diff --git a/bionetdb-app/pom.xml b/bionetdb-app/pom.xml index 50ec08d..f474552 100644 --- a/bionetdb-app/pom.xml +++ b/bionetdb-app/pom.xml @@ -23,7 +23,7 @@ org.opencb.bionetdb - bionetdb-core + bionetdb-lib org.opencb.bionetdb diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java index ca0a475..2549cab 100644 --- a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java +++ b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/CliOptionsParser.java @@ -20,7 +20,7 @@ import com.beust.jcommander.Parameter; import com.beust.jcommander.ParameterDescription; import com.beust.jcommander.ParameterException; -import org.opencb.bionetdb.core.BioNetDbManager; +import org.opencb.bionetdb.lib.BioNetDbManager; import java.io.InputStream; import java.util.Map; diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/LoadCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/LoadCommandExecutor.java index ecc1aa7..ab36643 100644 --- a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/LoadCommandExecutor.java +++ b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/admin/executors/LoadCommandExecutor.java @@ -3,7 +3,7 @@ import org.apache.commons.lang.StringUtils; import org.opencb.bionetdb.app.cli.CommandExecutor; import org.opencb.bionetdb.app.cli.admin.AdminCliOptionsParser; -import org.opencb.bionetdb.core.BioNetDbManager; +import org.opencb.bionetdb.lib.BioNetDbManager; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.commons.utils.FileUtils; diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/ExpressionCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/ExpressionCommandExecutor.java index f78b8cb..455cd88 100644 --- a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/ExpressionCommandExecutor.java +++ b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/ExpressionCommandExecutor.java @@ -2,11 +2,11 @@ import org.opencb.bionetdb.app.cli.main.BioNetDBCliOptionsParser; import org.opencb.bionetdb.app.cli.CommandExecutor; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.bionetdb.core.io.ExpressionParser; import org.opencb.bionetdb.core.models.Expression; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; import org.opencb.commons.utils.FileUtils; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/QueryCommandExecutor.java b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/QueryCommandExecutor.java index 97faf2c..366d9ac 100644 --- a/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/QueryCommandExecutor.java +++ b/bionetdb-app/src/main/java/org/opencb/bionetdb/app/cli/main/executors/QueryCommandExecutor.java @@ -3,9 +3,9 @@ import org.apache.commons.lang3.StringUtils; import org.opencb.bionetdb.app.cli.CommandExecutor; import org.opencb.bionetdb.app.cli.main.BioNetDBCliOptionsParser; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; import org.opencb.bionetdb.core.config.DatabaseConfiguration; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-client/pom.xml b/bionetdb-client/pom.xml new file mode 100644 index 0000000..dd5ccde --- /dev/null +++ b/bionetdb-client/pom.xml @@ -0,0 +1,51 @@ + + + 4.0.0 + + + bionetdb + org.opencb.bionetdb + 0.2.0-SNAPSHOT + + + bionetdb-client + ${bionetdb.version} + jar + + + + org.opencb.bionetdb + bionetdb-core + + + org.glassfish.jersey.core + jersey-client + + + org.glassfish.jersey.inject + jersey-hk2 + + + org.glassfish.jersey.containers + jersey-container-servlet + test + + + org.junit.jupiter + junit-jupiter-api + test + + + org.junit.platform + junit-platform-engine + test + + + org.junit.jupiter + junit-jupiter-engine + test + + + \ No newline at end of file diff --git a/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/ClientConfiguration.java b/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/ClientConfiguration.java new file mode 100644 index 0000000..b42a251 --- /dev/null +++ b/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/ClientConfiguration.java @@ -0,0 +1,103 @@ +/* + * Copyright 2015-2020 OpenCB + * + * 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 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.opencb.bionetdb.client.config; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.fasterxml.jackson.dataformat.yaml.YAMLFactory; + +import java.io.IOException; +import java.io.InputStream; +import java.io.OutputStream; + +/** + * Created by imedina on 12/05/16. + */ +public class ClientConfiguration { + + private String version; + private String logLevel; + private RestConfig rest; + + public ClientConfiguration() { + } + + public static ClientConfiguration load(InputStream configurationInputStream) throws IOException { + return load(configurationInputStream, "YAML"); + } + + public static ClientConfiguration load(InputStream configurationInputStream, String format) + throws IOException { + ClientConfiguration clientConfiguration; + ObjectMapper objectMapper; + switch (format.toUpperCase()) { + case "JSON": + objectMapper = new ObjectMapper(); + clientConfiguration = objectMapper.readValue(configurationInputStream, ClientConfiguration.class); + break; + case "YML": + case "YAML": + default: + objectMapper = new ObjectMapper(new YAMLFactory()); + clientConfiguration = objectMapper.readValue(configurationInputStream, ClientConfiguration.class); + break; + } + + return clientConfiguration; + } + + public void serialize(OutputStream configurationOutputStream) throws IOException { + ObjectMapper jsonMapper = new ObjectMapper(new YAMLFactory()); + jsonMapper.writerWithDefaultPrettyPrinter().writeValue(configurationOutputStream, this); + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("ClientConfiguration{"); + sb.append("version='").append(version).append('\''); + sb.append(", logLevel='").append(logLevel).append('\''); + sb.append(", rest=").append(rest); + sb.append('}'); + return sb.toString(); + } + + public String getVersion() { + return version; + } + + public ClientConfiguration setVersion(String version) { + this.version = version; + return this; + } + + public String getLogLevel() { + return logLevel; + } + + public ClientConfiguration setLogLevel(String logLevel) { + this.logLevel = logLevel; + return this; + } + + public RestConfig getRest() { + return rest; + } + + public ClientConfiguration setRest(RestConfig rest) { + this.rest = rest; + return this; + } +} diff --git a/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/RestConfig.java b/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/RestConfig.java new file mode 100644 index 0000000..804585b --- /dev/null +++ b/bionetdb-client/src/main/java/org/opencb/bionetdb/client/config/RestConfig.java @@ -0,0 +1,61 @@ +/* + * Copyright 2015-2020 OpenCB + * + * 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 + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.opencb.bionetdb.client.config; + +/** + * Created by imedina on 04/05/16. + */ +public class RestConfig { + + private String host; + private int timeout; + + public RestConfig() { + } + + public RestConfig(String host, int timeout) { + this.host = host; + this.timeout = timeout; + } + + @Override + public String toString() { + final StringBuilder sb = new StringBuilder("RestConfig{"); + sb.append("host=").append(host); + sb.append(", timeout=").append(timeout); + sb.append('}'); + return sb.toString(); + } + + public String getHosts() { + return host; + } + + public RestConfig setHosts(String host) { + this.host = host; + return this; + } + + public int getTimeout() { + return timeout; + } + + public RestConfig setTimeout(int timeout) { + this.timeout = timeout; + return this; + } +} diff --git a/bionetdb-client/src/main/python/README.md b/bionetdb-client/src/main/python/README.md new file mode 100644 index 0000000..e69de29 diff --git a/bionetdb-client/src/main/resources/client-configuration.yml b/bionetdb-client/src/main/resources/client-configuration.yml new file mode 100644 index 0000000..ed908b2 --- /dev/null +++ b/bionetdb-client/src/main/resources/client-configuration.yml @@ -0,0 +1,8 @@ +--- +version: "v1" + +## These are the RESTful configurations parameters +rest: + host: "localhost:8080/bionetdb" + timeout: 2000 + diff --git a/bionetdb-core/src/main/resources/configuration.yml b/bionetdb-core/src/main/resources/configuration.yml index da09c7d..29682f6 100644 --- a/bionetdb-core/src/main/resources/configuration.yml +++ b/bionetdb-core/src/main/resources/configuration.yml @@ -4,22 +4,25 @@ logFile: null ## More than one database can be defined, you can pass the database id to BioNetDbManager. ## If not passed the default database will always be the first one. -databases: -- id: "${BIONETDB.DB.DATABASE}" - species: "${BIONETDB.DB.SPECIES}" ## examples: hsapiens, mmusculus, ... +database: host: "${BIONETDB.DB.HOST}" port: "${BIONETDB.DB.PORT}" user: "${BIONETDB.DB.USER}" password: "${BIONETDB.DB.PASSWORD}" - options: null ## map containing specific database options +# options: null ## map containing specific database options + + +## Raw data download URLs download: + network: + ## In this version we are loading Ractome as default network + host: https://www.reactome.org/download/current/biopax.zip gene: host: http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v5/homo_sapiens_grch38/build/gene.json.gz protein: host: http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v5/homo_sapiens_grch38/build/protein.json.gz ## panel: ## host: ftp://mirbase.org/pub/mirbase/CURRENT/miRNA.xls.gz - clinvar: + clinicalVariant: host: http://bioinfo.hpc.cam.ac.uk/downloads/cellbase/v5/homo_sapiens_grch38/build/clinical_variants.json.gz - reactome: - host: https://www.reactome.org/download/current/biopax.zip \ No newline at end of file + diff --git a/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParserTest.java b/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParserTest.java index 7ec3a7e..dea56e6 100644 --- a/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParserTest.java +++ b/bionetdb-core/src/test/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParserTest.java @@ -1,9 +1,9 @@ package org.opencb.bionetdb.core.neo4j.query; import org.junit.Test; -import org.opencb.bionetdb.core.api.query.VariantQueryParam; -import org.opencb.bionetdb.core.api.query.NetworkPathQuery; -import org.opencb.bionetdb.core.api.query.NodeQuery; +import org.opencb.bionetdb.lib.api.iterators.query.VariantQueryParam; +import org.opencb.bionetdb.lib.api.iterators.query.NetworkPathQuery; +import org.opencb.bionetdb.lib.api.iterators.query.NodeQuery; import org.opencb.bionetdb.core.models.network.Node; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-lib/pom.xml b/bionetdb-lib/pom.xml new file mode 100644 index 0000000..1f9d77f --- /dev/null +++ b/bionetdb-lib/pom.xml @@ -0,0 +1,84 @@ + + + 4.0.0 + + + bionetdb + org.opencb.bionetdb + 0.2.0-SNAPSHOT + + + bionetdb-lib + ${bionetdb.version} + jar + + + + org.opencb.bionetdb + bionetdb-core + + + org.opencb.biodata + biodata-formats + + + org.opencb.biodata + biodata-tools + ${biodata.version} + + + org.opencb.commons + commons-lib + + + org.opencb.commons + commons-datastore-core + + + + org.neo4j + neo4j + 3.5.22 + + + org.neo4j + neo4j-kernel + 3.5.22 + + + org.neo4j + neo4j-kernel + 3.5.22 + + + org.neo4j.driver + neo4j-java-driver + 1.4.5 + + + org.biopax.paxtools + paxtools-core + + + com.fasterxml.jackson.core + jackson-databind + + + com.fasterxml.jackson.dataformat + jackson-dataformat-yaml + + + org.apache.commons + commons-math3 + + + junit + junit + test + + + + + \ No newline at end of file diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/BioNetDbManager.java similarity index 95% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/BioNetDbManager.java index f00356c..68710e1 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/BioNetDbManager.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/BioNetDbManager.java @@ -1,30 +1,30 @@ -package org.opencb.bionetdb.core; +package org.opencb.bionetdb.lib; import htsjdk.variant.variantcontext.VariantContext; import org.apache.commons.lang3.StringUtils; import org.neo4j.driver.v1.Session; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.tools.variant.converters.avro.VariantContextToVariantConverter; -import org.opencb.bionetdb.core.analysis.InterpretationAnalysis; -import org.opencb.bionetdb.core.analysis.NetworkAnalysis; -import org.opencb.bionetdb.core.analysis.VariantAnalysis; -import org.opencb.bionetdb.core.analysis.interpretation.TieringInterpretationAnalysis; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.iterators.NetworkPathIterator; -import org.opencb.bionetdb.core.api.iterators.NodeIterator; -import org.opencb.bionetdb.core.api.iterators.RowIterator; -import org.opencb.bionetdb.core.api.query.NetworkPathQuery; -import org.opencb.bionetdb.core.api.query.NodeQuery; -import org.opencb.bionetdb.core.api.query.NodeQueryParam; +import org.opencb.bionetdb.lib.analysis.InterpretationAnalysis; +import org.opencb.bionetdb.lib.analysis.NetworkAnalysis; +import org.opencb.bionetdb.lib.analysis.VariantAnalysis; +import org.opencb.bionetdb.lib.analysis.interpretation.TieringInterpretationAnalysis; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.iterators.NetworkPathIterator; +import org.opencb.bionetdb.lib.api.iterators.NodeIterator; +import org.opencb.bionetdb.lib.api.iterators.RowIterator; +import org.opencb.bionetdb.lib.api.query.NetworkPathQuery; +import org.opencb.bionetdb.lib.api.query.NodeQuery; +import org.opencb.bionetdb.lib.api.query.NodeQueryParam; import org.opencb.bionetdb.core.config.BioNetDBConfiguration; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.bionetdb.core.models.network.Network; import org.opencb.bionetdb.core.models.network.NetworkManager; import org.opencb.bionetdb.core.models.network.NetworkPath; import org.opencb.bionetdb.core.models.network.Node; -import org.opencb.bionetdb.core.neo4j.Neo4JBioPaxLoader; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; -import org.opencb.bionetdb.core.neo4j.Neo4JVariantLoader; +import org.opencb.bionetdb.lib.db.Neo4JBioPaxLoader; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.db.Neo4JVariantLoader; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/BioNetDBAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/BioNetDBAnalysis.java similarity index 68% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/BioNetDBAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/BioNetDBAnalysis.java index cdedeba..79e28f5 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/BioNetDBAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/BioNetDBAnalysis.java @@ -1,6 +1,6 @@ -package org.opencb.bionetdb.core.analysis; +package org.opencb.bionetdb.lib.analysis; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; public class BioNetDBAnalysis { diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/InterpretationAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/InterpretationAnalysis.java similarity index 84% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/InterpretationAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/InterpretationAnalysis.java index ed96895..10b1a84 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/InterpretationAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/InterpretationAnalysis.java @@ -1,11 +1,11 @@ -package org.opencb.bionetdb.core.analysis; +package org.opencb.bionetdb.lib.analysis; import org.opencb.biodata.models.clinical.ClinicalProperty; import org.opencb.biodata.models.clinical.Disorder; import org.opencb.biodata.models.clinical.pedigree.Pedigree; import org.opencb.biodata.models.variant.Variant; -import org.opencb.bionetdb.core.analysis.interpretation.ProteinNetworkInterpretationAnalysis; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.analysis.interpretation.ProteinNetworkInterpretationAnalysis; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/NetworkAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/NetworkAnalysis.java similarity index 62% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/NetworkAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/NetworkAnalysis.java index 1fcede3..fcac8ed 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/NetworkAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/NetworkAnalysis.java @@ -1,6 +1,6 @@ -package org.opencb.bionetdb.core.analysis; +package org.opencb.bionetdb.lib.analysis; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; public class NetworkAnalysis extends BioNetDBAnalysis { diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/VariantAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/VariantAnalysis.java similarity index 97% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/VariantAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/VariantAnalysis.java index 478b74e..09bf2b6 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/VariantAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/VariantAnalysis.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.analysis; +package org.opencb.bionetdb.lib.analysis; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang.StringUtils; @@ -6,9 +6,9 @@ import org.opencb.biodata.models.clinical.pedigree.Pedigree; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.tools.pedigree.ModeOfInheritance; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.iterators.NodeIterator; -import org.opencb.bionetdb.core.api.query.VariantQueryParam; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.iterators.NodeIterator; +import org.opencb.bionetdb.lib.api.query.VariantQueryParam; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.bionetdb.core.utils.NodeBuilder; import org.opencb.commons.datastore.core.Query; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java similarity index 94% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java index 3d56711..89cc1e5 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/ProteinNetworkInterpretationAnalysis.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.analysis.interpretation; +package org.opencb.bionetdb.lib.analysis.interpretation; import org.apache.commons.collections.CollectionUtils; import org.opencb.biodata.models.clinical.ClinicalProperty; @@ -6,8 +6,8 @@ import org.opencb.biodata.models.clinical.pedigree.Pedigree; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.tools.pedigree.ModeOfInheritance; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.query.VariantQueryParam; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.query.VariantQueryParam; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/TieringInterpretationAnalysis.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/TieringInterpretationAnalysis.java similarity index 98% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/TieringInterpretationAnalysis.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/TieringInterpretationAnalysis.java index 8edfb10..a98af98 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/analysis/interpretation/TieringInterpretationAnalysis.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/analysis/interpretation/TieringInterpretationAnalysis.java @@ -1,11 +1,11 @@ -package org.opencb.bionetdb.core.analysis.interpretation; +package org.opencb.bionetdb.lib.analysis.interpretation; import org.apache.commons.lang3.StringUtils; import org.neo4j.driver.v1.*; import org.opencb.biodata.models.clinical.pedigree.Member; import org.opencb.biodata.models.variant.Variant; -import org.opencb.bionetdb.core.neo4j.iterators.Neo4JVariantIterator; +import org.opencb.bionetdb.lib.db.iterators.Neo4JVariantIterator; import org.opencb.bionetdb.core.utils.NodeBuilder; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/NetworkDBAdaptor.java similarity index 94% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/NetworkDBAdaptor.java index 73f4ba8..13358a1 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/NetworkDBAdaptor.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/NetworkDBAdaptor.java @@ -1,12 +1,12 @@ -package org.opencb.bionetdb.core.api; +package org.opencb.bionetdb.lib.api; import org.opencb.biodata.models.variant.Variant; -import org.opencb.bionetdb.core.api.iterators.NetworkPathIterator; -import org.opencb.bionetdb.core.api.iterators.NodeIterator; -import org.opencb.bionetdb.core.api.iterators.RowIterator; -import org.opencb.bionetdb.core.api.iterators.VariantIterator; -import org.opencb.bionetdb.core.api.query.NetworkPathQuery; -import org.opencb.bionetdb.core.api.query.NodeQuery; +import org.opencb.bionetdb.lib.api.iterators.NetworkPathIterator; +import org.opencb.bionetdb.lib.api.iterators.NodeIterator; +import org.opencb.bionetdb.lib.api.iterators.RowIterator; +import org.opencb.bionetdb.lib.api.iterators.VariantIterator; +import org.opencb.bionetdb.lib.api.query.NetworkPathQuery; +import org.opencb.bionetdb.lib.api.query.NodeQuery; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.bionetdb.core.models.network.Network; import org.opencb.bionetdb.core.models.network.NetworkPath; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NetworkPathIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NetworkPathIterator.java similarity index 87% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NetworkPathIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NetworkPathIterator.java index 69b0df8..281a3e8 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NetworkPathIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NetworkPathIterator.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.iterators; +package org.opencb.bionetdb.lib.api.iterators; import org.opencb.bionetdb.core.models.network.NetworkPath; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NodeIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NodeIterator.java similarity index 86% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NodeIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NodeIterator.java index d58a9e2..a534b30 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/NodeIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/NodeIterator.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.iterators; +package org.opencb.bionetdb.lib.api.iterators; import org.opencb.bionetdb.core.models.network.Node; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/RowIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/RowIterator.java similarity index 85% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/RowIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/RowIterator.java index f30c669..5920415 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/RowIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/RowIterator.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.iterators; +package org.opencb.bionetdb.lib.api.iterators; import java.util.Iterator; import java.util.List; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/VariantIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/VariantIterator.java similarity index 74% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/VariantIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/VariantIterator.java index daa4aa6..d8d216a 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/iterators/VariantIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/iterators/VariantIterator.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.iterators; +package org.opencb.bionetdb.lib.api.iterators; import org.opencb.biodata.models.variant.Variant; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/GeneNodeQueryParam.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/GeneNodeQueryParam.java similarity index 95% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/GeneNodeQueryParam.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/GeneNodeQueryParam.java index d5767aa..c8d5ea7 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/GeneNodeQueryParam.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/GeneNodeQueryParam.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import static org.opencb.commons.datastore.core.QueryParam.Type.TEXT_ARRAY; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NetworkPathQuery.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NetworkPathQuery.java similarity index 96% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NetworkPathQuery.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NetworkPathQuery.java index 7737d3d..09386a8 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NetworkPathQuery.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NetworkPathQuery.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import org.opencb.commons.datastore.core.Query; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQuery.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQuery.java similarity index 91% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQuery.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQuery.java index 7ef6be8..cb7c808 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQuery.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQuery.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import org.opencb.bionetdb.core.models.network.Node; import org.opencb.commons.datastore.core.Query; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQueryParam.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQueryParam.java similarity index 97% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQueryParam.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQueryParam.java index 612a828..5c09616 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/NodeQueryParam.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/NodeQueryParam.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import org.opencb.commons.datastore.core.QueryParam; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantNodeQueryParam.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantNodeQueryParam.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantNodeQueryParam.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantNodeQueryParam.java index 16f7de9..07781ca 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantNodeQueryParam.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantNodeQueryParam.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import static org.opencb.commons.datastore.core.QueryParam.Type.TEXT_ARRAY; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantQueryParam.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantQueryParam.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantQueryParam.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantQueryParam.java index aeb984e..75a1a87 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/api/query/VariantQueryParam.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/api/query/VariantQueryParam.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.api.query; +package org.opencb.bionetdb.lib.api.query; import org.opencb.commons.datastore.core.QueryParam; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JBioPaxLoader.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JBioPaxLoader.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JBioPaxLoader.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JBioPaxLoader.java index 4f41c0d..0b52463 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JBioPaxLoader.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JBioPaxLoader.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.neo4j; +package org.opencb.bionetdb.lib.db; import org.apache.commons.lang3.StringUtils; import org.biopax.paxtools.io.BioPAXIOHandler; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JLoader.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JLoader.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JLoader.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JLoader.java index 43ab101..a73428f 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JLoader.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JLoader.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.neo4j; +package org.opencb.bionetdb.lib.db; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.collections.MapUtils; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JNetworkDBAdaptor.java similarity index 97% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JNetworkDBAdaptor.java index 92c4c78..a7e1562 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JNetworkDBAdaptor.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JNetworkDBAdaptor.java @@ -1,17 +1,10 @@ -package org.opencb.bionetdb.core.neo4j; +package org.opencb.bionetdb.lib.db; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.time.StopWatch; import org.neo4j.driver.v1.*; import org.opencb.biodata.models.variant.Variant; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.iterators.NetworkPathIterator; -import org.opencb.bionetdb.core.api.iterators.NodeIterator; -import org.opencb.bionetdb.core.api.iterators.RowIterator; -import org.opencb.bionetdb.core.api.iterators.VariantIterator; -import org.opencb.bionetdb.core.api.query.NetworkPathQuery; -import org.opencb.bionetdb.core.api.query.NodeQuery; import org.opencb.bionetdb.core.config.BioNetDBConfiguration; import org.opencb.bionetdb.core.config.DatabaseConfiguration; import org.opencb.bionetdb.core.exceptions.BioNetDBException; @@ -19,13 +12,20 @@ import org.opencb.bionetdb.core.models.network.NetworkPath; import org.opencb.bionetdb.core.models.network.Node; import org.opencb.bionetdb.core.models.network.Relation; -import org.opencb.bionetdb.core.neo4j.iterators.Neo4JNetworkPathIterator; -import org.opencb.bionetdb.core.neo4j.iterators.Neo4JNodeIterator; -import org.opencb.bionetdb.core.neo4j.iterators.Neo4JRowIterator; -import org.opencb.bionetdb.core.neo4j.iterators.Neo4JVariantIterator; -import org.opencb.bionetdb.core.neo4j.query.Neo4JQueryParser; -import org.opencb.bionetdb.core.neo4j.query.Neo4JVariantQueryParser; import org.opencb.bionetdb.core.utils.Neo4jConverter; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.iterators.NetworkPathIterator; +import org.opencb.bionetdb.lib.api.iterators.NodeIterator; +import org.opencb.bionetdb.lib.api.iterators.RowIterator; +import org.opencb.bionetdb.lib.api.iterators.VariantIterator; +import org.opencb.bionetdb.lib.api.query.NetworkPathQuery; +import org.opencb.bionetdb.lib.api.query.NodeQuery; +import org.opencb.bionetdb.lib.db.iterators.Neo4JNetworkPathIterator; +import org.opencb.bionetdb.lib.db.iterators.Neo4JNodeIterator; +import org.opencb.bionetdb.lib.db.iterators.Neo4JRowIterator; +import org.opencb.bionetdb.lib.db.iterators.Neo4JVariantIterator; +import org.opencb.bionetdb.lib.db.query.Neo4JQueryParser; +import org.opencb.bionetdb.lib.db.query.Neo4JVariantQueryParser; import org.opencb.commons.datastore.core.ObjectMap; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JVariantLoader.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JVariantLoader.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JVariantLoader.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JVariantLoader.java index 4eff692..b99a713 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/Neo4JVariantLoader.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/Neo4JVariantLoader.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.neo4j; +package org.opencb.bionetdb.lib.db; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.vcf.VCFHeader; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/UserDefinedProcedure.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/UserDefinedProcedure.java similarity index 98% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/UserDefinedProcedure.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/UserDefinedProcedure.java index aec2fb5..892ac8f 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/UserDefinedProcedure.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/UserDefinedProcedure.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.neo4j; +package org.opencb.bionetdb.lib.db; import org.neo4j.graphdb.GraphDatabaseService; import org.neo4j.logging.Log; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/converters/Neo4JRecordToVariantConverter.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/converters/Neo4JRecordToVariantConverter.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/converters/Neo4JRecordToVariantConverter.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/converters/Neo4JRecordToVariantConverter.java index be90536..4b396ce 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/converters/Neo4JRecordToVariantConverter.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/converters/Neo4JRecordToVariantConverter.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core.neo4j.converters; +package org.opencb.bionetdb.lib.db.converters; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.MapperFeature; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNetworkPathIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNetworkPathIterator.java similarity index 88% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNetworkPathIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNetworkPathIterator.java index bcc9b68..3fd3b58 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNetworkPathIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNetworkPathIterator.java @@ -1,9 +1,9 @@ -package org.opencb.bionetdb.core.neo4j.iterators; +package org.opencb.bionetdb.lib.db.iterators; import org.neo4j.driver.v1.StatementResult; -import org.opencb.bionetdb.core.api.iterators.NetworkPathIterator; import org.opencb.bionetdb.core.models.network.NetworkPath; import org.opencb.bionetdb.core.utils.Neo4jConverter; +import org.opencb.bionetdb.lib.api.iterators.NetworkPathIterator; import java.util.ArrayList; import java.util.List; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNodeIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNodeIterator.java similarity index 89% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNodeIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNodeIterator.java index 871f3d4..cbac52d 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JNodeIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JNodeIterator.java @@ -1,9 +1,9 @@ -package org.opencb.bionetdb.core.neo4j.iterators; +package org.opencb.bionetdb.lib.db.iterators; import org.neo4j.driver.v1.StatementResult; -import org.opencb.bionetdb.core.api.iterators.NodeIterator; import org.opencb.bionetdb.core.models.network.Node; import org.opencb.bionetdb.core.utils.Neo4jConverter; +import org.opencb.bionetdb.lib.api.iterators.NodeIterator; import java.util.ArrayList; import java.util.List; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JRowIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JRowIterator.java similarity index 85% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JRowIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JRowIterator.java index 36b6964..ccc477f 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JRowIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JRowIterator.java @@ -1,9 +1,9 @@ -package org.opencb.bionetdb.core.neo4j.iterators; +package org.opencb.bionetdb.lib.db.iterators; import org.neo4j.driver.v1.Record; import org.neo4j.driver.v1.StatementResult; -import org.opencb.bionetdb.core.api.iterators.RowIterator; import org.opencb.bionetdb.core.utils.Neo4jConverter; +import org.opencb.bionetdb.lib.api.iterators.RowIterator; import java.util.List; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JVariantIterator.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JVariantIterator.java similarity index 76% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JVariantIterator.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JVariantIterator.java index b40fcd8..b698e81 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/iterators/Neo4JVariantIterator.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/iterators/Neo4JVariantIterator.java @@ -1,9 +1,9 @@ -package org.opencb.bionetdb.core.neo4j.iterators; +package org.opencb.bionetdb.lib.db.iterators; import org.neo4j.driver.v1.StatementResult; import org.opencb.biodata.models.variant.Variant; -import org.opencb.bionetdb.core.api.iterators.VariantIterator; -import org.opencb.bionetdb.core.neo4j.converters.Neo4JRecordToVariantConverter; +import org.opencb.bionetdb.lib.api.iterators.VariantIterator; +import org.opencb.bionetdb.lib.db.converters.Neo4JRecordToVariantConverter; public class Neo4JVariantIterator implements VariantIterator { diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JGeneQueryParser.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JGeneQueryParser.java similarity index 86% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JGeneQueryParser.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JGeneQueryParser.java index 6324b86..8bfbc4f 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JGeneQueryParser.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JGeneQueryParser.java @@ -1,6 +1,6 @@ -package org.opencb.bionetdb.core.neo4j.query; +package org.opencb.bionetdb.lib.db.query; -import org.opencb.bionetdb.core.api.query.NodeQuery; +import org.opencb.bionetdb.lib.api.iterators.query.NodeQuery; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParser.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JQueryParser.java similarity index 98% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParser.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JQueryParser.java index 9883832..0dffae1 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JQueryParser.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JQueryParser.java @@ -1,10 +1,10 @@ -package org.opencb.bionetdb.core.neo4j.query; +package org.opencb.bionetdb.lib.db.query; import org.apache.commons.lang3.StringUtils; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.query.NetworkPathQuery; -import org.opencb.bionetdb.core.api.query.NodeQuery; import org.opencb.bionetdb.core.exceptions.BioNetDBException; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.query.NetworkPathQuery; +import org.opencb.bionetdb.lib.api.query.NodeQuery; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.commons.utils.ListUtils; diff --git a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JVariantQueryParser.java b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JVariantQueryParser.java similarity index 99% rename from bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JVariantQueryParser.java rename to bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JVariantQueryParser.java index d95fbf5..571f59c 100644 --- a/bionetdb-core/src/main/java/org/opencb/bionetdb/core/neo4j/query/Neo4JVariantQueryParser.java +++ b/bionetdb-lib/src/main/java/org/opencb/bionetdb/lib/db/query/Neo4JVariantQueryParser.java @@ -1,9 +1,9 @@ -package org.opencb.bionetdb.core.neo4j.query; +package org.opencb.bionetdb.lib.db.query; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang3.StringUtils; -import org.opencb.bionetdb.core.api.query.VariantQueryParam; import org.opencb.bionetdb.core.utils.NodeBuilder; +import org.opencb.bionetdb.lib.api.query.VariantQueryParam; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-core/src/test/java/org/opencb/bionetdb/core/BioNetDbManagerTest.java b/bionetdb-lib/src/test/java/org/opencb/bionetdb/lib/BioNetDbManagerTest.java similarity index 98% rename from bionetdb-core/src/test/java/org/opencb/bionetdb/core/BioNetDbManagerTest.java rename to bionetdb-lib/src/test/java/org/opencb/bionetdb/lib/BioNetDbManagerTest.java index 23d741a..5f07409 100644 --- a/bionetdb-core/src/test/java/org/opencb/bionetdb/core/BioNetDbManagerTest.java +++ b/bionetdb-lib/src/test/java/org/opencb/bionetdb/lib/BioNetDbManagerTest.java @@ -1,4 +1,4 @@ -package org.opencb.bionetdb.core; +package org.opencb.bionetdb.lib; import com.fasterxml.jackson.annotation.JsonInclude; import com.fasterxml.jackson.databind.MapperFeature; @@ -14,15 +14,15 @@ import org.opencb.biodata.models.clinical.pedigree.Pedigree; import org.opencb.biodata.models.variant.Variant; import org.opencb.biodata.models.variant.avro.ConsequenceType; -import org.opencb.bionetdb.core.analysis.VariantAnalysis; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.query.VariantQueryParam; +import org.opencb.bionetdb.lib.analysis.VariantAnalysis; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.query.VariantQueryParam; import org.opencb.bionetdb.core.config.BioNetDBConfiguration; import org.opencb.bionetdb.core.config.DatabaseConfiguration; import org.opencb.bionetdb.core.exceptions.BioNetDBException; import org.opencb.bionetdb.core.models.network.Network; import org.opencb.bionetdb.core.models.network.Node; -import org.opencb.bionetdb.core.neo4j.query.Neo4JQueryParser; +import org.opencb.bionetdb.lib.db.query.Neo4JQueryParser; import org.opencb.bionetdb.core.utils.CsvInfo; import org.opencb.bionetdb.core.utils.Neo4jCsvImporter; import org.opencb.bionetdb.core.utils.NodeBuilder; diff --git a/bionetdb-server/pom.xml b/bionetdb-server/pom.xml index 86942e8..6421897 100644 --- a/bionetdb-server/pom.xml +++ b/bionetdb-server/pom.xml @@ -18,7 +18,7 @@ org.opencb.bionetdb - bionetdb-core + bionetdb-lib org.opencb.commons diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java index cadf0bd..8cf6254 100644 --- a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java +++ b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/GenericRestWSServer.java @@ -9,8 +9,8 @@ import com.google.common.base.Splitter; import io.swagger.annotations.ApiParam; import org.apache.commons.lang3.StringUtils; -import org.opencb.bionetdb.core.BioNetDbManager; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.BioNetDbManager; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; import org.opencb.bionetdb.core.config.BioNetDBConfiguration; import org.opencb.bionetdb.core.config.DatabaseConfiguration; import org.opencb.bionetdb.core.exceptions.BioNetDBException; diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/NodeWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/NodeWSServer.java index 93b3eb5..281afc7 100644 --- a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/NodeWSServer.java +++ b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/NodeWSServer.java @@ -4,8 +4,8 @@ import io.swagger.annotations.ApiOperation; import io.swagger.annotations.ApiParam; import org.apache.commons.lang3.StringUtils; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; import org.opencb.bionetdb.server.exception.VersionException; import org.opencb.commons.datastore.core.Query; import org.opencb.commons.datastore.core.QueryOptions; diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/PathWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/PathWSServer.java index d993c94..fd226c3 100644 --- a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/PathWSServer.java +++ b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/PathWSServer.java @@ -2,9 +2,9 @@ import io.swagger.annotations.Api; import io.swagger.annotations.ApiOperation; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.iterators.NetworkPathIterator; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.iterators.NetworkPathIterator; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; import org.opencb.bionetdb.core.models.network.NetworkPath; import org.opencb.bionetdb.server.exception.VersionException; import org.opencb.commons.datastore.core.QueryResult; diff --git a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/TableWSServer.java b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/TableWSServer.java index f5e4332..de7bfdd 100644 --- a/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/TableWSServer.java +++ b/bionetdb-server/src/main/java/org/opencb/bionetdb/server/rest/TableWSServer.java @@ -3,9 +3,9 @@ import io.swagger.annotations.Api; import io.swagger.annotations.ApiOperation; import org.apache.commons.lang.StringUtils; -import org.opencb.bionetdb.core.api.NetworkDBAdaptor; -import org.opencb.bionetdb.core.api.iterators.RowIterator; -import org.opencb.bionetdb.core.neo4j.Neo4JNetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.NetworkDBAdaptor; +import org.opencb.bionetdb.lib.api.iterators.RowIterator; +import org.opencb.bionetdb.lib.db.Neo4JNetworkDBAdaptor; import org.opencb.bionetdb.server.exception.VersionException; import org.opencb.commons.datastore.core.QueryResult; diff --git a/pom.xml b/pom.xml index a930418..6b4ae6b 100644 --- a/pom.xml +++ b/pom.xml @@ -17,6 +17,8 @@ bionetdb-app bionetdb-core bionetdb-server + bionetdb-lib + bionetdb-client @@ -26,6 +28,8 @@ 2.1.0-SNAPSHOT 2.10.1 2.29.1 + 5.5.2 + 1.5.2 build @@ -76,6 +80,11 @@ bionetdb-core ${bionetdb.version} + + org.opencb.bionetdb + bionetdb-lib + ${bionetdb.version} + org.opencb.biodata biodata-formats @@ -152,6 +161,11 @@ jersey-client ${jersey.version} + + org.glassfish.jersey.inject + jersey-hk2 + ${jersey.version} + org.apache.commons commons-math3 @@ -163,6 +177,24 @@ 4.12 test + + org.junit.jupiter + junit-jupiter-api + ${junit.jupiter.version} + test + + + org.junit.platform + junit-platform-engine + ${junit.platform.version} + test + + + org.junit.jupiter + junit-jupiter-engine + ${junit.jupiter.version} + test +