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Merge pull request #359 from VEuPathDB/extended-meta
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Extend dataset meta.
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@Foxcapades
Foxcapades authored Feb 7, 2025
2 parents a5d1225 + 223db81 commit 5f2b5c0
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Showing 165 changed files with 3,229 additions and 1,238 deletions.
149 changes: 149 additions & 0 deletions docker-compose.dev.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@ networks:
external: false
rabbitmq:
external: false
traefik:
external: false

name: "vdi"

Expand Down Expand Up @@ -96,3 +98,150 @@ services:
- rabbitmq
ports:
- "8080:${VDI_SERVICE_HTTP_PORT:-80}"

plugin-example:
image: veupathdb/vdi-plugin-example:${VDI_PLUGIN_EXAMPLE_TAG:-latest}
networks:
internal:
aliases:
- example
monitoring-ext: {}
labels:
- "prometheus.scrape_enabled=true"
- "com.centurylinklabs.watchtower.enable=${PLUGIN_EXAMPLE_WATCHTOWER:-false}"
volumes:
- type: bind
source: ${DATASET_DIRECTORY_SOURCE_PATH:?}
target: ${DATASET_DIRECTORY_TARGET_PATH:?}
environment:
LDAP_SERVER: ${LDAP_SERVER:?}
ORACLE_BASE_DN: ${ORACLE_BASE_DN:?}
CUSTOM_PATH: ${PLUGIN_HANDLER_NOOP_CUSTOM_PATH}
SITE_BUILD: ${SITE_BUILD:?}
DATASET_INSTALL_ROOT: ${DATASET_DIRECTORY_TARGET_PATH:?}

IMPORT_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_IMPORT_SCRIPT_MAX_DURATION}
INSTALL_DATA_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_INSTALL_DATA_SCRIPT_MAX_DURATION}
INSTALL_META_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_INSTALL_META_SCRIPT_MAX_DURATION}
UNINSTALL_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_UNINSTALL_SCRIPT_MAX_DURATION}
CHECK_COMPAT_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_CHECK_COMPAT_SCRIPT_MAX_DURATION}

DB_CONNECTION_ENABLED_AMOEBA: ${DB_CONNECTION_ENABLED_AMOEBA}
DB_CONNECTION_NAME_AMOEBA: ${DB_CONNECTION_NAME_AMOEBA:?}
DB_CONNECTION_LDAP_AMOEBA: ${DB_CONNECTION_LDAP_AMOEBA:?}
DB_CONNECTION_PASS_AMOEBA: ${DB_CONNECTION_PASS_AMOEBA:?}
DB_CONNECTION_DATA_SCHEMA_AMOEBA: ${DB_CONNECTION_DATA_SCHEMA_AMOEBA:?}
DB_CONNECTION_CONTROL_SCHEMA_AMOEBA: ${DB_CONNECTION_CONTROL_SCHEMA_AMOEBA:?}
DB_CONNECTION_POOL_SIZE_AMOEBA: ${DB_CONNECTION_POOL_SIZE_AMOEBA}

DB_CONNECTION_ENABLED_CRYPTO: ${DB_CONNECTION_ENABLED_CRYPTO}
DB_CONNECTION_NAME_CRYPTO: ${DB_CONNECTION_NAME_CRYPTO:?}
DB_CONNECTION_LDAP_CRYPTO: ${DB_CONNECTION_LDAP_CRYPTO:?}
DB_CONNECTION_PASS_CRYPTO: ${DB_CONNECTION_PASS_CRYPTO:?}
DB_CONNECTION_DATA_SCHEMA_CRYPTO: ${DB_CONNECTION_DATA_SCHEMA_CRYPTO:?}
DB_CONNECTION_CONTROL_SCHEMA_CRYPTO: ${DB_CONNECTION_CONTROL_SCHEMA_CRYPTO:?}
DB_CONNECTION_POOL_SIZE_CRYPTO: ${DB_CONNECTION_POOL_SIZE_CRYPTO}

DB_CONNECTION_ENABLED_FUNGI: ${DB_CONNECTION_ENABLED_FUNGI}
DB_CONNECTION_NAME_FUNGI: ${DB_CONNECTION_NAME_FUNGI:?}
DB_CONNECTION_LDAP_FUNGI: ${DB_CONNECTION_LDAP_FUNGI:?}
DB_CONNECTION_PASS_FUNGI: ${DB_CONNECTION_PASS_FUNGI:?}
DB_CONNECTION_DATA_SCHEMA_FUNGI: ${DB_CONNECTION_DATA_SCHEMA_FUNGI:?}
DB_CONNECTION_CONTROL_SCHEMA_FUNGI: ${DB_CONNECTION_CONTROL_SCHEMA_FUNGI:?}
DB_CONNECTION_POOL_SIZE_FUNGI: ${DB_CONNECTION_POOL_SIZE_FUNGI}

DB_CONNECTION_ENABLED_GIARDIA: ${DB_CONNECTION_ENABLED_GIARDIA}
DB_CONNECTION_NAME_GIARDIA: ${DB_CONNECTION_NAME_GIARDIA:?}
DB_CONNECTION_LDAP_GIARDIA: ${DB_CONNECTION_LDAP_GIARDIA:?}
DB_CONNECTION_PASS_GIARDIA: ${DB_CONNECTION_PASS_GIARDIA:?}
DB_CONNECTION_DATA_SCHEMA_GIARDIA: ${DB_CONNECTION_DATA_SCHEMA_GIARDIA:?}
DB_CONNECTION_CONTROL_SCHEMA_GIARDIA: ${DB_CONNECTION_CONTROL_SCHEMA_GIARDIA:?}
DB_CONNECTION_POOL_SIZE_GIARDIA: ${DB_CONNECTION_POOL_SIZE_GIARDIA}

DB_CONNECTION_ENABLED_HOST: ${DB_CONNECTION_ENABLED_HOST}
DB_CONNECTION_NAME_HOST: ${DB_CONNECTION_NAME_HOST:?}
DB_CONNECTION_LDAP_HOST: ${DB_CONNECTION_LDAP_HOST:?}
DB_CONNECTION_PASS_HOST: ${DB_CONNECTION_PASS_HOST:?}
DB_CONNECTION_DATA_SCHEMA_HOST: ${DB_CONNECTION_DATA_SCHEMA_HOST:?}
DB_CONNECTION_CONTROL_SCHEMA_HOST: ${DB_CONNECTION_CONTROL_SCHEMA_HOST:?}
DB_CONNECTION_POOL_SIZE_HOST: ${DB_CONNECTION_POOL_SIZE_HOST}

DB_CONNECTION_ENABLED_MICROSPORIDIA: ${DB_CONNECTION_ENABLED_MICROSPORIDIA}
DB_CONNECTION_NAME_MICROSPORIDIA: ${DB_CONNECTION_NAME_MICROSPORIDIA:?}
DB_CONNECTION_LDAP_MICROSPORIDIA: ${DB_CONNECTION_LDAP_MICROSPORIDIA:?}
DB_CONNECTION_PASS_MICROSPORIDIA: ${DB_CONNECTION_PASS_MICROSPORIDIA:?}
DB_CONNECTION_DATA_SCHEMA_MICROSPORIDIA: ${DB_CONNECTION_DATA_SCHEMA_MICROSPORIDIA:?}
DB_CONNECTION_CONTROL_SCHEMA_MICROSPORIDIA: ${DB_CONNECTION_CONTROL_SCHEMA_MICROSPORIDIA:?}
DB_CONNECTION_POOL_SIZE_MICROSPORIDIA: ${DB_CONNECTION_POOL_SIZE_MICROSPORIDIA}

DB_CONNECTION_ENABLED_PIROPLASMA: ${DB_CONNECTION_ENABLED_PIROPLASMA}
DB_CONNECTION_NAME_PIROPLASMA: ${DB_CONNECTION_NAME_PIROPLASMA:?}
DB_CONNECTION_LDAP_PIROPLASMA: ${DB_CONNECTION_LDAP_PIROPLASMA:?}
DB_CONNECTION_PASS_PIROPLASMA: ${DB_CONNECTION_PASS_PIROPLASMA:?}
DB_CONNECTION_DATA_SCHEMA_PIROPLASMA: ${DB_CONNECTION_DATA_SCHEMA_PIROPLASMA:?}
DB_CONNECTION_CONTROL_SCHEMA_PIROPLASMA: ${DB_CONNECTION_CONTROL_SCHEMA_PIROPLASMA:?}
DB_CONNECTION_POOL_SIZE_PIROPLASMA: ${DB_CONNECTION_POOL_SIZE_PIROPLASMA}

DB_CONNECTION_ENABLED_PLASMO: ${DB_CONNECTION_ENABLED_PLASMO}
DB_CONNECTION_NAME_PLASMO: ${DB_CONNECTION_NAME_PLASMO:?}
DB_CONNECTION_LDAP_PLASMO: ${DB_CONNECTION_LDAP_PLASMO:?}
DB_CONNECTION_PASS_PLASMO: ${DB_CONNECTION_PASS_PLASMO:?}
DB_CONNECTION_DATA_SCHEMA_PLASMO: ${DB_CONNECTION_DATA_SCHEMA_PLASMO:?}
DB_CONNECTION_CONTROL_SCHEMA_PLASMO: ${DB_CONNECTION_CONTROL_SCHEMA_PLASMO:?}
DB_CONNECTION_POOL_SIZE_PLASMO: ${DB_CONNECTION_POOL_SIZE_PLASMO}

DB_CONNECTION_ENABLED_TOXO: ${DB_CONNECTION_ENABLED_TOXO}
DB_CONNECTION_NAME_TOXO: ${DB_CONNECTION_NAME_TOXO:?}
DB_CONNECTION_LDAP_TOXO: ${DB_CONNECTION_LDAP_TOXO:?}
DB_CONNECTION_PASS_TOXO: ${DB_CONNECTION_PASS_TOXO:?}
DB_CONNECTION_DATA_SCHEMA_TOXO: ${DB_CONNECTION_DATA_SCHEMA_TOXO:?}
DB_CONNECTION_CONTROL_SCHEMA_TOXO: ${DB_CONNECTION_CONTROL_SCHEMA_TOXO:?}
DB_CONNECTION_POOL_SIZE_TOXO: ${DB_CONNECTION_POOL_SIZE_TOXO}

DB_CONNECTION_ENABLED_TRICH: ${DB_CONNECTION_ENABLED_TRICH}
DB_CONNECTION_NAME_TRICH: ${DB_CONNECTION_NAME_TRICH:?}
DB_CONNECTION_LDAP_TRICH: ${DB_CONNECTION_LDAP_TRICH:?}
DB_CONNECTION_PASS_TRICH: ${DB_CONNECTION_PASS_TRICH:?}
DB_CONNECTION_DATA_SCHEMA_TRICH: ${DB_CONNECTION_DATA_SCHEMA_TRICH:?}
DB_CONNECTION_CONTROL_SCHEMA_TRICH: ${DB_CONNECTION_CONTROL_SCHEMA_TRICH:?}
DB_CONNECTION_POOL_SIZE_TRICH: ${DB_CONNECTION_POOL_SIZE_TRICH}

DB_CONNECTION_ENABLED_TRITRYP: ${DB_CONNECTION_ENABLED_TRITRYP}
DB_CONNECTION_NAME_TRITRYP: ${DB_CONNECTION_NAME_TRITRYP:?}
DB_CONNECTION_LDAP_TRITRYP: ${DB_CONNECTION_LDAP_TRITRYP:?}
DB_CONNECTION_PASS_TRITRYP: ${DB_CONNECTION_PASS_TRITRYP:?}
DB_CONNECTION_DATA_SCHEMA_TRITRYP: ${DB_CONNECTION_DATA_SCHEMA_TRITRYP:?}
DB_CONNECTION_CONTROL_SCHEMA_TRITRYP: ${DB_CONNECTION_CONTROL_SCHEMA_TRITRYP:?}
DB_CONNECTION_POOL_SIZE_TRITRYP: ${DB_CONNECTION_POOL_SIZE_TRITRYP}

DB_CONNECTION_ENABLED_VECTOR: ${DB_CONNECTION_ENABLED_VECTOR}
DB_CONNECTION_NAME_VECTOR: ${DB_CONNECTION_NAME_VECTOR:?}
DB_CONNECTION_LDAP_VECTOR: ${DB_CONNECTION_LDAP_VECTOR:?}
DB_CONNECTION_PASS_VECTOR: ${DB_CONNECTION_PASS_VECTOR:?}
DB_CONNECTION_DATA_SCHEMA_VECTOR: ${DB_CONNECTION_DATA_SCHEMA_VECTOR:?}
DB_CONNECTION_CONTROL_SCHEMA_VECTOR: ${DB_CONNECTION_CONTROL_SCHEMA_VECTOR:?}
DB_CONNECTION_POOL_SIZE_VECTOR: ${DB_CONNECTION_POOL_SIZE_VECTOR}

DB_CONNECTION_ENABLED_ORTHO: ${DB_CONNECTION_ENABLED_ORTHO}
DB_CONNECTION_NAME_ORTHO: ${DB_CONNECTION_NAME_ORTHO:?}
DB_CONNECTION_LDAP_ORTHO: ${DB_CONNECTION_LDAP_ORTHO:?}
DB_CONNECTION_PASS_ORTHO: ${DB_CONNECTION_PASS_ORTHO:?}
DB_CONNECTION_DATA_SCHEMA_ORTHO: ${DB_CONNECTION_DATA_SCHEMA_ORTHO:?}
DB_CONNECTION_CONTROL_SCHEMA_ORTHO: ${DB_CONNECTION_CONTROL_SCHEMA_ORTHO:?}
DB_CONNECTION_POOL_SIZE_ORTHO: ${DB_CONNECTION_POOL_SIZE_ORTHO}

DB_CONNECTION_ENABLED_CLINEPI: ${DB_CONNECTION_ENABLED_CLINEPI}
DB_CONNECTION_NAME_CLINEPI: ${DB_CONNECTION_NAME_CLINEPI:?}
DB_CONNECTION_LDAP_CLINEPI: ${DB_CONNECTION_LDAP_CLINEPI:?}
DB_CONNECTION_PASS_CLINEPI: ${DB_CONNECTION_PASS_CLINEPI:?}
DB_CONNECTION_DATA_SCHEMA_CLINEPI: ${DB_CONNECTION_DATA_SCHEMA_CLINEPI:?}
DB_CONNECTION_CONTROL_SCHEMA_CLINEPI: ${DB_CONNECTION_CONTROL_SCHEMA_CLINEPI:?}
DB_CONNECTION_POOL_SIZE_CLINEPI: ${DB_CONNECTION_POOL_SIZE_CLINEPI}

DB_CONNECTION_ENABLED_MICROBIOME: ${DB_CONNECTION_ENABLED_MICROBIOME}
DB_CONNECTION_NAME_MICROBIOME: ${DB_CONNECTION_NAME_MICROBIOME:?}
DB_CONNECTION_LDAP_MICROBIOME: ${DB_CONNECTION_LDAP_MICROBIOME:?}
DB_CONNECTION_PASS_MICROBIOME: ${DB_CONNECTION_PASS_MICROBIOME:?}
DB_CONNECTION_DATA_SCHEMA_MICROBIOME: ${DB_CONNECTION_DATA_SCHEMA_MICROBIOME:?}
DB_CONNECTION_CONTROL_SCHEMA_MICROBIOME: ${DB_CONNECTION_CONTROL_SCHEMA_MICROBIOME:?}
DB_CONNECTION_POOL_SIZE_MICROBIOME: ${DB_CONNECTION_POOL_SIZE_MICROBIOME}
147 changes: 0 additions & 147 deletions docker-compose.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -380,153 +380,6 @@ services:
- "traefik.http.routers.${TRAEFIK_SERVICE_ROUTER:-vdi-dev}.entrypoints=${TRAEFIK_ENTRYPOINTS:-local}"
- "traefik.docker.network=traefik"

plugin-example:
image: veupathdb/vdi-plugin-example:${VDI_PLUGIN_EXAMPLE_TAG:-latest}
networks:
internal:
aliases:
- example
monitoring-ext: {}
labels:
- "prometheus.scrape_enabled=true"
- "com.centurylinklabs.watchtower.enable=${PLUGIN_EXAMPLE_WATCHTOWER:-false}"
volumes:
- type: bind
source: ${DATASET_DIRECTORY_SOURCE_PATH:?}
target: ${DATASET_DIRECTORY_TARGET_PATH:?}
environment:
LDAP_SERVER: ${LDAP_SERVER:?}
ORACLE_BASE_DN: ${ORACLE_BASE_DN:?}
CUSTOM_PATH: ${PLUGIN_HANDLER_NOOP_CUSTOM_PATH}
SITE_BUILD: ${SITE_BUILD:?}
DATASET_INSTALL_ROOT: ${DATASET_DIRECTORY_TARGET_PATH:?}

IMPORT_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_IMPORT_SCRIPT_MAX_DURATION}
INSTALL_DATA_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_INSTALL_DATA_SCRIPT_MAX_DURATION}
INSTALL_META_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_INSTALL_META_SCRIPT_MAX_DURATION}
UNINSTALL_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_UNINSTALL_SCRIPT_MAX_DURATION}
CHECK_COMPAT_SCRIPT_MAX_DURATION: ${PLUGIN_HANDLER_NOOP_CHECK_COMPAT_SCRIPT_MAX_DURATION}

DB_CONNECTION_ENABLED_AMOEBA: ${DB_CONNECTION_ENABLED_AMOEBA}
DB_CONNECTION_NAME_AMOEBA: ${DB_CONNECTION_NAME_AMOEBA:?}
DB_CONNECTION_LDAP_AMOEBA: ${DB_CONNECTION_LDAP_AMOEBA:?}
DB_CONNECTION_PASS_AMOEBA: ${DB_CONNECTION_PASS_AMOEBA:?}
DB_CONNECTION_DATA_SCHEMA_AMOEBA: ${DB_CONNECTION_DATA_SCHEMA_AMOEBA:?}
DB_CONNECTION_CONTROL_SCHEMA_AMOEBA: ${DB_CONNECTION_CONTROL_SCHEMA_AMOEBA:?}
DB_CONNECTION_POOL_SIZE_AMOEBA: ${DB_CONNECTION_POOL_SIZE_AMOEBA}

DB_CONNECTION_ENABLED_CRYPTO: ${DB_CONNECTION_ENABLED_CRYPTO}
DB_CONNECTION_NAME_CRYPTO: ${DB_CONNECTION_NAME_CRYPTO:?}
DB_CONNECTION_LDAP_CRYPTO: ${DB_CONNECTION_LDAP_CRYPTO:?}
DB_CONNECTION_PASS_CRYPTO: ${DB_CONNECTION_PASS_CRYPTO:?}
DB_CONNECTION_DATA_SCHEMA_CRYPTO: ${DB_CONNECTION_DATA_SCHEMA_CRYPTO:?}
DB_CONNECTION_CONTROL_SCHEMA_CRYPTO: ${DB_CONNECTION_CONTROL_SCHEMA_CRYPTO:?}
DB_CONNECTION_POOL_SIZE_CRYPTO: ${DB_CONNECTION_POOL_SIZE_CRYPTO}

DB_CONNECTION_ENABLED_FUNGI: ${DB_CONNECTION_ENABLED_FUNGI}
DB_CONNECTION_NAME_FUNGI: ${DB_CONNECTION_NAME_FUNGI:?}
DB_CONNECTION_LDAP_FUNGI: ${DB_CONNECTION_LDAP_FUNGI:?}
DB_CONNECTION_PASS_FUNGI: ${DB_CONNECTION_PASS_FUNGI:?}
DB_CONNECTION_DATA_SCHEMA_FUNGI: ${DB_CONNECTION_DATA_SCHEMA_FUNGI:?}
DB_CONNECTION_CONTROL_SCHEMA_FUNGI: ${DB_CONNECTION_CONTROL_SCHEMA_FUNGI:?}
DB_CONNECTION_POOL_SIZE_FUNGI: ${DB_CONNECTION_POOL_SIZE_FUNGI}

DB_CONNECTION_ENABLED_GIARDIA: ${DB_CONNECTION_ENABLED_GIARDIA}
DB_CONNECTION_NAME_GIARDIA: ${DB_CONNECTION_NAME_GIARDIA:?}
DB_CONNECTION_LDAP_GIARDIA: ${DB_CONNECTION_LDAP_GIARDIA:?}
DB_CONNECTION_PASS_GIARDIA: ${DB_CONNECTION_PASS_GIARDIA:?}
DB_CONNECTION_DATA_SCHEMA_GIARDIA: ${DB_CONNECTION_DATA_SCHEMA_GIARDIA:?}
DB_CONNECTION_CONTROL_SCHEMA_GIARDIA: ${DB_CONNECTION_CONTROL_SCHEMA_GIARDIA:?}
DB_CONNECTION_POOL_SIZE_GIARDIA: ${DB_CONNECTION_POOL_SIZE_GIARDIA}

DB_CONNECTION_ENABLED_HOST: ${DB_CONNECTION_ENABLED_HOST}
DB_CONNECTION_NAME_HOST: ${DB_CONNECTION_NAME_HOST:?}
DB_CONNECTION_LDAP_HOST: ${DB_CONNECTION_LDAP_HOST:?}
DB_CONNECTION_PASS_HOST: ${DB_CONNECTION_PASS_HOST:?}
DB_CONNECTION_DATA_SCHEMA_HOST: ${DB_CONNECTION_DATA_SCHEMA_HOST:?}
DB_CONNECTION_CONTROL_SCHEMA_HOST: ${DB_CONNECTION_CONTROL_SCHEMA_HOST:?}
DB_CONNECTION_POOL_SIZE_HOST: ${DB_CONNECTION_POOL_SIZE_HOST}

DB_CONNECTION_ENABLED_MICROSPORIDIA: ${DB_CONNECTION_ENABLED_MICROSPORIDIA}
DB_CONNECTION_NAME_MICROSPORIDIA: ${DB_CONNECTION_NAME_MICROSPORIDIA:?}
DB_CONNECTION_LDAP_MICROSPORIDIA: ${DB_CONNECTION_LDAP_MICROSPORIDIA:?}
DB_CONNECTION_PASS_MICROSPORIDIA: ${DB_CONNECTION_PASS_MICROSPORIDIA:?}
DB_CONNECTION_DATA_SCHEMA_MICROSPORIDIA: ${DB_CONNECTION_DATA_SCHEMA_MICROSPORIDIA:?}
DB_CONNECTION_CONTROL_SCHEMA_MICROSPORIDIA: ${DB_CONNECTION_CONTROL_SCHEMA_MICROSPORIDIA:?}
DB_CONNECTION_POOL_SIZE_MICROSPORIDIA: ${DB_CONNECTION_POOL_SIZE_MICROSPORIDIA}

DB_CONNECTION_ENABLED_PIROPLASMA: ${DB_CONNECTION_ENABLED_PIROPLASMA}
DB_CONNECTION_NAME_PIROPLASMA: ${DB_CONNECTION_NAME_PIROPLASMA:?}
DB_CONNECTION_LDAP_PIROPLASMA: ${DB_CONNECTION_LDAP_PIROPLASMA:?}
DB_CONNECTION_PASS_PIROPLASMA: ${DB_CONNECTION_PASS_PIROPLASMA:?}
DB_CONNECTION_DATA_SCHEMA_PIROPLASMA: ${DB_CONNECTION_DATA_SCHEMA_PIROPLASMA:?}
DB_CONNECTION_CONTROL_SCHEMA_PIROPLASMA: ${DB_CONNECTION_CONTROL_SCHEMA_PIROPLASMA:?}
DB_CONNECTION_POOL_SIZE_PIROPLASMA: ${DB_CONNECTION_POOL_SIZE_PIROPLASMA}

DB_CONNECTION_ENABLED_PLASMO: ${DB_CONNECTION_ENABLED_PLASMO}
DB_CONNECTION_NAME_PLASMO: ${DB_CONNECTION_NAME_PLASMO:?}
DB_CONNECTION_LDAP_PLASMO: ${DB_CONNECTION_LDAP_PLASMO:?}
DB_CONNECTION_PASS_PLASMO: ${DB_CONNECTION_PASS_PLASMO:?}
DB_CONNECTION_DATA_SCHEMA_PLASMO: ${DB_CONNECTION_DATA_SCHEMA_PLASMO:?}
DB_CONNECTION_CONTROL_SCHEMA_PLASMO: ${DB_CONNECTION_CONTROL_SCHEMA_PLASMO:?}
DB_CONNECTION_POOL_SIZE_PLASMO: ${DB_CONNECTION_POOL_SIZE_PLASMO}

DB_CONNECTION_ENABLED_TOXO: ${DB_CONNECTION_ENABLED_TOXO}
DB_CONNECTION_NAME_TOXO: ${DB_CONNECTION_NAME_TOXO:?}
DB_CONNECTION_LDAP_TOXO: ${DB_CONNECTION_LDAP_TOXO:?}
DB_CONNECTION_PASS_TOXO: ${DB_CONNECTION_PASS_TOXO:?}
DB_CONNECTION_DATA_SCHEMA_TOXO: ${DB_CONNECTION_DATA_SCHEMA_TOXO:?}
DB_CONNECTION_CONTROL_SCHEMA_TOXO: ${DB_CONNECTION_CONTROL_SCHEMA_TOXO:?}
DB_CONNECTION_POOL_SIZE_TOXO: ${DB_CONNECTION_POOL_SIZE_TOXO}

DB_CONNECTION_ENABLED_TRICH: ${DB_CONNECTION_ENABLED_TRICH}
DB_CONNECTION_NAME_TRICH: ${DB_CONNECTION_NAME_TRICH:?}
DB_CONNECTION_LDAP_TRICH: ${DB_CONNECTION_LDAP_TRICH:?}
DB_CONNECTION_PASS_TRICH: ${DB_CONNECTION_PASS_TRICH:?}
DB_CONNECTION_DATA_SCHEMA_TRICH: ${DB_CONNECTION_DATA_SCHEMA_TRICH:?}
DB_CONNECTION_CONTROL_SCHEMA_TRICH: ${DB_CONNECTION_CONTROL_SCHEMA_TRICH:?}
DB_CONNECTION_POOL_SIZE_TRICH: ${DB_CONNECTION_POOL_SIZE_TRICH}

DB_CONNECTION_ENABLED_TRITRYP: ${DB_CONNECTION_ENABLED_TRITRYP}
DB_CONNECTION_NAME_TRITRYP: ${DB_CONNECTION_NAME_TRITRYP:?}
DB_CONNECTION_LDAP_TRITRYP: ${DB_CONNECTION_LDAP_TRITRYP:?}
DB_CONNECTION_PASS_TRITRYP: ${DB_CONNECTION_PASS_TRITRYP:?}
DB_CONNECTION_DATA_SCHEMA_TRITRYP: ${DB_CONNECTION_DATA_SCHEMA_TRITRYP:?}
DB_CONNECTION_CONTROL_SCHEMA_TRITRYP: ${DB_CONNECTION_CONTROL_SCHEMA_TRITRYP:?}
DB_CONNECTION_POOL_SIZE_TRITRYP: ${DB_CONNECTION_POOL_SIZE_TRITRYP}

DB_CONNECTION_ENABLED_VECTOR: ${DB_CONNECTION_ENABLED_VECTOR}
DB_CONNECTION_NAME_VECTOR: ${DB_CONNECTION_NAME_VECTOR:?}
DB_CONNECTION_LDAP_VECTOR: ${DB_CONNECTION_LDAP_VECTOR:?}
DB_CONNECTION_PASS_VECTOR: ${DB_CONNECTION_PASS_VECTOR:?}
DB_CONNECTION_DATA_SCHEMA_VECTOR: ${DB_CONNECTION_DATA_SCHEMA_VECTOR:?}
DB_CONNECTION_CONTROL_SCHEMA_VECTOR: ${DB_CONNECTION_CONTROL_SCHEMA_VECTOR:?}
DB_CONNECTION_POOL_SIZE_VECTOR: ${DB_CONNECTION_POOL_SIZE_VECTOR}

DB_CONNECTION_ENABLED_ORTHO: ${DB_CONNECTION_ENABLED_ORTHO}
DB_CONNECTION_NAME_ORTHO: ${DB_CONNECTION_NAME_ORTHO:?}
DB_CONNECTION_LDAP_ORTHO: ${DB_CONNECTION_LDAP_ORTHO:?}
DB_CONNECTION_PASS_ORTHO: ${DB_CONNECTION_PASS_ORTHO:?}
DB_CONNECTION_DATA_SCHEMA_ORTHO: ${DB_CONNECTION_DATA_SCHEMA_ORTHO:?}
DB_CONNECTION_CONTROL_SCHEMA_ORTHO: ${DB_CONNECTION_CONTROL_SCHEMA_ORTHO:?}
DB_CONNECTION_POOL_SIZE_ORTHO: ${DB_CONNECTION_POOL_SIZE_ORTHO}

DB_CONNECTION_ENABLED_CLINEPI: ${DB_CONNECTION_ENABLED_CLINEPI}
DB_CONNECTION_NAME_CLINEPI: ${DB_CONNECTION_NAME_CLINEPI:?}
DB_CONNECTION_LDAP_CLINEPI: ${DB_CONNECTION_LDAP_CLINEPI:?}
DB_CONNECTION_PASS_CLINEPI: ${DB_CONNECTION_PASS_CLINEPI:?}
DB_CONNECTION_DATA_SCHEMA_CLINEPI: ${DB_CONNECTION_DATA_SCHEMA_CLINEPI:?}
DB_CONNECTION_CONTROL_SCHEMA_CLINEPI: ${DB_CONNECTION_CONTROL_SCHEMA_CLINEPI:?}
DB_CONNECTION_POOL_SIZE_CLINEPI: ${DB_CONNECTION_POOL_SIZE_CLINEPI}

DB_CONNECTION_ENABLED_MICROBIOME: ${DB_CONNECTION_ENABLED_MICROBIOME}
DB_CONNECTION_NAME_MICROBIOME: ${DB_CONNECTION_NAME_MICROBIOME:?}
DB_CONNECTION_LDAP_MICROBIOME: ${DB_CONNECTION_LDAP_MICROBIOME:?}
DB_CONNECTION_PASS_MICROBIOME: ${DB_CONNECTION_PASS_MICROBIOME:?}
DB_CONNECTION_DATA_SCHEMA_MICROBIOME: ${DB_CONNECTION_DATA_SCHEMA_MICROBIOME:?}
DB_CONNECTION_CONTROL_SCHEMA_MICROBIOME: ${DB_CONNECTION_CONTROL_SCHEMA_MICROBIOME:?}
DB_CONNECTION_POOL_SIZE_MICROBIOME: ${DB_CONNECTION_POOL_SIZE_MICROBIOME}

plugin-genelist:
image: veupathdb/vdi-plugin-genelist:${VDI_PLUGIN_GENELIST_TAG:-latest}
networks:
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24 changes: 12 additions & 12 deletions docs/vdi-api.html
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2 changes: 1 addition & 1 deletion gradle/libs.versions.toml
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Expand Up @@ -6,7 +6,7 @@ fgputil-db = { group = "org.gusdb", name = "fgputil-db", version = "2.14.2-jakar
container-core = { group = "org.veupathdb.lib", name = "jaxrs-container-core", version = "8.0.0" }
container-multipart = { group = "org.veupathdb.lib", name = "multipart-jackson-pojo", version = "1.1.7" }

vdi-common = { group = "org.veupathdb.vdi", name = "vdi-component-common", version = "14.2.1" }
vdi-common = { group = "org.veupathdb.vdi", name = "vdi-component-common", version = "17.0.0" }
vdi-json = { group = "org.veupathdb.vdi", name = "vdi-component-json", version = "1.0.2" }

# Database
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3 changes: 2 additions & 1 deletion gradle/wrapper/gradle-wrapper.properties
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@@ -1,6 +1,7 @@
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
distributionUrl=https\://services.gradle.org/distributions/gradle-8.12-bin.zip
networkTimeout=10000
validateDistributionUrl=true
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
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