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fix disk image paths #68

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fix disk image paths #68

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4 changes: 2 additions & 2 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ steps:
opensearch_tarball:
- name: tarball opensearch
source: /mnt/opensearch
destination: disk_images/opensearch.tar.gz
destination: disk_images/opensearch.tgz
open_search_prep_all:
- name: sync_bucket etl output files
source: ${data_source}/output
Expand Down Expand Up @@ -195,7 +195,7 @@ steps:
clickhouse_tarball:
- name: tarball clickhouse
source: /mnt/clickhouse
destination: disk_images/clickhouse.tar.gz
destination: disk_images/clickhouse.tgz
clickhouse_disk_snapshot:
- name: create_gcp_disk_snapshot clickhouse
gcp_project_id: open-targets-eu-dev
Expand Down
205 changes: 42 additions & 163 deletions deployment/pos_config.tftpl
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,9 @@ scratchpad:
# temp file locations
local_data: release_data
prepared_data: prepared_data
# croissant
release_ftp_output: ${RELEASE_FTP_OUTPUT}
release_gcs_output: ${RELEASE_GCS_OUTPUT}
# opensearch
opensearch_version: ${OPENSEARCH_VERSION}
opensearch_java_opts: ${OPENSEARCH_JAVA_OPTS}
Expand All @@ -24,8 +27,8 @@ scratchpad:
# bigquery
bq_prod_project_id: open-targets-prod
bq_parquet_path: ${BQ_DATA_SOURCE}
steps:

steps:
################################################################################################
# Sync data
################################################################################################
Expand All @@ -50,53 +53,53 @@ steps:
- name: ot_croissant generate release metadata
requires:
- sync_bucket etl output files
ftp_address: http://ftp.ebi.ac.uk/pub/databases/opentargets/platform/${release}/output/
gcp_address: gs://open-targets-data-releases/${release}/output/
date_published: "2025-02-12"
ftp_address: ${release_ftp_output}
gcp_address: ${release_gcs_output}
date_published: '2025-02-12'
dataset_path: ${local_data}/output
output: croissant.json
prepared_data_parent: ${prepared_data}

################################################################################################
# OpenSearch
################################################################################################

open_search_start:
- name: open_search_start opensearch start
opensearch_start:
- name: opensearch_start data loading instance
service_name: os-pos
volume_data: ${opensearch_data}
volume_logs: ${opensearch_logs}
opensearch_version: ${opensearch_version}
opensearch_java_opts: ${opensearch_java_opts}
open_search_disk_snapshot:
opensearch_disk_snapshot:
- name: create_gcp_disk_snapshot opensearch
gcp_project_id: open-targets-eu-dev
gcp_disk_name: ${opensearch_disk_name}
gcp_snapshot_name: ${opensearch_disk_snapshot_name}
gcp_disk_zone: europe-west1-d
open_search_stop:
- name: open_search_stop opensearch stop
gcp_disk_zone: europe-west1-d
opensearch_stop:
- name: opensearch_stop data loading instance
service_name: os-pos
open_search_tarball:
opensearch_tarball:
- name: tarball opensearch
source: /mnt/opensearch
destination: disk_images/opensearch.tar.gz
destination: disk_images/opensearch.tgz
open_search_prep_all:
- name: sync_bucket etl output files
source: ${data_source}/output
source: ${data_source}/output
destination: ${local_data}/output
- name: sync_bucket etl view files
source: ${data_source}/view/
destination: ${local_data}/view
- name: explode prep all datasets
requires:
- sync_bucket etl output files
- sync_bucket etl view files
foreach:
- sync_bucket pipeline output files
- sync_bucket pipeline view files
foreach: &opensearch_datasets
- biosample
- colocalisation_coloc
- colocalisation_ecaviar
- credible_set
- croissant
- disease
- disease_hpo
- drug
Expand Down Expand Up @@ -162,119 +165,56 @@ steps:
dataset: ${each}
parquet_parent: ${local_data}
json_parent: ${prepared_data}
open_search_load_all:
- name: open_search_start opensearch start
opensearch_load_all:
- name: opensearch_start data loading instance
volume_data: ${opensearch_data}
volume_logs: ${opensearch_logs}
opensearch_version: ${opensearch_version}
opensearch_java_opts: ${opensearch_java_opts}
- name: explode load all datasets
foreach:
- biosample
- colocalisation_coloc
- colocalisation_ecaviar
- credible_set
- croissant
- disease
- disease_hpo
- drug
- drug_warnings
- evidence_cancer_biomarkers
- evidence_cancer_gene_census
- evidence_chembl
- evidence_clingen
- evidence_crispr
- evidence_crispr_screen
- evidence_encore
- evidence_europepmc
- evidence_eva
- evidence_eva
- evidence_eva_somatic
- evidence_expression_atlas
- evidence_gene_burden
- evidence_gene2phenotype
- evidence_genomics_england
- evidence_gwas_credible_sets
- evidence_impc
- evidence_intogen
- evidence_orphanet
- evidence_ot_crispr
- evidence_ot_crispr_validation
- evidence_ot_genetics_portal
- evidence_progeny
- evidence_reactome
- evidence_slapenrich
- evidence_sysbio
- evidence_uniprot_literature
- evidence_uniprot_variants
- expression
- facet_search_disease
- facet_search_target
- go
- gwas_index
- hpo
- indication
- interaction
- interaction_evidence
- known_drugs
- l2g_predictions
- mechanism_of_action
- mouse_phenotypes
- openfda_faers
- otar_projects
- pharmacogenomics
- protein_coding_coords
- reactome
- search_disease
- search_drug
- search_study
- search_target
- search_variant
- so
- target
- target_essentiality
- target_prioritisation
- variant_index
foreach: *opensearch_datasets
do:
- name: open_search_create_index opensearch create index ${each}
- name: opensearch_create_index ${each}
requires:
- open_search_start opensearch start
- opensearch_start data loading instance
dataset: ${each}
- name: open_search_load opensearch load ${each}
- name: opensearch_load dataset ${each}
requires:
- open_search_create_index opensearch create index ${each}
- opensearch_create_index opensearch ${each}
dataset: ${each}
json_parent: ${prepared_data}

################################################################################################
# ClickHouse
################################################################################################
clickhouse_start:
- name: clickhouse_start clickhouse start
- name: clickhouse_start data loading instance
volume_data: ${clickhouse_data}
volume_logs: ${clickhouse_logs}
clickhouse_version: ${clickhouse_version}
clickhouse_tarball:
- name: tarball clickhouse
source: /mnt/clickhouse
destination: disk_images/clickhouse.tar.gz
destination: disk_images/clickhouse.tgz
clickhouse_disk_snapshot:
- name: create_gcp_disk_snapshot clickhouse
gcp_project_id: open-targets-eu-dev
gcp_disk_name: ${clickhouse_disk_name}
gcp_snapshot_name: ${clickhouse_disk_snapshot_name}
gcp_disk_zone: europe-west1-d
gcp_disk_zone: europe-west1-d
clickhouse_stop:
- name: clickhouse_stop clickhouse stop
- name: clickhouse_stop data loading instance
clickhouse_load_all:
- name: sync_bucket etl output files
source: ${data_source}/output
destination: ${local_data}/output
- name: sync_bucket etl view files
source: ${data_source}/view
source: ${data_source}/view
destination: ${local_data}/view
- name: sync_bucket etl intermediate files
source: ${data_source}/intermediate/literature_sentence
destination: ${local_data}/intermediate/literature_sentence
- name: clickhouse_start clickhouse start
- name: clickhouse_start data loading instance
volume_data: ${clickhouse_data}
volume_logs: ${clickhouse_logs}
clickhouse_version: ${clickhouse_version}
Expand All @@ -287,13 +227,13 @@ steps:
do:
- name: clickhouse_load clickhouse load ${each}
requires:
- clickhouse_start clickhouse start
- sync_bucket etl output files
- sync_bucket etl view files
- sync_bucket etl intermediate files
- clickhouse_start data loading instance
- sync_bucket pipeline output files
- sync_bucket pipeline view files
- sync_bucket pipeline intermediate files
dataset: ${each}
data_dir_parent: ${local_data}

########################################################################################
# BigQuery
bigquery_dev_load_all:
Expand All @@ -303,7 +243,7 @@ steps:
location: eu
release: ${release}
- name: explode load bigquery tables
foreach:
foreach: &bigquery_datasets
- association_by_datasource_direct
- association_by_datasource_indirect
- association_by_datatype_direct
Expand Down Expand Up @@ -381,68 +321,7 @@ steps:
location: eu
release: ${release}
- name: explode load bigquery tables
foreach:
- association_by_datasource_direct
- association_by_datasource_indirect
- association_by_datatype_direct
- association_by_datatype_indirect
- association_by_overall_indirect
- association_overall_direct
- biosample
- colocalisation_coloc
- colocalisation_ecaviar
- credible_set
- disease
- disease_hpo
- disease_phenotype
- drug_indication
- drug_mechanism_of_action
- drug_molecule
- drug_warning
- evidence_cancer_biomarkers
- evidence_cancer_gene_census
- evidence_chembl
- evidence_clingen
- evidence_crispr
- evidence_crispr_screen
- evidence_encore
- evidence_europepmc
- evidence_eva
- evidence_eva_somatic
- evidence_expression_atlas
- evidence_gene2phenotype
- evidence_gene_burden
- evidence_genomics_england
- evidence_gwas_credible_sets
- evidence_impc
- evidence_intogen
- evidence_orphanet
- evidence_progeny
- evidence_reactome
- evidence_slapenrich
- evidence_sysbio
- evidence_uniprot_literature
- evidence_uniprot_variants
- expression
- go
- interaction
- interaction_evidence
- known_drug
- l2g_prediction
- literature
- literature_vector
- mouse_phenotype
- openfda_significant_adverse_drug_reactions
- openfda_significant_adverse_target_reactions
- pharmacogenomics
- protein_coding_coords
- reactome
- so
- study
- target
- target_essentiality
- target_prioritisation
- variant
foreach: *bigquery_datasets
do:
- name: bigquery_load prod ${each}
requires:
Expand Down