<commit_before>## ================= General denfinitions =================
spring:
  profiles:
    include: httpServer
  lifecycle:
    timeout-per-shutdown-phase: 5m

logging:
  level:
    root: INFO
    uk.ac.ebi.quickgo.annotation: DEBUG

## ================= Tomcat definitions =================
server:
  tomcat:
    threads:
      max: 0
  max-http-header-size: 64000
  shutdown: graceful

## ================= Solr =================
## DEV solr server
solr:
  #host: http://ves-hx-ac.ebi.ac.uk:8090/solr
  host: http://wp-p2m-c5.ebi.ac.uk:8090/solr/
  timeoutMilliSeconds: 120000

## =============== Validation =================
geneproduct:
  db:
    xref:
      valid:
        regexes: /home/rizwan/tools/quickgo-local/ff/DB_XREFS_ENTITIES.dat.gz
        casesensitive: false

## =============== Search =================
## the fields that are compatible with being interpreted as a terms "LocalParams" query
## note: see use of these fields in, uk.ac.ebi.quickgo.rest.search.query.UnsortedSolrQuerySerializer
annotation:
  terms:
    query:
      compatible:
        fields: ['assignedBy', 'evidenceCode', 'goEvidence', 'goId', 'dbSubset', 'geneProductType', 'qualifier',
                 'targetSet', 'taxonId', 'geneProductId']
  validation:
    validationResource: file:/home/rizwan/tools/quickgo-local/ff/DB_XREFS_ENTITIES.dat.gz
    chunk: 30
    headerLines: 1
    reference_dbs: ['pmid', 'doi', 'go_ref', 'reactome']
  download:
    sort:
      fields: 'id'
    ontologySource: file:/home/rizwan/tools/quickgo-local/ff/ONTOLOGY_IRI.dat.gz
    taskExecutor:
      corePoolSize: 10
      maxPoolSize: 20
      queueCapacity: 100
      keepAliveSeconds: 600
      allowCoreThreadTimeout: true
      waitForTasksToCompleteOnShutdown: true
  metadata:
    source: file:/home/rizwan/tools/quickgo-local/ff/goa_uniprot.gpa-version
  stats:
    typeLimits:
      goId: 11
      taxonId: 1
      reference: 8
      typeDoesNotExist: 12

# the fields to return in search results from a solr query<commit_msg>overrides download time to 5 hours<commit_after>## ================= General denfinitions =================
spring:
  profiles:
    include: httpServer
  lifecycle:
    timeout-per-shutdown-phase: 5m

logging:
  level:
    root: INFO
    uk.ac.ebi.quickgo.annotation: DEBUG

## ================= Tomcat definitions =================
server:
  tomcat:
    threads:
      max: 0
  max-http-header-size: 64000
  shutdown: graceful

## ================= Solr =================
## DEV solr server
solr:
  #host: http://ves-hx-ac.ebi.ac.uk:8090/solr
  host: http://wp-p2m-c5.ebi.ac.uk:8090/solr/
  timeoutMilliSeconds: 120000

## =============== Validation =================
geneproduct:
  db:
    xref:
      valid:
        regexes: /home/rizwan/tools/quickgo-local/ff/DB_XREFS_ENTITIES.dat.gz
        casesensitive: false

## =============== Search =================
## the fields that are compatible with being interpreted as a terms "LocalParams" query
## note: see use of these fields in, uk.ac.ebi.quickgo.rest.search.query.UnsortedSolrQuerySerializer
annotation:
  terms:
    query:
      compatible:
        fields: ['assignedBy', 'evidenceCode', 'goEvidence', 'goId', 'dbSubset', 'geneProductType', 'qualifier',
                 'targetSet', 'taxonId', 'geneProductId']
  validation:
    validationResource: file:/home/rizwan/tools/quickgo-local/ff/DB_XREFS_ENTITIES.dat.gz
    chunk: 30
    headerLines: 1
    reference_dbs: ['pmid', 'doi', 'go_ref', 'reactome']
  download:
    sort:
      fields: 'id'
    ontologySource: file:/home/rizwan/tools/quickgo-local/ff/ONTOLOGY_IRI.dat.gz
    taskExecutor:
      corePoolSize: 10
      maxPoolSize: 20
      queueCapacity: 100
      keepAliveSeconds: 600
      allowCoreThreadTimeout: true
      waitForTasksToCompleteOnShutdown: true
    defaultEmitterTimeout: 18000000
  metadata:
    source: file:/home/rizwan/tools/quickgo-local/ff/goa_uniprot.gpa-version
  stats:
    typeLimits:
      goId: 11
      taxonId: 1
      reference: 8
      typeDoesNotExist: 12

# the fields to return in search results from a solr query
{'fraction_non_alphanumeric': 0.18032786885245902, 'fraction_numerical': 0.022755077073648152, 'mean_word_length': 3.472647702407002, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 3, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3307966', 'n_tokens_mistral': 1429, 'n_tokens_neox': 1324, 'n_words': 284}