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DO NOT MERGE - PENDING QA SIGN OFF: TheAnvil Release Q3 1598473585 (#…
…1986) * copying etlMapping.yaml to gen3.theanvil.io * copying manifest.json to gen3.theanvil.io * copying manifests/hatchery/hatchery.json to gen3.theanvil.io * copying portal/gitops-favicon.ico to gen3.theanvil.io * copying portal/gitops-logo.png to gen3.theanvil.io * copying portal/gitops.css to gen3.theanvil.io * copying portal/gitops.json to gen3.theanvil.io * fix etlMapping so it will reference prod values as expected * set 2020.08 for hatchery component * match fence version from internal staging Co-authored-by: Marcelo Costa <marceloc@uchicago.edu>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,119 +1,121 @@ | ||
| mappings: | ||
| - name: gen3.theanvil.io_subject | ||
| doc_type: subject | ||
| type: aggregator | ||
| root: subject | ||
| props: | ||
| - name: submitter_id | ||
| - name: project_id | ||
| - name: sex | ||
| - name: age_value | ||
| - name: ancestry | ||
| - name: disease_description | ||
| - name: phenotype_present | ||
| - name: phenotype_absent | ||
| - name: disease_id | ||
| - name: solve_state | ||
| - name: congenital_status | ||
| - name: age_of_onset | ||
| aggregated_props: | ||
| - name: sample_provider | ||
| path: samples | ||
| src: sample_provider | ||
| fn: set | ||
| - name: tissue_affected_status | ||
| path: samples | ||
| src: tissue_affected_status | ||
| fn: set | ||
| - name: tissue_type | ||
| path: samples | ||
| src: tissue_type | ||
| fn: set | ||
| - name: sample_type | ||
| path: samples | ||
| src: sample_type | ||
| fn: set | ||
| - name: original_material_type | ||
| path: samples | ||
| src: original_material_type | ||
| fn: set | ||
| - name: exome_capture_platform | ||
| path: samples.sequencings | ||
| src: exome_capture_platform | ||
| fn: set | ||
| - name: library_prep_kit_method | ||
| path: samples.sequencings | ||
| src: library_prep_kit_method | ||
| fn: set | ||
| - name: capture_region_bed_file | ||
| path: samples.sequencings | ||
| src: capture_region_bed_file | ||
| fn: set | ||
| - name: reference_genome_build | ||
| path: samples.sequencings | ||
| src: reference_genome_build | ||
| fn: set | ||
| - name: sequencing_assay | ||
| path: samples.sequencings | ||
| src: sequencing_assay | ||
| fn: set | ||
| - name: alignment_method | ||
| path: samples.sequencings | ||
| src: alignment_method | ||
| fn: set | ||
| - name: data_processing_pipeline | ||
| path: samples.sequencings | ||
| src: data_processing_pipeline | ||
| fn: set | ||
| - name: _samples_count | ||
| path: samples | ||
| fn: count | ||
| - name: _sequencings_count | ||
| path: samples.sequencings | ||
| fn: count | ||
| joining_props: | ||
| - index: file | ||
| join_on: subject_id | ||
| - name: gen3.theanvil.io_subject | ||
| doc_type: subject | ||
| type: aggregator | ||
| root: subject | ||
| props: | ||
| - name: data_format | ||
| src: data_format | ||
| fn: set | ||
| - name: data_type | ||
| src: data_type | ||
| fn: set | ||
| parent_props: | ||
| - path: projects[project_code:code] | ||
| - path: projects[project_name:name] | ||
| - path: projects[project_dbgap_phs:dbgap_phs] | ||
| - path: projects[project_dbgap_consent_text:dbgap_consent_text] | ||
| - path: projects[project_short_name:short_name] | ||
| - path: projects[project_dbgap_accession_number:dbgap_accession_number] | ||
| - name: gen3.theanvil.io_file | ||
| doc_type: file | ||
| type: collector | ||
| root: None | ||
| category: data_file | ||
| props: | ||
| - name: project_id | ||
| - name: submitter_id | ||
| - name: object_id | ||
| - name: md5sum | ||
| - name: file_name | ||
| - name: file_size | ||
| - name: data_format | ||
| - name: data_type | ||
| - name: state | ||
| - name: data_category | ||
| - name: analyte_type | ||
| - name: sequencing_assay | ||
| injecting_props: | ||
| subject: | ||
| props: | ||
| - name: subject_id | ||
| src: id | ||
| - name: submitter_id | ||
| - name: project_id | ||
| - name: sex | ||
| - name: age_value | ||
| - name: ancestry | ||
| - name: disease_description | ||
| - name: phenotype_present | ||
| - name: phenotype_absent | ||
| - name: disease_id | ||
| - name: solve_state | ||
| - name: congenital_status | ||
| - name: age_of_onset | ||
| # flatten_props: | ||
| aggregated_props: | ||
| - name: sample_provider | ||
| path: samples | ||
| src: sample_provider | ||
| fn: set | ||
| - name: subject_submitter_id | ||
| src: submitter_id | ||
| - name: tissue_affected_status | ||
| path: samples | ||
| src: tissue_affected_status | ||
| fn: set | ||
| - name: project_id | ||
| - name: tissue_type | ||
| path: samples | ||
| src: tissue_type | ||
| fn: set | ||
| - name: sample_type | ||
| path: samples | ||
| src: sample_type | ||
| fn: set | ||
| - name: original_material_type | ||
| path: samples | ||
| src: original_material_type | ||
| fn: set | ||
| - name: exome_capture_platform | ||
| path: samples.sequencings | ||
| src: exome_capture_platform | ||
| fn: set | ||
| - name: library_prep_kit_method | ||
| path: samples.sequencings | ||
| src: library_prep_kit_method | ||
| fn: set | ||
| - name: capture_region_bed_file | ||
| path: samples.sequencings | ||
| src: capture_region_bed_file | ||
| fn: set | ||
| - name: reference_genome_build | ||
| path: samples.sequencings | ||
| src: reference_genome_build | ||
| fn: set | ||
| - name: sequencing_assay | ||
| path: samples.sequencings | ||
| src: sequencing_assay | ||
| fn: set | ||
| - name: alignment_method | ||
| path: samples.sequencings | ||
| src: alignment_method | ||
| fn: set | ||
| - name: data_processing_pipeline | ||
| path: samples.sequencings | ||
| src: data_processing_pipeline | ||
| fn: set | ||
| - name: _samples_count | ||
| path: samples | ||
| fn: count | ||
| - name: _sequencings_count | ||
| path: samples.sequencings | ||
| fn: count | ||
| joining_props: | ||
| - index: file | ||
| join_on: subject_id | ||
| props: | ||
| - name: data_format | ||
| src: data_format | ||
| fn: set | ||
| - name: data_type | ||
| src: data_type | ||
| fn: set | ||
| parent_props: | ||
| - path: projects[project_code:code] | ||
| - path: projects[project_name:name] | ||
| - path: projects[project_dbgap_phs:dbgap_phs] | ||
| - path: projects[project_dbgap_consent_text:dbgap_consent_text] | ||
| - path: projects[project_short_name:short_name] | ||
| - path: projects[project_dbgap_accession_number:dbgap_accession_number] | ||
|
|
||
| - name: gen3.theanvil.io_file | ||
| doc_type: file | ||
| type: collector | ||
| root: None | ||
| category: data_file | ||
| props: | ||
| - name: project_id | ||
| - name: submitter_id | ||
| - name: object_id | ||
| - name: md5sum | ||
| - name: file_name | ||
| - name: file_size | ||
| - name: data_format | ||
| - name: data_type | ||
| - name: state | ||
| - name: data_category | ||
| - name: analyte_type | ||
| - name: sequencing_assay | ||
| injecting_props: | ||
| subject: | ||
| props: | ||
| - name: subject_id | ||
| src: id | ||
| fn: set | ||
| - name: subject_submitter_id | ||
| src: submitter_id | ||
| fn: set | ||
| - name: project_id | ||
| fn: set |
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