From 94f22796ba0e3fb5560bf1d8335a017625ff02a4 Mon Sep 17 00:00:00 2001 From: Andres Silva Date: Tue, 24 Nov 2020 22:37:13 +0000 Subject: [PATCH 1/5] add tests --- eva-release/pom.xml | 4 + .../ReleaseInfoControllerTest.java | 57 ++ .../ReleaseStatsControllerTest.java | 64 +++ .../src/test/resources/application.properties | 10 + eva-release/src/test/resources/data.sql | 504 ++++++++++++++++++ 5 files changed, 639 insertions(+) create mode 100644 eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoControllerTest.java create mode 100644 eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java create mode 100644 eva-release/src/test/resources/application.properties create mode 100644 eva-release/src/test/resources/data.sql diff --git a/eva-release/pom.xml b/eva-release/pom.xml index 81affb54..2501b03c 100644 --- a/eva-release/pom.xml +++ b/eva-release/pom.xml @@ -55,6 +55,10 @@ springfox-swagger2 compile + + org.hsqldb + hsqldb + diff --git a/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoControllerTest.java b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoControllerTest.java new file mode 100644 index 00000000..f5146ddb --- /dev/null +++ b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoControllerTest.java @@ -0,0 +1,57 @@ +/* + * Copyright 2020 EMBL - European Bioinformatics Institute + * + * 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 uk.ac.ebi.eva.release.controllers; + +import org.assertj.core.util.IterableUtil; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.junit4.SpringRunner; + +import uk.ac.ebi.eva.release.Application; +import uk.ac.ebi.eva.release.models.ReleaseInfo; + +import static org.junit.Assert.assertEquals; + +@SpringBootTest(classes = Application.class) +@RunWith(SpringRunner.class) +public class ReleaseInfoControllerTest { + + @Autowired + private ReleaseInfoController releaseInfoController; + + @Test + public void getOneReleaseInfo() { + int releaseVersion = 1; + Iterable releaseInfo = releaseInfoController.getReleaseInfo(releaseVersion); + assertEquals(releaseVersion, releaseInfo.iterator().next().getReleaseVersion()); + } + + @Test + public void getAllReleasesInfo() { + Integer releaseVersion = null; + Iterable releaseInfo = releaseInfoController.getReleaseInfo(releaseVersion); + assertEquals(2, IterableUtil.sizeOf(releaseInfo)); + } + + @Test + public void getLatestReleaseInfo() { + int latestReleaseVersion = 2; + ReleaseInfo latestReleaseInfo = releaseInfoController.getLatestReleaseInfo(); + assertEquals(latestReleaseVersion, latestReleaseInfo.getReleaseVersion()); + } +} \ No newline at end of file diff --git a/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java new file mode 100644 index 00000000..e219b2cc --- /dev/null +++ b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java @@ -0,0 +1,64 @@ +/* + * Copyright 2020 EMBL - European Bioinformatics Institute + * + * 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 uk.ac.ebi.eva.release.controllers; + +import org.assertj.core.util.IterableUtil; +import org.junit.Test; +import org.junit.runner.RunWith; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.test.context.junit4.SpringRunner; + +import uk.ac.ebi.eva.release.Application; +import uk.ac.ebi.eva.release.dto.ReleaseStatsPerSpeciesDto; + +import static org.junit.Assert.assertEquals; + +@SpringBootTest(classes = Application.class) +@RunWith(SpringRunner.class) +public class ReleaseStatsControllerTest { + + @Autowired + private ReleaseStatsController releaseStatsController; + + @Test + public void getAllSpeciesStats() { + int totalNumberOfRecords = 417; + Iterable allRecords = releaseStatsController.getReleaseStatsPerSpecies(null, false); + assertEquals(totalNumberOfRecords, IterableUtil.sizeOf(allRecords)); + } + + @Test + public void getStatsByReleaseVersion() { + int speciesInRelease2 = 218; + Iterable allRecords = releaseStatsController.getReleaseStatsPerSpecies(2, false); + assertEquals(speciesInRelease2, IterableUtil.sizeOf(allRecords)); + } + + @Test + public void getStatsByReleaseVersionNoUnmapped() { + int speciesInRelease2ExcludingUnmapped = 22; + Iterable allRecords = releaseStatsController.getReleaseStatsPerSpecies(2, true); + assertEquals(speciesInRelease2ExcludingUnmapped, IterableUtil.sizeOf(allRecords)); + } + + @Test + public void getStatsForNewVariantsOnlyInSpecificRelease() { + int numberOfSpeciesWithNewVariants = 29; + Iterable allRecords = releaseStatsController.getSpeciesWithNewRsIds(2); + assertEquals(numberOfSpeciesWithNewVariants, IterableUtil.sizeOf(allRecords)); + } +} \ No newline at end of file diff --git a/eva-release/src/test/resources/application.properties b/eva-release/src/test/resources/application.properties new file mode 100644 index 00000000..a389a16b --- /dev/null +++ b/eva-release/src/test/resources/application.properties @@ -0,0 +1,10 @@ +spring.datasource.driver-class-name=org.hsqldb.jdbcDriver +spring.datasource.url=jdbc:hsqldb:mem:db;sql.syntax_pgs=true;DB_CLOSE_DELAY=-1 +spring.datasource.username=SA +spring.datasource.password= + +spring.jpa.generate-ddl=true +spring.jpa.show-sql=true + +# See https://github.com/spring-projects/spring-boot/wiki/Spring-Boot-2.1-Release-Notes#bean-overriding +spring.main.allow-bean-definition-overriding=true \ No newline at end of file diff --git a/eva-release/src/test/resources/data.sql b/eva-release/src/test/resources/data.sql new file mode 100644 index 00000000..0c53b665 --- /dev/null +++ b/eva-release/src/test/resources/data.sql @@ -0,0 +1,504 @@ +INSERT INTO release_rs (release_version, release_date, release_description, release_ftp) VALUES (1, '2019-11-12', 'Initial EVA released. This release is the culmination of a year long process to import all non-human RefSNP (RS) accessioned variants from dbSNP.', 'ftp://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_1/'); +INSERT INTO release_rs (release_version, release_date, release_description, release_ftp) VALUES (2, '2020-11-03', 'RS Release 2 contains variants submitted directly to EVA in addition to those submitted to dbSNP up to September 2017 and made available in the first RS Release.', 'ftp://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_2/'); + +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(31971,'Absiella dolichum','Absiella_dolichum_31971',1,0,0,0,0,0,26337,0,0,0,0,0,26337,0) +,(905,'Acidaminococcus fermentans','Acidaminococcus_fermentans_905',1,0,0,0,0,0,9689,0,0,0,0,0,9689,0) +,(563191,'Acidaminococcus intestini','Acidaminococcus_intestini_563191',1,0,0,0,0,0,16445,0,0,0,0,0,16445,0) +,(470,'Acinetobacter baumannii','Acinetobacter_baumannii_470',1,0,0,0,0,0,1104226,0,0,0,0,0,1104226,0) +,(202950,'Acinetobacter baylyi','Acinetobacter_baylyi_202950',1,0,0,0,0,0,15414,0,0,0,0,0,15414,0) +,(471,'Acinetobacter calcoaceticus','Acinetobacter_calcoaceticus_471',1,0,0,0,0,0,1124336,0,0,0,0,0,1124336,0) +,(40214,'Acinetobacter johnsonii','Acinetobacter_johnsonii_40214',1,0,0,0,0,0,289070,0,0,0,0,0,289070,0) +,(106654,'Acinetobacter nosocomialis','Acinetobacter_nosocomialis_106654',1,0,0,0,0,0,712343,0,0,0,0,0,712343,0) +,(48296,'Acinetobacter pittii','Acinetobacter_pittii_48296',1,0,0,0,0,0,1138848,0,0,0,0,0,1138848,0) +,(472,'Acinetobacter sp.','Acinetobacter_sp__472',1,0,0,0,0,0,1064900,0,0,0,0,0,1064900,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(7165,'Anopheles gambiae','African_malaria_mosquito_7165',1,1250185,0,681,329724,202,2316,1250185,0,681,329724,202,2316,2243275) +,(51953,'Elaeis guineensis','African_oil_palm_51953',1,52383,0,0,59977,0,0,52383,0,0,59977,0,0,112484) +,(239935,'Akkermansia muciniphila','Akkermansia_muciniphila_239935',1,0,0,0,0,0,145318,0,0,0,0,0,145318,0) +,(28117,'Alistipes putredinis','Alistipes_putredinis_28117',1,0,0,0,0,0,77371,0,0,0,0,0,77371,0) +,(328814,'Alistipes shahii','Alistipes_shahii_328814',1,0,0,0,0,0,168531,0,0,0,0,0,168531,0) +,(169435,'Anaerotruncus colihominis','Anaerotruncus_colihominis_169435',1,0,0,0,0,0,49524,0,0,0,0,0,49524,0) +,(3750,'Malus domestica','Apple_3750',1,222929,0,0,113373,7,7914,222929,0,0,113373,7,7914,453768) +,(34274,'Gossypium herbaceum','Arabian_cotton_34274',1,0,0,0,0,0,10947,0,0,0,0,0,10947,0) +,(330879,'Aspergillus fumigatus','Ascomycetes_746128',1,114904,0,8,15,1,153,114904,0,8,15,1,153,878475) +,(469796,'Ovis orientalis','Asiatic_mouflon_469796',1,29257919,0,31936,126219,441,0,29257919,0,31936,126219,441,0,29547898) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(8237,'Thunnus thynnus','Atlantic_bluefin_tuna_8237',1,0,0,0,0,0,5,0,0,0,0,0,5,0) +,(7950,'Clupea harengus','Atlantic_herring_7950',1,0,0,0,43,0,5,0,0,0,43,0,5,44) +,(8030,'Salmo salar','Atlantic_salmon_8030',1,1004096,0,0,30229,2,4427,1004096,0,0,30229,2,4427,1163379) +,(246787,'Bacteroides cellulosilyticus','Bacteroides_cellulosilyticus_246787',1,0,0,0,0,0,321173,0,0,0,0,0,321173,0) +,(310298,'Bacteroides coprocola','Bacteroides_coprocola_310298',1,0,0,0,0,0,131900,0,0,0,0,0,131900,0) +,(387090,'Bacteroides coprophilus','Bacteroides_coprophilus_387090',1,0,0,0,0,0,92288,0,0,0,0,0,92288,0) +,(28111,'Bacteroides eggerthii','Bacteroides_eggerthii_28111',1,0,0,0,0,0,118877,0,0,0,0,0,118877,0) +,(469587,'Bacteroides fragilis','Bacteroides_fragilis_469587',1,0,0,0,0,0,155955,0,0,0,0,0,155955,0) +,(28116,'Bacteroides ovatus','Bacteroides_ovatus_28116',1,0,0,0,0,0,349999,0,0,0,0,0,349999,0) +,(384638,'Bacteroides pectinophilus','Bacteroides_pectinophilus_384638',1,0,0,0,0,0,74106,0,0,0,0,0,74106,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(310297,'Bacteroides plebeius','Bacteroides_plebeius_310297',1,0,0,0,0,0,246162,0,0,0,0,0,246162,0) +,(469586,'Bacteroides thetaiotaomicron','Bacteroides_thetaiotaomicron_469586',1,0,0,0,0,0,302092,0,0,0,0,0,302092,0) +,(820,'Bacteroides uniformis','Bacteroides_uniformis_820',1,0,0,0,0,0,187334,0,0,0,0,0,187334,0) +,(821,'Bacteroides vulgatus','Bacteroides_vulgatus_821',1,0,0,0,0,0,156681,0,0,0,0,0,156681,0) +,(3880,'Medicago truncatula','Barrel_medic_3880',1,16,0,0,1,0,12,16,0,0,1,0,12,19) +,(1680,'Bifidobacterium adolescentis','Bifidobacterium_adolescentis_1680',1,0,0,0,0,0,69505,0,0,0,0,0,69505,0) +,(28025,'Bifidobacterium animalis','Bifidobacterium_animalis_28025',1,0,0,0,0,0,804,0,0,0,0,0,804,0) +,(1681,'Bifidobacterium bifidum','Bifidobacterium_bifidum_1681',1,0,0,0,0,0,23723,0,0,0,0,0,23723,0) +,(1685,'Bifidobacterium breve','Bifidobacterium_breve_1685',1,0,0,0,0,0,11655,0,0,0,0,0,11655,0) +,(216816,'Bifidobacterium longum','Bifidobacterium_longum_216816',1,0,0,0,0,0,57525,0,0,0,0,0,57525,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(28026,'Bifidobacterium pseudocatenulatum','Bifidobacterium_pseudocatenulatum_28026',1,0,0,0,0,0,53797,0,0,0,0,0,53797,0) +,(3694,'Populus trichocarpa','Black_cottonwood_3694',1,9187468,0,99625,3170860,137577,0,9187468,0,99625,3170860,137577,0,15970398) +,(5039,'Blastomyces dermatitidis','Blastomyces_dermatitidis_5039',1,0,0,0,0,0,41892,0,0,0,0,0,41892,0) +,(1322,'Blautia hansenii','Blautia_hansenii_1322',1,0,0,0,0,0,40234,0,0,0,0,0,40234,0) +,(53443,'Blautia hydrogenotrophica','Blautia_hydrogenotrophica_53443',1,0,0,0,0,0,10349,0,0,0,0,0,10349,0) +,(40520,'Blautia obeum','Blautia_obeum_40520',1,0,0,0,0,0,331355,0,0,0,0,0,331355,0) +,(6183,'Schistosoma mansoni','Blood_fluke_6183',1,0,0,0,0,0,8,0,0,0,0,0,8,0) +,(9600,'Pongo pygmaeus','Bornean_orangutan_9600',1,0,0,0,0,0,7854083,0,0,0,0,0,7854083,0) +,(36855,'Brucella canis','Brucella_canis_36855',1,0,0,0,0,0,1212,0,0,0,0,0,1212,0) +,(236,'Brucella ovis','Brucella_ovis_236',1,0,0,0,0,0,1648,0,0,0,0,0,1648,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(52132,'Brucella sp.','Brucella_sp__52132',1,0,0,0,0,0,45294,0,0,0,0,0,45294,0) +,(245014,'Butyrate-producing bacterium ss3/4','Butyrate_producing_bacterium_ss3_4_245014',1,0,0,0,0,0,204100,0,0,0,0,0,204100,0) +,(45851,'Butyrivibrio crossotus','Butyrivibrio_crossotus_45851',1,0,0,0,0,0,86728,0,0,0,0,0,86728,0) +,(6238,'Caenorhabditis briggsae','Caenorhabditis_briggsae_6238',1,0,0,0,0,0,34403,0,0,0,0,0,34403,0) +,(216498,'Hydroides elegans','Calcareous_tube_worm_216498',1,0,0,0,0,0,8,0,0,0,0,0,8,0) +,(5476,'Candida albicans','Candida_albicans_5476',1,0,0,0,0,0,206514,0,0,0,0,0,206514,0) +,(79200,'Daucus carota subsp. sativus','Carrot_79200',1,1378278,0,0,15029,0,0,1378278,0,0,15029,0,0,1420001) +,(9685,'Felis catus','Cat_9685',1,3531201,0,12854,64779,4063,3392,3531201,0,12854,64779,4063,3392,4272123) +,(100886,'Catenibacterium mitsuokai','Catenibacterium_mitsuokai_100886',1,0,0,0,0,0,90734,0,0,0,0,0,90734,0) +,(9031,'Gallus gallus','Chicken_9031',1,23793669,0,140478,320088,4992,26701,23793669,0,140478,320088,4992,26701,73155330) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(3827,'Cicer arietinum','Chickpea_3827',1,327311,0,0,191755,0,0,327311,0,0,191755,0,0,531214) +,(9598,'Pan troglodytes','Chimpanzee_9598',1,1592108,0,36818,54763,1469,4238,1592108,0,36818,54763,1469,4238,2443966) +,(74940,'Oncorhynchus tshawytscha','Chinook_salmon_74940',1,0,0,0,0,0,935,0,0,0,0,0,935,0) +,(8018,'Oncorhynchus keta','Chum_salmon_8018',1,0,0,0,0,0,212,0,0,0,0,0,212,0) +,(457421,'Clostridiales bacterium 1_7_47FAA','Clostridiales_bacterium_1_7_47FAA_457421',1,0,0,0,0,0,55909,0,0,0,0,0,55909,0) +,(333367,'Clostridium asparagiforme','Clostridium_asparagiforme_333367',1,0,0,0,0,0,81007,0,0,0,0,0,81007,0) +,(208479,'Clostridium bolteae','Clostridium_bolteae_208479',1,0,0,0,0,0,171820,0,0,0,0,0,171820,0) +,(1535,'Clostridium leptum','Clostridium_leptum_1535',1,0,0,0,0,0,84248,0,0,0,0,0,84248,0) +,(29348,'Clostridium spiroforme','Clostridium_spiroforme_29348',1,0,0,0,0,0,57003,0,0,0,0,0,57003,0) +,(411489,'Clostridium sp. L2-50','Clostridium_sp__L2_50_411489',1,0,0,0,0,0,138575,0,0,0,0,0,138575,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(411486,'Clostridium sp. M62/1','Clostridium_sp__M62_1_411486',1,0,0,0,0,0,72510,0,0,0,0,0,72510,0) +,(411484,'Clostridium sp. SS2/1','Clostridium_sp__SS2_1_411484',1,0,0,0,0,0,154708,0,0,0,0,0,154708,0) +,(8019,'Oncorhynchus kisutch','Coho_salmon_8019',1,0,0,0,0,0,75,0,0,0,0,0,75,0) +,(59894,'Ficedula albicollis','Collared_flycatcher_59894',1,37728,0,0,682,0,119,37728,0,0,682,0,119,38483) +,(74426,'Collinsella aerofaciens','Collinsella_aerofaciens_74426',1,0,0,0,0,0,250405,0,0,0,0,0,250405,0) +,(147207,'Collinsella intestinalis','Collinsella_intestinalis_147207',1,0,0,0,0,0,28650,0,0,0,0,0,28650,0) +,(147206,'Collinsella stercoris','Collinsella_stercoris_147206',1,0,0,0,0,0,15863,0,0,0,0,0,15863,0) +,(9483,'Callithrix jacchus','Common_marmoset_9483',1,16049148,0,0,0,0,10,16049148,0,0,0,0,10,16049148) +,(27828,'Cooperia oncophora','Cooperia_oncophora_27828',1,0,0,0,0,0,426,0,0,0,0,0,426,0) +,(556270,'Coprobacillus sp. D7','Coprobacillus_sp__D7_556270',1,0,0,0,0,0,11975,0,0,0,0,0,11975,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(116085,'Coprococcus catus','Coprococcus_catus_116085',1,0,0,0,0,0,136694,0,0,0,0,0,136694,0) +,(410072,'Coprococcus comes','Coprococcus_comes_410072',1,0,0,0,0,0,181703,0,0,0,0,0,181703,0) +,(33043,'Coprococcus eutactus','Coprococcus_eutactus_33043',1,0,0,0,0,0,117168,0,0,0,0,0,117168,0) +,(3635,'Gossypium hirsutum','Cotton_3635',1,85757,0,0,14754,2,20652,85757,0,0,14754,2,20652,104499) +,(9913,'Bos taurus','Cow_9913',1,102813585,0,287864,1058111,6564,106113,102813585,0,287864,1058111,6564,106113,517045414) +,(9541,'Macaca fascicularis','Crab_eating_macaque_9541',1,1651397,0,0,21730,0,395866,1651397,0,0,21730,0,395866,1693894) +,(42345,'Phoenix dactylifera','Date_palm_42345',1,0,0,0,0,0,983553,0,0,0,0,0,983553,0) +,(901,'Desulfovibrio piger','Desulfovibrio_piger_901',1,0,0,0,0,0,46517,0,0,0,0,0,46517,0) +,(218538,'Dialister invisus','Dialister_invisus_218538',1,0,0,0,0,0,110981,0,0,0,0,0,110981,0) +,(9615,'Canis lupus familiaris','Dog_9615',1,5706844,0,50182,170432,13903,16975,5706844,0,50182,170432,13903,16975,8254195) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(39486,'Dorea formicigenerans','Dorea_formicigenerans_39486',1,0,0,0,0,0,58216,0,0,0,0,0,58216,0) +,(84112,'Eggerthella lenta','Eggerthella_lenta_84112',1,0,0,0,0,0,27993,0,0,0,0,0,27993,0) +,(1351,'Enterococcus faecalis','Enterococcus_faecalis_1351',1,0,0,0,0,0,1311,0,0,0,0,0,1311,0) +,(1352,'Enterococcus faecium','Enterococcus_faecium_1352',1,0,0,0,0,0,2777,0,0,0,0,0,2777,0) +,(552396,'Erysipelotrichaceae bacterium 5_2_54FAA','Erysipelotrichaceae_bacterium_5_2_54FAA_552396',1,0,0,0,0,0,49237,0,0,0,0,0,49237,0) +,(39485,'Eubacterium eligens','Eubacterium_eligens_39485',1,0,0,0,0,0,132024,0,0,0,0,0,132024,0) +,(39488,'Eubacterium hallii','Eubacterium_hallii_39488',1,0,0,0,0,0,104412,0,0,0,0,0,104412,0) +,(39491,'Eubacterium rectale','Eubacterium_rectale_39491',1,0,0,0,0,0,223111,0,0,0,0,0,223111,0) +,(39492,'Eubacterium siraeum','Eubacterium_siraeum_39492',1,0,0,0,0,0,207186,0,0,0,0,0,207186,0) +,(39496,'Eubacterium ventriosum','Eubacterium_ventriosum_39496',1,0,0,0,0,0,113243,0,0,0,0,0,113243,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(39483,'Faecalitalea cylindroides','Faecalitalea_cylindroides_39483',1,0,0,0,0,0,31085,0,0,0,0,0,31085,0) +,(46689,'Ficedula hypoleuca','Ficedula_hypoleuca_46689',1,0,0,0,0,0,230,0,0,0,0,0,230,0) +,(3711,'Brassica rapa','Field_mustard_3711',1,164,0,0,3,0,0,164,0,0,3,0,0,200) +,(7227,'Drosophila melanogaster','Fruit_fly_7227',1,5618530,0,41,1728,0,0,5618530,0,41,1728,0,0,6980418) +,(850,'Fusobacterium mortiferum','Fusobacterium_mortiferum_850',1,0,0,0,0,0,25244,0,0,0,0,0,25244,0) +,(2702,'Gardnerella vaginalis','Gardnerella_vaginalis_2702',1,0,0,0,0,0,668,0,0,0,0,0,668,0) +,(9925,'Capra hircus','Goat_9925',1,40690028,0,12472767,1097154,321788,56,40690028,0,12472767,1097154,321788,56,37568472) +,(9593,'Gorilla gorilla','Gorilla_9593',1,4,0,0,0,0,1,4,0,0,0,0,1,4) +,(13616,'Monodelphis domestica','Gray_short_tailed_opossum_13616',1,0,0,0,0,0,1086,0,0,0,0,0,1086,0) +,(9157,'Parus major','Great_tit_9157',1,6169,0,0,30,0,1645,6169,0,0,30,0,1645,6204) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(1735,'Holdemanella biformis','Holdemanella_biformis_1735',1,0,0,0,0,0,109232,0,0,0,0,0,109232,0) +,(61171,'Holdemania filiformis','Holdemania_filiformis_61171',1,0,0,0,0,0,128406,0,0,0,0,0,128406,0) +,(7460,'Apis mellifera','Honey_bee_7460',1,3834597,0,356,403905,109,10368,3834597,0,356,403905,109,10368,4732640) +,(9796,'Equus caballus','Horse_9796',1,21553652,0,56460,12229,117,488,21553652,0,56460,12229,117,488,26529883) +,(48849,'Passer domesticus','House_sparrow_48849',1,0,0,0,0,0,8491,0,0,0,0,0,8491,0) +,(154046,'Hungatella hathewayi','Hungatella_hathewayi_154046',1,0,0,0,0,0,71313,0,0,0,0,0,71313,0) +,(30522,'Bos indicus x Bos taurus','Hybrid_cattle_30522',1,0,0,0,0,0,100,0,0,0,0,0,100,0) +,(261299,'Intestinibacter bartlettii','Intestinibacter_bartlettii_261299',1,0,0,0,0,0,46123,0,0,0,0,0,46123,0) +,(93934,'Coturnix japonica','Japanese_quail_93934',1,8665,0,0,81,0,7567,8665,0,0,81,0,7567,8780) +,(3885,'Phaseolus vulgaris','Kidney_bean_3885',1,0,0,0,0,0,11989,0,0,0,0,0,11989,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(573,'Klebsiella pneumoniae','Klebsiella_pneumoniae_573',1,0,0,0,0,0,42709,0,0,0,0,0,42709,0) +,(1598,'Lactobacillus reuteri','Lactobacillus_reuteri_1598',1,0,0,0,0,0,2172,0,0,0,0,0,2172,0) +,(1623,'Lactobacillus ruminis','Lactobacillus_ruminis_1623',1,0,0,0,0,0,27388,0,0,0,0,0,27388,0) +,(1358,'Lactococcus lactis','Lactococcus_lactis_1358',1,0,0,0,0,0,9353,0,0,0,0,0,9353,0) +,(4577,'Zea mays','Maize_4577',1,57647260,0,6,960597,456,337986,57647260,0,6,960597,456,337986,86816709) +,(8839,'Anas platyrhynchos','Mallard_8839',1,0,0,0,1273017,0,301,0,0,0,1273017,0,301,1305529) +,(158847,'Megamonas hypermegale','Megamonas_hypermegale_158847',1,0,0,0,0,0,39236,0,0,0,0,0,39236,0) +,(2173,'Methanobrevibacter smithii','Methanobrevibacter_smithii_2173',1,0,0,0,0,0,47709,0,0,0,0,0,47709,0) +,(7994,'Astyanax mexicanus','Mexican_tetra_7994',1,0,0,0,507,0,0,0,0,0,507,0,0,518) +,(52226,'Mitsuokella multacida','Mitsuokella_multacida_52226',1,0,0,0,0,0,39465,0,0,0,0,0,39465,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(10090,'Mus musculus','Mouse_10090',1,83711318,0,381152,105979,3935,125898,83711318,0,381152,105979,3935,125898,178530053) +,(8128,'Oreochromis niloticus','Nile_tilapia_8128',1,254,0,0,71,0,17,254,0,0,71,0,17,412) +,(7175,'Culex pipiens','Northern_house_mosquito_7175',1,0,0,0,0,0,1,0,0,0,0,0,1,0) +,(61853,'Nomascus leucogenys','Northern_white_cheeked_gibbon_61853',1,1114820,0,0,58397,0,0,1114820,0,0,58397,0,0,1173217) +,(4679,'Allium cepa','Onion_4679',1,0,0,0,0,0,45,0,0,0,0,0,45,0) +,(9601,'Pongo abelii','Orangutan_9601',1,9745325,0,24188,197914,7974,62266,9745325,0,24188,197914,7974,62266,10517500) +,(847,'Oxalobacter formigenes','Oxalobacter_formigenes_847',1,0,0,0,0,0,10043,0,0,0,0,0,10043,0) +,(46503,'Parabacteroides merdae','Parabacteroides_merdae_46503',1,0,0,0,0,0,168534,0,0,0,0,0,168534,0) +,(563193,'Parabacteroides sp. D13','Parabacteroides_sp__D13_563193',1,0,0,0,0,0,196960,0,0,0,0,0,196960,0) +,(1255,'Pediococcus pentosaceus','Pediococcus_pentosaceus_1255',1,0,0,0,0,0,1149,0,0,0,0,0,1149,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(4072,'Capsicum annuum','Pepper_4072',1,17352,0,0,1923,1,3576,17352,0,0,1923,1,3576,19484) +,(1261,'Peptostreptococcus anaerobius','Peptostreptococcus_anaerobius_1261',1,0,0,0,0,0,3662,0,0,0,0,0,3662,0) +,(9823,'Sus scrofa','Pig_9823',1,65906312,0,126611,1043834,3731,39087,65906312,0,126611,1043834,3731,39087,193784833) +,(71647,'Pinus pinaster','Pinus_pinaster_71647',1,0,0,0,0,0,5926,0,0,0,0,0,5926,0) +,(5833,'Plasmodium falciparum','Plasmodium_falciparum_5833',1,0,0,0,0,0,2504144,0,0,0,0,0,2504144,0) +,(5861,'Plasmodium yoelii','Plasmodium_yoelii_5861',1,0,0,0,0,0,206103,0,0,0,0,0,206103,0) +,(9258,'Ornithorhynchus anatinus','Platypus_9258',1,0,0,0,0,0,11810,0,0,0,0,0,11810,0) +,(29073,'Ursus maritimus','Polar_bear_29073',1,0,0,0,0,0,175,0,0,0,0,0,175,0) +,(281920,'Porphyromonas uenonis','Porphyromonas_uenonis_281920',1,0,0,0,0,0,16133,0,0,0,0,0,16133,0) +,(79684,'Microtus ochrogaster','Prairie_vole_79684',1,8281,0,0,3601,18,2646,8281,0,0,3601,18,2646,13179) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(165179,'Prevotella copri','Prevotella_copri_165179',1,0,0,0,0,0,225404,0,0,0,0,0,225404,0) +,(386414,'Prevotella timonensis','Prevotella_timonensis_386414',1,0,0,0,0,0,16820,0,0,0,0,0,16820,0) +,(9986,'Oryctolagus cuniculus','Rabbit_9986',1,35,0,0,0,0,3,35,0,0,0,0,3,35) +,(8022,'Oncorhynchus mykiss','Rainbow_trout_8022',1,0,0,0,0,0,146384,0,0,0,0,0,146384,0) +,(3708,'Brassica napus','Rapeseed_3708',1,262717,0,0,41912,27,596854,262717,0,0,41912,27,596854,316156) +,(10116,'Rattus norvegicus','Rat_10116',1,4985148,0,89912,19034,3044,43794,4985148,0,89912,19034,3044,43794,14373438) +,(7070,'Tribolium castaneum','Red_flour_beetle_7070',1,0,0,0,103,0,138,0,0,0,103,0,138,103) +,(6728,'Procambarus clarkii','Red_swamp_crayfish_6728',1,0,0,0,0,0,44,0,0,0,0,0,44,0) +,(39638,'Agelaius phoeniceus','Red_winged_blackbird_39638',1,0,0,0,0,0,47,0,0,0,0,0,47,0) +,(9544,'Macaca mulatta','Rhesus_monkey_9544',1,53021755,0,13619,361073,1605,542019,53021755,0,13619,361073,1605,542019,103303387) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(4530,'Oryza sativa','Rice_4530',1,12825093,0,370849,92540,1514,192282,12825093,0,370849,92540,1514,192282,39672715) +,(166486,'Roseburia intestinalis','Roseburia_intestinalis_166486',1,0,0,0,0,0,151208,0,0,0,0,0,151208,0) +,(360807,'Roseburia inulinivorans','Roseburia_inulinivorans_360807',1,0,0,0,0,0,230337,0,0,0,0,0,230337,0) +,(6239,'Caenorhabditis elegans','Roundworm_6239',1,0,0,0,0,0,1476,0,0,0,0,0,1476,0) +,(40518,'Ruminococcus bromii','Ruminococcus_bromii_40518',1,0,0,0,0,0,167002,0,0,0,0,0,167002,0) +,(1161942,'Ruminococcus champanellensis','Ruminococcus_champanellensis_1161942',1,0,0,0,0,0,46005,0,0,0,0,0,46005,0) +,(33038,'Ruminococcus gnavus','Ruminococcus_gnavus_33038',1,0,0,0,0,0,26851,0,0,0,0,0,26851,0) +,(46228,'Ruminococcus lactaris','Ruminococcus_lactaris_46228',1,0,0,0,0,0,83380,0,0,0,0,0,83380,0) +,(457412,'Ruminococcus sp. 5_1_39BFAA','Ruminococcus_sp__5_1_39BFAA_457412',1,0,0,0,0,0,214091,0,0,0,0,0,214091,0) +,(657323,'Ruminococcus sp. SR1/5','Ruminococcus_sp__SR1_5_657323',1,0,0,0,0,0,208300,0,0,0,0,0,208300,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(33039,'Ruminococcus torques','Ruminococcus_torques_33039',1,0,0,0,0,0,275154,0,0,0,0,0,275154,0) +,(128810,'Saccharum hybrid cultivar','Saccharum_hybrid_cultivar_128810',1,0,0,0,0,0,59552,0,0,0,0,0,59552,0) +,(28901,'Salmonella enterica','Salmonella_enterica_28901',1,0,0,0,0,0,250,0,0,0,0,0,250,0) +,(7719,'Ciona intestinalis','Sea_vase_7719',1,2154561,0,0,1035951,0,0,2154561,0,0,1035951,0,0,3233501) +,(9940,'Ovis aries','Sheep_9940',1,92323274,0,37219,510235,1663,94367,92323274,0,37219,510235,1663,94367,125937151) +,(8023,'Oncorhynchus nerka','Sockeye_salmon_8023',1,0,0,0,0,0,197,0,0,0,0,0,197,0) +,(4558,'Sorghum bicolor','Sorghum_4558',1,7109294,0,1328,5431,19,1018,7109294,0,1328,5431,19,1018,8523055) +,(3847,'Glycine max','Soybean_3847',1,16533712,0,287204,1074945,1897,1451,16533712,0,287204,1074945,1897,1451,40720517) +,(99883,'Tetraodon nigroviridis','Spotted_green_pufferfish_99883',1,0,0,0,0,0,903588,0,0,0,0,0,903588,0) +,(28037,'Streptococcus mitis','Streptococcus_mitis_28037',1,0,0,0,0,0,39112,0,0,0,0,0,39112,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(1318,'Streptococcus parasanguinis','Streptococcus_parasanguinis_1318',1,0,0,0,0,0,84497,0,0,0,0,0,84497,0) +,(1308,'Streptococcus thermophilus','Streptococcus_thermophilus_1308',1,0,0,0,0,0,59551,0,0,0,0,0,59551,0) +,(3702,'Arabidopsis thaliana','Thale_cress_3702',1,13378702,0,32366,1707,0,128,13378702,0,32366,1707,0,128,15365629) +,(4081,'Solanum lycopersicum','Tomato_4081',1,7768,0,0,21,0,85,7768,0,0,21,0,85,7964) +,(154288,'Turicibacter sanguinis','Turicibacter_sanguinis_154288',1,0,0,0,0,0,6373,0,0,0,0,0,6373,0) +,(9103,'Meleagris gallopavo','Turkey_9103',1,6169,0,1,1142,3,1962,6169,0,1,1142,3,1962,8903) +,(105023,'Nothobranchius furzeri','Turquoise_killifish_105023',1,288,0,0,18,0,15,288,0,0,18,0,15,319) +,(29361,'Tyzzerella nexilis','Tyzzerella_nexilis_29361',1,0,0,0,0,0,116888,0,0,0,0,0,116888,0) +,(29466,'Veillonella parvula','Veillonella_parvula_29466',1,0,0,0,0,0,90777,0,0,0,0,0,90777,0) +,(60711,'Chlorocebus sabaeus','Vervet_monkey_60711',1,507592,0,0,0,0,0,507592,0,0,0,0,0,507592) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(10096,'Mus spretus','Western_wild_mouse_10096',1,0,0,0,0,0,4,0,0,0,0,0,4,0) +,(9807,'Ceratotherium simum','White_rhinoceros_9807',1,0,0,0,0,0,11,0,0,0,0,0,11,0) +,(3330,'Picea glauca','White_spruce_3330',1,0,0,0,0,0,229187,0,0,0,0,0,229187,0) +,(3712,'Brassica oleracea','Wild_cabbage_3712',1,625798,0,0,0,0,0,625798,0,0,0,0,0,625798) +,(9923,'Capra aegagrus','Wild_goat_9923',1,40690028,0,12472767,1097154,321788,0,40690028,0,12472767,1097154,321788,0,17530681) +,(29760,'Vitis vinifera','Wine_grape_29760',1,442737,0,730,2313,162,2594,442737,0,730,2313,162,2594,524189) +,(59729,'Taeniopygia guttata','Zebra_finch_59729',1,1663282,0,176,85844,497,968,1663282,0,176,85844,497,968,1767120) +,(7955,'Danio rerio','Zebrafish_7955',1,17592388,0,14816,133974,131,28883,17592388,0,14816,133974,131,28883,18706603) +,(9915,'Bos indicus','Zebu_9915',1,0,0,0,0,0,292363,0,0,0,0,0,292363,32989380) +,(31971,'Absiella dolichum','absiella_dolichum',2,0,0,0,0,0,26337,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(905,'Acidaminococcus fermentans','acidaminococcus_fermentans',2,0,0,0,0,0,9689,0,0,0,0,0,0,0) +,(563191,'Acidaminococcus intestini','acidaminococcus_intestini',2,0,0,0,0,0,16445,0,0,0,0,0,0,0) +,(470,'Acinetobacter baumannii','acinetobacter_baumannii',2,0,0,0,0,0,1104226,0,0,0,0,0,0,0) +,(202950,'Acinetobacter baylyi','acinetobacter_baylyi',2,0,0,0,0,0,15414,0,0,0,0,0,0,0) +,(471,'Acinetobacter calcoaceticus','acinetobacter_calcoaceticus',2,0,0,0,0,0,1124336,0,0,0,0,0,0,0) +,(40214,'Acinetobacter johnsonii','acinetobacter_johnsonii',2,0,0,0,0,0,289070,0,0,0,0,0,0,0) +,(106654,'Acinetobacter nosocomialis','acinetobacter_nosocomialis',2,0,0,0,0,0,712343,0,0,0,0,0,0,0) +,(48296,'Acinetobacter pittii','acinetobacter_pittii',2,0,0,0,0,0,1138848,0,0,0,0,0,0,0) +,(472,'Acinetobacter sp.','acinetobacter_sp',2,0,0,0,0,0,1064900,0,0,0,0,0,0,0) +,(7159,'Aedes aegypti','aedes_aegypti',2,25589,0,0,0,0,0,25589,0,0,0,0,0,25589) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(39638,'Agelaius phoeniceus','agelaius_phoeniceus',2,0,0,0,0,0,47,0,0,0,0,0,0,0) +,(239935,'Akkermansia muciniphila','akkermansia_muciniphila',2,0,0,0,0,0,145318,0,0,0,0,0,0,0) +,(28117,'Alistipes putredinis','alistipes_putredinis',2,0,0,0,0,0,77371,0,0,0,0,0,0,0) +,(328814,'Alistipes shahii','alistipes_shahii',2,0,0,0,0,0,168531,0,0,0,0,0,0,0) +,(4679,'Allium cepa','allium_cepa',2,0,0,0,0,0,45,0,0,0,0,0,0,0) +,(169435,'Anaerotruncus colihominis','anaerotruncus_colihominis',2,0,0,0,0,0,49524,0,0,0,0,0,0,0) +,(4615,'Ananas comosus','ananas_comosus',2,14644,0,0,0,0,0,14644,0,0,0,0,0,14644) +,(8839,'Anas platyrhynchos','anas_platyrhynchos',2,0,0,0,1273017,0,301,0,0,0,0,0,0,0) +,(7165,'Anopheles gambiae','anopheles_gambiae',2,1215098,35087,681,329724,202,2316,0,35087,0,0,0,0,0) +,(8845,'Anser cygnoides','anser_cygnoides',2,6,0,0,0,0,0,6,0,0,0,0,0,6) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(7460,'Apis mellifera','apis_mellifera',2,3828753,5844,356,403905,109,10368,0,5844,0,0,0,0,0) +,(3702,'Arabidopsis thaliana','arabidopsis_thaliana',2,26315512,319,32366,1707,0,128,12959978,319,0,0,0,0,31963009) +,(330879,'Aspergillus fumigatus','aspergillus_fumigatus',2,114613,291,8,15,1,153,0,291,0,0,0,0,0) +,(7994,'Astyanax mexicanus','astyanax_mexicanus',2,0,0,0,507,0,0,0,0,0,0,0,0,0) +,(246787,'Bacteroides cellulosilyticus','bacteroides_cellulosilyticus',2,0,0,0,0,0,321173,0,0,0,0,0,0,0) +,(310298,'Bacteroides coprocola','bacteroides_coprocola',2,0,0,0,0,0,131900,0,0,0,0,0,0,0) +,(387090,'Bacteroides coprophilus','bacteroides_coprophilus',2,0,0,0,0,0,92288,0,0,0,0,0,0,0) +,(28111,'Bacteroides eggerthii','bacteroides_eggerthii',2,0,0,0,0,0,118877,0,0,0,0,0,0,0) +,(469587,'Bacteroides fragilis','bacteroides_fragilis',2,0,0,0,0,0,155955,0,0,0,0,0,0,0) +,(28116,'Bacteroides ovatus','bacteroides_ovatus',2,0,0,0,0,0,349999,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(384638,'Bacteroides pectinophilus','bacteroides_pectinophilus',2,0,0,0,0,0,74106,0,0,0,0,0,0,0) +,(310297,'Bacteroides plebeius','bacteroides_plebeius',2,0,0,0,0,0,246162,0,0,0,0,0,0,0) +,(469586,'Bacteroides thetaiotaomicron','bacteroides_thetaiotaomicron',2,0,0,0,0,0,302092,0,0,0,0,0,0,0) +,(820,'Bacteroides uniformis','bacteroides_uniformis',2,0,0,0,0,0,187334,0,0,0,0,0,0,0) +,(821,'Bacteroides vulgatus','bacteroides_vulgatus',2,0,0,0,0,0,156681,0,0,0,0,0,0,0) +,(1680,'Bifidobacterium adolescentis','bifidobacterium_adolescentis',2,0,0,0,0,0,69505,0,0,0,0,0,0,0) +,(28025,'Bifidobacterium animalis','bifidobacterium_animalis',2,0,0,0,0,0,804,0,0,0,0,0,0,0) +,(1681,'Bifidobacterium bifidum','bifidobacterium_bifidum',2,0,0,0,0,0,23723,0,0,0,0,0,0,0) +,(1685,'Bifidobacterium breve','bifidobacterium_breve',2,0,0,0,0,0,11655,0,0,0,0,0,0,0) +,(216816,'Bifidobacterium longum','bifidobacterium_longum',2,0,0,0,0,0,57525,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(28026,'Bifidobacterium pseudocatenulatum','bifidobacterium_pseudocatenulatum',2,0,0,0,0,0,53797,0,0,0,0,0,0,0) +,(5039,'Blastomyces dermatitidis','blastomyces_dermatitidis',2,0,0,0,0,0,41892,0,0,0,0,0,0,0) +,(1322,'Blautia hansenii','blautia_hansenii',2,0,0,0,0,0,40234,0,0,0,0,0,0,0) +,(53443,'Blautia hydrogenotrophica','blautia_hydrogenotrophica',2,0,0,0,0,0,10349,0,0,0,0,0,0,0) +,(40520,'Blautia obeum','blautia_obeum',2,0,0,0,0,0,331355,0,0,0,0,0,0,0) +,(9915,'Bos indicus','bos_indicus',2,0,0,0,0,0,292363,0,0,0,0,0,0,0) +,(30522,'Bos indicus x Bos taurus','bos_indicus_x_bos_taurus',2,0,0,0,0,0,100,0,0,0,0,0,0,0) +,(9913,'Bos taurus','bos_taurus',2,102605893,635955,287864,1058111,6564,106113,0,635955,0,0,0,0,0) +,(3708,'Brassica napus','brassica_napus',2,262717,0,0,41912,27,596854,0,0,0,0,0,0,0) +,(3712,'Brassica oleracea','brassica_oleracea',2,625798,0,0,0,0,0,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(3711,'Brassica rapa','brassica_rapa',2,164,0,0,3,0,0,0,0,0,0,0,0,0) +,(36855,'Brucella canis','brucella_canis',2,0,0,0,0,0,1212,0,0,0,0,0,0,0) +,(236,'Brucella ovis','brucella_ovis',2,0,0,0,0,0,1648,0,0,0,0,0,0,0) +,(52132,'Brucella sp.','brucella_sp',2,0,0,0,0,0,45294,0,0,0,0,0,0,0) +,(245014,'Butyrate-producing bacterium ss3/4','butyrate_producing_bacterium_ss3_4',2,0,0,0,0,0,204100,0,0,0,0,0,0,0) +,(45851,'Butyrivibrio crossotus','butyrivibrio_crossotus',2,0,0,0,0,0,86728,0,0,0,0,0,0,0) +,(6238,'Caenorhabditis briggsae','caenorhabditis_briggsae',2,0,0,0,0,0,34403,0,0,0,0,0,0,0) +,(6239,'Caenorhabditis elegans','caenorhabditis_elegans',2,0,0,0,0,0,1476,0,0,0,0,0,0,0) +,(3821,'Cajanus cajan','cajanus_cajan',2,734810,0,0,0,0,0,734810,0,0,0,0,0,734810) +,(9483,'Callithrix jacchus','callithrix_jacchus',2,17025118,0,0,0,0,10,975970,0,0,0,0,0,4590507) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(5476,'Candida albicans','candida_albicans',2,0,0,0,0,0,206514,0,0,0,0,0,0,0) +,(9615,'Canis lupus familiaris','canis_lupus_familiaris',2,5604336,102508,50182,170432,13903,16975,0,102508,0,0,0,0,0) +,(9923,'Capra aegagrus','capra_aegagrus',2,40689951,77,12472767,1097154,321788,0,0,77,0,0,0,0,0) +,(9925,'Capra hircus','capra_hircus',2,40689951,77,12472767,1097154,321788,56,0,77,0,0,0,0,0) +,(4072,'Capsicum annuum','capsicum_annuum',2,17357,0,0,1923,1,3576,5,0,0,0,0,0,6) +,(100886,'Catenibacterium mitsuokai','catenibacterium_mitsuokai',2,0,0,0,0,0,90734,0,0,0,0,0,0,0) +,(10141,'Cavia porcellus','cavia_porcellus',2,2,0,0,0,0,0,2,0,0,0,0,0,2) +,(9807,'Ceratotherium simum','ceratotherium_simum',2,0,0,0,0,0,11,0,0,0,0,0,0,0) +,(60711,'Chlorocebus sabaeus','chlorocebus_sabaeus',2,62811022,0,0,0,0,0,62303430,0,0,0,0,0,62781317) +,(3827,'Cicer arietinum','cicer_arietinum',2,327311,0,0,191755,0,0,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(7719,'Ciona intestinalis','ciona_intestinalis',2,2154561,0,0,1035951,0,0,0,0,0,0,0,0,0) +,(457421,'Clostridiales bacterium 1_7_47FAA','clostridiales_bacterium_1_7_47faa',2,0,0,0,0,0,55909,0,0,0,0,0,0,0) +,(333367,'Clostridium asparagiforme','clostridium_asparagiforme',2,0,0,0,0,0,81007,0,0,0,0,0,0,0) +,(208479,'Clostridium bolteae','clostridium_bolteae',2,0,0,0,0,0,171820,0,0,0,0,0,0,0) +,(1535,'Clostridium leptum','clostridium_leptum',2,0,0,0,0,0,84248,0,0,0,0,0,0,0) +,(29348,'Clostridium spiroforme','clostridium_spiroforme',2,0,0,0,0,0,57003,0,0,0,0,0,0,0) +,(411489,'Clostridium sp. L2-50','clostridium_sp_l2_50',2,0,0,0,0,0,138575,0,0,0,0,0,0,0) +,(411486,'Clostridium sp. M62/1','clostridium_sp_m62_1',2,0,0,0,0,0,72510,0,0,0,0,0,0,0) +,(411484,'Clostridium sp. SS2/1','clostridium_sp_ss2_1',2,0,0,0,0,0,154708,0,0,0,0,0,0,0) +,(7950,'Clupea harengus','clupea_harengus',2,0,0,0,43,0,5,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(74426,'Collinsella aerofaciens','collinsella_aerofaciens',2,0,0,0,0,0,250405,0,0,0,0,0,0,0) +,(147207,'Collinsella intestinalis','collinsella_intestinalis',2,0,0,0,0,0,28650,0,0,0,0,0,0,0) +,(147206,'Collinsella stercoris','collinsella_stercoris',2,0,0,0,0,0,15863,0,0,0,0,0,0,0) +,(27828,'Cooperia oncophora','cooperia_oncophora',2,0,0,0,0,0,426,0,0,0,0,0,0,0) +,(556270,'Coprobacillus sp. D7','coprobacillus_sp_d7',2,0,0,0,0,0,11975,0,0,0,0,0,0,0) +,(116085,'Coprococcus catus','coprococcus_catus',2,0,0,0,0,0,136694,0,0,0,0,0,0,0) +,(410072,'Coprococcus comes','coprococcus_comes',2,0,0,0,0,0,181703,0,0,0,0,0,0,0) +,(33043,'Coprococcus eutactus','coprococcus_eutactus',2,0,0,0,0,0,117168,0,0,0,0,0,0,0) +,(93934,'Coturnix japonica','coturnix_japonica',2,8665,0,0,81,0,7567,0,0,0,0,0,0,0) +,(7175,'Culex pipiens','culex_pipiens',2,0,0,0,0,0,1,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(7955,'Danio rerio','danio_rerio',2,17565652,26736,14816,133974,131,28883,0,26736,0,0,0,0,0) +,(79200,'Daucus carota subsp. sativus','daucus_carota_subsp_sativus',2,1378278,0,0,15029,0,0,0,0,0,0,0,0,0) +,(901,'Desulfovibrio piger','desulfovibrio_piger',2,0,0,0,0,0,46517,0,0,0,0,0,0,0) +,(218538,'Dialister invisus','dialister_invisus',2,0,0,0,0,0,110981,0,0,0,0,0,0,0) +,(39486,'Dorea formicigenerans','dorea_formicigenerans',2,0,0,0,0,0,58216,0,0,0,0,0,0,0) +,(7227,'Drosophila melanogaster','drosophila_melanogaster',2,5618489,41,41,1728,0,0,0,41,0,0,0,0,0) +,(84112,'Eggerthella lenta','eggerthella_lenta',2,0,0,0,0,0,27993,0,0,0,0,0,0,0) +,(51953,'Elaeis guineensis','elaeis_guineensis',2,52383,0,0,59977,0,0,0,0,0,0,0,0,0) +,(1351,'Enterococcus faecalis','enterococcus_faecalis',2,0,0,0,0,0,1311,0,0,0,0,0,0,0) +,(1352,'Enterococcus faecium','enterococcus_faecium',2,0,0,0,0,0,2777,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(9796,'Equus caballus','equus_caballus',2,22552742,62136,56460,12229,117,488,1061241,62136,0,0,0,0,11147394) +,(552396,'Erysipelotrichaceae bacterium 5_2_54FAA','erysipelotrichaceae_bacterium_5_2_54faa',2,0,0,0,0,0,49237,0,0,0,0,0,0,0) +,(39485,'Eubacterium eligens','eubacterium_eligens',2,0,0,0,0,0,132024,0,0,0,0,0,0,0) +,(39488,'Eubacterium hallii','eubacterium_hallii',2,0,0,0,0,0,104412,0,0,0,0,0,0,0) +,(39491,'Eubacterium rectale','eubacterium_rectale',2,0,0,0,0,0,223111,0,0,0,0,0,0,0) +,(39492,'Eubacterium siraeum','eubacterium_siraeum',2,0,0,0,0,0,207186,0,0,0,0,0,0,0) +,(39496,'Eubacterium ventriosum','eubacterium_ventriosum',2,0,0,0,0,0,113243,0,0,0,0,0,0,0) +,(39483,'Faecalitalea cylindroides','faecalitalea_cylindroides',2,0,0,0,0,0,31085,0,0,0,0,0,0,0) +,(9685,'Felis catus','felis_catus',2,3500633,30584,12854,64779,4063,3392,16,30584,0,0,0,0,16) +,(59894,'Ficedula albicollis','ficedula_albicollis',2,37728,0,0,682,0,119,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(46689,'Ficedula hypoleuca','ficedula_hypoleuca',2,0,0,0,0,0,230,0,0,0,0,0,0,0) +,(850,'Fusobacterium mortiferum','fusobacterium_mortiferum',2,0,0,0,0,0,25244,0,0,0,0,0,0,0) +,(9031,'Gallus gallus','gallus_gallus',2,23750269,43400,140478,320088,4992,26701,0,43400,0,0,0,0,0) +,(2702,'Gardnerella vaginalis','gardnerella_vaginalis',2,0,0,0,0,0,668,0,0,0,0,0,0,0) +,(3847,'Glycine max','glycine_max',2,16115243,418469,287204,1074945,12966,1451,0,418469,0,0,0,0,0) +,(9593,'Gorilla gorilla','gorilla_gorilla',2,4,0,0,0,0,1,0,0,0,0,0,0,0) +,(34274,'Gossypium herbaceum','gossypium_herbaceum',2,0,0,0,0,0,10947,0,0,0,0,0,0,0) +,(3635,'Gossypium hirsutum','gossypium_hirsutum',2,85757,0,0,14754,2,20652,0,0,0,0,0,0,0) +,(52644,'Haliaeetus leucocephalus','haliaeetus_leucocephalus',2,43596,0,0,0,0,0,43596,0,0,0,0,0,43596) +,(4232,'Helianthus annuus','helianthus_annuus',2,52,0,0,0,0,0,52,0,0,0,0,0,52) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(3981,'Hevea brasiliensis','hevea_brasiliensis',2,669,0,0,0,0,0,669,0,0,0,0,0,669) +,(1735,'Holdemanella biformis','holdemanella_biformis',2,0,0,0,0,0,109232,0,0,0,0,0,0,0) +,(61171,'Holdemania filiformis','holdemania_filiformis',2,0,0,0,0,0,128406,0,0,0,0,0,0,0) +,(154046,'Hungatella hathewayi','hungatella_hathewayi',2,0,0,0,0,0,71313,0,0,0,0,0,0,0) +,(216498,'Hydroides elegans','hydroides_elegans',2,0,0,0,0,0,8,0,0,0,0,0,0,0) +,(261299,'Intestinibacter bartlettii','intestinibacter_bartlettii',2,0,0,0,0,0,46123,0,0,0,0,0,0,0) +,(573,'Klebsiella pneumoniae','klebsiella_pneumoniae',2,0,0,0,0,0,42709,0,0,0,0,0,0,0) +,(84645,'Labeo rohita','labeo_rohita',2,2397236,0,0,0,0,0,2397236,0,0,0,0,0,2411259) +,(1598,'Lactobacillus reuteri','lactobacillus_reuteri',2,0,0,0,0,0,2172,0,0,0,0,0,0,0) +,(1623,'Lactobacillus ruminis','lactobacillus_ruminis',2,0,0,0,0,0,27388,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(1358,'Lactococcus lactis','lactococcus_lactis',2,0,0,0,0,0,9353,0,0,0,0,0,0,0) +,(334908,'Larimichthys polyactis','larimichthys_polyactis',2,6457,0,0,0,0,0,6457,0,0,0,0,0,6457) +,(72036,'Lepeophtheirus salmonis','lepeophtheirus_salmonis',2,12,0,0,0,0,0,12,0,0,0,0,0,12) +,(9541,'Macaca fascicularis','macaca_fascicularis',2,1651397,0,0,21730,0,395866,0,0,0,0,0,0,0) +,(9544,'Macaca mulatta','macaca_mulatta',2,52981764,68101,13619,361073,1605,542019,0,68101,0,0,0,0,0) +,(3750,'Malus domestica','malus_domestica',2,222929,0,0,113373,7,7914,0,0,0,0,0,0,0) +,(3880,'Medicago truncatula','medicago_truncatula',2,16,0,0,1,0,12,0,0,0,0,0,0,0) +,(158847,'Megamonas hypermegale','megamonas_hypermegale',2,0,0,0,0,0,39236,0,0,0,0,0,0,0) +,(9103,'Meleagris gallopavo','meleagris_gallopavo',2,5825,344,1,1142,3,1962,0,344,0,0,0,0,0) +,(2173,'Methanobrevibacter smithii','methanobrevibacter_smithii',2,0,0,0,0,0,47709,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(79684,'Microtus ochrogaster','microtus_ochrogaster',2,8166,115,0,3601,18,2646,0,115,0,0,0,0,0) +,(52226,'Mitsuokella multacida','mitsuokella_multacida',2,0,0,0,0,0,39465,0,0,0,0,0,0,0) +,(13616,'Monodelphis domestica','monodelphis_domestica',2,0,0,0,0,0,1086,0,0,0,0,0,0,0) +,(46259,'Morone chrysops','morone_chrysops',2,3597,0,0,0,0,0,3597,0,0,0,0,0,3675) +,(10090,'Mus musculus','mus_musculus',2,81225786,2485532,381152,105979,3935,125898,0,2485532,0,0,0,0,0) +,(10096,'Mus spretus','mus_spretus',2,0,0,0,0,0,4,0,0,0,0,0,0,0) +,(7425,'Nasonia vitripennis','nasonia_vitripennis',2,205691,0,0,0,0,0,205691,0,0,0,0,0,205799) +,(452646,'Neovison vison','neovison_vison',2,34816,0,0,0,0,0,34816,0,0,0,0,0,34816) +,(61853,'Nomascus leucogenys','nomascus_leucogenys',2,1114820,0,0,58397,0,0,0,0,0,0,0,0,0) +,(105023,'Nothobranchius furzeri','nothobranchius_furzeri',2,288,0,0,18,0,15,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(8018,'Oncorhynchus keta','oncorhynchus_keta',2,0,0,0,0,0,212,0,0,0,0,0,0,0) +,(8019,'Oncorhynchus kisutch','oncorhynchus_kisutch',2,0,0,0,0,0,75,0,0,0,0,0,0,0) +,(8022,'Oncorhynchus mykiss','oncorhynchus_mykiss',2,0,0,0,0,0,146384,0,0,0,0,0,0,0) +,(8023,'Oncorhynchus nerka','oncorhynchus_nerka',2,0,0,0,0,0,197,0,0,0,0,0,0,0) +,(74940,'Oncorhynchus tshawytscha','oncorhynchus_tshawytscha',2,0,0,0,0,0,935,0,0,0,0,0,0,0) +,(8128,'Oreochromis niloticus','oreochromis_niloticus',2,240,14,0,71,0,17,0,14,0,0,0,0,0) +,(9258,'Ornithorhynchus anatinus','ornithorhynchus_anatinus',2,0,0,0,0,0,11810,0,0,0,0,0,0,0) +,(9986,'Oryctolagus cuniculus','oryctolagus_cuniculus',2,81103,0,0,0,0,3,81068,0,0,0,0,0,83295) +,(4530,'Oryza sativa','oryza_sativa',2,12163632,661755,370849,92540,1514,192282,0,661755,0,0,0,0,0) +,(9940,'Ovis aries','ovis_aries',2,92288816,34458,37219,510235,1663,94367,0,34458,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(469796,'Ovis orientalis','ovis_orientalis',2,29257919,0,31936,126219,441,0,0,0,0,0,0,0,0) +,(847,'Oxalobacter formigenes','oxalobacter_formigenes',2,0,0,0,0,0,10043,0,0,0,0,0,0,0) +,(9598,'Pan troglodytes','pan_troglodytes',2,1424055,198703,36818,54763,1469,4238,0,198703,0,0,0,0,0) +,(46503,'Parabacteroides merdae','parabacteroides_merdae',2,0,0,0,0,0,168534,0,0,0,0,0,0,0) +,(563193,'Parabacteroides sp. D13','parabacteroides_sp_d13',2,0,0,0,0,0,196960,0,0,0,0,0,0,0) +,(9157,'Parus major','parus_major',2,6169,0,0,30,0,1645,0,0,0,0,0,0,0) +,(48849,'Passer domesticus','passer_domesticus',2,0,0,0,0,0,8491,0,0,0,0,0,0,0) +,(1255,'Pediococcus pentosaceus','pediococcus_pentosaceus',2,0,0,0,0,0,1149,0,0,0,0,0,0,0) +,(1261,'Peptostreptococcus anaerobius','peptostreptococcus_anaerobius',2,0,0,0,0,0,3662,0,0,0,0,0,0,0) +,(3885,'Phaseolus vulgaris','phaseolus_vulgaris',2,41606443,0,0,0,0,11989,41606443,0,0,0,0,0,43323448) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(42345,'Phoenix dactylifera','phoenix_dactylifera',2,0,0,0,0,0,983553,0,0,0,0,0,0,0) +,(3330,'Picea glauca','picea_glauca',2,0,0,0,0,0,229187,0,0,0,0,0,0,0) +,(71647,'Pinus pinaster','pinus_pinaster',2,0,0,0,0,0,5926,0,0,0,0,0,0,0) +,(5833,'Plasmodium falciparum','plasmodium_falciparum',2,12648,0,0,0,0,2504144,12648,0,0,0,0,0,12656) +,(5861,'Plasmodium yoelii','plasmodium_yoelii',2,0,0,0,0,0,206103,0,0,0,0,0,0,0) +,(9601,'Pongo abelii','pongo_abelii',2,9745325,0,24188,197914,7974,62266,0,0,0,0,0,0,0) +,(9600,'Pongo pygmaeus','pongo_pygmaeus',2,0,0,0,0,0,7854083,0,0,0,0,0,0,0) +,(3694,'Populus trichocarpa','populus_trichocarpa',2,8129782,1057686,99625,3170860,137577,0,0,1057686,0,0,0,0,0) +,(281920,'Porphyromonas uenonis','porphyromonas_uenonis',2,0,0,0,0,0,16133,0,0,0,0,0,0,0) +,(165179,'Prevotella copri','prevotella_copri',2,0,0,0,0,0,225404,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(386414,'Prevotella timonensis','prevotella_timonensis',2,0,0,0,0,0,16820,0,0,0,0,0,0,0) +,(6728,'Procambarus clarkii','procambarus_clarkii',2,0,0,0,0,0,44,0,0,0,0,0,0,0) +,(10116,'Rattus norvegicus','rattus_norvegicus',2,4864846,217417,89912,19034,3044,43794,0,217417,0,0,0,0,0) +,(166486,'Roseburia intestinalis','roseburia_intestinalis',2,0,0,0,0,0,151208,0,0,0,0,0,0,0) +,(360807,'Roseburia inulinivorans','roseburia_inulinivorans',2,0,0,0,0,0,230337,0,0,0,0,0,0,0) +,(40518,'Ruminococcus bromii','ruminococcus_bromii',2,0,0,0,0,0,167002,0,0,0,0,0,0,0) +,(1161942,'Ruminococcus champanellensis','ruminococcus_champanellensis',2,0,0,0,0,0,46005,0,0,0,0,0,0,0) +,(33038,'Ruminococcus gnavus','ruminococcus_gnavus',2,0,0,0,0,0,26851,0,0,0,0,0,0,0) +,(46228,'Ruminococcus lactaris','ruminococcus_lactaris',2,0,0,0,0,0,83380,0,0,0,0,0,0,0) +,(457412,'Ruminococcus sp. 5_1_39BFAA','ruminococcus_sp_5_1_39bfaa',2,0,0,0,0,0,214091,0,0,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(657323,'Ruminococcus sp. SR1/5','ruminococcus_sp_sr1_5',2,0,0,0,0,0,208300,0,0,0,0,0,0,0) +,(33039,'Ruminococcus torques','ruminococcus_torques',2,0,0,0,0,0,275154,0,0,0,0,0,0,0) +,(128810,'Saccharum hybrid cultivar','saccharum_hybrid_cultivar',2,0,0,0,0,0,59552,0,0,0,0,0,0,0) +,(28901,'Salmonella enterica','salmonella_enterica',2,0,0,0,0,0,250,0,0,0,0,0,0,0) +,(8030,'Salmo salar','salmo_salar',2,19688096,0,0,30229,2,4427,18684000,0,0,0,0,0,19184796) +,(6183,'Schistosoma mansoni','schistosoma_mansoni',2,0,0,0,0,0,8,0,0,0,0,0,0,0) +,(4896,'Schizosaccharomyces pombe','schizosaccharomyces_pombe',2,254389,0,0,0,0,0,254389,0,0,0,0,0,264186) +,(41447,'Seriola dumerili','seriola_dumerili',2,8425456,0,0,0,0,0,8425456,0,0,0,0,0,9094931) +,(4081,'Solanum lycopersicum','solanum_lycopersicum',2,7768,0,0,21,0,85,0,0,0,0,0,0,0) +,(4558,'Sorghum bicolor','sorghum_bicolor',2,7088672,20622,1328,5431,19,1018,0,20622,0,0,0,0,0) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(28037,'Streptococcus mitis','streptococcus_mitis',2,0,0,0,0,0,39112,0,0,0,0,0,0,0) +,(1318,'Streptococcus parasanguinis','streptococcus_parasanguinis',2,0,0,0,0,0,84497,0,0,0,0,0,0,0) +,(1308,'Streptococcus thermophilus','streptococcus_thermophilus',2,0,0,0,0,0,59551,0,0,0,0,0,0,0) +,(9823,'Sus scrofa','sus_scrofa',2,65680333,225979,126611,1043834,3731,39087,0,225979,0,0,0,0,0) +,(59729,'Taeniopygia guttata','taeniopygia_guttata',2,1658572,4710,176,85844,497,968,0,4710,0,0,0,0,0) +,(99883,'Tetraodon nigroviridis','tetraodon_nigroviridis',2,0,0,0,0,0,903588,0,0,0,0,0,0,0) +,(8237,'Thunnus thynnus','thunnus_thynnus',2,0,0,0,0,0,5,0,0,0,0,0,0,0) +,(7070,'Tribolium castaneum','tribolium_castaneum',2,0,0,0,103,0,138,0,0,0,0,0,0,0) +,(4565,'Triticum aestivum','triticum_aestivum',2,9673090,0,0,0,0,0,9673090,0,0,0,0,0,13882990) +,(85692,'Triticum dicoccoides','triticum_dicoccoides',2,1755051,0,0,0,0,0,1755051,0,0,0,0,0,1755051) +; +INSERT INTO release_rs_statistics_per_species (taxonomy_id,scientific_name,release_folder,release_version,current_rs,multi_mapped_rs,merged_rs,deprecated_rs,merged_deprecated_rs,unmapped_rs,new_current_rs,new_multi_mapped_rs,new_merged_rs,new_deprecated_rs,new_merged_deprecated_rs,new_unmapped_rs,new_ss_clustered) VALUES +(154288,'Turicibacter sanguinis','turicibacter_sanguinis',2,0,0,0,0,0,6373,0,0,0,0,0,0,0) +,(29361,'Tyzzerella nexilis','tyzzerella_nexilis',2,0,0,0,0,0,116888,0,0,0,0,0,0,0) +,(29073,'Ursus maritimus','ursus_maritimus',2,0,0,0,0,0,175,0,0,0,0,0,0,0) +,(29466,'Veillonella parvula','veillonella_parvula',2,0,0,0,0,0,90777,0,0,0,0,0,0,0) +,(30538,'Vicugna pacos','vicugna_pacos',2,400,0,0,0,0,0,400,0,0,0,0,0,400) +,(29760,'Vitis vinifera','vitis_vinifera',2,425136,17601,730,2313,162,2594,0,17601,0,0,0,0,0) +,(4577,'Zea mays','zea_mays',2,57647260,0,6,960597,456,337986,0,0,0,0,0,0,0) +; \ No newline at end of file From d618bc9147a63bf7d8333f2e770c279d9fde9b16 Mon Sep 17 00:00:00 2001 From: Andres Silva Date: Tue, 24 Nov 2020 23:33:19 +0000 Subject: [PATCH 2/5] swagger support --- .../release/{ => configuration}/SwaggerConfiguration.java | 6 +++--- .../ebi/eva/release/controllers/ReleaseInfoController.java | 3 ++- .../ebi/eva/release/controllers/ReleaseStatsController.java | 4 ++++ 3 files changed, 9 insertions(+), 4 deletions(-) rename eva-release/src/main/java/uk/ac/ebi/eva/release/{ => configuration}/SwaggerConfiguration.java (92%) diff --git a/eva-release/src/main/java/uk/ac/ebi/eva/release/SwaggerConfiguration.java b/eva-release/src/main/java/uk/ac/ebi/eva/release/configuration/SwaggerConfiguration.java similarity index 92% rename from eva-release/src/main/java/uk/ac/ebi/eva/release/SwaggerConfiguration.java rename to eva-release/src/main/java/uk/ac/ebi/eva/release/configuration/SwaggerConfiguration.java index cf81422b..fdcafe4c 100644 --- a/eva-release/src/main/java/uk/ac/ebi/eva/release/SwaggerConfiguration.java +++ b/eva-release/src/main/java/uk/ac/ebi/eva/release/configuration/SwaggerConfiguration.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package uk.ac.ebi.eva.release; +package uk.ac.ebi.eva.release.configuration; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; @@ -47,8 +47,8 @@ private ApiInfo getApiInfo() { .licenseUrl("http://www.apache.org/licenses/LICENSE-2.0") .title("EVA RS Release API") .description( - "API to retrieve information about clustered variant identifiers (usually called RefSNP or RS)" + - "released by the EVA") + "API to retrieve information about clustered variant identifiers (usually called RefSNP or " + + "RS) released by the EVA") .version("0.1") .build(); } diff --git a/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoController.java b/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoController.java index 3b4633fa..12026aaa 100644 --- a/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoController.java +++ b/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseInfoController.java @@ -16,6 +16,7 @@ package uk.ac.ebi.eva.release.controllers; import io.swagger.annotations.Api; +import io.swagger.annotations.ApiParam; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestParam; @@ -24,7 +25,6 @@ import uk.ac.ebi.eva.release.models.ReleaseInfo; import uk.ac.ebi.eva.release.repositories.ReleaseInfoRepository; -import javax.websocket.server.PathParam; import java.util.Collections; @RestController @@ -40,6 +40,7 @@ public ReleaseInfoController(ReleaseInfoRepository releaseInfoRepository) { @GetMapping public Iterable getReleaseInfo( + @ApiParam(value = "Version of the RS Release, e.g.: 2") @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion) { if (releaseVersion != null) { return Collections.singleton(releaseInfoRepository.findById(releaseVersion).get()); diff --git a/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsController.java b/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsController.java index c516f4b1..5b925a40 100644 --- a/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsController.java +++ b/eva-release/src/main/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsController.java @@ -16,6 +16,7 @@ package uk.ac.ebi.eva.release.controllers; import io.swagger.annotations.Api; +import io.swagger.annotations.ApiParam; import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestParam; @@ -37,13 +38,16 @@ public ReleaseStatsController(ReleaseStatsService releaseStatsService) { @GetMapping("/per-species") public Iterable getReleaseStatsPerSpecies( + @ApiParam(value = "Version of the RS Release, e.g.: 2") @RequestParam(name = "releaseVersion", required = false) Integer releaseVersion, + @ApiParam(value = "Flag to indicate if unmapped variants should be excluded from statistics") @RequestParam(name = "excludeUnmappedOnly", required = false) boolean excludeUnmappedOnly) { return releaseStatsService.getReleaseStatsPerSpecies(releaseVersion, excludeUnmappedOnly); } @GetMapping("/per-species/new") public Iterable getSpeciesWithNewRsIds( + @ApiParam(value = "Version of the RS Release, e.g.: 2") @RequestParam(name = "releaseVersion") Integer releaseVersion) { return releaseStatsService.getSpeciesWithNewRsIds(releaseVersion); } From 40e0951336adf20b286fa6108806cd11e3d6ec6b Mon Sep 17 00:00:00 2001 From: Andres Silva Date: Wed, 25 Nov 2020 01:39:55 +0000 Subject: [PATCH 3/5] change long jpa methods for sql native queries --- .../ReleaseStatsPerSpeciesRepository.java | 31 +++++++++++-------- .../release/services/ReleaseStatsService.java | 23 ++------------ .../ReleaseStatsControllerTest.java | 20 ++++++++---- 3 files changed, 35 insertions(+), 39 deletions(-) diff --git a/eva-release/src/main/java/uk/ac/ebi/eva/release/repositories/ReleaseStatsPerSpeciesRepository.java b/eva-release/src/main/java/uk/ac/ebi/eva/release/repositories/ReleaseStatsPerSpeciesRepository.java index 17e679af..03dee0be 100644 --- a/eva-release/src/main/java/uk/ac/ebi/eva/release/repositories/ReleaseStatsPerSpeciesRepository.java +++ b/eva-release/src/main/java/uk/ac/ebi/eva/release/repositories/ReleaseStatsPerSpeciesRepository.java @@ -15,6 +15,7 @@ */ package uk.ac.ebi.eva.release.repositories; +import org.springframework.data.jpa.repository.Query; import org.springframework.data.repository.CrudRepository; import org.springframework.stereotype.Repository; @@ -27,17 +28,21 @@ public interface ReleaseStatsPerSpeciesRepository extends CrudRepository findAllByReleaseVersion(int releaseVersion); - //All release data excluding rows with only unmapped data - Iterable findByCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan( - long currentRs, long multiMappedRs, long mergedRs, long deprecatedRs, long mergedDeprecatedRs, - long unmappedRs); - - //Data by release version excluding rows with only unmapped data - Iterable findByReleaseVersionAndCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan( - int releaseVersion, long currentRs, long multiMappedRs, long mergedRs, long deprecatedRs, - long mergedDeprecatedRs, long unmappedRs); - - Iterable findByNewCurrentRsGreaterThan(long currentRs); - - Iterable findByReleaseVersionAndNewCurrentRsGreaterThan(int releaseVersion, long currentRs); + //All released species stats excluding the unmapped only + @Query(value = "select * from release_rs_statistics_per_species " + + "where not (current_rs = 0 and multi_mapped_rs = 0 and merged_rs = 0 and deprecated_rs = 0 " + + "and merged_deprecated_rs = 0 and unmapped_rs > 0)", nativeQuery=true) + Iterable getAllExcludingUnmappedOnly(); + + //Species stats by release version excluding the unmapped only + @Query(value = "select * from release_rs_statistics_per_species " + + "where release_version = ?1 and not (current_rs = 0 and multi_mapped_rs = 0 and merged_rs = 0 " + + "and deprecated_rs = 0 and merged_deprecated_rs = 0 and unmapped_rs > 0)", nativeQuery=true) + Iterable getAllByVersionExcludingUnmappedOnly(int releaseVersion); + + //Species that introduced new variants in specified release + @Query(value = "select * from release_rs_statistics_per_species where release_version = ?1 " + + "and (new_current_rs > 0 or new_merged_rs > 0 or new_deprecated_rs > 0 or new_merged_deprecated_rs > 0 " + + "or new_unmapped_rs > 0)", nativeQuery=true) + Iterable getSpeciesWithVariantsInRelease(int releaseVersion); } diff --git a/eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsService.java b/eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsService.java index 728a9740..5d2007a7 100644 --- a/eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsService.java +++ b/eva-release/src/main/java/uk/ac/ebi/eva/release/services/ReleaseStatsService.java @@ -44,13 +44,13 @@ public Iterable getReleaseStatsPerSpecies(Integer rel Iterable releaseData; if (releaseVersion != null) { if (excludeUnmappedOnly) { - releaseData = getReleaseDataByVersionExcludingUnmappedOnly(releaseVersion); + releaseData = releaseStatsPerSpeciesRepository.getAllByVersionExcludingUnmappedOnly(releaseVersion); } else { releaseData = releaseStatsPerSpeciesRepository.findAllByReleaseVersion(releaseVersion); } } else { if (excludeUnmappedOnly) { - releaseData = getReleaseDataExcludingUnmappedOnly(); + releaseData = releaseStatsPerSpeciesRepository.getAllExcludingUnmappedOnly(); } else { releaseData = releaseStatsPerSpeciesRepository.findAll(); } @@ -58,18 +58,6 @@ public Iterable getReleaseStatsPerSpecies(Integer rel return toDto(releaseData); } - private Iterable getReleaseDataByVersionExcludingUnmappedOnly(Integer releaseVersion) { - return releaseStatsPerSpeciesRepository - .findByReleaseVersionAndCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan( - releaseVersion, 0, 0, 0, 0, 0, 0); - } - - private Iterable getReleaseDataExcludingUnmappedOnly() { - return releaseStatsPerSpeciesRepository - .findByCurrentRsNotAndMultiMappedRsNotAndMergedRsNotAndDeprecatedRsNotAndMergedDeprecatedRsNotAndUnmappedRsGreaterThan( - 0, 0, 0, 0, 0, 0); - } - private Iterable toDto(Iterable releaseStatsPerSpecies) { List releaseStatsPerSpeciesDtos = new ArrayList(); for (ReleaseStatsPerSpecies species : releaseStatsPerSpecies) { @@ -105,11 +93,6 @@ private ReleaseStatsPerSpeciesDto toDto(ReleaseStatsPerSpecies releaseStatsPerSp } public Iterable getSpeciesWithNewRsIds(Integer releaseVersion) { - if (releaseVersion != null) { - return toDto(releaseStatsPerSpeciesRepository - .findByReleaseVersionAndNewCurrentRsGreaterThan(releaseVersion, 0L)); - } else { - return toDto(releaseStatsPerSpeciesRepository.findByNewCurrentRsGreaterThan(0L)); - } + return toDto(releaseStatsPerSpeciesRepository.getSpeciesWithVariantsInRelease(releaseVersion)); } } diff --git a/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java index e219b2cc..7f5127dc 100644 --- a/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java +++ b/eva-release/src/test/java/uk/ac/ebi/eva/release/controllers/ReleaseStatsControllerTest.java @@ -50,15 +50,23 @@ public void getStatsByReleaseVersion() { @Test public void getStatsByReleaseVersionNoUnmapped() { - int speciesInRelease2ExcludingUnmapped = 22; - Iterable allRecords = releaseStatsController.getReleaseStatsPerSpecies(2, true); - assertEquals(speciesInRelease2ExcludingUnmapped, IterableUtil.sizeOf(allRecords)); + int speciesInRelease1ExcludingUnmapped = 58; + Iterable release1 = releaseStatsController.getReleaseStatsPerSpecies(1, true); + assertEquals(speciesInRelease1ExcludingUnmapped, IterableUtil.sizeOf(release1)); + + int speciesInRelease2ExcludingUnmapped = 79; + Iterable release2 = releaseStatsController.getReleaseStatsPerSpecies(2, true); + assertEquals(speciesInRelease2ExcludingUnmapped, IterableUtil.sizeOf(release2)); } @Test public void getStatsForNewVariantsOnlyInSpecificRelease() { - int numberOfSpeciesWithNewVariants = 29; - Iterable allRecords = releaseStatsController.getSpeciesWithNewRsIds(2); - assertEquals(numberOfSpeciesWithNewVariants, IterableUtil.sizeOf(allRecords)); + int numberOfSpeciesWithNewVariantsRelease1 = 199; + Iterable Release1 = releaseStatsController.getSpeciesWithNewRsIds(1); + assertEquals(numberOfSpeciesWithNewVariantsRelease1, IterableUtil.sizeOf(Release1)); + + int numberOfSpeciesWithNewVariantsRelease2 = 29; + Iterable Release2 = releaseStatsController.getSpeciesWithNewRsIds(2); + assertEquals(numberOfSpeciesWithNewVariantsRelease2, IterableUtil.sizeOf(Release2)); } } \ No newline at end of file From dff105bdd0983307ba3f4497d232a3f4c384a622 Mon Sep 17 00:00:00 2001 From: Andres Silva Date: Wed, 25 Nov 2020 01:45:02 +0000 Subject: [PATCH 4/5] update gitlab ci/cd to include eva-release module --- .gitlab-ci.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 33f6a956..81df2f0d 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -5,6 +5,7 @@ stages: variables: WS_ARTIFACT_PATH: eva-server/target/eva-$ENVIRONMENT_NAME.war + WS_RS_RELEASE_ARTIFACT_PATH: eva-release/target/eva-$ENVIRONMENT_NAME.war MAVEN_SETTINGS: maven-settings.xml URL_MAVEN_SETTINGS: https://api.github.com/repos/EBIvariation/configuration/contents/eva-maven-settings.xml MEDIA_TYPE: application/vnd.github.raw @@ -16,7 +17,7 @@ test: - mongo:4.0.18 script: # Gitlab exposes services under their own hostnames. So test host should be "mongo" instead of "localhost". - - mvn clean test --projects 'eva-lib,eva-server' -Deva.mongo.host.test=mongo + - mvn clean test --projects 'eva-lib,eva-server,eva-release' -Deva.mongo.host.test=mongo only: - master - tags @@ -34,11 +35,13 @@ test: script: - mvn package --projects 'eva-lib,eva-server' --settings $MAVEN_SETTINGS -P $MAVEN_PROFILE -DskipTests -Dtimestamp=$DATETIME - cp eva-server/target/eva-*.war $WS_ARTIFACT_PATH + - cp eva-release/target/eva-*.war $WS_RS_RELEASE_ARTIFACT_PATH after_script: - rm $MAVEN_SETTINGS artifacts: paths: - $WS_ARTIFACT_PATH + - $WS_RS_RELEASE_ARTIFACT_PATH package-internal: extends: .package @@ -74,6 +77,7 @@ package-production: - DATETIME=$(date +%Y-%m-%dT%H-%M-%S) - apk add --update curl - curl -u $TOMCAT_USER:$TOMCAT_PASSWORD -T "$WS_ARTIFACT_PATH" "http://$TOMCAT_HOST/manager/text/deploy?update=true&path=/eva&version=$DATETIME" | grep "OK - Deployed application" + - curl -u $TOMCAT_USER:$TOMCAT_PASSWORD -T "$WS_RS_RELEASE_ARTIFACT_PATH" "http://$TOMCAT_HOST/manager/text/deploy?update=true&path=/eva/webservices/release&version=$DATETIME" | grep "OK - Deployed application" deploy-tomcat-internal: extends: .deploy-tomcat From bf2a4a1a22958de9f3941b4f3d7ca9b021b76ec8 Mon Sep 17 00:00:00 2001 From: Andres Silva Date: Wed, 25 Nov 2020 10:00:22 +0000 Subject: [PATCH 5/5] use complete name in eva-release artifacts --- .gitlab-ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 81df2f0d..269fea83 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -5,7 +5,7 @@ stages: variables: WS_ARTIFACT_PATH: eva-server/target/eva-$ENVIRONMENT_NAME.war - WS_RS_RELEASE_ARTIFACT_PATH: eva-release/target/eva-$ENVIRONMENT_NAME.war + WS_RS_RELEASE_ARTIFACT_PATH: eva-release/target/eva-release-$ENVIRONMENT_NAME.war MAVEN_SETTINGS: maven-settings.xml URL_MAVEN_SETTINGS: https://api.github.com/repos/EBIvariation/configuration/contents/eva-maven-settings.xml MEDIA_TYPE: application/vnd.github.raw @@ -35,7 +35,7 @@ test: script: - mvn package --projects 'eva-lib,eva-server' --settings $MAVEN_SETTINGS -P $MAVEN_PROFILE -DskipTests -Dtimestamp=$DATETIME - cp eva-server/target/eva-*.war $WS_ARTIFACT_PATH - - cp eva-release/target/eva-*.war $WS_RS_RELEASE_ARTIFACT_PATH + - cp eva-release/target/eva-release-*.war $WS_RS_RELEASE_ARTIFACT_PATH after_script: - rm $MAVEN_SETTINGS artifacts: