) { + + List collect = map.entrySet().stream() + .map(e -> toRows(e.getKey(), e.getValue())) + .flatMap(Collection::stream) + .collect(Collectors.toList()); + IntStream.range(0, collect.size()).forEach(i -> collect.get(i).setNum(i)); + return collect; + } + + private List toRows(Entity entity, Map> map) { + + return map.entrySet().stream().map(e -> toRow(entity, e)).collect(Collectors.toList()); + } + + private Row toRow(Entity entity, Map.Entry> e) { + Row row = new Row(); + row.setEntityIdx(entity.getEntityIdx().getRepetitions()); + row.setArchetypeId(entity.getArchetypeId()); + row.setEntityPath(entity.getPathFromRoot()); + row.setFields(e.getValue()); + row.setFieldIdx(e.getKey().getRepetitions()); + return row; + } + + private List toEntryList(String csv) { + + try { + return CSV_FORMAT.parse(new StringReader(csv)).stream() + .skip(1) + .map(this::toRow) + .map(this::toEntryList) + .flatMap(Collection::stream) + .collect(Collectors.toList()); + } catch (IOException e) { + throw new SdkException(e.getMessage(), e); + } + } + + private List toEntryList(Row row) { + + return row.getFields().entrySet().stream() + .map(e -> { + ToWalkerDto toWalkerDto = new ToWalkerDto(); + + toWalkerDto.path = row.getEntityPath().addEnd(e.getKey()); + toWalkerDto.index = new ArrayList<>(Arrays.asList(row.getEntityIdx())); + toWalkerDto.index.addAll(Arrays.asList(row.getFieldIdx())); + toWalkerDto.value = e.getValue(); + return toWalkerDto; + }) + .collect(Collectors.toList()); + } + + private Row toRow(CSVRecord csvRecord) { + + Row row = new Row(); + row.setNum(Integer.parseInt(csvRecord.get(HEADERS.NUM))); + row.setEntityIdx(buildArray(csvRecord.get(HEADERS.ENTITY_IDX))); + row.setFieldIdx(buildArray(csvRecord.get(HEADERS.FIELD_IDX))); + row.setArchetypeId(csvRecord.get(HEADERS.ENTITY_CONCEPT)); + row.setEntityPath(AqlPath.parse(csvRecord.get(HEADERS.ENTITY_PATH))); + try { + Map map = MAPPER.readValue( + csvRecord.get(HEADERS.FIELDS), + MAPPER.getTypeFactory().constructMapType(LinkedHashMap.class, String.class, Object.class)); + row.setFields(map.entrySet().stream() + .collect(Collectors.toMap(e -> AqlPath.parse(e.getKey()), Map.Entry::getValue))); + } catch (JsonProcessingException e) { + throw new SdkException(e.getMessage(), e); + } + + if (encoder != null) { + decode(row); + } + + return row; + } + + private static Integer[] buildArray(String s) { + + String s1 = StringUtils.substringBetween(s, "{", "}"); + + if (StringUtils.isEmpty(s1)) { + return new Integer[] {}; + } + + return Arrays.stream(s1.split(",")).map(Integer::parseInt).toArray(Integer[]::new); + } + + @Override + public String marshal(RMObject rmObject) { + if (rmObject instanceof Composition) { + + StringBuilder sb = new StringBuilder(); + try (CSVPrinter printer = new CSVPrinter(sb, CSV_FORMAT)) { + for (Row r : toTable((Composition) rmObject)) { + printRow(printer, r); + } + } catch (IOException e) { + throw new SdkException(e.getMessage(), e); + } + + return sb.toString(); + } else { + throw new UnsupportedOperationException(); + } + } + + private static void printRow(CSVPrinter printer, Row r) { + try { + printer.printRecord( + r.getNum(), + r.getArchetypeId(), + findTypeName(r.getArchetypeId()), + r.getEntityPath().format(AqlPath.OtherPredicatesFormat.SHORTED, true), + printArray(r.getEntityIdx()), + printArray(r.getFieldIdx()), + ArrayUtils.isEmpty(r.getFieldIdx()) ? 0 : r.getFieldIdx().length, + MAPPER.writerFor(MAPPER.getTypeFactory().constructMapType(Map.class, AqlPath.class, Object.class)) + .writeValueAsString(r.getFields())); + } catch (IOException e) { + throw new SdkException(e.getMessage()); + } + } + + private static String printArray(Integer[] index) { + return ArrayUtils.isEmpty(index) + ? "{}" + : "{" + Arrays.stream(index).map(Objects::toString).collect(Collectors.joining(",")) + "}"; + } + + @Override + public T unmarshal(String value, Class clazz) { + + List entries = toEntryList(value); + + String templateId = + MatrixToCompositionWalker.filter( + entries, AqlPath.parse("/archetype_details/template_id/value"), false, null) + .stream() + .findAny() + .orElseThrow() + .value + .toString(); + + MatrixToCompositionWalker matrixToCompositionWalker = new MatrixToCompositionWalker(); + + Composition composition = new Composition(); + matrixToCompositionWalker.walk( + composition, + entries, + templateProvider.buildIntrospect(templateId).orElseThrow(), + null, + templateId); + + return (T) composition; + } + + private void encode(Row row) { + + row.setEntityPath(encoder.encode(row.getEntityPath())); + row.setFields(row.getFields().entrySet().stream() + .collect(Collectors.toMap( + e -> encoder.encode(e.getKey()), + Map.Entry::getValue, + (u, v) -> { + throw new IllegalStateException(String.format("Duplicate key %s", u)); + }, + LinkedHashMap::new))); + } + + private void decode(Row row) { + + row.setEntityPath(encoder.decode(row.getEntityPath())); + row.setFields(row.getFields().entrySet().stream() + .collect(Collectors.toMap( + e -> encoder.decode(e.getKey()), + Map.Entry::getValue, + (u, v) -> { + throw new IllegalStateException(String.format("Duplicate key %s", u)); + }, + LinkedHashMap::new))); + } + + private static class AqlPathKeyStdSerializer extends StdSerializer { + + public AqlPathKeyStdSerializer() { + super((Class) null); + } + + @Override + public void serialize(AqlPath value, JsonGenerator gen, SerializerProvider provider) throws IOException { + gen.writeFieldName(value.format(AqlPath.OtherPredicatesFormat.SHORTED, true)); + } + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixToCompositionWalker.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixToCompositionWalker.java new file mode 100644 index 000000000..03b1f0267 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixToCompositionWalker.java @@ -0,0 +1,349 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.ehrbase.serialisation.jsonencoding.CanonicalJson.MARSHAL_OM; +import static org.ehrbase.util.rmconstants.RmConstants.DV_TEXT; +import static org.ehrbase.util.rmconstants.RmConstants.FEEDER_AUDIT; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.nedap.archie.rm.RMObject; +import com.nedap.archie.rm.archetyped.Archetyped; +import com.nedap.archie.rm.archetyped.Link; +import com.nedap.archie.rm.archetyped.Locatable; +import com.nedap.archie.rm.archetyped.TemplateId; +import com.nedap.archie.rm.composition.Activity; +import com.nedap.archie.rm.composition.EventContext; +import com.nedap.archie.rm.datastructures.Element; +import com.nedap.archie.rm.datastructures.IntervalEvent; +import com.nedap.archie.rm.datavalues.quantity.DvInterval; +import com.nedap.archie.rm.support.identification.ArchetypeID; +import java.util.List; +import java.util.Map; +import java.util.function.Consumer; +import java.util.stream.Collectors; +import org.apache.commons.lang3.tuple.Pair; +import org.ehrbase.aql.dto.path.AqlPath; +import org.ehrbase.building.webtemplateskeletnbuilder.WebTemplateSkeletonBuilder; +import org.ehrbase.serialisation.walker.Context; +import org.ehrbase.serialisation.walker.ToCompositionWalker; +import org.ehrbase.util.exception.SdkException; +import org.ehrbase.webtemplate.model.WebTemplateNode; + +/** + * @author Stefan Spiska + */ +public class MatrixToCompositionWalker extends ToCompositionWalker> { + + public static final String OTHER_REFERENCE_RANGES = "other_reference_ranges"; + // These subparts are saved as arrays. + public static final List> ARRAY_ELEMENTS = List.of( + Pair.of(AqlPath.parse("mappings"), DV_TEXT), + Pair.of(AqlPath.parse("mappings"), "DV_CODED_TEXT"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_QUANTITY"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_DURATION"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_ORDINAL"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_PROPORTION"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_COUNT"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_DATE"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_DATE_TIME"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_TIME"), + Pair.of(AqlPath.parse(OTHER_REFERENCE_RANGES), "DV_CODED_TEXT"), + Pair.of(AqlPath.parse("feeder_system_item_ids"), FEEDER_AUDIT), + Pair.of(AqlPath.parse("originating_system_item_ids"), FEEDER_AUDIT), + Pair.of(AqlPath.parse("performer/identifiers"), "PARTICIPATION"), + Pair.of(AqlPath.parse("identifiers"), "PARTY_IDENTIFIED"), + Pair.of(AqlPath.parse("identifiers"), "PARTY_RELATED"), + Pair.of(AqlPath.parse("originating_system_audit/provider/identifiers"), FEEDER_AUDIT), + Pair.of(AqlPath.parse("originating_system_audit/subject/identifiers"), FEEDER_AUDIT), + Pair.of(AqlPath.parse("feeder_system_audit/provider/identifiers"), FEEDER_AUDIT), + Pair.of(AqlPath.parse("feeder_system_audit/subject/identifiers"), FEEDER_AUDIT), + Pair.of(AqlPath.parse(""), "LINK")); + public static final String STRING = "STRING"; + public static final String BOOLEAN = "BOOLEAN"; + + @Override + protected List extract( + Context> context, WebTemplateNode child, boolean isChoice, Integer i) { + + // If primitive return null + if (List.of(STRING, "LONG", BOOLEAN).contains(child.getRmType())) { + + return null; + } + + List filter = filter(context.getObjectDeque().peek(), child.getAqlPathDto(), i != null, i); + + // Check that the type is correct + if (isChoice + && filter(filter, child.getAqlPathDto().addEnd("/_type"), false, null).stream() + .noneMatch(e -> e.value.equals(child.getRmType()))) { + return null; + } + + MatrixUtil.addMissingChildren(child); + + if (filter.isEmpty()) { + return null; + } + return filter; + } + + @Override + protected void preHandle(Context> context) { + + WebTemplateNode node = context.getNodeDeque().peek(); + + if (!visitChildren(node)) { + + Map unflatten = unflatten( + node.getRmType(), + node.getAqlPathDto(), + context.getObjectDeque().peek()); + + RMObject peek = context.getRmObjectDeque().peek(); + + // We do not correctly serialise Link and Archetyped and thus have to do that manually. (see + // https://github.com/ehrbase/ehrbase/issues/924) + if (peek instanceof Link) { + unflatten.put("_type", "LINK"); + } + if (peek instanceof Archetyped) { + + ((Archetyped) peek).setRmVersion(unflatten.get("rm_version").toString()); + + ((Archetyped) peek) + .setArchetypeId( + new ArchetypeID(unflatten.get("archetype_id").toString())); + if (unflatten.containsKey("template_id")) { + + TemplateId templateId = new TemplateId(); + templateId.setValue(unflatten.get("template_id").toString()); + ((Archetyped) peek).setTemplateId(templateId); + } + } else { + + Object newRmObject; + newRmObject = buildObject(unflatten); + + RMObject oldRM = context.getRmObjectDeque().poll(); + RMObject parentRM = context.getRmObjectDeque().peek(); + WebTemplateNode currentNode = context.getNodeDeque().poll(); + WebTemplateNode parentNode = context.getNodeDeque().peek(); + + WebTemplateSkeletonBuilder.remove(parentNode, parentRM, currentNode, oldRM); + WebTemplateSkeletonBuilder.insert(parentNode, parentRM, currentNode, newRmObject); + context.getRmObjectDeque().push((RMObject) wrap(newRmObject)); + context.getNodeDeque().push(currentNode); + } + } + } + + private static Object buildObject(Map unflatten) { + + Object newRmObject; + if (unflatten.size() > 1 || unflatten.containsKey("_type")) { + newRmObject = MARSHAL_OM.convertValue(unflatten, RMObject.class); + } else { + newRmObject = unflatten.values().stream().findAny().orElseThrow(); + } + return newRmObject; + } + + private static Map unflatten(String rmType, AqlPath aqlPath, List entries) { + List collect = entries.stream() + .map(o -> { + ToWalkerDto toWalkerDto = new ToWalkerDto(); + toWalkerDto.path = o.path.removeStart(aqlPath); + if (isJsonArray(toWalkerDto, rmType)) { + try { + toWalkerDto.value = MARSHAL_OM.readValue(o.value.toString(), List.class); + } catch (JsonProcessingException e) { + throw new SdkException(e.getMessage()); + } + } else { + toWalkerDto.value = o.value; + } + + toWalkerDto.index = o.index; + return toWalkerDto; + }) + .collect(Collectors.toList()); + return unflatten(collect); + } + + private static boolean isJsonArray(ToWalkerDto toWalkerDto, String rmType) { + + return ARRAY_ELEMENTS.stream() + .anyMatch(p -> p.getRight().equals(rmType) && toWalkerDto.path.equals(p.getLeft())); + } + + private static Map unflatten(List entries) { + + Map> collect = entries.stream() + .collect(Collectors.groupingBy(e -> e.path.getBaseNode().getName())); + + return collect.entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, e -> { + // Elementar Value found + if (e.getValue().size() == 1 && e.getValue().get(0).path.getNodeCount() <= 1) { + return e.getValue().get(0).value; + } + // unfaltten sub-values + else { + return unflatten(e.getValue().stream() + .map(o -> { + ToWalkerDto toWalkerDto = new ToWalkerDto(); + toWalkerDto.value = o.value; + toWalkerDto.path = o.path.removeStart(1); + toWalkerDto.index = o.index; + return toWalkerDto; + }) + .collect(Collectors.toList())); + } + })); + } + + @Override + protected void postHandle(Context> context) { + super.postHandle(context); + + RMObject rmObject = context.getRmObjectDeque().peek(); + + // missing in the webtemplate and thus have to be handled manually + if (rmObject instanceof Locatable) { + + add( + ((Locatable) rmObject)::setUid, + context.getObjectDeque().peek(), + "HIER_OBJECT_ID", + context.getNodeDeque().peek().getAqlPathDto().addEnd("/uid")); + } + + if (rmObject instanceof Element) { + + add( + ((Element) rmObject)::setNullReason, + context.getObjectDeque().peek(), + DV_TEXT, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/null_reason")); + } + + if (rmObject instanceof IntervalEvent) { + + add( + ((IntervalEvent) rmObject)::setSampleCount, + context.getObjectDeque().peek(), + "LONG", + context.getNodeDeque().peek().getAqlPathDto().addEnd("/sample_count")); + } + + if (rmObject instanceof EventContext) { + + add( + ((EventContext) rmObject)::setLocation, + context.getObjectDeque().peek(), + STRING, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/location")); + } + + if (rmObject instanceof Activity) { + + add( + ((Activity) rmObject)::setActionArchetypeId, + context.getObjectDeque().peek(), + STRING, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/action_archetype_id")); + } + + if (rmObject instanceof DvInterval) { + + add( + ((DvInterval) rmObject)::setLowerIncluded, + context.getObjectDeque().peek(), + BOOLEAN, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/lower_included")); + add( + ((DvInterval) rmObject)::setUpperIncluded, + context.getObjectDeque().peek(), + BOOLEAN, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/upper_included")); + add( + ((DvInterval) rmObject)::setLowerUnbounded, + context.getObjectDeque().peek(), + BOOLEAN, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/lower_unbounded")); + add( + ((DvInterval) rmObject)::setUpperUnbounded, + context.getObjectDeque().peek(), + BOOLEAN, + context.getNodeDeque().peek().getAqlPathDto().addEnd("/upper_unbounded")); + } + } + + @Override + protected int calculateSize(Context> context, WebTemplateNode childNode) { + + return filter(context.getObjectDeque().peek(), childNode.getAqlPathDto(), true, null).stream() + .mapToInt(e -> e.index.get(0) + 1) + .max() + .orElse(0); + } + + private static void add(Consumer setter, List toWalkerDtoList, String rmType, AqlPath aqlPath) { + + List filter = filter(toWalkerDtoList, aqlPath, false, null); + + if (!filter.isEmpty()) { + Map unflaten = unflatten(rmType, aqlPath, filter); + + Object object = buildObject(unflaten); + + if (object instanceof Integer && rmType.equals("LONG")) { + object = ((Integer) object).longValue(); + } + + setter.accept((T) object); + } + } + + /** + * Return + * @param list + * @param path + * @param checkIndex + * @param index + * @return + */ + static List filter(List list, AqlPath path, boolean checkIndex, Integer index) { + + return list.stream().filter(e -> matches(e, path, checkIndex, index)).collect(Collectors.toList()); + } + + private static boolean matches(ToWalkerDto toWalkerDto, AqlPath path, boolean checkIndex, Integer index) { + + if (!toWalkerDto.path.startsWith(path)) { + return false; + } + + if (checkIndex && toWalkerDto.index.isEmpty()) { + return false; + } + + return index == null || toWalkerDto.index.get(0).equals(index); + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixUtil.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixUtil.java new file mode 100644 index 000000000..427e38e59 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/MatrixUtil.java @@ -0,0 +1,60 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.ehrbase.util.rmconstants.RmConstants.DV_TEXT; + +import org.ehrbase.util.rmconstants.RmConstants; +import org.ehrbase.webtemplate.model.WebTemplateNode; + +/** + * @author Stefan Spiska + */ +class MatrixUtil { + + private MatrixUtil() { + // util class + } + + static void addMissingChildren(WebTemplateNode child) { + // Webtemplate is missing "link" for Element thus we add it here + if (child.getRmType().equals(RmConstants.ELEMENT)) { + + WebTemplateNode links = new WebTemplateNode(); + + links.setRmType("LINK"); + links.setAqlPath(child.getAqlPathDto().addEnd("/links")); + links.setId("links"); + child.getChildren().add(links); + child.setMax(1); + child.setMin(0); + } + // Webtemplate is missing "reason" for ISM_TRANSITION thus we add it here + if (child.getRmType().equals(RmConstants.ISM_TRANSITION)) { + + WebTemplateNode reason = new WebTemplateNode(); + + reason.setRmType(DV_TEXT); + reason.setAqlPath(child.getAqlPathDto().addEnd("/reason")); + reason.setId("reason"); + child.getChildren().add(reason); + child.setMax(1); + child.setMin(0); + } + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Row.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Row.java new file mode 100644 index 000000000..c408dfc7d --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/Row.java @@ -0,0 +1,122 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.Arrays; +import java.util.Map; +import java.util.Objects; +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * @author Stefan Spiska + */ +public class Row { + + private int num; + private AqlPath entityPath; + private String archetypeId; + + private Integer[] entityIdx; + + private Integer[] fieldIdx; + private Map fields; + + public AqlPath getEntityPath() { + return entityPath; + } + + public void setEntityPath(AqlPath entityPath) { + this.entityPath = entityPath; + } + + public String getArchetypeId() { + return archetypeId; + } + + public void setArchetypeId(String archetypeId) { + this.archetypeId = archetypeId; + } + + public Integer[] getEntityIdx() { + return entityIdx; + } + + public void setEntityIdx(Integer[] entityIdx) { + this.entityIdx = entityIdx; + } + + public Integer[] getFieldIdx() { + return fieldIdx; + } + + public void setFieldIdx(Integer[] fieldIdx) { + this.fieldIdx = fieldIdx; + } + + public Map getFields() { + return fields; + } + + public void setFields(Map fields) { + this.fields = fields; + } + + public int getNum() { + return num; + } + + public void setNum(int num) { + this.num = num; + } + + @Override + public boolean equals(Object o) { + if (this == o) { + return true; + } + if (o == null || getClass() != o.getClass()) { + return false; + } + Row row = (Row) o; + return num == row.num + && Objects.equals(entityPath, row.entityPath) + && Objects.equals(archetypeId, row.archetypeId) + && Arrays.equals(entityIdx, row.entityIdx) + && Arrays.equals(fieldIdx, row.fieldIdx) + && Objects.equals(fields, row.fields); + } + + @Override + public int hashCode() { + int result = Objects.hash(num, entityPath, archetypeId, fields); + result = 31 * result + Arrays.hashCode(entityIdx); + result = 31 * result + Arrays.hashCode(fieldIdx); + return result; + } + + @Override + public String toString() { + return "Row{" + "num=" + + num + ", pathFromRoot=" + + entityPath + ", archetypeId='" + + archetypeId + '\'' + ", count=" + + Arrays.toString(entityIdx) + ", index=" + + Arrays.toString(fieldIdx) + ", other=" + + fields + '}'; + } +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/ToWalkerDto.java b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/ToWalkerDto.java new file mode 100644 index 000000000..ea52cb3e2 --- /dev/null +++ b/serialisation/src/main/java/org/ehrbase/serialisation/matrixencoding/ToWalkerDto.java @@ -0,0 +1,31 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.util.List; +import org.ehrbase.aql.dto.path.AqlPath; + +/** + * @author Stefan Spiska + */ +class ToWalkerDto { + + AqlPath path; + List index; + Object value; +} diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/walker/ItemExtractor.java b/serialisation/src/main/java/org/ehrbase/serialisation/walker/ItemExtractor.java index 30cf396c1..7097155e1 100644 --- a/serialisation/src/main/java/org/ehrbase/serialisation/walker/ItemExtractor.java +++ b/serialisation/src/main/java/org/ehrbase/serialisation/walker/ItemExtractor.java @@ -122,7 +122,7 @@ public ItemExtractor invoke() { } } - if ((childNode.getMax() == 1 || currentNode.getRmType().equals(RmConstants.ELEMENT)) && child instanceof List) { + if (!RMHelper.isMulti(currentNode, childNode) && child instanceof List) { child = ((List) child).stream().findFirst().orElse(null); } diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/walker/RMHelper.java b/serialisation/src/main/java/org/ehrbase/serialisation/walker/RMHelper.java index 3ec0cb504..e4bff32b1 100644 --- a/serialisation/src/main/java/org/ehrbase/serialisation/walker/RMHelper.java +++ b/serialisation/src/main/java/org/ehrbase/serialisation/walker/RMHelper.java @@ -17,6 +17,8 @@ */ package org.ehrbase.serialisation.walker; +import static org.ehrbase.util.rmconstants.RmConstants.ELEMENT; + import com.nedap.archie.rm.archetyped.FeederAudit; import com.nedap.archie.rm.archetyped.FeederAuditDetails; import com.nedap.archie.rm.composition.IsmTransition; @@ -31,6 +33,7 @@ import java.util.Collection; import org.apache.commons.collections4.CollectionUtils; import org.apache.commons.lang3.StringUtils; +import org.ehrbase.webtemplate.model.WebTemplateNode; public class RMHelper { @@ -93,4 +96,15 @@ public static boolean isEmpty(Object rmObject) { } return false; } + + /** + * Do to historic Reasons, the value for max (and min) are pushed down from Element to value. Thus, checken the max of a child gives the wrong result. A child of Element is multivalued if and only if it is 'link' + * @param parent + * @param child + * @return + */ + static boolean isMulti(WebTemplateNode parent, WebTemplateNode child) { + + return parent.getRmType().equals(ELEMENT) ? child.getId().equals("link") : child.isMulti(); + } } diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/walker/Walker.java b/serialisation/src/main/java/org/ehrbase/serialisation/walker/Walker.java index edaf10ef7..d00bc5019 100644 --- a/serialisation/src/main/java/org/ehrbase/serialisation/walker/Walker.java +++ b/serialisation/src/main/java/org/ehrbase/serialisation/walker/Walker.java @@ -102,8 +102,7 @@ private void handle(Context context) { for (List childrenForPath : childrenByPath.values()) { - boolean isMulti = !currentNode.getRmType().equals(ELEMENT) - && childrenForPath.stream().anyMatch(WebTemplateNode::isMulti); + boolean isMulti = childrenForPath.stream().anyMatch(n -> RMHelper.isMulti(currentNode, n)); Stream childConstellations; if (!isMulti) { diff --git a/serialisation/src/main/java/org/ehrbase/serialisation/walker/defaultvalues/defaultinserter/EntryDefaultValueInserter.java b/serialisation/src/main/java/org/ehrbase/serialisation/walker/defaultvalues/defaultinserter/EntryDefaultValueInserter.java index 6c4b9f7ad..49a0228bd 100644 --- a/serialisation/src/main/java/org/ehrbase/serialisation/walker/defaultvalues/defaultinserter/EntryDefaultValueInserter.java +++ b/serialisation/src/main/java/org/ehrbase/serialisation/walker/defaultvalues/defaultinserter/EntryDefaultValueInserter.java @@ -56,6 +56,7 @@ public void insert(Entry rmObject, DefaultValues defaultValues, WebTemplateNode if (rmObject.getOtherParticipations() != null) { rmObject.getOtherParticipations().stream() .map(Participation::getPerformer) + .filter(Objects::nonNull) .map(PartyProxy::getExternalRef) .filter(Objects::nonNull) .filter(ref -> ref.getId() != null) diff --git a/serialisation/src/main/resources/encoder/pathencoding.csv b/serialisation/src/main/resources/encoder/pathencoding.csv new file mode 100644 index 000000000..fa2a5f84b --- /dev/null +++ b/serialisation/src/main/resources/encoder/pathencoding.csv @@ -0,0 +1,38 @@ +path,code +items,a +data,b +value,c +_type,d +events,e +name,f +description,g +content,h +protocol,i +defining_code,j +archetype_node_id,k +magnitude,l +terminology_id,m +archetype_details,n +origin,o +time,p +activities,q +code_string,r +rm_version,y +archetype_id,z +units,1 +media_type,2 +type,3 +issuer,4 +id,5 +assigner,6 +precision,7 +uri,8 +math_function,9 +alternate_text,0 +size,ba +timing,bb +width,bc +formalism,bd +action_archetype_id,be +denominator,bf +numerator,bg diff --git a/serialisation/src/main/resources/encoder/totalpathencoding.csv b/serialisation/src/main/resources/encoder/totalpathencoding.csv new file mode 100644 index 000000000..7ce656a24 --- /dev/null +++ b/serialisation/src/main/resources/encoder/totalpathencoding.csv @@ -0,0 +1,99 @@ +path,code +/other_participations/performer/external_ref/id/scheme,"!a" +/other_participations/performer/_type,"!b" +/other_participations/mode/defining_code/terminology_id/_type,"!c" +/other_participations/mode/defining_code/terminology_id/value,"!d" +/other_participations/_type,"!e" +/other_participations/performer/external_ref/namespace,"!f" +/other_participations/mode/defining_code/_type,"!g" +/other_participations/performer/name,"!h" +/other_participations/function/value,"!i" +/other_participations/function/_type,"!j" +/other_participations/performer/external_ref/type,"!k" +/other_participations/mode/value,"!l" +/other_participations/performer/external_ref/id/value,"!m" +/other_participations/mode/defining_code/code_string,"!n" +/other_participations/performer/external_ref/id/_type,"!o" +/other_participations/mode/_type,"!p" +/other_participations/performer/external_ref/_type,"!q" +/name/_type,"!r" +/language/code_string,"!y" +/archetype_details/_type,"!z" +/name/value,"!1" +/archetype_node_id,"!2" +/archetype_details/archetype_id/value,"!3" +/language/terminology_id/_type,"!4" +/_type,"!5" +/language/_type,"!6" +/language/terminology_id/value,"!7" +/archetype_details/rm_version,"!8" +/encoding/terminology_id/_type,"!9" +/subject/_type,"!0" +/encoding/_type,"!ba" +/encoding/terminology_id/value,"!bb" +/encoding/code_string,"!bc" +/ism_transition/current_state/defining_code/terminology_id/_type,"!bd" +/ism_transition/current_state/value,"!be" +/ism_transition/current_state/_type,"!bf" +/time/magnitude,"!bg" +/ism_transition/_type,"!bh" +/time/_type,"!bi" +/ism_transition/current_state/defining_code/terminology_id/value,"!bj" +/ism_transition/current_state/defining_code/code_string,"!bk" +/time/value,"!bl" +/ism_transition/current_state/defining_code/_type,"!bm" +/uid/value,"!bn" +/uid/_type,"!bo" +/context/participations/mode/defining_code/terminology_id/_type,"!bp" +/category/defining_code/terminology_id/_type,"!bq" +/context/participations/function/value,"!br" +/context/participations/performer/external_ref/namespace,"!by" +/context/participations/mode/defining_code/_type,"!bz" +/territory/terminology_id/value,"!b1" +/archetype_details/template_id/value,"!b2" +/territory/code_string,"!b3" +/context/_type,"!b4" +/context/setting/defining_code/terminology_id/_type,"!b5" +/category/defining_code/_type,"!b6" +/territory/_type,"!b7" +/category/defining_code/code_string,"!b8" +/category/_type,"!b9" +/context/setting/value,"!b0" +/context/participations/function/_type,"!ca" +/context/setting/_type,"!cb" +/context/participations/performer/external_ref/id/_type,"!cc" +/context/setting/defining_code/terminology_id/value,"!cd" +/context/participations/performer/external_ref/type,"!ce" +/context/participations/performer/name,"!cf" +/context/start_time/magnitude,"!cg" +/context/participations/performer/_type,"!ch" +/category/value,"!ci" +/context/participations/performer/external_ref/id/value,"!cj" +/context/start_time/_type,"!ck" +/context/setting/defining_code/_type,"!cl" +/context/participations/_type,"!cm" +/composer/_type,"!cn" +/context/participations/performer/external_ref/_type,"!co" +/composer/name,"!cp" +/context/participations/mode/defining_code/terminology_id/value,"!cq" +/context/start_time/value,"!cr" +/category/defining_code/terminology_id/value,"!cy" +/context/participations/mode/value,"!cz" +/context/participations/performer/external_ref/id/scheme,"!c1" +/territory/terminology_id/_type,"!c2" +/context/setting/defining_code/code_string,"!c3" +/context/participations/mode/defining_code/code_string,"!c4" +/context/participations/mode/_type,"!c5" +/context/health_care_facility/external_ref/_type,"!c6" +/context/health_care_facility/external_ref/namespace,"!c7" +/narrative/_type,"!c8" +/context/health_care_facility/external_ref/id/_type,"!c9" +/narrative/value,"!c0" +/expiry_time/magnitude,"!da" +/expiry_time/_type,"!db" +/context/health_care_facility/external_ref/id/value,"!dc" +/context/health_care_facility/name,"!dd" +/context/health_care_facility/_type,"!de" +/context/health_care_facility/external_ref/type,"!df" +/expiry_time/value,"!dg" +/context/health_care_facility/external_ref/id/scheme,"!dh" diff --git a/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/EncoderToolTest.java b/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/EncoderToolTest.java new file mode 100644 index 000000000..1a222496d --- /dev/null +++ b/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/EncoderToolTest.java @@ -0,0 +1,106 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import org.apache.commons.csv.CSVFormat; +import org.apache.commons.csv.CSVPrinter; +import org.apache.commons.io.IOUtils; +import org.ehrbase.serialisation.jsonencoding.CanonicalJson; +import org.ehrbase.serialisation.templateprovider.TestDataTemplateProvider; +import org.ehrbase.test_data.composition.CompositionTestDataCanonicalJson; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +/** + * @author Stefan Spiska + */ +class EncoderToolTest { + + @Test + @Disabled("Helper to create the mappings") + void createTotalMap() throws IOException { + + List rowList = new ArrayList<>(); + + rowList.addAll(getRows(CompositionTestDataCanonicalJson.CORONA)); + rowList.addAll(getRows(CompositionTestDataCanonicalJson.IPS)); + + EncoderTool encoderTool = new EncoderTool(); + + Map stringStringMap = encoderTool.buildTotalEncodingMap(rowList); + + StringBuilder appendable = new StringBuilder(); + try (CSVPrinter cv = new CSVPrinter( + appendable, + CSVFormat.DEFAULT.builder().setHeader("path", "code").build())) { + + stringStringMap.forEach((k, v) -> { + try { + cv.printRecord(k, v); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + } + + System.out.println(appendable.toString()); + } + + @Test + @Disabled("Helper to create the mappings") + void createPathMap() throws IOException { + + List rowList = new ArrayList<>(); + + rowList.addAll(getRows(CompositionTestDataCanonicalJson.CORONA)); + rowList.addAll(getRows(CompositionTestDataCanonicalJson.IPS)); + + EncoderTool encoderTool = new EncoderTool(); + + Map stringStringMap = encoderTool.buildPathEncodingMap(rowList); + + StringBuilder appendable = new StringBuilder(); + try (CSVPrinter cv = new CSVPrinter( + appendable, + CSVFormat.DEFAULT.builder().setHeader("path", "code").build())) { + + stringStringMap.forEach((k, v) -> { + try { + cv.printRecord(k, v); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + } + + System.out.println(appendable.toString()); + } + + private static List getRows(CompositionTestDataCanonicalJson dataCanonicalJson) throws IOException { + String corona = IOUtils.toString(dataCanonicalJson.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider()); + + return cut.toTable(new CanonicalJson().unmarshal(corona)); + } +} diff --git a/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/MatrixFormatTest.java b/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/MatrixFormatTest.java new file mode 100644 index 000000000..a10fe72ab --- /dev/null +++ b/serialisation/src/test/java/org/ehrbase/serialisation/matrixencoding/MatrixFormatTest.java @@ -0,0 +1,120 @@ +/* + * Copyright (c) 2022 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.serialisation.matrixencoding; + +import static org.assertj.core.api.Assertions.assertThat; + +import com.nedap.archie.rm.composition.Composition; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import org.apache.commons.io.IOUtils; +import org.ehrbase.serialisation.jsonencoding.CanonicalJson; +import org.ehrbase.serialisation.templateprovider.TestDataTemplateProvider; +import org.ehrbase.test_data.composition.CompositionTestDataCanonicalJson; +import org.junit.jupiter.api.Test; + +/** + * @author Stefan Spiska + */ +class MatrixFormatTest { + + @Test + void toMatrix() throws IOException { + + String corona = + IOUtils.toString(CompositionTestDataCanonicalJson.MULTI_OCCURRENCE.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider()); + + String actual = cut.marshal(new CanonicalJson().unmarshal(corona)); + + String expected = IOUtils.toString( + MatrixFormat.class.getResourceAsStream("/csv/MULTI_OCCURRENCE.csv"), StandardCharsets.UTF_8); + + assertThat(actual).isEqualToNormalizingNewlines(expected); + } + + @Test + void toMatrixCorona() throws IOException { + + String corona = IOUtils.toString(CompositionTestDataCanonicalJson.CORONA.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider()); + + String actual = cut.marshal(new CanonicalJson().unmarshal(corona)); + + String expected = + IOUtils.toString(MatrixFormat.class.getResourceAsStream("/csv/CORONA.csv"), StandardCharsets.UTF_8); + + assertThat(actual).isEqualToNormalizingNewlines(expected); + } + + @Test + void toMatrixIPS() throws IOException { + + String corona = IOUtils.toString(CompositionTestDataCanonicalJson.IPS.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider()); + + String actual = cut.marshal(new CanonicalJson().unmarshal(corona)); + + String expected = + IOUtils.toString(MatrixFormat.class.getResourceAsStream("/csv/IPS.csv"), StandardCharsets.UTF_8); + + assertThat(actual).isEqualToNormalizingNewlines(expected); + } + + @Test + void toMatrixIPSEncode() throws IOException { + + String corona = IOUtils.toString(CompositionTestDataCanonicalJson.IPS.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider(), new FixedCodeSetEncoder()); + + String actual = cut.marshal(new CanonicalJson().unmarshal(corona)); + + String expected = + IOUtils.toString(MatrixFormat.class.getResourceAsStream("/csv/IPSEncode.csv"), StandardCharsets.UTF_8); + + assertThat(actual).isEqualToNormalizingNewlines(expected); + } + + @Test + void toMatrixCoronaEncode() throws IOException { + + String corona = IOUtils.toString(CompositionTestDataCanonicalJson.CORONA.getStream(), StandardCharsets.UTF_8); + + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider(), new FixedCodeSetEncoder()); + + String actual = cut.marshal(new CanonicalJson().unmarshal(corona)); + + String expected = IOUtils.toString( + MatrixFormat.class.getResourceAsStream("/csv/CORONAEncode.csv"), StandardCharsets.UTF_8); + + assertThat(actual).isEqualToNormalizingNewlines(expected); + } + + @Test + void fromMatrix() throws IOException { + MatrixFormat cut = new MatrixFormat(new TestDataTemplateProvider()); + Composition actual = cut.unmarshal( + IOUtils.toString(MatrixFormat.class.getResourceAsStream("/csv/IPS.csv"), StandardCharsets.UTF_8)); + + assertThat(actual.getContent()).size().isEqualTo(14); + } +} diff --git a/serialisation/src/test/resources/csv/CORONA.csv b/serialisation/src/test/resources/csv/CORONA.csv new file mode 100644 index 000000000..d21b53823 --- /dev/null +++ b/serialisation/src/test/resources/csv/CORONA.csv @@ -0,0 +1,18 @@ +NUM,ENTITY_CONCEPT,RM_ENTITY,ENTITY_PATH,ENTITY_IDX,FIELD_IDX,FIELD_IDX_LEN,FIELDS +0,openEHR-EHR-COMPOSITION.report.v1,COMPOSITION,/,{},{},0,"{""/_type"":""COMPOSITION"",""/category/_type"":""DV_CODED_TEXT"",""/category/value"":""event"",""/category/defining_code/_type"":""CODE_PHRASE"",""/category/defining_code/terminology_id/_type"":""TERMINOLOGY_ID"",""/category/defining_code/terminology_id/value"":""openehr"",""/category/defining_code/code_string"":""433"",""/context/_type"":""EVENT_CONTEXT"",""/context/start_time/_type"":""DV_DATE_TIME"",""/context/start_time/value"":""2020-05-11T22:53:12.039139+02:00"",""/context/start_time/magnitude"":63724827192,""/context/setting/_type"":""DV_CODED_TEXT"",""/context/setting/value"":""other 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event"",""/data[at0002]/events[at0003]/time/_type"":""DV_DATE_TIME"",""/data[at0002]/events[at0003]/time/value"":""2020-10-06T13:30:34.328873+02:00"",""/data[at0002]/events[at0003]/time/magnitude"":63737580634}" diff --git a/serialisation_conformance_test/src/test/java/org/ehrbase/conformance_test/matrix/MatrixConformanceTest.java b/serialisation_conformance_test/src/test/java/org/ehrbase/conformance_test/matrix/MatrixConformanceTest.java new file mode 100644 index 000000000..5d8a9255f --- /dev/null +++ b/serialisation_conformance_test/src/test/java/org/ehrbase/conformance_test/matrix/MatrixConformanceTest.java @@ -0,0 +1,172 @@ +/* + * Copyright (c) 2021 vitasystems GmbH and Hannover Medical School. + * + * This file is part of project openEHR_SDK + * + * Licensed 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 + * + * https://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.ehrbase.conformance_test.matrix; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.nedap.archie.rm.composition.Composition; +import java.io.IOException; +import java.nio.charset.StandardCharsets; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.ArrayUtils; +import org.assertj.core.api.SoftAssertions; +import org.ehrbase.conformance_test.templateprovider.TestDataTemplateProvider; +import org.ehrbase.serialisation.RMDataFormat; +import org.ehrbase.serialisation.flatencoding.FlatFormat; +import org.ehrbase.serialisation.flatencoding.FlatJasonProvider; +import org.ehrbase.serialisation.jsonencoding.ArchieObjectMapperProvider; +import org.ehrbase.serialisation.matrixencoding.FixedCodeSetEncoder; +import org.ehrbase.serialisation.matrixencoding.MatrixFormat; +import org.ehrbase.test_data.composition.CompositionTestDataConformanceSDTJson; +import org.ehrbase.test_data.composition.CompositionTestDataSimSDTJson; +import org.ehrbase.test_data.composition.CompositionTestDataSimSDTJsonInterface; +import org.ehrbase.validation.CompositionValidator; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.Arguments; +import org.junit.jupiter.params.provider.MethodSource; + +class MatrixConformanceTest { + + private static final TestDataTemplateProvider TEMPLATE_PROVIDER = new TestDataTemplateProvider(); + + private static List testRoundTripArguments() { + List arguments = new ArrayList<>(); + + Arrays.stream(CompositionTestDataConformanceSDTJson.values()).forEach(test -> { + switch (test) { + default: + arguments.add(Arguments.of(test, new String[] {}, new String[] {}, new String[] {})); + } + }); + arguments.add(Arguments.of( + CompositionTestDataSimSDTJson.ALL_TYPES, + new String[] { + "Missing path: test_all_types/test_all_types:0/identifier|id, value: 55175056", + "Missing path: test_all_types/test_all_types:0/proportion_any|type, value: 1" + }, + new String[] { + "Extra path: test_all_types/test_all_types:0/identifier, value: 55175056", + "Extra path: test_all_types/test_all_types:0/proportion_any|type, value: 1.0" + }, + new String[] {})); + return arguments; + } + + @ParameterizedTest + @MethodSource("testRoundTripArguments") + void testRoundTrip( + CompositionTestDataSimSDTJsonInterface testData, + String[] expectedMissing, + String[] expectedExtra, + String[] expectedValidationErrorPath) + throws IOException { + + MatrixFormat cut = new MatrixFormat(TEMPLATE_PROVIDER); + + test(testData, expectedMissing, expectedExtra, expectedValidationErrorPath, cut); + } + + @ParameterizedTest + @MethodSource("testRoundTripArguments") + void testRoundTripEncoding( + CompositionTestDataSimSDTJsonInterface testData, + String[] expectedMissing, + String[] expectedExtra, + String[] expectedValidationErrorPath) + throws IOException { + + MatrixFormat cut = new MatrixFormat(TEMPLATE_PROVIDER, new FixedCodeSetEncoder()); + + test(testData, expectedMissing, expectedExtra, expectedValidationErrorPath, cut); + } + + private void test( + CompositionTestDataSimSDTJsonInterface testData, + String[] expectedMissing, + String[] expectedExtra, + String[] expectedValidationErrorPath, + MatrixFormat cut) + throws IOException { + String templateId = testData.getTemplate().getTemplateId(); + + RMDataFormat flatJson = new FlatJasonProvider(TEMPLATE_PROVIDER).buildFlatJson(FlatFormat.SIM_SDT, templateId); + + String flat = IOUtils.toString(testData.getStream(), StandardCharsets.UTF_8); + Composition composition = flatJson.unmarshal(flat); + + String db_encoded = cut.marshal(composition); + + Composition actual = cut.unmarshal(db_encoded); + + SoftAssertions softAssertions = new SoftAssertions(); + + softAssertions.assertThat(actual).isNotNull(); + + CompositionValidator rmObjectValidator = new CompositionValidator(); + + softAssertions + .assertThat(rmObjectValidator.validate( + actual, TEMPLATE_PROVIDER.buildIntrospect(templateId).orElseThrow())) + .filteredOn(d -> !ArrayUtils.contains(expectedValidationErrorPath, d.getAqlPath())) + .isEmpty(); + + String actualString = flatJson.marshal(actual); + + String expected = IOUtils.toString(testData.getStream(), StandardCharsets.UTF_8); + + List errors = compere(actualString, expected); + + softAssertions + .assertThat(errors) + .filteredOn(s -> s.startsWith("Missing")) + .containsExactlyInAnyOrder(expectedMissing); + + softAssertions + .assertThat(errors) + .filteredOn(s -> s.startsWith("Extra")) + .containsExactlyInAnyOrder(expectedExtra); + + softAssertions.assertAll(); + } + + private List compere(String actualJson, String expectedJson) throws JsonProcessingException { + List errors = new ArrayList<>(); + ObjectMapper objectMapper = ArchieObjectMapperProvider.getObjectMapper(); + + Map actual = objectMapper.readValue(actualJson, Map.class); + Map expected = objectMapper.readValue(expectedJson, Map.class); + + actual.forEach((key, value) -> { + if (!expected.containsKey(key) || !expected.get(key).equals(value)) { + errors.add(String.format("Missing path: %s, value: %s", key, value)); + } + }); + + expected.forEach((key, value) -> { + if (!actual.containsKey(key) || !actual.get(key).equals(value)) { + errors.add(String.format("Extra path: %s, value: %s", key, value)); + } + }); + + return errors; + } +} diff --git a/util/src/main/java/org/ehrbase/util/rmconstants/RmConstants.java b/util/src/main/java/org/ehrbase/util/rmconstants/RmConstants.java index b02ba3aa6..0a065637f 100644 --- a/util/src/main/java/org/ehrbase/util/rmconstants/RmConstants.java +++ b/util/src/main/java/org/ehrbase/util/rmconstants/RmConstants.java @@ -38,4 +38,5 @@ private RmConstants() {} public static final String EVENT = "EVENT"; public static final String POINT_EVENT = "POINT_EVENT"; public static final String INTERVAL_EVENT = "INTERVAL_EVENT"; + public static final String FEEDER_AUDIT = "FEEDER_AUDIT"; } diff --git a/web-template/pom.xml b/web-template/pom.xml index c60ead903..037aa1d37 100644 --- a/web-template/pom.xml +++ b/web-template/pom.xml @@ -63,6 +63,10 @@ com.jayway.jsonpath json-path + + org.apache.commons + commons-csv + org.ehrbase.openehr.sdk test-data