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Remove tissue_type, specimen_type, and realted pieces
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@yuanzhou
yuanzhou committed Nov 11, 2023
1 parent 8be60a6 commit 83a4b57
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28 changes: 0 additions & 28 deletions src/schema/provenance_schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -897,33 +897,6 @@ ENTITIES:
- validate_sample_category
before_property_update_validators:
- validate_sample_category

# No logner required on create, specimen_type -> sample_category 12/15/2022
specimen_type:
type: string
#required_on_create: true # Only required for create via POST, not update via PUT
description: "A code representing the type of specimen. Must be one of the codes specified in: [tissue sample types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml)"
# Validate the given value against the definitions: https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml
# Disabled validation 12/15/2022
# before_property_create_validators:
# - validate_specimen_type
# before_property_update_validators:
# - validate_specimen_type
specimen_type_other:
type: string
description: "The user provided sample type if the 'other' sample_type is chosen."


# specimen_type no logner required on create, will remove this field when removing specimen_type
# Simply always set to 'Unknown' and no need to update 12/15/2022
tissue_type:
type: string
generated: true # Can not be updated via the PUT
#auto_update: true # Will always update automatically if the entity gets updated
description: 'The type of the tissue based on the mapping between type (Block/Section/Suspension) and the specimen_type, default is Unknown'
before_create_trigger: set_tissue_type
#before_update_trigger: set_tissue_type

portal_metadata_upload_files:
type: json_string
description: "A list of relative paths to metadata files"
Expand All @@ -949,7 +922,6 @@ ENTITIES:
immutable: true
description: "The displayname of globus group which the user who created this entity is a member of"
before_create_trigger: set_group_name
# Should be required on create only when specimen_type==organ
organ:
type: string
description: "Organ code specifier, only set if sample_type == organ. Valid values found in: [organ types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml)"
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5 changes: 0 additions & 5 deletions src/schema/schema_constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,11 @@
class SchemaConstants(object):
MEMCACHED_TTL = 7200

# Constants used by validators
INGEST_API_APP = 'ingest-api'
INGEST_PIPELINE_APP = 'ingest-pipeline'
HUBMAP_APP_HEADER = 'X-Hubmap-Application'
DATASET_STATUS_PUBLISHED = 'published'

# Used by triggers, all lowercase for easy comparision
ACCESS_LEVEL_PUBLIC = 'public'
ACCESS_LEVEL_CONSORTIUM = 'consortium'
ACCESS_LEVEL_PROTECTED = 'protected'
Expand All @@ -19,9 +17,6 @@ class SchemaConstants(object):
ONTOLOGY_API_ASSAY_TYPES_ENDPOINT = '/assaytype?application_context=HuBMAP'
ONTOLOGY_API_ORGAN_TYPES_ENDPOINT = '/organs?application_context=HuBMAP'

# For generating Sample.tissue_type
TISSUE_TYPES_YAML = 'https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml'

DOI_BASE_URL = 'https://doi.org/'

# Define an enumeration to classify an entity's visibility, which can be combined with
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99 changes: 0 additions & 99 deletions src/schema/schema_triggers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1562,105 +1562,6 @@ def get_sample_direct_ancestor(property_key, normalized_type, user_token, existi
return property_key, schema_manager.normalize_entity_result_for_response(direct_ancestor_dict)


"""
Trigger event method of generating the type of the tissue based on the mapping between type (Block/Section/Suspension) and the specimen_type
This method applies to both the create and update triggers
Rererence:
- https://docs.google.com/spreadsheets/d/1OODo8QK852txSNSmfIe0ua4A7nPFSgKq6h46grmrpto/edit#gid=0
- https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml
Parameters
----------
property_key : str
The target property key of the value to be generated
normalized_type : str
One of the types defined in the schema yaml: Sample
user_token: str
The user's globus nexus token
existing_data_dict : dict
A dictionary that contains all existing entity properties
new_data_dict : dict
A merged dictionary that contains all possible input data to be used
Returns
-------
str: The target property key
str: The type of the tissue
"""
def set_tissue_type(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
# specimen_type is no logner required on create 12/15/2022, set to Unknown
# Default to use 'Unknown'
tissue_type = 'Unknown'

# # The `specimen_type` field is required on entity creation via POST
# # thus should be available on existing entity update via PUT
# # We do a double check here just in case
# if ('specimen_type' not in new_data_dict) and ('specimen_type' not in existing_data_dict):
# raise KeyError("Missing 'specimen_type' key in both 'new_data_dict' and 'existing_data_dict' during calling 'set_tissue_type()' trigger method.")

# # Always calculate the tissue_type value no matter new creation or update existing
# # The `specimen_type` field can be used in a PUT
# # But if it's not in the request JSON of a PUT, it must be in the existing data
# if 'specimen_type' in new_data_dict:
# # The `specimen_type` value validation is handled in the `schema_validators.validate_specimen_type()`
# # and that gets called before this trigger method
# specimen_type = new_data_dict['specimen_type'].lower()
# else:
# # Use lowercase in case someone manually updated the neo4j filed with incorrect case
# specimen_type = existing_data_dict['specimen_type'].lower()

# # Categories: Block, Section, Suspension
# block_category = [
# 'pbmc',
# 'biopsy',
# 'segment',
# 'ffpe_block',
# 'organ_piece',
# 'fresh_tissue',
# 'clarity_hydrogel',
# 'fixed_tissue_piece',
# 'fresh_frozen_tissue',
# 'fresh_frozen_oct_block',
# 'formalin_fixed_oct_block',
# 'pfa_fixed_frozen_oct_block',
# 'flash_frozen_liquid_nitrogen',
# 'frozen_cell_pellet_buffy_coat'
# ]

# section_category = [
# 'ffpe_slide',
# 'fixed_frozen_section_slide',
# 'fresh_frozen_section_slide',
# 'fresh_frozen_tissue_section',
# 'cryosections_curls_rnalater',
# 'cryosections_curls_from_fresh_frozen_oct'
# ]

# suspension_category = [
# 'gdna',
# 'serum',
# 'plasma',
# 'nuclei',
# 'protein',
# 'rna_total',
# 'cell_lysate',
# 'tissue_lysate',
# 'sequence_library',
# 'ran_poly_a_enriched',
# 'single_cell_cryopreserved'
# ]

# # Capitalized type, default is 'Unknown' if no match
# if specimen_type in block_category:
# tissue_type = 'Block'
# elif specimen_type in section_category:
# tissue_type = 'Section'
# elif specimen_type in suspension_category:
# tissue_type = 'Suspension'

return property_key, tissue_type


####################################################################################################
## Trigger methods specific to Publication - DO NOT RENAME
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71 changes: 0 additions & 71 deletions src/schema/schema_validators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -430,33 +430,6 @@ def validate_upload_status_value(property_key, normalized_entity_type, request,
raise ValueError(f"Invalid status value: {new_status}")


"""
NOTE: TO BE REMOVED when we remove specimen_type field
Validate the provided value of Sample.specimen_type on create via POST and update via PUT
Parameters
----------
property_key : str
The target property key
normalized_type : str
Submission
request: Flask request object
The instance of Flask request passed in from application request
existing_data_dict : dict
A dictionary that contains all existing entity properties
new_data_dict : dict
The json data in request body, already after the regular validations
"""
def validate_specimen_type(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
# Use lowercase for comparison
defined_tissue_types = _get_tissue_types()
specimen_type = new_data_dict[property_key].lower()

if specimen_type not in defined_tissue_types:
raise ValueError(f"Invalid specimen_type value: {specimen_type}")


"""
Validate the provided value of Sample.sample_category on create via POST and update via PUT
Expand Down Expand Up @@ -562,47 +535,3 @@ def _validate_application_header(applications_allowed, request_headers):
msg = f"Unable to proceed due to invalid {SchemaConstants.HUBMAP_APP_HEADER} header value: {app_header}"
raise schema_errors.InvalidApplicationHeaderException(msg)


"""
Get the complete list of defined tissue types
Returns
-------
list: The list of defined tissue types
"""
def _get_tissue_types():
yaml_file_url = SchemaConstants.TISSUE_TYPES_YAML

# Use Memcached to improve performance
response = schema_manager.make_request_get(yaml_file_url)

if response.status_code == 200:
yaml_file = response.text

try:
tissue_types_dict = yaml.safe_load(response.text)

# We don't need the description here, just a list of tissue types
# Note: dict.keys() returns a dict, need to typecast to list
tissue_types_list = list(tissue_types_dict.keys())

# Add the 'other'
tissue_types_list.append('other')

return tissue_types_list
except yaml.YAMLError as e:
raise yaml.YAMLError(e)
else:
msg = f"Unable to fetch the: {yaml_file_url}"
# Log the full stack trace, prepend a line with our message
logger.exception(msg)

logger.debug("======_get_tissue_types() status code======")
logger.debug(response.status_code)

logger.debug("======_get_tissue_types() response text======")
logger.debug(response.text)

# Also bubble up the error message
raise requests.exceptions.RequestException(response.text)

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