From 75e600df28862f17ab13c0c586623c295e3db9f1 Mon Sep 17 00:00:00 2001 From: brendagutman Date: Wed, 27 May 2026 12:21:08 -0500 Subject: [PATCH 1/4] Insert the utils generated pipeline --- dbt_project/dbt_project.yml | 8 + .../inc_chr_18_src_chr_18_phenotype_data.sql | 86 ++++ .../inc_chr_18_src_s3_scrape_cody.sql | 12 + ...c_chr_18_src_ha_delivery_manifest_6735.sql | 19 + .../chr_18/src/_column_descriptions.md | 395 ++++++++++++++++++ .../models/kids_first/chr_18/src/sources.yml | 215 ++++++++++ .../stb/inc_chr_18_stb_accesspolicy.sql | 12 + .../stb/inc_chr_18_stb_activitydefinition.sql | 10 + ..._18_stb_activitydefinition_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_aliquot.sql | 14 + .../inc_chr_18_stb_aliquot_external_id.sql | 7 + .../inc_chr_18_stb_biospecimencollection.sql | 14 + ..._stb_biospecimencollection_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_concept.sql | 7 + .../chr_18/stb/inc_chr_18_stb_dataset.sql | 11 + .../stb/inc_chr_18_stb_dataset_file_id.sql | 7 + .../inc_chr_18_stb_dataset_publication.sql | 7 + .../stb/inc_chr_18_stb_demographics.sql | 14 + ...nc_chr_18_stb_demographics_external_id.sql | 7 + .../stb/inc_chr_18_stb_demographics_race.sql | 7 + .../chr_18/stb/inc_chr_18_stb_doi.sql | 9 + .../stb/inc_chr_18_stb_doi_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_encounter.sql | 11 + .../inc_chr_18_stb_encounter_external_id.sql | 7 + .../inc_chr_18_stb_encounterdefinition.sql | 10 + ...unterdefinition_activity_definition_id.sql | 7 + ...18_stb_encounterdefinition_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_family.sql | 12 + .../stb/inc_chr_18_stb_family_external_id.sql | 7 + .../stb/inc_chr_18_stb_familymember.sql | 11 + ...nc_chr_18_stb_familymember_external_id.sql | 7 + .../stb/inc_chr_18_stb_familyrelationship.sql | 11 + ..._18_stb_familyrelationship_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_file.sql | 17 + .../stb/inc_chr_18_stb_file_external_id.sql | 7 + .../stb/inc_chr_18_stb_file_sample_id.sql | 7 + .../stb/inc_chr_18_stb_file_subject_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_filehash.sql | 8 + .../stb/inc_chr_18_stb_investigator.sql | 12 + ...nc_chr_18_stb_investigator_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_publication.sql | 10 + ...inc_chr_18_stb_publication_external_id.sql | 7 + .../stb/inc_chr_18_stb_record_external_id.sql | 7 + .../chr_18/stb/inc_chr_18_stb_sample.sql | 14 + .../stb/inc_chr_18_stb_sample_external_id.sql | 7 + .../stb/inc_chr_18_stb_sample_processing.sql | 7 + .../inc_chr_18_stb_sample_storage_method.sql | 7 + .../chr_18/stb/inc_chr_18_stb_study.sql | 16 + ...18_stb_study_clinical_data_source_type.sql | 7 + .../stb/inc_chr_18_stb_study_contact.sql | 7 + .../inc_chr_18_stb_study_data_category.sql | 7 + .../stb/inc_chr_18_stb_study_external_id.sql | 7 + .../inc_chr_18_stb_study_funding_source.sql | 7 + ...8_stb_study_participant_lifespan_stage.sql | 7 + ...hr_18_stb_study_principal_investigator.sql | 7 + .../stb/inc_chr_18_stb_study_program.sql | 7 + .../stb/inc_chr_18_stb_study_publication.sql | 7 + .../inc_chr_18_stb_study_research_domain.sql | 7 + .../stb/inc_chr_18_stb_study_study_design.sql | 7 + .../stb/inc_chr_18_stb_studymetadata.sql | 11 + ...tudymetadata_clinical_data_source_type.sql | 7 + ...chr_18_stb_studymetadata_data_category.sql | 7 + ...c_chr_18_stb_studymetadata_external_id.sql | 7 + ...udymetadata_participant_lifespan_stage.sql | 7 + ...r_18_stb_studymetadata_research_domain.sql | 7 + ..._chr_18_stb_studymetadata_study_design.sql | 7 + .../chr_18/stb/inc_chr_18_stb_subject.sql | 10 + .../inc_chr_18_stb_subject_external_id.sql | 7 + .../stb/inc_chr_18_stb_subjectassertion.sql | 19 + ...nc_chr_18_stb_subjectassertion_concept.sql | 7 + ...hr_18_stb_subjectassertion_external_id.sql | 7 + ..._18_stb_subjectassertion_value_concept.sql | 7 + .../inc_chr_18_stb_virtualbiorepository.sql | 12 + ...hr_18_stb_virtualbiorepository_contact.sql | 7 + ...8_stb_virtualbiorepository_external_id.sql | 7 + .../scripts/run_version_placeholder.sh | 199 +++++++++ 76 files changed, 1531 insertions(+) create mode 100644 dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql create mode 100644 dbt_project/models/kids_first/chr_18/src/_column_descriptions.md create mode 100644 dbt_project/models/kids_first/chr_18/src/sources.yml create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql create mode 100644 dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql create mode 100755 dbt_project/scripts/run_version_placeholder.sh diff --git a/dbt_project/dbt_project.yml b/dbt_project/dbt_project.yml index dd9070b..7ece3e1 100644 --- a/dbt_project/dbt_project.yml +++ b/dbt_project/dbt_project.yml @@ -24,6 +24,11 @@ models: +schema: inc_aadsc_src int: +schema: inc_aadsc_int + chr_18: + src: + +schema: inc_chr_18_src + int: + +schema: inc_chr_18_int kids_first: +tags: [study_stage,kids_first] sd_1nns3k8v: @@ -32,6 +37,9 @@ models: +schema: kf_sd_1nns3k8v_src int: +schema: kf_sd_1nns3k8v_int + chr_18: + +tags: + - chr_18 access: +tags: [access_stage] +schema: access diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql new file mode 100644 index 0000000..d136438 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql @@ -0,0 +1,86 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "Family ID"::text as "family_id", + "Participant ID"::text as "participant_id", + "Family Relationship Target Participant ID"::text as "family_relationship_target_participant_id", + "alliquot_id"::text as "alliquot_id", + "Consent Group"::text as "consent_group", + "Age at Sample"::text as "age_at_sample", + "Sample Composition"::text as "sample_composition", + "Race"::text as "race", + "Sex"::text as "sex", + "Ethnicity"::text as "ethnicity", + "Analyte Type"::text as "analyte_type", + "Age at Phenotype"::text as "age_at_phenotype", + "Affected Status"::text as "affected_status", + "Vital Status"::text as "vital_status", + "chiari 2"::text as "chiari_2", + "pituitary gland abn"::text as "pituitary_gland_abn", + "cleft palate"::text as "cleft_palate", + "hearing loss"::text as "hearing_loss", + "tetralogy of fallot"::text as "tetralogy_of_fallot", + "conductive hearing loss"::text as "conductive_hearing_loss", + "holoprosencephaly"::text as "holoprosencephaly", + "choanal atresia"::text as "choanal_atresia", + "aural atresia"::text as "aural_atresia", + "midface hypoplasia"::text as "midface_hypoplasia", + "dysmyelination"::text as "dysmyelination", + "polymicrogyria"::text as "polymicrogyria", + "cryptorchidism"::text as "cryptorchidism", + "sensorineural hearing loss"::text as "sensorineural_hearing_loss", + "cleft lip"::text as "cleft_lip", + "imperforate anus"::text as "imperforate_anus", + "microcephaly"::text as "microcephaly", + "vertical talus"::text as "vertical_talus", + "hypospadias"::text as "hypospadias", + "rocker bottom foot"::text as "rocker_bottom_foot", + "chiari 1"::text as "chiari_1", + "ptosis"::text as "ptosis", + "strabismus"::text as "strabismus", + "bilateral coxa valga"::text as "bilateral_coxa_valga", + "cardiac_nos"::text as "cardiac_nos", + "corpus callosum abn"::text as "corpus_callosum_abn", + "pulmonary valve stenosis"::text as "pulmonary_valve_stenosis", + "metatarsus varus"::text as "metatarsus_varus", + "decreased white matter volume"::text as "decreased_white_matter_volume", + "macrocephaly"::text as "macrocephaly", + "suprasellar cyst"::text as "suprasellar_cyst", + "hydrocephalus"::text as "hydrocephalus", + "micropenis"::text as "micropenis", + "anal stenosis"::text as "anal_stenosis", + "congenital heart malformation"::text as "congenital_heart_malformation", + "bilateral choanal atresia"::text as "bilateral_choanal_atresia", + "dandy walker malformation"::text as "dandy_walker_malformation", + "dandy walker"::text as "dandy_walker", + "congenital heart defect"::text as "congenital_heart_defect", + "aural stenosis"::text as "aural_stenosis", + "kidney malform"::text as "kidney_malform", + "pituitary fossa enlargement"::text as "pituitary_fossa_enlargement", + "submucous cleft"::text as "submucous_cleft", + "virchow robins spaces"::text as "virchow_robins_spaces", + "retinal coloboma"::text as "retinal_coloboma", + "corneal staphyloma"::text as "corneal_staphyloma", + "club foot"::text as "club_foot", + "macroglossia"::text as "macroglossia", + "dandy walker variant"::text as "dandy_walker_variant", + "coanal atresia"::text as "coanal_atresia", + "occipatal lobe abn"::text as "occipatal_lobe_abn", + "asd"::text as "asd", + "vsd"::text as "vsd", + "pectus excavatum"::text as "pectus_excavatum", + "peripherial pulmonary stenosis"::text as "peripherial_pulmonary_stenosis", + "sagittal stenosis"::text as "sagittal_stenosis", + "hydronephrosis"::text as "hydronephrosis", + "patent ductus arteriosus"::text as "patent_ductus_arteriosus", + "duanes syndrome"::text as "duanes_syndrome", + "laryngomalacia"::text as "laryngomalacia", + "metatarsus adductus"::text as "metatarsus_adductus", + "ptosisbilateral"::text as "ptosisbilateral", + "microphallus"::text as "microphallus", + "sacral agenesis"::text as "sacral_agenesis", + "situs inversus"::text as "situs_inversus", + "Sample Tissue Type"::text as "sample_tissue_type" + from {{ source('chr_18', 'chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql new file mode 100644 index 0000000..70a74d8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "Size"::integer as "size", + "Key"::text as "key", + "ETag"::text as "etag", + "Bucket"::text as "bucket", + "LastModified"::text as "lastmodified", + "StorageClass"::text as "storageclass" + from {{ source('chr_18', 's3_scrape_cody') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql new file mode 100644 index 0000000..1e0c119 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + ROW_NUMBER() OVER () AS "kf_index", + "type"::text as "type", + "sample.sample_id"::text as "sample", + "file_name"::text as "file_name", + "file_type"::text as "file_type", + "file_description"::text as "file_description", + "file_size"::integer as "file_size", + "md5sum"::text as "md5sum", + "library_id"::text as "library_id", + "library_strategy"::text as "library_strategy", + "library_layout"::text as "library_layout", + "library_source"::text as "library_source", + "platform"::text as "platform", + "instrument_model"::text as "instrument_model" + from {{ source('chr_18', 'ha_delivery_manifest_6735') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md new file mode 100644 index 0000000..787b36d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/_column_descriptions.md @@ -0,0 +1,395 @@ +{% docs chr_18_phenotype_data_family_id %} +Family ID +{% enddocs %} + +{% docs chr_18_phenotype_data_participant_id %} +Participant ID +{% enddocs %} + +{% docs chr_18_phenotype_data_family_relationship_target_pa_59d6df7d %} +Family Relationship Target Participant ID +{% enddocs %} + +{% docs chr_18_phenotype_data_alliquot_id %} +alliquot_id +{% enddocs %} + +{% docs chr_18_phenotype_data_consent_group %} +Consent Group +{% enddocs %} + +{% docs chr_18_phenotype_data_age_at_sample %} +Age at Sample +{% enddocs %} + +{% docs chr_18_phenotype_data_sample_composition %} +Sample Composition +{% enddocs %} + +{% docs chr_18_phenotype_data_race %} +Race +{% enddocs %} + +{% docs chr_18_phenotype_data_sex %} +Sex +{% enddocs %} + +{% docs chr_18_phenotype_data_ethnicity %} +Ethnicity +{% enddocs %} + +{% docs chr_18_phenotype_data_analyte_type %} +Analyte Type +{% enddocs %} + +{% docs chr_18_phenotype_data_age_at_phenotype %} +Age at Phenotype +{% enddocs %} + +{% docs chr_18_phenotype_data_affected_status %} +Affected Status +{% enddocs %} + +{% docs chr_18_phenotype_data_vital_status %} +Vital Status +{% enddocs %} + +{% docs chr_18_phenotype_data_chiari_2 %} +chiari 2 +{% enddocs %} + +{% docs chr_18_phenotype_data_pituitary_gland_abn %} +pituitary gland abn +{% enddocs %} + +{% docs chr_18_phenotype_data_cleft_palate %} +cleft palate +{% enddocs %} + +{% docs chr_18_phenotype_data_hearing_loss %} +hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_tetralogy_of_fallot %} +tetralogy of fallot +{% enddocs %} + +{% docs chr_18_phenotype_data_conductive_hearing_loss %} +conductive hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_holoprosencephaly %} +holoprosencephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_choanal_atresia %} +choanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_aural_atresia %} +aural atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_midface_hypoplasia %} +midface hypoplasia +{% enddocs %} + +{% docs chr_18_phenotype_data_dysmyelination %} +dysmyelination +{% enddocs %} + +{% docs chr_18_phenotype_data_polymicrogyria %} +polymicrogyria +{% enddocs %} + +{% docs chr_18_phenotype_data_cryptorchidism %} +cryptorchidism +{% enddocs %} + +{% docs chr_18_phenotype_data_sensorineural_hearing_loss %} +sensorineural hearing loss +{% enddocs %} + +{% docs chr_18_phenotype_data_cleft_lip %} +cleft lip +{% enddocs %} + +{% docs chr_18_phenotype_data_imperforate_anus %} +imperforate anus +{% enddocs %} + +{% docs chr_18_phenotype_data_microcephaly %} +microcephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_vertical_talus %} +vertical talus +{% enddocs %} + +{% docs chr_18_phenotype_data_hypospadias %} +hypospadias +{% enddocs %} + +{% docs chr_18_phenotype_data_rocker_bottom_foot %} +rocker bottom foot +{% enddocs %} + +{% docs chr_18_phenotype_data_chiari_1 %} +chiari 1 +{% enddocs %} + +{% docs chr_18_phenotype_data_ptosis %} +ptosis +{% enddocs %} + +{% docs chr_18_phenotype_data_strabismus %} +strabismus +{% enddocs %} + +{% docs chr_18_phenotype_data_bilateral_coxa_valga %} +bilateral coxa valga +{% enddocs %} + +{% docs chr_18_phenotype_data_cardiac_nos %} +cardiac_nos +{% enddocs %} + +{% docs chr_18_phenotype_data_corpus_callosum_abn %} +corpus callosum abn +{% enddocs %} + +{% docs chr_18_phenotype_data_pulmonary_valve_stenosis %} +pulmonary valve stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_metatarsus_varus %} +metatarsus varus +{% enddocs %} + +{% docs chr_18_phenotype_data_decreased_white_matter_volume %} +decreased white matter volume +{% enddocs %} + +{% docs chr_18_phenotype_data_macrocephaly %} +macrocephaly +{% enddocs %} + +{% docs chr_18_phenotype_data_suprasellar_cyst %} +suprasellar cyst +{% enddocs %} + +{% docs chr_18_phenotype_data_hydrocephalus %} +hydrocephalus +{% enddocs %} + +{% docs chr_18_phenotype_data_micropenis %} +micropenis +{% enddocs %} + +{% docs chr_18_phenotype_data_anal_stenosis %} +anal stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_congenital_heart_malformation %} +congenital heart malformation +{% enddocs %} + +{% docs chr_18_phenotype_data_bilateral_choanal_atresia %} +bilateral choanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker_malformation %} +dandy walker malformation +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker %} +dandy walker +{% enddocs %} + +{% docs chr_18_phenotype_data_congenital_heart_defect %} +congenital heart defect +{% enddocs %} + +{% docs chr_18_phenotype_data_aural_stenosis %} +aural stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_kidney_malform %} +kidney malform +{% enddocs %} + +{% docs chr_18_phenotype_data_pituitary_fossa_enlargement %} +pituitary fossa enlargement +{% enddocs %} + +{% docs chr_18_phenotype_data_submucous_cleft %} +submucous cleft +{% enddocs %} + +{% docs chr_18_phenotype_data_virchow_robins_spaces %} +virchow robins spaces +{% enddocs %} + +{% docs chr_18_phenotype_data_retinal_coloboma %} +retinal coloboma +{% enddocs %} + +{% docs chr_18_phenotype_data_corneal_staphyloma %} +corneal staphyloma +{% enddocs %} + +{% docs chr_18_phenotype_data_club_foot %} +club foot +{% enddocs %} + +{% docs chr_18_phenotype_data_macroglossia %} +macroglossia +{% enddocs %} + +{% docs chr_18_phenotype_data_dandy_walker_variant %} +dandy walker variant +{% enddocs %} + +{% docs chr_18_phenotype_data_coanal_atresia %} +coanal atresia +{% enddocs %} + +{% docs chr_18_phenotype_data_occipatal_lobe_abn %} +occipatal lobe abn +{% enddocs %} + +{% docs chr_18_phenotype_data_asd %} +asd +{% enddocs %} + +{% docs chr_18_phenotype_data_vsd %} +vsd +{% enddocs %} + +{% docs chr_18_phenotype_data_pectus_excavatum %} +pectus excavatum +{% enddocs %} + +{% docs chr_18_phenotype_data_peripherial_pulmonary_stenosis %} +peripherial pulmonary stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_sagittal_stenosis %} +sagittal stenosis +{% enddocs %} + +{% docs chr_18_phenotype_data_hydronephrosis %} +hydronephrosis +{% enddocs %} + +{% docs chr_18_phenotype_data_patent_ductus_arteriosus %} +patent ductus arteriosus +{% enddocs %} + +{% docs chr_18_phenotype_data_duanes_syndrome %} +duanes syndrome +{% enddocs %} + +{% docs chr_18_phenotype_data_laryngomalacia %} +laryngomalacia +{% enddocs %} + +{% docs chr_18_phenotype_data_metatarsus_adductus %} +metatarsus adductus +{% enddocs %} + +{% docs chr_18_phenotype_data_ptosisbilateral %} +ptosisbilateral +{% enddocs %} + +{% docs chr_18_phenotype_data_microphallus %} +microphallus +{% enddocs %} + +{% docs chr_18_phenotype_data_sacral_agenesis %} +sacral agenesis +{% enddocs %} + +{% docs chr_18_phenotype_data_situs_inversus %} +situs inversus +{% enddocs %} + +{% docs chr_18_phenotype_data_sample_tissue_type %} +Sample Tissue Type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_type %} +type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_sample %} +sample.sample_id +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_name %} +file_name +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_type %} +file_type +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_description %} +file_description +{% enddocs %} + +{% docs ha_delivery_manifest_6735_file_size %} +file_size +{% enddocs %} + +{% docs ha_delivery_manifest_6735_md5sum %} +md5sum +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_id %} +library_id +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_strategy %} +library_strategy +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_layout %} +library_layout +{% enddocs %} + +{% docs ha_delivery_manifest_6735_library_source %} +library_source +{% enddocs %} + +{% docs ha_delivery_manifest_6735_platform %} +platform +{% enddocs %} + +{% docs ha_delivery_manifest_6735_instrument_model %} +instrument_model +{% enddocs %} + +{% docs s3_scrape_cody_size %} +Size +{% enddocs %} + +{% docs s3_scrape_cody_key %} +Key +{% enddocs %} + +{% docs s3_scrape_cody_etag %} +ETag +{% enddocs %} + +{% docs s3_scrape_cody_bucket %} +Bucket +{% enddocs %} + +{% docs s3_scrape_cody_lastmodified %} +LastModified +{% enddocs %} + +{% docs s3_scrape_cody_storageclass %} +StorageClass +{% enddocs %} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/sources.yml b/dbt_project/models/kids_first/chr_18/src/sources.yml new file mode 100644 index 0000000..d60f199 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/src/sources.yml @@ -0,0 +1,215 @@ +sources: +- name: chr_18 + schema: inc_chr_18_src + tables: + - name: chr_18_phenotype_data + description: Source table for chr_18_phenotype_data. + columns: + - name: Family ID + description: '{{ doc("chr_18_phenotype_data_family_id") }}' + - name: Participant ID + description: '{{ doc("chr_18_phenotype_data_participant_id") }}' + - name: Family Relationship Target Participant ID + description: '{{ doc("chr_18_phenotype_data_family_relationship_target_pa_59d6df7d") + }}' + - name: alliquot_id + description: '{{ doc("chr_18_phenotype_data_alliquot_id") }}' + - name: Consent Group + description: '{{ doc("chr_18_phenotype_data_consent_group") }}' + - name: Age at Sample + description: '{{ doc("chr_18_phenotype_data_age_at_sample") }}' + - name: Sample Composition + description: '{{ doc("chr_18_phenotype_data_sample_composition") }}' + - name: Race + description: '{{ doc("chr_18_phenotype_data_race") }}' + - name: Sex + description: '{{ doc("chr_18_phenotype_data_sex") }}' + - name: Ethnicity + description: '{{ doc("chr_18_phenotype_data_ethnicity") }}' + - name: Analyte Type + description: '{{ doc("chr_18_phenotype_data_analyte_type") }}' + - name: Age at Phenotype + description: '{{ doc("chr_18_phenotype_data_age_at_phenotype") }}' + - name: Affected Status + description: '{{ doc("chr_18_phenotype_data_affected_status") }}' + - name: Vital Status + description: '{{ doc("chr_18_phenotype_data_vital_status") }}' + - name: chiari 2 + description: '{{ doc("chr_18_phenotype_data_chiari_2") }}' + - name: pituitary gland abn + description: '{{ doc("chr_18_phenotype_data_pituitary_gland_abn") }}' + - name: cleft palate + description: '{{ doc("chr_18_phenotype_data_cleft_palate") }}' + - name: hearing loss + description: '{{ doc("chr_18_phenotype_data_hearing_loss") }}' + - name: tetralogy of fallot + description: '{{ doc("chr_18_phenotype_data_tetralogy_of_fallot") }}' + - name: conductive hearing loss + description: '{{ doc("chr_18_phenotype_data_conductive_hearing_loss") }}' + - name: holoprosencephaly + description: '{{ doc("chr_18_phenotype_data_holoprosencephaly") }}' + - name: choanal atresia + description: '{{ doc("chr_18_phenotype_data_choanal_atresia") }}' + - name: aural atresia + description: '{{ doc("chr_18_phenotype_data_aural_atresia") }}' + - name: midface hypoplasia + description: '{{ doc("chr_18_phenotype_data_midface_hypoplasia") }}' + - name: dysmyelination + description: '{{ doc("chr_18_phenotype_data_dysmyelination") }}' + - name: polymicrogyria + description: '{{ doc("chr_18_phenotype_data_polymicrogyria") }}' + - name: cryptorchidism + description: '{{ doc("chr_18_phenotype_data_cryptorchidism") }}' + - name: sensorineural hearing loss + description: '{{ doc("chr_18_phenotype_data_sensorineural_hearing_loss") }}' + - name: cleft lip + description: '{{ doc("chr_18_phenotype_data_cleft_lip") }}' + - name: imperforate anus + description: '{{ doc("chr_18_phenotype_data_imperforate_anus") }}' + - name: microcephaly + description: '{{ doc("chr_18_phenotype_data_microcephaly") }}' + - name: vertical talus + description: '{{ doc("chr_18_phenotype_data_vertical_talus") }}' + - name: hypospadias + description: '{{ doc("chr_18_phenotype_data_hypospadias") }}' + - name: rocker bottom foot + description: '{{ doc("chr_18_phenotype_data_rocker_bottom_foot") }}' + - name: chiari 1 + description: '{{ doc("chr_18_phenotype_data_chiari_1") }}' + - name: ptosis + description: '{{ doc("chr_18_phenotype_data_ptosis") }}' + - name: strabismus + description: '{{ doc("chr_18_phenotype_data_strabismus") }}' + - name: bilateral coxa valga + description: '{{ doc("chr_18_phenotype_data_bilateral_coxa_valga") }}' + - name: cardiac_nos + description: '{{ doc("chr_18_phenotype_data_cardiac_nos") }}' + - name: corpus callosum abn + description: '{{ doc("chr_18_phenotype_data_corpus_callosum_abn") }}' + - name: pulmonary valve stenosis + description: '{{ doc("chr_18_phenotype_data_pulmonary_valve_stenosis") }}' + - name: metatarsus varus + description: '{{ doc("chr_18_phenotype_data_metatarsus_varus") }}' + - name: decreased white matter volume + description: '{{ doc("chr_18_phenotype_data_decreased_white_matter_volume") + }}' + - name: macrocephaly + description: '{{ doc("chr_18_phenotype_data_macrocephaly") }}' + - name: suprasellar cyst + description: '{{ doc("chr_18_phenotype_data_suprasellar_cyst") }}' + - name: hydrocephalus + description: '{{ doc("chr_18_phenotype_data_hydrocephalus") }}' + - name: micropenis + description: '{{ doc("chr_18_phenotype_data_micropenis") }}' + - name: anal stenosis + description: '{{ doc("chr_18_phenotype_data_anal_stenosis") }}' + - name: congenital heart malformation + description: '{{ doc("chr_18_phenotype_data_congenital_heart_malformation") + }}' + - name: bilateral choanal atresia + description: '{{ doc("chr_18_phenotype_data_bilateral_choanal_atresia") }}' + - name: dandy walker malformation + description: '{{ doc("chr_18_phenotype_data_dandy_walker_malformation") }}' + - name: dandy walker + description: '{{ doc("chr_18_phenotype_data_dandy_walker") }}' + - name: congenital heart defect + description: '{{ doc("chr_18_phenotype_data_congenital_heart_defect") }}' + - name: aural stenosis + description: '{{ doc("chr_18_phenotype_data_aural_stenosis") }}' + - name: kidney malform + description: '{{ doc("chr_18_phenotype_data_kidney_malform") }}' + - name: pituitary fossa enlargement + description: '{{ doc("chr_18_phenotype_data_pituitary_fossa_enlargement") }}' + - name: submucous cleft + description: '{{ doc("chr_18_phenotype_data_submucous_cleft") }}' + - name: virchow robins spaces + description: '{{ doc("chr_18_phenotype_data_virchow_robins_spaces") }}' + - name: retinal coloboma + description: '{{ doc("chr_18_phenotype_data_retinal_coloboma") }}' + - name: corneal staphyloma + description: '{{ doc("chr_18_phenotype_data_corneal_staphyloma") }}' + - name: club foot + description: '{{ doc("chr_18_phenotype_data_club_foot") }}' + - name: macroglossia + description: '{{ doc("chr_18_phenotype_data_macroglossia") }}' + - name: dandy walker variant + description: '{{ doc("chr_18_phenotype_data_dandy_walker_variant") }}' + - name: coanal atresia + description: '{{ doc("chr_18_phenotype_data_coanal_atresia") }}' + - name: occipatal lobe abn + description: '{{ doc("chr_18_phenotype_data_occipatal_lobe_abn") }}' + - name: asd + description: '{{ doc("chr_18_phenotype_data_asd") }}' + - name: vsd + description: '{{ doc("chr_18_phenotype_data_vsd") }}' + - name: pectus excavatum + description: '{{ doc("chr_18_phenotype_data_pectus_excavatum") }}' + - name: peripherial pulmonary stenosis + description: '{{ doc("chr_18_phenotype_data_peripherial_pulmonary_stenosis") + }}' + - name: sagittal stenosis + description: '{{ doc("chr_18_phenotype_data_sagittal_stenosis") }}' + - name: hydronephrosis + description: '{{ doc("chr_18_phenotype_data_hydronephrosis") }}' + - name: patent ductus arteriosus + description: '{{ doc("chr_18_phenotype_data_patent_ductus_arteriosus") }}' + - name: duanes syndrome + description: '{{ doc("chr_18_phenotype_data_duanes_syndrome") }}' + - name: laryngomalacia + description: '{{ doc("chr_18_phenotype_data_laryngomalacia") }}' + - name: metatarsus adductus + description: '{{ doc("chr_18_phenotype_data_metatarsus_adductus") }}' + - name: ptosisbilateral + description: '{{ doc("chr_18_phenotype_data_ptosisbilateral") }}' + - name: microphallus + description: '{{ doc("chr_18_phenotype_data_microphallus") }}' + - name: sacral agenesis + description: '{{ doc("chr_18_phenotype_data_sacral_agenesis") }}' + - name: situs inversus + description: '{{ doc("chr_18_phenotype_data_situs_inversus") }}' + - name: Sample Tissue Type + description: '{{ doc("chr_18_phenotype_data_sample_tissue_type") }}' + - name: ha_delivery_manifest_6735 + description: Source table for ha_delivery_manifest_6735. + columns: + - name: type + description: '{{ doc("ha_delivery_manifest_6735_type") }}' + - name: sample.sample_id + description: '{{ doc("ha_delivery_manifest_6735_sample") }}' + - name: file_name + description: '{{ doc("ha_delivery_manifest_6735_file_name") }}' + - name: file_type + description: '{{ doc("ha_delivery_manifest_6735_file_type") }}' + - name: file_description + description: '{{ doc("ha_delivery_manifest_6735_file_description") }}' + - name: file_size + description: '{{ doc("ha_delivery_manifest_6735_file_size") }}' + - name: md5sum + description: '{{ doc("ha_delivery_manifest_6735_md5sum") }}' + - name: library_id + description: '{{ doc("ha_delivery_manifest_6735_library_id") }}' + - name: library_strategy + description: '{{ doc("ha_delivery_manifest_6735_library_strategy") }}' + - name: library_layout + description: '{{ doc("ha_delivery_manifest_6735_library_layout") }}' + - name: library_source + description: '{{ doc("ha_delivery_manifest_6735_library_source") }}' + - name: platform + description: '{{ doc("ha_delivery_manifest_6735_platform") }}' + - name: instrument_model + description: '{{ doc("ha_delivery_manifest_6735_instrument_model") }}' + - name: s3_scrape_cody + description: Source table for s3_scrape_cody. + columns: + - name: Size + description: '{{ doc("s3_scrape_cody_size") }}' + - name: Key + description: '{{ doc("s3_scrape_cody_key") }}' + - name: ETag + description: '{{ doc("s3_scrape_cody_etag") }}' + - name: Bucket + description: '{{ doc("s3_scrape_cody_bucket") }}' + - name: LastModified + description: '{{ doc("s3_scrape_cody_lastmodified") }}' + - name: StorageClass + description: '{{ doc("s3_scrape_cody_storageclass") }}' diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql new file mode 100644 index 0000000..7f9f41d --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "access_policy_id", + null::text as "data_use_accession", + null::text as "data_use_permission", + null::text as "data_use_modifier", + null::text as "disease_limitation", + null::text as "access_description", + null::text as "website" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql new file mode 100644 index 0000000..570da50 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "activity_definition_id", + null::text as "name", + null::text as "description", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql new file mode 100644 index 0000000..7ecb81a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "activitydefinition_activity_definition_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql new file mode 100644 index 0000000..b2f7bd2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "aliquot_id", + null::text as "sample_id", + null::text as "availablity_status", + null::text as "quantity_number", + null::text as "quantity_unit", + null::text as "concentration_number", + null::text as "concentration_unit", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql new file mode 100644 index 0000000..02bf1a0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "aliquot_aliquot_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql new file mode 100644 index 0000000..eb9b027 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "biospecimen_collection_id", + null::text as "age_at_collection", + null::text as "method", + null::text as "site", + null::text as "spatial_qualifier", + null::text as "laterality", + null::text as "encounter_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql new file mode 100644 index 0000000..11e8404 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "biospecimencollection_biospecimen_collection_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql new file mode 100644 index 0000000..4350c7e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "concept_curie", + null::text as "display" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql new file mode 100644 index 0000000..33091c0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_id", + null::text as "name", + null::text as "description", + null::text as "do_id", + null::text as "data_collection_start", + null::text as "data_collection_end" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql new file mode 100644 index 0000000..9f8eaa0 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_dataset_id", + null::text as "file_id_file_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql new file mode 100644 index 0000000..41fd529 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "dataset_dataset_id", + null::integer as "publication_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql new file mode 100644 index 0000000..4c0bf43 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_id", + null::text as "sex", + null::text as "ethnicity", + null::text as "down_syndrome_status", + null::integer as "age_at_last_vital_status", + null::text as "vital_status", + null::integer as "age_at_first_engagement", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql new file mode 100644 index 0000000..953521b --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "demographics_subject_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql new file mode 100644 index 0000000..1bcfae1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "demographics_subject_id", + null::text as "race" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql new file mode 100644 index 0000000..e330e15 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql @@ -0,0 +1,9 @@ +{{ config(materialized='table') }} + + select + null::text as "do_id", + null::text as "bibliographic_reference", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql new file mode 100644 index 0000000..6dec0dc --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "doi_do_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql new file mode 100644 index 0000000..fbb8dc2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_id", + null::text as "subject_id", + null::text as "encounter_definition_id", + null::integer as "age_at_event", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql new file mode 100644 index 0000000..a8f3dc9 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_encounter_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql new file mode 100644 index 0000000..492dbe3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "encounter_definition_id", + null::text as "name", + null::text as "description", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql new file mode 100644 index 0000000..a19a472 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounterdefinition_encounter_definition_id", + null::text as "activity_definition_id_activity_definition_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql new file mode 100644 index 0000000..b283c9c --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "encounterdefinition_encounter_definition_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql new file mode 100644 index 0000000..affd9d3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "family_id", + null::text as "family_type", + null::text as "family_description", + null::text as "consanguinity", + null::text as "family_study_focus", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql new file mode 100644 index 0000000..ed70b01 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "family_family_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql new file mode 100644 index 0000000..673f8a2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "family_id", + null::text as "subject_id", + null::text as "family_role", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql new file mode 100644 index 0000000..4e41c3e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "familymember_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql new file mode 100644 index 0000000..0161392 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "family_relationship_id", + null::text as "family_member_id", + null::text as "relationship", + null::text as "subject_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql new file mode 100644 index 0000000..881cab5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "familyrelationship_family_relationship_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql new file mode 100644 index 0000000..5cba39e --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql @@ -0,0 +1,17 @@ +{{ config(materialized='table') }} + + select + null::text as "file_id", + null::text as "filename", + null::text as "format", + null::text as "data_category", + null::text as "data_type", + null::integer as "size", + null::text as "staging_url", + null::text as "release_url", + null::text as "drs_uri", + null::text as "access_policy_id", + null::text as "study_id", + null::integer as "hash_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql new file mode 100644 index 0000000..cca4563 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql new file mode 100644 index 0000000..c209f6a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "sample_id_sample_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql new file mode 100644 index 0000000..ab988fd --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "file_file_id", + null::text as "subject_id_subject_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql new file mode 100644 index 0000000..aea7743 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql @@ -0,0 +1,8 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "hash_type", + null::text as "hash_value" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql new file mode 100644 index 0000000..f37fca3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "name", + null::text as "institution", + null::text as "investigator_title", + null::text as "email", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql new file mode 100644 index 0000000..8a6d70f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "investigator_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql new file mode 100644 index 0000000..99f9165 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::integer as "id", + null::text as "bibliographic_reference", + null::text as "website", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql new file mode 100644 index 0000000..d433a31 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "publication_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql new file mode 100644 index 0000000..2d24622 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::integer as "record_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql new file mode 100644 index 0000000..539c076 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql @@ -0,0 +1,14 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_id", + null::text as "biospecimen_collection_id", + null::text as "parent_sample_id", + null::text as "sample_type", + null::text as "availablity_status", + null::text as "quantity_number", + null::text as "quantity_unit", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql new file mode 100644 index 0000000..800dae1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql new file mode 100644 index 0000000..4c4aaf7 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "processing" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql new file mode 100644 index 0000000..96163f6 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "sample_sample_id", + null::text as "storage_method" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql new file mode 100644 index 0000000..eec3536 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql @@ -0,0 +1,16 @@ +{{ config(materialized='table') }} + + select + null::text as "parent_study", + null::text as "study_title", + null::text as "study_code", + null::text as "study_short_name", + null::text as "study_description", + null::text as "website", + null::text as "acknowledgments", + null::text as "citation_statement", + null::text as "do_id", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql new file mode 100644 index 0000000..8b5f04b --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "clinical_data_source_type" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql new file mode 100644 index 0000000..51ea7a5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "contact_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql new file mode 100644 index 0000000..47c5f42 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "data_category" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql new file mode 100644 index 0000000..9431889 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql new file mode 100644 index 0000000..fd0f9f5 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "funding_source" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql new file mode 100644 index 0000000..18a0694 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "participant_lifespan_stage" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql new file mode 100644 index 0000000..323f069 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "principal_investigator_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql new file mode 100644 index 0000000..d2ba0e2 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "program" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql new file mode 100644 index 0000000..e543e60 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::integer as "publication_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql new file mode 100644 index 0000000..38790ef --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "research_domain" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql new file mode 100644 index 0000000..c6487a4 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "study_study_id", + null::text as "study_design" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql new file mode 100644 index 0000000..3be97a7 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql @@ -0,0 +1,11 @@ +{{ config(materialized='table') }} + + select + null::text as "study_id", + null::text as "selection_criteria", + null::text as "vbr_id", + null::integer as "expected_number_of_participants", + null::integer as "actual_number_of_participants", + null::text as "access_policy_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql new file mode 100644 index 0000000..3147a0a --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "clinical_data_source_type" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql new file mode 100644 index 0000000..cf9793f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "data_category" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql new file mode 100644 index 0000000..d59f31c --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql new file mode 100644 index 0000000..b69a575 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "participant_lifespan_stage" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql new file mode 100644 index 0000000..9807a99 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "research_domain" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql new file mode 100644 index 0000000..e60ea85 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "studymetadata_study_id", + null::text as "study_design" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql new file mode 100644 index 0000000..4e05b34 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql @@ -0,0 +1,10 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_id", + null::text as "subject_type", + null::text as "organism_type", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql new file mode 100644 index 0000000..7dfc140 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subject_subject_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql new file mode 100644 index 0000000..e7e3e65 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + null::text as "assertion_id", + null::text as "subject_id", + null::text as "encounter_id", + null::text as "assertion_provenance", + null::integer as "age_at_assertion", + null::integer as "age_at_event", + null::integer as "age_at_resolution", + null::text as "concept_source", + null::text as "value_number", + null::text as "value_source", + null::text as "value_unit", + null::text as "value_unit_source", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql new file mode 100644 index 0000000..a24c514 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "concept_concept_curie" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql new file mode 100644 index 0000000..715abdb --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql new file mode 100644 index 0000000..3b170a1 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "subjectassertion_assertion_id", + null::text as "value_concept_concept_curie" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql new file mode 100644 index 0000000..93927d3 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + null::text as "vbr_id", + null::text as "name", + null::text as "institution", + null::text as "website", + null::text as "vbr_readme", + null::text as "access_policy_id", + null::text as "study_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql new file mode 100644 index 0000000..25da532 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "virtualbiorepository_vbr_id", + null::integer as "contact_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql new file mode 100644 index 0000000..3d2a785 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql @@ -0,0 +1,7 @@ +{{ config(materialized='table') }} + + select + null::text as "virtualbiorepository_vbr_id", + null::text as "external_id" + from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + \ No newline at end of file diff --git a/dbt_project/scripts/run_version_placeholder.sh b/dbt_project/scripts/run_version_placeholder.sh new file mode 100755 index 0000000..e46bff5 --- /dev/null +++ b/dbt_project/scripts/run_version_placeholder.sh @@ -0,0 +1,199 @@ +#!/bin/bash +set -e +dbt clean +dbt deps || { echo "Error: dbt deps failed. Exiting..."; exit 1; } +dbt seed #--full-refresh +# Source tables +dbt run --select inc_chr_18_src_chr_18_phenotype_data +dbt run --select inc_chr_18_src_ha_delivery_manifest_6735 +dbt run --select inc_chr_18_src_s3_scrape_cody +# Stable tables +dbt run --select inc_chr_18_stb_accesspolicy +dbt run --select inc_chr_18_stb_activitydefinition +dbt run --select inc_chr_18_stb_activitydefinition_external_id +dbt run --select inc_chr_18_stb_aliquot +dbt run --select inc_chr_18_stb_aliquot_external_id +dbt run --select inc_chr_18_stb_biospecimencollection +dbt run --select inc_chr_18_stb_biospecimencollection_external_id +dbt run --select inc_chr_18_stb_concept +dbt run --select inc_chr_18_stb_doi +dbt run --select inc_chr_18_stb_doi_external_id +dbt run --select inc_chr_18_stb_dataset +dbt run --select inc_chr_18_stb_dataset_file_id +dbt run --select inc_chr_18_stb_dataset_publication +dbt run --select inc_chr_18_stb_demographics +dbt run --select inc_chr_18_stb_demographics_external_id +dbt run --select inc_chr_18_stb_demographics_race +dbt run --select inc_chr_18_stb_encounter +dbt run --select inc_chr_18_stb_encounterdefinition +dbt run --select inc_chr_18_stb_encounterdefinition_activity_definition_id +dbt run --select inc_chr_18_stb_encounterdefinition_external_id +dbt run --select inc_chr_18_stb_encounter_external_id +dbt run --select inc_chr_18_stb_family +dbt run --select inc_chr_18_stb_familymember +dbt run --select inc_chr_18_stb_familymember_external_id +dbt run --select inc_chr_18_stb_familyrelationship +dbt run --select inc_chr_18_stb_familyrelationship_external_id +dbt run --select inc_chr_18_stb_family_external_id +dbt run --select inc_chr_18_stb_file +dbt run --select inc_chr_18_stb_filehash +dbt run --select inc_chr_18_stb_file_external_id +dbt run --select inc_chr_18_stb_file_sample_id +dbt run --select inc_chr_18_stb_file_subject_id +dbt run --select inc_chr_18_stb_investigator +dbt run --select inc_chr_18_stb_investigator_external_id +dbt run --select inc_chr_18_stb_publication +dbt run --select inc_chr_18_stb_publication_external_id +dbt run --select inc_chr_18_stb_record_external_id +dbt run --select inc_chr_18_stb_sample +dbt run --select inc_chr_18_stb_sample_external_id +dbt run --select inc_chr_18_stb_sample_processing +dbt run --select inc_chr_18_stb_sample_storage_method +dbt run --select inc_chr_18_stb_study +dbt run --select inc_chr_18_stb_studymetadata +dbt run --select inc_chr_18_stb_studymetadata_clinical_data_source_type +dbt run --select inc_chr_18_stb_studymetadata_data_category +dbt run --select inc_chr_18_stb_studymetadata_external_id +dbt run --select inc_chr_18_stb_studymetadata_participant_lifespan_stage +dbt run --select inc_chr_18_stb_studymetadata_research_domain +dbt run --select inc_chr_18_stb_studymetadata_study_design +dbt run --select inc_chr_18_stb_study_clinical_data_source_type +dbt run --select inc_chr_18_stb_study_contact +dbt run --select inc_chr_18_stb_study_data_category +dbt run --select inc_chr_18_stb_study_external_id +dbt run --select inc_chr_18_stb_study_funding_source +dbt run --select inc_chr_18_stb_study_participant_lifespan_stage +dbt run --select inc_chr_18_stb_study_principal_investigator +dbt run --select inc_chr_18_stb_study_program +dbt run --select inc_chr_18_stb_study_publication +dbt run --select inc_chr_18_stb_study_research_domain +dbt run --select inc_chr_18_stb_study_study_design +dbt run --select inc_chr_18_stb_subject +dbt run --select inc_chr_18_stb_subjectassertion +dbt run --select inc_chr_18_stb_subjectassertion_concept +dbt run --select inc_chr_18_stb_subjectassertion_external_id +dbt run --select inc_chr_18_stb_subjectassertion_value_concept +dbt run --select inc_chr_18_stb_subject_external_id +dbt run --select inc_chr_18_stb_virtualbiorepository +dbt run --select inc_chr_18_stb_virtualbiorepository_contact +dbt run --select inc_chr_18_stb_virtualbiorepository_external_id +# Combined tables +dbt run --select combined_accesspolicy +dbt run --select combined_activitydefinition +dbt run --select combined_activitydefinition_external_id +dbt run --select combined_aliquot +dbt run --select combined_aliquot_external_id +dbt run --select combined_biospecimencollection +dbt run --select combined_biospecimencollection_external_id +dbt run --select combined_concept +dbt run --select combined_doi +dbt run --select combined_doi_external_id +dbt run --select combined_dataset +dbt run --select combined_dataset_file_id +dbt run --select combined_dataset_publication +dbt run --select combined_demographics +dbt run --select combined_demographics_external_id +dbt run --select combined_demographics_race +dbt run --select combined_encounter +dbt run --select combined_encounterdefinition +dbt run --select combined_encounterdefinition_activity_definition_id +dbt run --select combined_encounterdefinition_external_id +dbt run --select combined_encounter_external_id +dbt run --select combined_family +dbt run --select combined_familymember +dbt run --select combined_familymember_external_id +dbt run --select combined_familyrelationship +dbt run --select combined_familyrelationship_external_id +dbt run --select combined_family_external_id +dbt run --select combined_file +dbt run --select combined_filehash +dbt run --select combined_file_external_id +dbt run --select combined_file_sample_id +dbt run --select combined_file_subject_id +dbt run --select combined_investigator +dbt run --select combined_investigator_external_id +dbt run --select combined_publication +dbt run --select combined_publication_external_id +dbt run --select combined_record_external_id +dbt run --select combined_sample +dbt run --select combined_sample_external_id +dbt run --select combined_sample_processing +dbt run --select combined_sample_storage_method +dbt run --select combined_study +dbt run --select combined_studymetadata +dbt run --select combined_studymetadata_clinical_data_source_type +dbt run --select combined_studymetadata_data_category +dbt run --select combined_studymetadata_external_id +dbt run --select combined_studymetadata_participant_lifespan_stage +dbt run --select combined_studymetadata_research_domain +dbt run --select combined_studymetadata_study_design +dbt run --select combined_study_clinical_data_source_type +dbt run --select combined_study_contact +dbt run --select combined_study_data_category +dbt run --select combined_study_external_id +dbt run --select combined_study_funding_source +dbt run --select combined_study_participant_lifespan_stage +dbt run --select combined_study_principal_investigator +dbt run --select combined_study_program +dbt run --select combined_study_publication +dbt run --select combined_study_research_domain +dbt run --select combined_study_study_design +dbt run --select combined_subject +dbt run --select combined_subjectassertion +dbt run --select combined_subjectassertion_concept +dbt run --select combined_subjectassertion_external_id +dbt run --select combined_subjectassertion_value_concept +dbt run --select combined_subject_external_id +dbt run --select combined_virtualbiorepository +dbt run --select combined_virtualbiorepository_contact +dbt run --select combined_virtualbiorepository_external_id +# Export tables +dbt run --select fhir_accesspolicy +dbt run --select fhir_accesspolicy_access_policy_code +dbt run --select fhir_ageat +dbt run --select fhir_aliquot +dbt run --select fhir_aliquot_external_id +dbt run --select fhir_associatedparty +dbt run --select fhir_associatedparty_classifier +dbt run --select fhir_associatedparty_period_id +dbt run --select fhir_family +dbt run --select fhir_familyrelationship +dbt run --select fhir_family_external_id +dbt run --select fhir_filelocation +dbt run --select fhir_filemetadata +dbt run --select fhir_filemetadata_samples +dbt run --select fhir_hasexternalid_external_id +dbt run --select fhir_institution +dbt run --select fhir_institution_external_id +dbt run --select fhir_ncpifile +dbt run --select fhir_ncpifile_external_id +dbt run --select fhir_ncpifile_file_location_id +dbt run --select fhir_ncpifile_file_meta_data_id +dbt run --select fhir_participant +dbt run --select fhir_participantassertion +dbt run --select fhir_participant_external_id +dbt run --select fhir_participant_race +dbt run --select fhir_participant_sample_id +dbt run --select fhir_period +dbt run --select fhir_person +dbt run --select fhir_person_participant_id +dbt run --select fhir_practitioner +dbt run --select fhir_practitionerrole +dbt run --select fhir_practitioner_external_id +dbt run --select fhir_relativedatetime +dbt run --select fhir_researchstudy +dbt run --select fhir_researchstudycollection +dbt run --select fhir_researchstudycollection_external_id +dbt run --select fhir_researchstudycollection_label +dbt run --select fhir_researchstudycollection_research_study_collection_member_id +dbt run --select fhir_researchstudy_external_id +dbt run --select fhir_researchstudy_study_acknowledgement +dbt run --select fhir_researchstudy_study_condition +dbt run --select fhir_researchstudy_study_design +dbt run --select fhir_researchstudy_study_focus +dbt run --select fhir_researchstudy_study_personnel +dbt run --select fhir_researchsubject +dbt run --select fhir_sample +dbt run --select fhir_sample_external_id +dbt run --select fhir_sample_processing +dbt run --select fhir_studymembership From 12ba9a00ec27849a2ac1bc9e2c90c724fdee737f Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 09:30:26 -0400 Subject: [PATCH 2/4] =?UTF-8?q?=F0=9F=9A=A7=20WIP?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ...ql => kf_chr_18_src_chr_18_phenotype_data.sql} | 0 ..._cody.sql => kf_chr_18_src_s3_scrape_cody.sql} | 0 ...> kf_chr_18_src_ha_delivery_manifest_6735.sql} | 0 .../chr_18/stb/inc_chr_18_stb_demographics.sql | 12 ++++++------ .../stb/inc_chr_18_stb_demographics_race.sql | 4 ++-- .../kids_first/chr_18/stb/inc_chr_18_stb_file.sql | 15 ++++++++------- .../chr_18/stb/inc_chr_18_stb_filehash.sql | 6 +++--- .../chr_18/stb/inc_chr_18_stb_sample.sql | 6 +++--- 8 files changed, 22 insertions(+), 21 deletions(-) rename dbt_project/models/kids_first/chr_18/src/Clinical_Data/{inc_chr_18_src_chr_18_phenotype_data.sql => kf_chr_18_src_chr_18_phenotype_data.sql} (100%) rename dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/{inc_chr_18_src_s3_scrape_cody.sql => kf_chr_18_src_s3_scrape_cody.sql} (100%) rename dbt_project/models/kids_first/chr_18/src/Sequencing_Data/{inc_chr_18_src_ha_delivery_manifest_6735.sql => kf_chr_18_src_ha_delivery_manifest_6735.sql} (100%) diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/Clinical_Data/inc_chr_18_src_chr_18_phenotype_data.sql rename to dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/inc_chr_18_src_s3_scrape_cody.sql rename to dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/src/Sequencing_Data/inc_chr_18_src_ha_delivery_manifest_6735.sql rename to dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql index 4c0bf43..06cd0c2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql @@ -2,13 +2,13 @@ select null::text as "subject_id", - null::text as "sex", - null::text as "ethnicity", - null::text as "down_syndrome_status", + sex as "sex", + ethnicity as "ethnicity", + null::text as "down_syndrome_status", -- could map to Not Applicable? null::integer as "age_at_last_vital_status", - null::text as "vital_status", - null::integer as "age_at_first_engagement", + vital_status as "vital_status", + null::integer as "age_at_first_engagement", -- age at phenotype? or sample? null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql index 1bcfae1..0e0b421 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql @@ -2,6 +2,6 @@ select null::text as "demographics_subject_id", - null::text as "race" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + race as "race" + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql index 5cba39e..f79e037 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql @@ -2,16 +2,17 @@ select null::text as "file_id", - null::text as "filename", + file_name as "filename", null::text as "format", null::text as "data_category", - null::text as "data_type", - null::integer as "size", - null::text as "staging_url", - null::text as "release_url", - null::text as "drs_uri", + file_type as "data_type", + file_size as "size", + -- Need to determine when DRS indexing will happen + -- null::text as "staging_url", + -- null::text as "release_url", + -- null::text as "drs_uri", null::text as "access_policy_id", null::text as "study_id", null::integer as "hash_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql index aea7743..3e09bd4 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql @@ -2,7 +2,7 @@ select null::integer as "id", - null::text as "hash_type", - null::text as "hash_value" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + 'md5sum' as "hash_type", + md5sum as "hash_value" + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql index 539c076..1ea159e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql +++ b/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql @@ -1,14 +1,14 @@ {{ config(materialized='table') }} select - null::text as "sample_id", + sample as "sample_id", null::text as "biospecimen_collection_id", null::text as "parent_sample_id", - null::text as "sample_type", + type as "sample_type", null::text as "availablity_status", null::text as "quantity_number", null::text as "quantity_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_ha_delivery_manifest_6735') }} \ No newline at end of file From 014c0b0635704e7eeb66d1678f2b77e8832c8e00 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 14:14:35 -0400 Subject: [PATCH 3/4] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20reorganizing=20src=20a?= =?UTF-8?q?nd=20int?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../chr_18/int/kf_chr_18_int_clinical.sql | 118 +++++++++++++ .../chr_18/int/kf_chr_18_int_s3.sql | 12 ++ .../chr_18/int/kf_chr_18_int_sequencing.sql | 19 ++ .../kf_chr_18_src_chr_18_phenotype_data.sql | 162 +++++++++--------- .../kf_chr_18_src_s3_scrape_cody.sql | 14 +- ...f_chr_18_src_ha_delivery_manifest_6735.sql | 28 +-- 6 files changed, 251 insertions(+), 102 deletions(-) create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql create mode 100644 dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql new file mode 100644 index 0000000..06a0e9f --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_clinical.sql @@ -0,0 +1,118 @@ +{{ config(materialized='table') }} + +with base_data as ( + select * from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} +), +phenotype_list as ( + select phenotype from ( + values + ('chiari_2'), ('pituitary_gland_abn'), ('cleft_palate'), ('hearing_loss'), + ('tetralogy_of_fallot'), ('conductive_hearing_loss'), ('holoprosencephaly'), ('choanal_atresia'), + ('aural_atresia'), ('midface_hypoplasia'), ('dysmyelination'), ('polymicrogyria'), + ('cryptorchidism'), ('sensorineural_hearing_loss'), ('cleft_lip'), ('imperforate_anus'), + ('microcephaly'), ('vertical_talus'), ('hypospadias'), ('rocker_bottom_foot'), + ('chiari_1'), ('ptosis'), ('strabismus'), ('bilateral_coxa_valga'), + ('cardiac_nos'), ('corpus_callosum_abn'), ('pulmonary_valve_stenosis'), ('metatarsus_varus'), + ('decreased_white_matter_volume'), ('macrocephaly'), ('suprasellar_cyst'), ('hydrocephalus'), + ('micropenis'), ('anal_stenosis'), ('congenital_heart_malformation'), ('bilateral_choanal_atresia'), + ('dandy_walker_malformation'), ('dandy_walker'), ('congenital_heart_defect'), ('aural_stenosis'), + ('kidney_malform'), ('pituitary_fossa_enlargement'), ('submucous_cleft'), ('virchow_robins_spaces'), + ('retinal_coloboma'), ('corneal_staphyloma'), ('club_foot'), ('macroglossia'), + ('dandy_walker_variant'), ('coanal_atresia'), ('occipatal_lobe_abn'), ('asd'), + ('vsd'), ('pectus_excavatum'), ('peripherial_pulmonary_stenosis'), ('sagittal_stenosis'), + ('hydronephrosis'), ('patent_ductus_arteriosus'), ('duanes_syndrome'), ('laryngomalacia'), + ('metatarsus_adductus'), ('ptosisbilateral'), ('microphallus'), ('sacral_agenesis'), + ('situs_inversus') + ) as t(phenotype) +), +unpivoted_phenotypes as ( + select + bd.family_id, + bd.participant_id, + bd.family_relationship_target_participant_id, + bd.aliquot_id, + bd.consent_group, + bd.age_at_sample, + bd.sample_composition, + bd.race, + bd.sex, + bd.ethnicity, + bd.analyte_type, + bd.age_at_phenotype, + bd.affected_status, + bd.vital_status, + bd.sample_tissue_type, + pl.phenotype + from base_data bd + cross join phenotype_list pl + where case pl.phenotype + when 'chiari_2' then bd.chiari_2 + when 'pituitary_gland_abn' then bd.pituitary_gland_abn + when 'cleft_palate' then bd.cleft_palate + when 'hearing_loss' then bd.hearing_loss + when 'tetralogy_of_fallot' then bd.tetralogy_of_fallot + when 'conductive_hearing_loss' then bd.conductive_hearing_loss + when 'holoprosencephaly' then bd.holoprosencephaly + when 'choanal_atresia' then bd.choanal_atresia + when 'aural_atresia' then bd.aural_atresia + when 'midface_hypoplasia' then bd.midface_hypoplasia + when 'dysmyelination' then bd.dysmyelination + when 'polymicrogyria' then bd.polymicrogyria + when 'cryptorchidism' then bd.cryptorchidism + when 'sensorineural_hearing_loss' then bd.sensorineural_hearing_loss + when 'cleft_lip' then bd.cleft_lip + when 'imperforate_anus' then bd.imperforate_anus + when 'microcephaly' then bd.microcephaly + when 'vertical_talus' then bd.vertical_talus + when 'hypospadias' then bd.hypospadias + when 'rocker_bottom_foot' then bd.rocker_bottom_foot + when 'chiari_1' then bd.chiari_1 + when 'ptosis' then bd.ptosis + when 'strabismus' then bd.strabismus + when 'bilateral_coxa_valga' then bd.bilateral_coxa_valga + when 'cardiac_nos' then bd.cardiac_nos + when 'corpus_callosum_abn' then bd.corpus_callosum_abn + when 'pulmonary_valve_stenosis' then bd.pulmonary_valve_stenosis + when 'metatarsus_varus' then bd.metatarsus_varus + when 'decreased_white_matter_volume' then bd.decreased_white_matter_volume + when 'macrocephaly' then bd.macrocephaly + when 'suprasellar_cyst' then bd.suprasellar_cyst + when 'hydrocephalus' then bd.hydrocephalus + when 'micropenis' then bd.micropenis + when 'anal_stenosis' then bd.anal_stenosis + when 'congenital_heart_malformation' then bd.congenital_heart_malformation + when 'bilateral_choanal_atresia' then bd.bilateral_choanal_atresia + when 'dandy_walker_malformation' then bd.dandy_walker_malformation + when 'dandy_walker' then bd.dandy_walker + when 'congenital_heart_defect' then bd.congenital_heart_defect + when 'aural_stenosis' then bd.aural_stenosis + when 'kidney_malform' then bd.kidney_malform + when 'pituitary_fossa_enlargement' then bd.pituitary_fossa_enlargement + when 'submucous_cleft' then bd.submucous_cleft + when 'virchow_robins_spaces' then bd.virchow_robins_spaces + when 'retinal_coloboma' then bd.retinal_coloboma + when 'corneal_staphyloma' then bd.corneal_staphyloma + when 'club_foot' then bd.club_foot + when 'macroglossia' then bd.macroglossia + when 'dandy_walker_variant' then bd.dandy_walker_variant + when 'coanal_atresia' then bd.coanal_atresia + when 'occipatal_lobe_abn' then bd.occipatal_lobe_abn + when 'asd' then bd.asd + when 'vsd' then bd.vsd + when 'pectus_excavatum' then bd.pectus_excavatum + when 'peripherial_pulmonary_stenosis' then bd.peripherial_pulmonary_stenosis + when 'sagittal_stenosis' then bd.sagittal_stenosis + when 'hydronephrosis' then bd.hydronephrosis + when 'patent_ductus_arteriosus' then bd.patent_ductus_arteriosus + when 'duanes_syndrome' then bd.duanes_syndrome + when 'laryngomalacia' then bd.laryngomalacia + when 'metatarsus_adductus' then bd.metatarsus_adductus + when 'ptosisbilateral' then bd.ptosisbilateral + when 'microphallus' then bd.microphallus + when 'sacral_agenesis' then bd.sacral_agenesis + when 'situs_inversus' then bd.situs_inversus + end = 'present' +) + +select * from unpivoted_phenotypes + diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql new file mode 100644 index 0000000..bedc2f8 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_s3.sql @@ -0,0 +1,12 @@ +{{ config(materialized='table') }} + + select + kf_index, + size, + key, + etag, + bucket, + lastmodified, + storageclass + from {{ ref('kf_chr_18_src_s3_scrape_cody') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql new file mode 100644 index 0000000..7446e88 --- /dev/null +++ b/dbt_project/models/kids_first/chr_18/int/kf_chr_18_int_sequencing.sql @@ -0,0 +1,19 @@ +{{ config(materialized='table') }} + + select + kf_index, + type, + sample, + file_name, + file_type, + file_description, + file_size, + md5sum, + library_id, + library_strategy, + library_layout, + library_source, + platform, + instrument_model + from {{ source('chr_18', 'ha_delivery_manifest_6735') }} + \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql index d136438..cfb1d99 100644 --- a/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql +++ b/dbt_project/models/kids_first/chr_18/src/Clinical_Data/kf_chr_18_src_chr_18_phenotype_data.sql @@ -1,86 +1,86 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "Family ID"::text as "family_id", - "Participant ID"::text as "participant_id", - "Family Relationship Target Participant ID"::text as "family_relationship_target_participant_id", - "alliquot_id"::text as "alliquot_id", - "Consent Group"::text as "consent_group", - "Age at Sample"::text as "age_at_sample", - "Sample Composition"::text as "sample_composition", - "Race"::text as "race", - "Sex"::text as "sex", - "Ethnicity"::text as "ethnicity", - "Analyte Type"::text as "analyte_type", - "Age at Phenotype"::text as "age_at_phenotype", - "Affected Status"::text as "affected_status", - "Vital Status"::text as "vital_status", - "chiari 2"::text as "chiari_2", - "pituitary gland abn"::text as "pituitary_gland_abn", - "cleft palate"::text as "cleft_palate", - "hearing loss"::text as "hearing_loss", - "tetralogy of fallot"::text as "tetralogy_of_fallot", - "conductive hearing loss"::text as "conductive_hearing_loss", - "holoprosencephaly"::text as "holoprosencephaly", - "choanal atresia"::text as "choanal_atresia", - "aural atresia"::text as "aural_atresia", - "midface hypoplasia"::text as "midface_hypoplasia", - "dysmyelination"::text as "dysmyelination", - "polymicrogyria"::text as "polymicrogyria", - "cryptorchidism"::text as "cryptorchidism", - "sensorineural hearing loss"::text as "sensorineural_hearing_loss", - "cleft lip"::text as "cleft_lip", - "imperforate anus"::text as "imperforate_anus", - "microcephaly"::text as "microcephaly", - "vertical talus"::text as "vertical_talus", - "hypospadias"::text as "hypospadias", - "rocker bottom foot"::text as "rocker_bottom_foot", - "chiari 1"::text as "chiari_1", - "ptosis"::text as "ptosis", - "strabismus"::text as "strabismus", - "bilateral coxa valga"::text as "bilateral_coxa_valga", - "cardiac_nos"::text as "cardiac_nos", - "corpus callosum abn"::text as "corpus_callosum_abn", - "pulmonary valve stenosis"::text as "pulmonary_valve_stenosis", - "metatarsus varus"::text as "metatarsus_varus", - "decreased white matter volume"::text as "decreased_white_matter_volume", - "macrocephaly"::text as "macrocephaly", - "suprasellar cyst"::text as "suprasellar_cyst", - "hydrocephalus"::text as "hydrocephalus", - "micropenis"::text as "micropenis", - "anal stenosis"::text as "anal_stenosis", - "congenital heart malformation"::text as "congenital_heart_malformation", - "bilateral choanal atresia"::text as "bilateral_choanal_atresia", - "dandy walker malformation"::text as "dandy_walker_malformation", - "dandy walker"::text as "dandy_walker", - "congenital heart defect"::text as "congenital_heart_defect", - "aural stenosis"::text as "aural_stenosis", - "kidney malform"::text as "kidney_malform", - "pituitary fossa enlargement"::text as "pituitary_fossa_enlargement", - "submucous cleft"::text as "submucous_cleft", - "virchow robins spaces"::text as "virchow_robins_spaces", - "retinal coloboma"::text as "retinal_coloboma", - "corneal staphyloma"::text as "corneal_staphyloma", - "club foot"::text as "club_foot", - "macroglossia"::text as "macroglossia", - "dandy walker variant"::text as "dandy_walker_variant", - "coanal atresia"::text as "coanal_atresia", - "occipatal lobe abn"::text as "occipatal_lobe_abn", - "asd"::text as "asd", - "vsd"::text as "vsd", - "pectus excavatum"::text as "pectus_excavatum", - "peripherial pulmonary stenosis"::text as "peripherial_pulmonary_stenosis", - "sagittal stenosis"::text as "sagittal_stenosis", - "hydronephrosis"::text as "hydronephrosis", - "patent ductus arteriosus"::text as "patent_ductus_arteriosus", - "duanes syndrome"::text as "duanes_syndrome", - "laryngomalacia"::text as "laryngomalacia", - "metatarsus adductus"::text as "metatarsus_adductus", - "ptosisbilateral"::text as "ptosisbilateral", - "microphallus"::text as "microphallus", - "sacral agenesis"::text as "sacral_agenesis", - "situs inversus"::text as "situs_inversus", - "Sample Tissue Type"::text as "sample_tissue_type" + ROW_NUMBER() OVER () AS kf_index, + "Family ID"::text as family_id, + "Participant ID"::text as participant_id, + "Family Relationship Target Participant ID"::text as family_relationship_target_participant_id, + "alliquot_id"::text as aliquot_id, + "Consent Group"::text as consent_group, + "Age at Sample"::text as age_at_sample, + "Sample Composition"::text as sample_composition, + "Race"::text as race, + "Sex"::text as sex, + "Ethnicity"::text as ethnicity, + "Analyte Type"::text as analyte_type, + "Age at Phenotype"::text as age_at_phenotype, + "Affected Status"::text as affected_status, + "Vital Status"::text as vital_status, + "chiari 2"::text as chiari_2, + "pituitary gland abn"::text as pituitary_gland_abn, + "cleft palate"::text as cleft_palate, + "hearing loss"::text as hearing_loss, + "tetralogy of fallot"::text as tetralogy_of_fallot, + "conductive hearing loss"::text as conductive_hearing_loss, + "holoprosencephaly"::text as holoprosencephaly, + "choanal atresia"::text as choanal_atresia, + "aural atresia"::text as aural_atresia, + "midface hypoplasia"::text as midface_hypoplasia, + "dysmyelination"::text as dysmyelination, + "polymicrogyria"::text as polymicrogyria, + "cryptorchidism"::text as cryptorchidism, + "sensorineural hearing loss"::text as sensorineural_hearing_loss, + "cleft lip"::text as cleft_lip, + "imperforate anus"::text as imperforate_anus, + "microcephaly"::text as microcephaly, + "vertical talus"::text as vertical_talus, + "hypospadias"::text as hypospadias, + "rocker bottom foot"::text as rocker_bottom_foot, + "chiari 1"::text as chiari_1, + "ptosis"::text as ptosis, + "strabismus"::text as strabismus, + "bilateral coxa valga"::text as bilateral_coxa_valga, + "cardiac_nos"::text as cardiac_nos, + "corpus callosum abn"::text as corpus_callosum_abn, + "pulmonary valve stenosis"::text as pulmonary_valve_stenosis, + "metatarsus varus"::text as metatarsus_varus, + "decreased white matter volume"::text as decreased_white_matter_volume, + "macrocephaly"::text as macrocephaly, + "suprasellar cyst"::text as suprasellar_cyst, + "hydrocephalus"::text as hydrocephalus, + "micropenis"::text as micropenis, + "anal stenosis"::text as anal_stenosis, + "congenital heart malformation"::text as congenital_heart_malformation, + "bilateral choanal atresia"::text as bilateral_choanal_atresia, + "dandy walker malformation"::text as dandy_walker_malformation, + "dandy walker"::text as dandy_walker, + "congenital heart defect"::text as congenital_heart_defect, + "aural stenosis"::text as aural_stenosis, + "kidney malform"::text as kidney_malform, + "pituitary fossa enlargement"::text as pituitary_fossa_enlargement, + "submucous cleft"::text as submucous_cleft, + "virchow robins spaces"::text as virchow_robins_spaces, + "retinal coloboma"::text as retinal_coloboma, + "corneal staphyloma"::text as corneal_staphyloma, + "club foot"::text as club_foot, + "macroglossia"::text as macroglossia, + "dandy walker variant"::text as dandy_walker_variant, + "coanal atresia"::text as coanal_atresia, + "occipatal lobe abn"::text as occipatal_lobe_abn, + "asd"::text as asd, + "vsd"::text as vsd, + "pectus excavatum"::text as pectus_excavatum, + "peripherial pulmonary stenosis"::text as peripherial_pulmonary_stenosis, + "sagittal stenosis"::text as sagittal_stenosis, + "hydronephrosis"::text as hydronephrosis, + "patent ductus arteriosus"::text as patent_ductus_arteriosus, + "duanes syndrome"::text as duanes_syndrome, + "laryngomalacia"::text as laryngomalacia, + "metatarsus adductus"::text as metatarsus_adductus, + "ptosisbilateral"::text as ptosisbilateral, + "microphallus"::text as microphallus, + "sacral agenesis"::text as sacral_agenesis, + "situs inversus"::text as situs_inversus, + "Sample Tissue Type"::text as sample_tissue_type from {{ source('chr_18', 'chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql index 70a74d8..3267410 100644 --- a/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql +++ b/dbt_project/models/kids_first/chr_18/src/S3_Bucket_Scrape/kf_chr_18_src_s3_scrape_cody.sql @@ -1,12 +1,12 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "Size"::integer as "size", - "Key"::text as "key", - "ETag"::text as "etag", - "Bucket"::text as "bucket", - "LastModified"::text as "lastmodified", - "StorageClass"::text as "storageclass" + ROW_NUMBER() OVER () AS kf_index, + "Size"::integer as size, + "Key"::text as key, + "ETag"::text as etag, + "Bucket"::text as bucket, + "LastModified"::text as lastmodified, + "StorageClass"::text as storageclass from {{ source('chr_18', 's3_scrape_cody') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql index 1e0c119..6cb41ba 100644 --- a/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql +++ b/dbt_project/models/kids_first/chr_18/src/Sequencing_Data/kf_chr_18_src_ha_delivery_manifest_6735.sql @@ -1,19 +1,19 @@ {{ config(materialized='table') }} select - ROW_NUMBER() OVER () AS "kf_index", - "type"::text as "type", - "sample.sample_id"::text as "sample", - "file_name"::text as "file_name", - "file_type"::text as "file_type", - "file_description"::text as "file_description", - "file_size"::integer as "file_size", - "md5sum"::text as "md5sum", - "library_id"::text as "library_id", - "library_strategy"::text as "library_strategy", - "library_layout"::text as "library_layout", - "library_source"::text as "library_source", - "platform"::text as "platform", - "instrument_model"::text as "instrument_model" + ROW_NUMBER() OVER () AS kf_index, + "type"::text as type, + "sample.sample_id"::text as sample, + "file_name"::text as file_name, + "file_type"::text as file_type, + "file_description"::text as file_description, + "file_size"::integer as file_size, + "md5sum"::text as md5sum, + "library_id"::text as library_id, + "library_strategy"::text as library_strategy, + "library_layout"::text as library_layout, + "library_source"::text as library_source, + "platform"::text as platform, + "instrument_model"::text as instrument_model from {{ source('chr_18', 'ha_delivery_manifest_6735') }} \ No newline at end of file From 0ac30b677e08a92745a1b009b5f03eb5b7291d88 Mon Sep 17 00:00:00 2001 From: Amanda Warkow Date: Mon, 22 Jun 2026 14:25:12 -0400 Subject: [PATCH 4/4] =?UTF-8?q?=E2=9C=8F=EF=B8=8F=20rename=20all=20models?= =?UTF-8?q?=20to=20KF?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- ...18_stb_accesspolicy.sql => kf_chr_18_stb_accesspolicy.sql} | 2 +- ...itydefinition.sql => kf_chr_18_stb_activitydefinition.sql} | 2 +- ...d.sql => kf_chr_18_stb_activitydefinition_external_id.sql} | 2 +- .../{inc_chr_18_stb_aliquot.sql => kf_chr_18_stb_aliquot.sql} | 2 +- ..._external_id.sql => kf_chr_18_stb_aliquot_external_id.sql} | 2 +- ...collection.sql => kf_chr_18_stb_biospecimencollection.sql} | 2 +- ...ql => kf_chr_18_stb_biospecimencollection_external_id.sql} | 2 +- .../{inc_chr_18_stb_concept.sql => kf_chr_18_stb_concept.sql} | 2 +- .../{inc_chr_18_stb_dataset.sql => kf_chr_18_stb_dataset.sql} | 2 +- ..._dataset_file_id.sql => kf_chr_18_stb_dataset_file_id.sql} | 2 +- ..._publication.sql => kf_chr_18_stb_dataset_publication.sql} | 2 +- ...18_stb_demographics.sql => kf_chr_18_stb_demographics.sql} | 0 ...rnal_id.sql => kf_chr_18_stb_demographics_external_id.sql} | 2 +- ...ographics_race.sql => kf_chr_18_stb_demographics_race.sql} | 0 .../stb/{inc_chr_18_stb_doi.sql => kf_chr_18_stb_doi.sql} | 2 +- ..._doi_external_id.sql => kf_chr_18_stb_doi_external_id.sql} | 2 +- ...c_chr_18_stb_encounter.sql => kf_chr_18_stb_encounter.sql} | 2 +- ...xternal_id.sql => kf_chr_18_stb_encounter_external_id.sql} | 2 +- ...erdefinition.sql => kf_chr_18_stb_encounterdefinition.sql} | 2 +- ...chr_18_stb_encounterdefinition_activity_definition_id.sql} | 2 +- ....sql => kf_chr_18_stb_encounterdefinition_external_id.sql} | 2 +- .../{inc_chr_18_stb_family.sql => kf_chr_18_stb_family.sql} | 2 +- ...y_external_id.sql => kf_chr_18_stb_family_external_id.sql} | 2 +- ...18_stb_familymember.sql => kf_chr_18_stb_familymember.sql} | 2 +- ...rnal_id.sql => kf_chr_18_stb_familymember_external_id.sql} | 2 +- ...yrelationship.sql => kf_chr_18_stb_familyrelationship.sql} | 2 +- ...d.sql => kf_chr_18_stb_familyrelationship_external_id.sql} | 2 +- .../stb/{inc_chr_18_stb_file.sql => kf_chr_18_stb_file.sql} | 0 ...ile_external_id.sql => kf_chr_18_stb_file_external_id.sql} | 2 +- ...tb_file_sample_id.sql => kf_chr_18_stb_file_sample_id.sql} | 2 +- ..._file_subject_id.sql => kf_chr_18_stb_file_subject_id.sql} | 2 +- ...inc_chr_18_stb_filehash.sql => kf_chr_18_stb_filehash.sql} | 0 ...18_stb_investigator.sql => kf_chr_18_stb_investigator.sql} | 2 +- ...rnal_id.sql => kf_chr_18_stb_investigator_external_id.sql} | 2 +- ...r_18_stb_publication.sql => kf_chr_18_stb_publication.sql} | 2 +- ...ernal_id.sql => kf_chr_18_stb_publication_external_id.sql} | 2 +- ...d_external_id.sql => kf_chr_18_stb_record_external_id.sql} | 2 +- .../{inc_chr_18_stb_sample.sql => kf_chr_18_stb_sample.sql} | 0 ...e_external_id.sql => kf_chr_18_stb_sample_external_id.sql} | 2 +- ...ple_processing.sql => kf_chr_18_stb_sample_processing.sql} | 2 +- ...age_method.sql => kf_chr_18_stb_sample_storage_method.sql} | 2 +- .../stb/{inc_chr_18_stb_study.sql => kf_chr_18_stb_study.sql} | 2 +- ....sql => kf_chr_18_stb_study_clinical_data_source_type.sql} | 2 +- ..._stb_study_contact.sql => kf_chr_18_stb_study_contact.sql} | 2 +- ...ata_category.sql => kf_chr_18_stb_study_data_category.sql} | 2 +- ...dy_external_id.sql => kf_chr_18_stb_study_external_id.sql} | 2 +- ...ding_source.sql => kf_chr_18_stb_study_funding_source.sql} | 2 +- ...sql => kf_chr_18_stb_study_participant_lifespan_stage.sql} | 2 +- ...tor.sql => kf_chr_18_stb_study_principal_investigator.sql} | 2 +- ..._stb_study_program.sql => kf_chr_18_stb_study_program.sql} | 2 +- ...dy_publication.sql => kf_chr_18_stb_study_publication.sql} | 2 +- ...rch_domain.sql => kf_chr_18_stb_study_research_domain.sql} | 2 +- ..._study_design.sql => kf_chr_18_stb_study_study_design.sql} | 2 +- ..._stb_studymetadata.sql => kf_chr_18_stb_studymetadata.sql} | 2 +- ...kf_chr_18_stb_studymetadata_clinical_data_source_type.sql} | 2 +- ...gory.sql => kf_chr_18_stb_studymetadata_data_category.sql} | 2 +- ...nal_id.sql => kf_chr_18_stb_studymetadata_external_id.sql} | 2 +- ...f_chr_18_stb_studymetadata_participant_lifespan_stage.sql} | 2 +- ...in.sql => kf_chr_18_stb_studymetadata_research_domain.sql} | 2 +- ...esign.sql => kf_chr_18_stb_studymetadata_study_design.sql} | 2 +- .../{inc_chr_18_stb_subject.sql => kf_chr_18_stb_subject.sql} | 2 +- ..._external_id.sql => kf_chr_18_stb_subject_external_id.sql} | 2 +- ...ubjectassertion.sql => kf_chr_18_stb_subjectassertion.sql} | 2 +- ...concept.sql => kf_chr_18_stb_subjectassertion_concept.sql} | 2 +- ..._id.sql => kf_chr_18_stb_subjectassertion_external_id.sql} | 2 +- ...t.sql => kf_chr_18_stb_subjectassertion_value_concept.sql} | 2 +- ...orepository.sql => kf_chr_18_stb_virtualbiorepository.sql} | 2 +- ...act.sql => kf_chr_18_stb_virtualbiorepository_contact.sql} | 2 +- ...sql => kf_chr_18_stb_virtualbiorepository_external_id.sql} | 2 +- dbt_project/package-lock.yml | 4 ++++ 70 files changed, 68 insertions(+), 64 deletions(-) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_accesspolicy.sql => kf_chr_18_stb_accesspolicy.sql} (84%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_activitydefinition.sql => kf_chr_18_stb_activitydefinition.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_activitydefinition_external_id.sql => kf_chr_18_stb_activitydefinition_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_aliquot.sql => kf_chr_18_stb_aliquot.sql} (86%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_aliquot_external_id.sql => kf_chr_18_stb_aliquot_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_biospecimencollection.sql => kf_chr_18_stb_biospecimencollection.sql} (86%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_biospecimencollection_external_id.sql => kf_chr_18_stb_biospecimencollection_external_id.sql} (72%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_concept.sql => kf_chr_18_stb_concept.sql} (65%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset.sql => kf_chr_18_stb_dataset.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset_file_id.sql => kf_chr_18_stb_dataset_file_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_dataset_publication.sql => kf_chr_18_stb_dataset_publication.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics.sql => kf_chr_18_stb_demographics.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics_external_id.sql => kf_chr_18_stb_demographics_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_demographics_race.sql => kf_chr_18_stb_demographics_race.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_doi.sql => kf_chr_18_stb_doi.sql} (76%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_doi_external_id.sql => kf_chr_18_stb_doi_external_id.sql} (65%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounter.sql => kf_chr_18_stb_encounter.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounter_external_id.sql => kf_chr_18_stb_encounter_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition.sql => kf_chr_18_stb_encounterdefinition.sql} (79%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition_activity_definition_id.sql => kf_chr_18_stb_encounterdefinition_activity_definition_id.sql} (75%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_encounterdefinition_external_id.sql => kf_chr_18_stb_encounterdefinition_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_family.sql => kf_chr_18_stb_family.sql} (83%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_family_external_id.sql => kf_chr_18_stb_family_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familymember.sql => kf_chr_18_stb_familymember.sql} (80%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familymember_external_id.sql => kf_chr_18_stb_familymember_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familyrelationship.sql => kf_chr_18_stb_familyrelationship.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_familyrelationship_external_id.sql => kf_chr_18_stb_familyrelationship_external_id.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file.sql => kf_chr_18_stb_file.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_external_id.sql => kf_chr_18_stb_file_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_sample_id.sql => kf_chr_18_stb_file_sample_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_file_subject_id.sql => kf_chr_18_stb_file_subject_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_filehash.sql => kf_chr_18_stb_filehash.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_investigator.sql => kf_chr_18_stb_investigator.sql} (82%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_investigator_external_id.sql => kf_chr_18_stb_investigator_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_publication.sql => kf_chr_18_stb_publication.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_publication_external_id.sql => kf_chr_18_stb_publication_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_record_external_id.sql => kf_chr_18_stb_record_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample.sql => kf_chr_18_stb_sample.sql} (100%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_external_id.sql => kf_chr_18_stb_sample_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_processing.sql => kf_chr_18_stb_sample_processing.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_sample_storage_method.sql => kf_chr_18_stb_sample_storage_method.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study.sql => kf_chr_18_stb_study.sql} (87%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_clinical_data_source_type.sql => kf_chr_18_stb_study_clinical_data_source_type.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_contact.sql => kf_chr_18_stb_study_contact.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_data_category.sql => kf_chr_18_stb_study_data_category.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_external_id.sql => kf_chr_18_stb_study_external_id.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_funding_source.sql => kf_chr_18_stb_study_funding_source.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_participant_lifespan_stage.sql => kf_chr_18_stb_study_participant_lifespan_stage.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_principal_investigator.sql => kf_chr_18_stb_study_principal_investigator.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_program.sql => kf_chr_18_stb_study_program.sql} (66%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_publication.sql => kf_chr_18_stb_study_publication.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_research_domain.sql => kf_chr_18_stb_study_research_domain.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_study_study_design.sql => kf_chr_18_stb_study_study_design.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata.sql => kf_chr_18_stb_studymetadata.sql} (83%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_clinical_data_source_type.sql => kf_chr_18_stb_studymetadata_clinical_data_source_type.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_data_category.sql => kf_chr_18_stb_studymetadata_data_category.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_external_id.sql => kf_chr_18_stb_studymetadata_external_id.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql => kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_research_domain.sql => kf_chr_18_stb_studymetadata_research_domain.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_studymetadata_study_design.sql => kf_chr_18_stb_studymetadata_study_design.sql} (68%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subject.sql => kf_chr_18_stb_subject.sql} (78%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subject_external_id.sql => kf_chr_18_stb_subject_external_id.sql} (67%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion.sql => kf_chr_18_stb_subjectassertion.sql} (90%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_concept.sql => kf_chr_18_stb_subjectassertion_concept.sql} (70%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_external_id.sql => kf_chr_18_stb_subjectassertion_external_id.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_subjectassertion_value_concept.sql => kf_chr_18_stb_subjectassertion_value_concept.sql} (71%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository.sql => kf_chr_18_stb_virtualbiorepository.sql} (81%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository_contact.sql => kf_chr_18_stb_virtualbiorepository_contact.sql} (69%) rename dbt_project/models/kids_first/chr_18/stb/{inc_chr_18_stb_virtualbiorepository_external_id.sql => kf_chr_18_stb_virtualbiorepository_external_id.sql} (69%) create mode 100644 dbt_project/package-lock.yml diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql similarity index 84% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql index 7f9f41d..00f3c1b 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_accesspolicy.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_accesspolicy.sql @@ -8,5 +8,5 @@ null::text as "disease_limitation", null::text as "access_description", null::text as "website" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql index 570da50..1cd2bc3 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition.sql @@ -6,5 +6,5 @@ null::text as "description", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql index 7ecb81a..0a0bf91 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_activitydefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_activitydefinition_external_id.sql @@ -3,5 +3,5 @@ select null::text as "activitydefinition_activity_definition_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql similarity index 86% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql index b2f7bd2..d5e2293 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot.sql @@ -10,5 +10,5 @@ null::text as "concentration_unit", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql index 02bf1a0..2c49464 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_aliquot_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_aliquot_external_id.sql @@ -3,5 +3,5 @@ select null::text as "aliquot_aliquot_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql similarity index 86% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql index eb9b027..abbf60c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection.sql @@ -10,5 +10,5 @@ null::text as "encounter_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql similarity index 72% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql index 11e8404..11ab9f9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_biospecimencollection_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_biospecimencollection_external_id.sql @@ -3,5 +3,5 @@ select null::text as "biospecimencollection_biospecimen_collection_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql similarity index 65% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql index 4350c7e..436c7e0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_concept.sql @@ -3,5 +3,5 @@ select null::text as "concept_curie", null::text as "display" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql index 33091c0..a1e8495 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset.sql @@ -7,5 +7,5 @@ null::text as "do_id", null::text as "data_collection_start", null::text as "data_collection_end" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql index 9f8eaa0..1ddf2d6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_file_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_file_id.sql @@ -3,5 +3,5 @@ select null::text as "dataset_dataset_id", null::text as "file_id_file_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql index 41fd529..2d08182 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_dataset_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_dataset_publication.sql @@ -3,5 +3,5 @@ select null::text as "dataset_dataset_id", null::integer as "publication_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql index 953521b..3b9d002 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_external_id.sql @@ -3,5 +3,5 @@ select null::text as "demographics_subject_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_demographics_race.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_demographics_race.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql similarity index 76% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql index e330e15..632d186 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi.sql @@ -5,5 +5,5 @@ null::text as "bibliographic_reference", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql similarity index 65% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql index 6dec0dc..4d79e71 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_doi_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_doi_external_id.sql @@ -3,5 +3,5 @@ select null::text as "doi_do_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql index fbb8dc2..2698417 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter.sql @@ -7,5 +7,5 @@ null::integer as "age_at_event", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql index a8f3dc9..a8f68a4 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounter_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounter_external_id.sql @@ -3,5 +3,5 @@ select null::text as "encounter_encounter_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql similarity index 79% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql index 492dbe3..b82f63a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition.sql @@ -6,5 +6,5 @@ null::text as "description", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql similarity index 75% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql index a19a472..d1b003e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_activity_definition_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_activity_definition_id.sql @@ -3,5 +3,5 @@ select null::text as "encounterdefinition_encounter_definition_id", null::text as "activity_definition_id_activity_definition_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql index b283c9c..ea0f884 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_encounterdefinition_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_encounterdefinition_external_id.sql @@ -3,5 +3,5 @@ select null::text as "encounterdefinition_encounter_definition_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql similarity index 83% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql index affd9d3..1497d0c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family.sql @@ -8,5 +8,5 @@ null::text as "family_study_focus", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql index ed70b01..3567c7f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_family_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_family_external_id.sql @@ -3,5 +3,5 @@ select null::text as "family_family_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql similarity index 80% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql index 673f8a2..efbcb26 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember.sql @@ -7,5 +7,5 @@ null::text as "family_role", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql index 4e41c3e..a7117d0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familymember_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familymember_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "familymember_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql index 0161392..9e84927 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship.sql @@ -7,5 +7,5 @@ null::text as "subject_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql index 881cab5..d64ec62 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_familyrelationship_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_familyrelationship_external_id.sql @@ -3,5 +3,5 @@ select null::text as "familyrelationship_family_relationship_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql index cca4563..25567a8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_external_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql index c209f6a..e6f5a31 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_sample_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_sample_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "sample_id_sample_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql index ab988fd..8554e3b 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_file_subject_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_file_subject_id.sql @@ -3,5 +3,5 @@ select null::text as "file_file_id", null::text as "subject_id_subject_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_filehash.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_filehash.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql similarity index 82% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql index f37fca3..f1161de 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator.sql @@ -8,5 +8,5 @@ null::text as "email", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql index 8a6d70f..1e6c882 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_investigator_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_investigator_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "investigator_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql index 99f9165..758fc43 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication.sql @@ -6,5 +6,5 @@ null::text as "website", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql index d433a31..478f978 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_publication_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_publication_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "publication_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql index 2d24622..6873693 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_record_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_record_external_id.sql @@ -3,5 +3,5 @@ select null::integer as "record_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql similarity index 100% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample.sql diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql index 800dae1..9f53c14 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_external_id.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql index 4c4aaf7..0ca6c7c 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_processing.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_processing.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "processing" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql index 96163f6..09f1a7e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_sample_storage_method.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_sample_storage_method.sql @@ -3,5 +3,5 @@ select null::text as "sample_sample_id", null::text as "storage_method" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql similarity index 87% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql index eec3536..b851fe6 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study.sql @@ -12,5 +12,5 @@ null::text as "do_id", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql index 8b5f04b..ad84524 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_clinical_data_source_type.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "clinical_data_source_type" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql index 51ea7a5..5f2874e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_contact.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "contact_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql index 47c5f42..5997d77 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_data_category.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "data_category" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql index 9431889..d7324a2 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_external_id.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql index fd0f9f5..d345ec8 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_funding_source.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_funding_source.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "funding_source" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql index 18a0694..23c43c9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_participant_lifespan_stage.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "participant_lifespan_stage" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql index 323f069..dffdf06 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_principal_investigator.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_principal_investigator.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "principal_investigator_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql similarity index 66% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql index d2ba0e2..e04a170 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_program.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_program.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "program" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql index e543e60..35f2187 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_publication.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_publication.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::integer as "publication_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql index 38790ef..20ebb9f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_research_domain.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "research_domain" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql index c6487a4..2473ea5 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_study_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_study_study_design.sql @@ -3,5 +3,5 @@ select null::text as "study_study_id", null::text as "study_design" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql similarity index 83% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql index 3be97a7..b666f04 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata.sql @@ -7,5 +7,5 @@ null::integer as "expected_number_of_participants", null::integer as "actual_number_of_participants", null::text as "access_policy_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql index 3147a0a..c21df2f 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_clinical_data_source_type.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_clinical_data_source_type.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "clinical_data_source_type" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql index cf9793f..e956c06 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_data_category.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_data_category.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "data_category" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql index d59f31c..6f21f7a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_external_id.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql index b69a575..d351a23 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_participant_lifespan_stage.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_participant_lifespan_stage.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "participant_lifespan_stage" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql index 9807a99..cf2c675 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_research_domain.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_research_domain.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "research_domain" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql similarity index 68% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql index e60ea85..7edc780 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_studymetadata_study_design.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_studymetadata_study_design.sql @@ -3,5 +3,5 @@ select null::text as "studymetadata_study_id", null::text as "study_design" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql similarity index 78% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql index 4e05b34..0941c6a 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject.sql @@ -6,5 +6,5 @@ null::text as "organism_type", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql similarity index 67% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql index 7dfc140..8080cab 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subject_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subject_external_id.sql @@ -3,5 +3,5 @@ select null::text as "subject_subject_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql similarity index 90% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql index e7e3e65..2ae5ad0 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion.sql @@ -15,5 +15,5 @@ null::text as "value_unit_source", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql similarity index 70% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql index a24c514..9771ae9 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_concept.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "concept_concept_curie" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql index 715abdb..f6af07d 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_external_id.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql similarity index 71% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql index 3b170a1..b6a1e23 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_subjectassertion_value_concept.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_subjectassertion_value_concept.sql @@ -3,5 +3,5 @@ select null::text as "subjectassertion_assertion_id", null::text as "value_concept_concept_curie" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql similarity index 81% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql index 93927d3..dd14313 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository.sql @@ -8,5 +8,5 @@ null::text as "vbr_readme", null::text as "access_policy_id", null::text as "study_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql index 25da532..7d01c0e 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_contact.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_contact.sql @@ -3,5 +3,5 @@ select null::text as "virtualbiorepository_vbr_id", null::integer as "contact_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql similarity index 69% rename from dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql rename to dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql index 3d2a785..ccbfcfa 100644 --- a/dbt_project/models/kids_first/chr_18/stb/inc_chr_18_stb_virtualbiorepository_external_id.sql +++ b/dbt_project/models/kids_first/chr_18/stb/kf_chr_18_stb_virtualbiorepository_external_id.sql @@ -3,5 +3,5 @@ select null::text as "virtualbiorepository_vbr_id", null::text as "external_id" - from {{ ref('inc_chr_18_src_chr_18_phenotype_data') }} + from {{ ref('kf_chr_18_src_chr_18_phenotype_data') }} \ No newline at end of file diff --git a/dbt_project/package-lock.yml b/dbt_project/package-lock.yml new file mode 100644 index 0000000..ac29b3f --- /dev/null +++ b/dbt_project/package-lock.yml @@ -0,0 +1,4 @@ +packages: + - package: dbt-labs/dbt_utils + version: 1.3.3 +sha1_hash: 5ffdb7983bbd653b524c5344daf6cb5fd9eaf293