gistfile1.txt

(mtx-api--EuOzVbW) bash-3.2$ docker-compose run --rm web ./manage.py importdatasets ./mtx-dataset-13.zip
WARNING: The DJANGO_CORS_ORIGIN_WHITELIST variable is not set. Defaulting to a blank string.
Starting mtx-api_postgres_1 ... done
Generating import commands:
- Generated import for `datasets_datasets` from datasets.tsv.
- Generated import for `datasets_biopsy_batches` from biopsy_batches.tsv.
- Generated import for `datasets_tumor_sites` from tumor_sites.tsv.
- Generated import for `datasets_treatments` from treatments.tsv.
- Generated import for `datasets_outcomes` from outcomes.tsv.
- Generated import for `datasets_cancer_types` from cancer_types.tsv.
- Generated import for `datasets_genes` from genes.tsv.
- Generated import for `datasets_gene_mutation_variants` from gene_mutation_variants.tsv.
- Generated import for `datasets_gene_traits` from gene_traits.tsv.
- Generated import for `datasets_rules` from rules.tsv.
- Generated import for `datasets_rules_gene_traits` from rules_gene_traits.tsv.
- Generated import for `datasets_rulesets` from rulesets.tsv.
- Generated import for `datasets_rulesets_rules` from ruleset_rules.tsv.
- Generated import for `datasets_biopsies` from biopsies.tsv.
- Generated import for `datasets_biopsies_treatments` from biopsies_treatments.tsv.
- Generated import for `datasets_biopsies_rules` from biopsies_rules.tsv.
- Generated import for `datasets_biopsy_cancer_types` from biopsies_cancer_types.tsv.
- Generated import for `datasets_biopsy_gene_traits` from biopsies_gene_traits.tsv.
- Generated import for `datasets_biopsies_outcomes` from biopsies_outcomes.tsv.

Starting import:
START TRANSACTION;
START TRANSACTION
COPY datasets_datasets (id,label) FROM '/code/.import_data/datasets.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  could not open file "/code/.import_data/datasets.tsv" for reading: No such file or directory
COPY datasets_biopsy_batches (id,dataset_id,label,patient_count) FROM '/code/.import_data/biopsy_batches.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_tumor_sites (id,label,biopsy_batch_id) FROM '/code/.import_data/tumor_sites.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_treatments (id,label,biopsy_batch_id) FROM '/code/.import_data/treatments.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_outcomes (id,label,treatment_id,survival_metric,biopsy_batch_id) FROM '/code/.import_data/outcomes.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_cancer_types (id,label,biopsy_batch_id) FROM '/code/.import_data/cancer_types.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_genes (id,label,biopsy_batch_id) FROM '/code/.import_data/genes.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_gene_mutation_variants (id,label,biopsy_batch_id) FROM '/code/.import_data/gene_mutation_variants.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_gene_traits (id,label,gene_id,gene_mutation_variant_id,position,mutated,biopsy_batch_id) FROM '/code/.import_data/gene_traits.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_rules (id,label,biopsy_batch_id) FROM '/code/.import_data/rules.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_rules_gene_traits (rule_id,gene_trait_id,biopsy_batch_id) FROM '/code/.import_data/rules_gene_traits.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_rulesets (id,outcome_id,label,meta,biopsy_batch_id) FROM '/code/.import_data/rulesets.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_rulesets_rules (id,rule_id,ruleset_id,meta,biopsy_batch_id) FROM '/code/.import_data/ruleset_rules.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsies (id,biopsy_batch_id,tumor_site_id,patient_meta) FROM '/code/.import_data/biopsies.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsies_treatments (id,biopsy_id,treatment_id,days_to_start,days_to_stop,dose_value,dose_units,biopsy_batch_id) FROM '/code/.import_data/biopsies_treatments.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsies_rules (ruleset_id,biopsy_id,rule_id,meta,biopsy_batch_id) FROM '/code/.import_data/biopsies_rules.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsy_cancer_types (id,biopsy_id,cancer_type_id) FROM '/code/.import_data/biopsies_cancer_types.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsy_gene_traits (id,biopsy_id,gene_trait_id,biopsy_batch_id) FROM '/code/.import_data/biopsies_gene_traits.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COPY datasets_biopsies_outcomes (id,biopsy_id,outcome_id,duration,event_observed) FROM '/code/.import_data/biopsies_outcomes.tsv' WITH DELIMITER E'	' CSV HEADER;
ERROR:  current transaction is aborted, commands ignored until end of transaction block
COMMIT;
ROLLBACK

Cleaning up.

Import completed.