From dfd0181774ce9d491256fb41c49d464b2dc8f6b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Meier?= Date: Thu, 18 Apr 2024 14:59:02 +0200 Subject: [PATCH] Remove API stub. MassBank3 API is more advanced --- MassBank-Project/MassBank-OpenAPI/LICENSE.txt | 339 ------------------ MassBank-Project/MassBank-OpenAPI/generate.sh | 3 - .../openapi-generator-config.json | 15 - MassBank-Project/MassBank-OpenAPI/pom.xml | 123 ------- .../java/massbank/RecordSearchParser.java | 9 - .../RecordSearchParserDefinition.java | 125 ------- .../openapi/api/RecordApiDelegateImpl.java | 49 --- .../src/main/resources/application.properties | 1 - .../src/main/resources/openapi.yaml | 273 -------------- 9 files changed, 937 deletions(-) delete mode 100644 MassBank-Project/MassBank-OpenAPI/LICENSE.txt delete mode 100644 MassBank-Project/MassBank-OpenAPI/generate.sh delete mode 100644 MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json delete mode 100644 MassBank-Project/MassBank-OpenAPI/pom.xml delete mode 100644 MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParser.java delete mode 100644 MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParserDefinition.java delete mode 100644 MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/openapi/api/RecordApiDelegateImpl.java delete mode 100644 MassBank-Project/MassBank-OpenAPI/src/main/resources/application.properties delete mode 100644 MassBank-Project/MassBank-OpenAPI/src/main/resources/openapi.yaml diff --git a/MassBank-Project/MassBank-OpenAPI/LICENSE.txt b/MassBank-Project/MassBank-OpenAPI/LICENSE.txt deleted file mode 100644 index d511905c..00000000 --- a/MassBank-Project/MassBank-OpenAPI/LICENSE.txt +++ /dev/null @@ -1,339 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 2, June 1991 - - Copyright (C) 1989, 1991 Free Software Foundation, Inc., - 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The licenses for most software are designed to take away your -freedom to share and change it. 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If this is what you want to do, use the GNU Lesser General -Public License instead of this License. diff --git a/MassBank-Project/MassBank-OpenAPI/generate.sh b/MassBank-Project/MassBank-OpenAPI/generate.sh deleted file mode 100644 index 761d1987..00000000 --- a/MassBank-Project/MassBank-OpenAPI/generate.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -#wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.4.0/openapi-generator-cli-5.4.0.jar -O openapi-generator-cli.jar -java -jar openapi-generator-cli.jar generate -g spring -i src/main/resources/openapi.yaml -c openapi-generator-config.json -o ../spring-boot-codegenerator diff --git a/MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json b/MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json deleted file mode 100644 index e3268e11..00000000 --- a/MassBank-Project/MassBank-OpenAPI/openapi-generator-config.json +++ /dev/null @@ -1,15 +0,0 @@ -{ - "basePackage": "massbank.openapi", - "configPackage": "massbank.openapi.config", - "apiPackage": "massbank.openapi.api", - "modelPackage": "massbank.openapi.model", - "parentArtifactId": "MassBank-Project", - "parentGroupId": "de.ipb-halle.msbi", - "parentVersion": "2.1.11-SNAPSHOT", - "artifactId": "MassBank-OpenAPI", - "groupId": "de.ipb-halle.msbi", - "artifactVersion": "2.1.11-SNAPSHOT", - "delegatePattern": true - -} - diff --git a/MassBank-Project/MassBank-OpenAPI/pom.xml b/MassBank-Project/MassBank-OpenAPI/pom.xml deleted file mode 100644 index 87fc1a52..00000000 --- a/MassBank-Project/MassBank-OpenAPI/pom.xml +++ /dev/null @@ -1,123 +0,0 @@ - - 4.0.0 - - de.ipb-halle.msbi - MassBank-Project - 2.2.6-SNAPSHOT - - - MassBank-OpenAPI - jar - - MassBank OpenAPI REST interface - - - ${project.basedir}/src/main/resources/openapi.yaml - 1.7.0 - - - - - - org.openapitools - openapi-generator-maven-plugin - - - - generate - - - ${yaml.file} - spring - - massbank.openapi - massbank.openapi.config - massbank.openapi.api - massbank.openapi.model - true - true - - - - - - - org.springframework.boot - spring-boot-maven-plugin - - - - repackage - - - - - - - - - - - de.ipb-halle.msbi - MassBank-lib - - - org.springframework.boot - spring-boot-starter-web - - - org.springframework.data - spring-data-commons - - - - org.springdoc - springdoc-openapi-ui - ${springdoc.version} - - - - com.google.code.findbugs - jsr305 - 3.0.2 - - - com.fasterxml.jackson.dataformat - jackson-dataformat-yaml - - - com.fasterxml.jackson.datatype - jackson-datatype-jsr310 - - - org.openapitools - jackson-databind-nullable - 0.2.6 - - - - org.springframework.boot - spring-boot-starter-validation - - - com.fasterxml.jackson.core - jackson-databind - - - org.springframework.boot - spring-boot-devtools - - - - - - - org.springframework.boot - spring-boot-dependencies - ${spring-boot.version} - pom - import - - - - diff --git a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParser.java b/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParser.java deleted file mode 100644 index 5fbdf7f4..00000000 --- a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParser.java +++ /dev/null @@ -1,9 +0,0 @@ -package massbank; - -import org.petitparser.tools.GrammarParser; - -public class RecordSearchParser extends GrammarParser { - public RecordSearchParser() { - super(new RecordSearchParserDefinition()); - } -} \ No newline at end of file diff --git a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParserDefinition.java b/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParserDefinition.java deleted file mode 100644 index b8eba1e3..00000000 --- a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/RecordSearchParserDefinition.java +++ /dev/null @@ -1,125 +0,0 @@ -package massbank; - -import java.util.List; - -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.petitparser.parser.primitive.CharacterParser; -import org.petitparser.parser.primitive.StringParser; -import org.petitparser.tools.GrammarDefinition; - -public class RecordSearchParserDefinition extends GrammarDefinition { - private static final Logger logger = LogManager.getLogger(RecordSearchParserDefinition.class); - - public RecordSearchParserDefinition() { - def("start", - ref("name") - .map((List value) -> { - System.out.println(value); - return value; - }) - .end() - ); - - //Comparison operators in FIQL notation or alternative notation: - //Equal to : == - def("eq", StringParser.of("==")); - //Not equal to : != - def("ne", StringParser.of("!=")); - //Less than : =lt= - def("lt", StringParser.of("=lt=").or(StringParser.of("<"))); - //Less than or equal to : =le= - def("le", StringParser.of("=le=").or(StringParser.of("<="))); - //Greater than operator : =gt= - def("gt", StringParser.of("=gt=").or(StringParser.of(">"))); - //Greater than or equal to : =ge= - def("ge", StringParser.of("=ge=").or(StringParser.of(">="))); - //In : =in= - def("in", StringParser.of("=in=")); - //Not in : =out= - def("out", StringParser.of("=out=")); - - - def("input", - StringParser.of("ACCESSION") - ); - - def("constraint", - - StringParser.of("ACCESSION") - ); - - - def("comparison", - ref("selector") - .seq(ref("comparison-op")) - .seq(ref("arguments")) - ); - - def("selector", - ref("unreserved-str") - ); - - def("comparison-op", - ref("comp-fiql") - .or(ref("comp-alt")) - ); - - def("name", - StringParser.of("name") - .seq(ref("eq")) - .seq(ref("value")) - ); - - def("value", - ref("unreserved-str") - .or(ref("double-quoted")) - //.or(ref("single-quoted")) - - ); - def("unreserved-str", - CharacterParser.noneOf("\"\'();, ").plus().flatten() - .map((List value) -> { - System.out.println("unreserved-str"); - System.out.println(value); - return value; - }) - ); - def("double-quoted", - CharacterParser.of('"') - .seq( - CharacterParser.noneOf("\\\"") - .or(StringParser.of("\\\"")) - .or(StringParser.of("\\\\")) - .star().flatten() - ) - .seq(CharacterParser.of('"')) - .map((List value) -> { - System.out.println("double-quoted"); - System.out.println(value); - return value; - }) - ); - - } -} - - -//input = or, EOF; -//or = and, { "," , and }; -//and = constraint, { ";" , constraint }; -//constraint = ( group | comparison ); -//group = "(", or, ")"; - - -//arguments = ( "(", value, { "," , value }, ")" ) | value; -//unreserved-str = unreserved, { unreserved } -//single-quoted = "'", { ( escaped | all-chars - ( "'" | "\" ) ) }, "'"; -//double-quoted = '"', { ( escaped | all-chars - ( '"' | "\" ) ) }, '"'; -// -//reserved = '"' | "'" | "(" | ")" | ";" | "," | "=" | "!" | "~" | "<" | ">"; -//unreserved = all-chars - reserved - " "; -//escaped = "\", all-chars; -//all-chars = ? all unicode characters ?; - - diff --git a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/openapi/api/RecordApiDelegateImpl.java b/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/openapi/api/RecordApiDelegateImpl.java deleted file mode 100644 index fa0c682f..00000000 --- a/MassBank-Project/MassBank-OpenAPI/src/main/java/massbank/openapi/api/RecordApiDelegateImpl.java +++ /dev/null @@ -1,49 +0,0 @@ -package massbank.openapi.api; - -import org.springframework.http.HttpStatus; -import org.springframework.http.MediaType; -import org.springframework.http.ResponseEntity; -import org.springframework.stereotype.Service; - -import massbank.Record; -import massbank.db.DatabaseManager; - -/** - * A delegate to be called by the {@link RecordApiController}}. - * Implement this interface with a {@link org.springframework.stereotype.Service} annotated class. - */ -@Service -public class RecordApiDelegateImpl implements RecordApiDelegate { - /** - * GET /record/{recordId} : Returns the content of one record - * Returns the content of the record in MassBank format - * - * @param recordId The record id (required) - * @return successful operation (status code 200) - * or The record with the recordId was not found (status code 404) - * or There was in internal error during database access (status code 500) - * @see RecordApi#getRecord - */ - public ResponseEntity getRecord(String recordId) { - getRequest().ifPresent(request -> { - for (MediaType mediaType: MediaType.parseMediaTypes(request.getHeader("Accept"))) { - if (mediaType.isCompatibleWith(MediaType.valueOf(""))) { - String exampleString = ""; - ApiUtil.setExampleResponse(request, "", exampleString); - break; - } - } - }); - Record record = null; - // load record from database - record = DatabaseManager.getAccessionData(recordId); - if (record == null) { - return new ResponseEntity<>("Record \"" + recordId + "\" not found", HttpStatus.NOT_FOUND); - } - String recordstring = record.toString(); - return new ResponseEntity<>(recordstring, HttpStatus.OK); - } - -} - - diff --git a/MassBank-Project/MassBank-OpenAPI/src/main/resources/application.properties b/MassBank-Project/MassBank-OpenAPI/src/main/resources/application.properties deleted file mode 100644 index 4ef5c891..00000000 --- a/MassBank-Project/MassBank-OpenAPI/src/main/resources/application.properties +++ /dev/null @@ -1 +0,0 @@ -server.port = 8081 diff --git a/MassBank-Project/MassBank-OpenAPI/src/main/resources/openapi.yaml b/MassBank-Project/MassBank-OpenAPI/src/main/resources/openapi.yaml deleted file mode 100644 index 3101771c..00000000 --- a/MassBank-Project/MassBank-OpenAPI/src/main/resources/openapi.yaml +++ /dev/null @@ -1,273 +0,0 @@ -openapi: 3.0.3 -info: - title: MassBank-OpenAPI - description: This is the MassBank REST API - version: "0.0.1" - termsOfService: 'https://massbank.eu' - contact: - email: denbi-mash@ipb-halle.de - license: - name: GPL - url: http://www.gnu.org/licenses/gpl-3.0 - -servers: - - url: https://msbi.ipb-halle.de/MassBank-OpenAPI/ - description: dev server - - url: http://localhost:8080/MassBank-OpenAPI - description: local dev server - -tags: - - name: record - description: Add and Search records - -components: - securitySchemes: - changeBearerAuth: - type: http - scheme: bearer - bearerFormat: JWT #JSON Web Token - responses: - UnauthorizedError: - description: Access token is missing or invalid - ForbiddenError: - description: Access token does not allow the operation - NotFoundError: - description: The record with the recordId was not found - DatabaseError: - description: There was in internal error during database access - SyntaxError: - description: The record or query was invalid - content: - application/json: - schema: - type: string - description: error message - example: "The value for ACCESSION is not valid." - schemas: - record: - type: string - description: a full massBank record file as a string - example: | - ACCESSION: UPA00001 - RECORD_TITLE: FLAVOXATE; ESI-QTOF; MS2; CE 23 eV; [M+H]+ - DATE: 2016.01.19 (Created 2015.06.23) - AUTHORS: K. Wilkinson, S. Miranda - LICENSE: CC BY - COPYRIGHT: UPAO - COMMENT: This spectrum was obtained at The Multidisciplinary Research Laboratory at Antenor Orrego Private University, Trujillo, La Libertad, Peru.The sample was obtained from a pharmacy. The sample was dissolved in 1:1 acetonitrile:water and infused at a rate of 10 uL/min. - COMMENT: Contact us: http://www.upao.edu.pe/labinm/ - CH$NAME: FLAVOXATE - CH$COMPOUND_CLASS: Non-Natural Product - CH$FORMULA: C24H25NO4 - CH$EXACT_MASS: 391.17836 - CH$SMILES: C(C4)CCN(C4)CCOC(=O)c(c3)c(O1)c(cc3)C(=O)C(C)=C(c(c2)cccc2)1 - CH$IUPAC: InChI=1S/C24H25NO4/c1-17-21(26)19-11-8-12-20(23(19)29-22(17)18-9-4-2-5-10-18)24(27)28-16-15-25-13-6-3-7-14-25/h2,4-5,8-12H,3,6-7,13-16H2,1H3 - CH$LINK: CAS 15301-69-6 - CH$LINK: CHEBI 5088 - CH$LINK: CHEMSPIDER 3237 - CH$LINK: INCHIKEY SPIUTQOUKAMGCX-UHFFFAOYSA-N - CH$LINK: COMPTOX DTXSID3023053 - CH$LINK: PUBCHEM CID:3354 - AC$INSTRUMENT: Xevo G2 XS QTOF waters - AC$INSTRUMENT_TYPE: ESI-QTOF - AC$MASS_SPECTROMETRY: MS_TYPE MS2 - AC$MASS_SPECTROMETRY: ION_MODE POSITIVE - AC$MASS_SPECTROMETRY: COLLISION_ENERGY 23 eV - AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 600 L/h - AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 300 C - AC$MASS_SPECTROMETRY: IONIZATION ESI - MS$FOCUSED_ION: PRECURSOR_M/Z 392.18563 - MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ - MS$DATA_PROCESSING: FIND_PEAK centroid - MS$DATA_PROCESSING: WHOLE Mass++ 2.7.5 - PK$SPLASH: splash10-03di-0958000000-36f8ecae0c5b45da3a93 - PK$ANNOTATION: m/z tentative_formula formula_count mass error(ppm) - 105.0704 C8H9+ 1 105.0704 0.24 - 112.1128 C7H14N+ 1 112.1126 -1.57 - 119.0860 C9H11+ 1 119.0861 0.63 - 147.0082 C8H3O3+ 1 147.0082 0.13 - 199.1345 C11H19O3+ 1 199.1334 -5.43 - 263.0709 C17H11O3+ 1 263.0708 -0.31 - 272.1635 C17H22NO2+ 1 272.1651 5.71 - 295.1947 C20H25NO+ 1 295.1936 -3.68 - 307.0971 C19H15O4+ 1 307.0970 -0.22 - 310.1708 C24H22+ 1 310.1722 4.35 - 392.1862 C24H26NO4+ 1 392.1862 -0.04 - PK$NUM_PEAK: 26 - PK$PEAK: m/z int. rel.int. - 105.0704 338200 14 - 112.1128 23870000 999 - 119.0860 118500 5 - 131.0021 378500 16 - 139.0336 258400 11 - 147.0082 1529000 64 - 191.0311 107900 5 - 198.1268 120200 5 - 199.1345 265600 11 - 203.0231 139600 6 - 236.1349 133000 6 - 250.1505 376400 16 - 258.1478 278600 12 - 263.0709 14100000 590 - 272.1635 643600 27 - 272.6651 112700 5 - 295.1947 281100 12 - 307.0971 14130000 591 - 310.1708 139300 6 - 323.2260 1326000 55 - 324.2293 135500 6 - 341.2370 153000 6 - 341.3050 274800 12 - 392.1862 9717000 407 - 392.2480 125800 5 - 392.2755 107100 4 - // - recordId: - type: string - description: a massBank id - example: "PR030008" - -paths: - /record: - post: - summary: Uploads a record to the database - description: Uploads a new record to the massBank database if the ACCESSION in the record is unique - operationId: postRecord - tags: - - record - security: - - changeBearerAuth: [] - responses: - 201: - description: Created a new record - headers: - Location: - schema: - type: string - format: url - example: 'https://msbi.ipb-halle.de/MassBank-OpenAPI/record/PR030008' - 401: - $ref: '#/components/responses/UnauthorizedError' - 403: - $ref: '#/components/responses/ForbiddenError' - 409: - description: Could not insert dataset, because it already exists - 400: - $ref: '#/components/responses/SyntaxError' - 500: - $ref: '#/components/responses/DatabaseError' - requestBody: - required: true - content: - text/plain: - schema: - '$ref': '#/components/schemas/record' - - get: - summary: Returns all records matching the search - description: This resource reports all record ids which fulfill the criteria in the search parameters, - or all records if the query parameters are missing or empty - operationId: getRecordsIds - tags: - - record - parameters: - - in: query - name: name - schema: - type: string - example: '*nicotine*' - description: Search records with the specified string in RECORD_TITLE or CH$NAME. - - in: query - name: formula - schema: - type: string - example: 'C9H15NO3S' - description: Search records with the specified formula CH$FORMULA. - responses: - '200': - description: successful operation - content: - application/json: - schema: - type: array - items: - $ref: '#/components/schemas/recordId' - 400: - $ref: '#/components/responses/SyntaxError' - 500: - $ref: '#/components/responses/DatabaseError' - - /record/{recordId}: - parameters: - - in: path - name: recordId - required: true - schema: - $ref: '#/components/schemas/recordId' - description: The record id - get: - summary: Returns the content of one record - description: Returns the content of the record in MassBank format - operationId: getRecord - tags: - - record - responses: - 200: - description: successful operation - content: - text/plain; charset=utf-8: - schema: - '$ref': '#/components/schemas/record' - 404: - $ref: '#/components/responses/NotFoundError' - 500: - $ref: '#/components/responses/DatabaseError' - put: - summary: replace a record - description: replaces the record in with the specified id by a new record, which must have the same ACCESSION - operationId: replaceRecord - security: - - changeBearerAuth: [] - tags: - - record - requestBody: - content: - text/plain: - schema: - $ref: '#/components/schemas/record' - responses: - 204: - description: the record was successfully replaced - 400: - $ref: '#/components/responses/SyntaxError' - 401: - $ref: '#/components/responses/UnauthorizedError' - 403: - $ref: '#/components/responses/ForbiddenError' - 404: - $ref: '#/components/responses/NotFoundError' - 500: - $ref: '#/components/responses/DatabaseError' - delete: - summary: delete a record - description: deletes the record with the specified id from the massBank database - operationId: deleteRecord - security: - - changeBearerAuth: [] - tags: - - record - responses: - 204: - description: the record was successfully deleted - 401: - $ref: '#/components/responses/UnauthorizedError' - 403: - $ref: '#/components/responses/ForbiddenError' - 404: - $ref: '#/components/responses/NotFoundError' - 500: - $ref: '#/components/responses/DatabaseError' - - - -