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Refactor czi_hosted and server into backend directory, pull common code into backend/common, refactor tests (#2102)

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* move local_server -> backend/server server-> backend/czi_hosted, pull common code into backend/common update imports, tests and make commands
This commit is contained in:
Madison Dunitz
2021-03-26 00:27:07 -05:00
committed by GitHub
parent e6e358ddc8
commit 78c9d24ed4
425 changed files with 734 additions and 5317 deletions
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backend/server/converters/schema/schema_definitions/1_0_0.yaml
+95
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title: Corpora schema version 1.0.0
type: anndata
components:
uns:
type: dict
keys:
version:
type: dict
keys:
corpora_schema_version: null
corpora_encoding_version: null
title:
type: string
contributors:
type: stringified list of dicts
layer_descriptions:
type: dict
keys:
X: null
organism:
type: string
nullable: false
organism_ontology_term_id:
type: curie
prefixes:
- NCBITaxon
var:
type: dataframe
index:
type: human-readable string
unique: true
obs:
type: dataframe
index:
unique: true
columns:
tissue:
type: human-readable string
nullable: false
tissue_ontology_term_id:
type: suffixed curie
nullable: true
prefixes:
- UBERON
assay:
type: human-readable string
nullable: false
assay_ontology_term_id:
type: curie
nullable: true
prefixes:
- EFO
disease:
type: human-readable string
nullable: false
disease_ontology_term_id:
type: curie
nullable: true
prefixes:
- MONDO
- PATO
cell_type:
type: human-readable string
nullable: false
cell_type_ontology_term_id:
type: curie
nullable: true
prefixes:
- CL
- UBERON
sex:
type: string
enum:
- male
- female
- mixed
- unknown
- other
ethnicity:
type: human-readable string
nullable: false
ethnicity_ontology_term_id:
type: curie
nullable: true
prefixes:
- HANCESTRO
development_stage:
type: human-readable string
nullable: false
development_stage_ontology_term_id:
type: curie
nullable: true
prefixes:
- HsapDv
- EFO
backend/server/converters/schema/schema_definitions/1_1_0.yaml
+93
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@@ -0,0 +1,93 @@
title: Corpora schema version 1.1.0
type: anndata
components:
uns:
type: dict
keys:
version:
type: dict
keys:
corpora_schema_version: null
corpora_encoding_version: null
title:
type: string
layer_descriptions:
type: dict
keys:
X: null
organism:
type: string
nullable: false
organism_ontology_term_id:
type: curie
prefixes:
- NCBITaxon
var:
type: dataframe
index:
type: human-readable string
unique: true
obs:
type: dataframe
index:
unique: true
columns:
tissue:
type: human-readable string
nullable: false
tissue_ontology_term_id:
type: suffixed curie
nullable: true
prefixes:
- UBERON
assay:
type: human-readable string
nullable: false
assay_ontology_term_id:
type: curie
nullable: true
prefixes:
- EFO
disease:
type: human-readable string
nullable: false
disease_ontology_term_id:
type: curie
nullable: true
prefixes:
- MONDO
- PATO
cell_type:
type: human-readable string
nullable: false
cell_type_ontology_term_id:
type: curie
nullable: true
prefixes:
- CL
- UBERON
sex:
type: string
enum:
- male
- female
- mixed
- unknown
- other
ethnicity:
type: human-readable string
nullable: false
ethnicity_ontology_term_id:
type: curie
nullable: true
prefixes:
- HANCESTRO
development_stage:
type: human-readable string
nullable: false
development_stage_ontology_term_id:
type: curie
nullable: true
prefixes:
- HsapDv
- EFO