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Validate config changes #552

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Validate config changes #552

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533b6ef
Initial commit with changes to Tab.
ptth222 Jan 30, 2024
3d3e036
Added no_config parameter to Tab validate.
ptth222 Feb 23, 2024
52c376f
no_config added everywhere and tests fixed
ptth222 Mar 15, 2024
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87 changes: 49 additions & 38 deletions isatools/isajson/validate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -693,11 +693,12 @@ def check_measurement_technology_types(assay_json, configs):
)


def check_study_and_assay_graphs(study_json, configs):
def check_assay_graph(process_sequence_json, config):
def check_study_and_assay_graphs(study_json, configs, no_config):
def check_assay_graph(process_sequence_json, config, no_config):
list_of_last_processes_in_sequence = [i for i in process_sequence_json if "nextProcess" not in i.keys()]
log.info("Checking against assay protocol sequence configuration {}".format(config["description"]))
config_protocol_sequence = [i["protocol"] for i in config["protocols"]]
if not no_config:
log.info("Checking against assay protocol sequence configuration {}".format(config["description"]))
config_protocol_sequence = [i["protocol"] for i in config["protocols"]]
for process in list_of_last_processes_in_sequence: # build graphs backwards
assay_graph = list()
try:
Expand Down Expand Up @@ -727,40 +728,48 @@ def check_assay_graph(process_sequence_json, config):
break
except KeyError: # this happens when we can"t find a previousProcess
pass
assay_graph.reverse()
assay_protocol_sequence = [[j for j in i if not j.startswith("#")] for i in assay_graph]
assay_protocol_sequence = [i for j in assay_protocol_sequence for i in j] # flatten list
assay_protocol_sequence_of_interest = [i for i in assay_protocol_sequence if i in config_protocol_sequence]
# filter out protocols in sequence that are not of interest (additional ones to required by config)
squished_assay_protocol_sequence_of_interest = list()
prev_prot = None
for prot in assay_protocol_sequence_of_interest: # remove consecutive same protocols
if prev_prot != prot:
squished_assay_protocol_sequence_of_interest.append(prot)
prev_prot = prot
from isatools.utils import contains
if not contains(squished_assay_protocol_sequence_of_interest, config_protocol_sequence):
warnings.append({
"message": "Process sequence is not valid against configuration",
"supplemental": "Config protocol sequence {} does not in assay protocol sequence {}".format(
config_protocol_sequence,
squished_assay_protocol_sequence_of_interest),
"code": 4004
})
log.warning("Configuration protocol sequence {} does not match study graph found in {}"
.format(config_protocol_sequence, assay_protocol_sequence))

if not no_config:
assay_graph.reverse()
assay_protocol_sequence = [[j for j in i if not j.startswith("#")] for i in assay_graph]
assay_protocol_sequence = [i for j in assay_protocol_sequence for i in j] # flatten list
assay_protocol_sequence_of_interest = [i for i in assay_protocol_sequence if i in config_protocol_sequence]
# filter out protocols in sequence that are not of interest (additional ones to required by config)
squished_assay_protocol_sequence_of_interest = list()
prev_prot = None
for prot in assay_protocol_sequence_of_interest: # remove consecutive same protocols
if prev_prot != prot:
squished_assay_protocol_sequence_of_interest.append(prot)
prev_prot = prot
from isatools.utils import contains
if not contains(squished_assay_protocol_sequence_of_interest, config_protocol_sequence):
warnings.append({
"message": "Process sequence is not valid against configuration",
"supplemental": "Config protocol sequence {} does not in assay protocol sequence {}".format(
config_protocol_sequence,
squished_assay_protocol_sequence_of_interest),
"code": 4004
})
log.warning("Configuration protocol sequence {} does not match study graph found in {}"
.format(config_protocol_sequence, assay_protocol_sequence))

protocols_and_types = dict([(i["@id"], i["protocolType"]["annotationValue"]) for i in study_json["protocols"]])
# first check study graph
log.info("Loading configuration (study)")
config = configs["study"]
check_assay_graph(study_json["processSequence"], config)
if not no_config:
log.info("Loading configuration (study)")
config = configs["study"]
else:
config = {}
check_assay_graph(study_json["processSequence"], config, no_config)
for assay_json in study_json["assays"]:
m = assay_json["measurementType"]["annotationValue"]
t = assay_json["technologyType"]["annotationValue"]
log.info("Loading configuration ({}, {})".format(m, t))
config = configs[(m, t)]
check_assay_graph(assay_json["processSequence"], config)
if not no_config:
log.info("Loading configuration ({}, {})".format(m, t))
config = configs[(m, t)]
else:
config = {}
check_assay_graph(assay_json["processSequence"], config, no_config)


def check_study_groups(study_or_assay):
Expand Down Expand Up @@ -811,7 +820,8 @@ def validate(
fp,
config_dir=default_config_dir,
log_level=None,
base_schemas_dir="isa_model_version_1_0_schemas"
base_schemas_dir="isa_model_version_1_0_schemas",
no_config: bool = False
):
if config_dir is None:
config_dir = default_config_dir
Expand Down Expand Up @@ -887,10 +897,11 @@ def validate(
check_term_accession_used_no_source_ref(isa_json) # Rule 3010
log.info("Loading configurations from " + config_dir)
configs = load_config(config_dir) # Rule 4001
log.info("Checking measurement and technology types...")
for study_json in isa_json["studies"]:
for assay_json in study_json["assays"]:
check_measurement_technology_types(assay_json, configs) # Rule 4002
if not no_config:
log.info("Checking measurement and technology types...")
for study_json in isa_json["studies"]:
for assay_json in study_json["assays"]:
check_measurement_technology_types(assay_json, configs) # Rule 4002
log.info("Checking against configuration schemas...")
check_isa_schemas(
isa_json=isa_json,
Expand All @@ -907,7 +918,7 @@ def validate(
fp.seek(0) # reset file pointer
log.info("Checking study and assay graphs...")
for study_json in isa_json["studies"]:
check_study_and_assay_graphs(study_json, configs) # Rule 4004
check_study_and_assay_graphs(study_json, configs, no_config) # Rule 4004
fp.seek(0)
# try load and do study groups check
log.info("Checking study groups...")
Expand Down
5 changes: 4 additions & 1 deletion isatools/isatab/validate/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,14 +169,16 @@ def validate(fp: TextIO,
config_dir: str = default_config_dir,
origin: str or None = None,
rules: dict = None,
log_level=None) -> dict:
log_level=None,
no_config: bool = False) -> dict:
"""
A function to validate an ISA investigation tab file
:param fp: the investigation file handler
:param config_dir: the XML configuration directory
:param origin: value accepted = mzml2isa or None
:param rules: optional rules to run (default: all rules)
:param log_level: optional log level (default: INFO)
:param no_config: whether or not to validate against configs (default: False)
:return: a dictionary of the validation results (errors, warnings and info)
"""
if not log_level:
Expand All @@ -191,6 +193,7 @@ def validate(fp: TextIO,
"investigation_df_dict": i_df_dict,
"dir_context": path.dirname(fp.name),
"configs": config_dir,
"no_config": no_config
}
investigation_validator = ISAInvestigationValidator(**params, **built_rules['investigation'])

Expand Down
21 changes: 15 additions & 6 deletions isatools/isatab/validate/rules/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@

from pandas import DataFrame

from isatools.io import isatab_configurator
from isatools.utils import utf8_text_file_open
from isatools.isatab.defaults import NUMBER_OF_STUDY_GROUPS
from isatools.isatab.load import load_table
Expand Down Expand Up @@ -112,22 +113,25 @@ def __init__(self,
dir_context: str,
configs: str,
available_rules: list = INVESTIGATION_RULES_MAPPING,
rules_to_run: tuple = DEFAULT_INVESTIGATION_RULES):
rules_to_run: tuple = DEFAULT_INVESTIGATION_RULES,
no_config: bool = False):
""" The ISA investigation validator class

:param investigation_df_dict: a dictionary of DataFrames and lists of DataFrames representing the investigation file
:param dir_context: the directory of the investigation
:param configs: directory of the XML config files
:param available_rules: a customizable list of all available rules for investigation objects
:param rules_to_run: a customizable tuple of rules identifiers to run for investigation objects
:param no_config: whether or not to validate against configs (default: False)
"""
self.all_rules = Rules(rules_to_run=rules_to_run, available_rules=available_rules)
self.has_validated = False
self.params = {
'investigation_df_dict': investigation_df_dict,
'dir_context': dir_context,
'configs': configs,
'term_source_refs': None
'term_source_refs': None,
"no_config": no_config
}
self.all_rules.validate_rules(validator=self)

Expand All @@ -140,7 +144,8 @@ def __init__(self,
study_filename: str,
study_df: DataFrame,
available_rules: List = STUDY_RULES_MAPPING,
rules_to_run: tuple = DEFAULT_STUDY_RULES):
rules_to_run: tuple = DEFAULT_STUDY_RULES,
no_config: bool = False):
"""
The ISA study validator class
:param validator: the investigation validator
Expand All @@ -149,13 +154,15 @@ def __init__(self,
:param study_df: the study dataframe
:param available_rules: a customizable list of all available rules for investigation objects
:param rules_to_run: a customizable tuple of rules identifiers to run for investigation objects
:param no_config: whether or not to validate against configs (default: False)
"""
self.all_rules = Rules(rules_to_run=rules_to_run, available_rules=available_rules)
self.has_validated = False
self.params = {
**validator.params,
'study_df': study_df,
'config': validator.params['configs'][('[sample]', '')],
'config': validator.params['configs'][('[sample]', '')] if ('[sample]', '') in validator.params['configs']
else isatab_configurator.IsaTabConfigFileType(),
'study_filename': study_filename
}
with utf8_text_file_open(path.join(self.params['dir_context'], study_filename)) as s_fp:
Expand Down Expand Up @@ -183,7 +190,8 @@ def __init__(self,
assay_filename: str = None,
assay_df: DataFrame = None,
available_rules: List = ASSAY_RULES_MAPPING,
rules_to_run: tuple = DEFAULT_ASSAY_RULES):
rules_to_run: tuple = DEFAULT_ASSAY_RULES,
no_config: bool = False):
"""
The ISA assay validator class
:param assay_tables: list of assay tables
Expand All @@ -193,6 +201,7 @@ def __init__(self,
:param assay_df: the assay dataframe
:param available_rules: a customizable list of all available rules for investigation objects
:param rules_to_run: a customizable tuple of rules identifiers to run for investigation objects
:param no_config: whether or not to validate against configs (default: False)
"""
self.all_rules = Rules(rules_to_run=rules_to_run, available_rules=available_rules)
self.has_validated = False
Expand All @@ -207,7 +216,7 @@ def __init__(self,
if assay_filename != '':
lowered_mt = assay_df['Study Assay Measurement Type'].tolist()[assay_index].lower()
lowered_tt = assay_df['Study Assay Technology Type'].tolist()[assay_index].lower()
self.params['config'] = self.params['configs'].get((lowered_mt, lowered_tt), None)
self.params['config'] = self.params['configs'].get((lowered_mt, lowered_tt), isatab_configurator.IsaTabConfigFileType())
if self.params['config']:
with utf8_text_file_open(path.join(self.params['dir_context'], assay_filename)) as a_fp:
self.params['assay_table'] = load_table(a_fp)
Expand Down
34 changes: 17 additions & 17 deletions isatools/isatab/validate/rules/defaults.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,9 @@
{'rule': check_pubmed_ids_format, 'params': ['investigation_df_dict'], 'identifier': '3003'},
{'rule': check_ontology_sources, 'params': ['investigation_df_dict'], 'identifier': '3008'},

{'rule': load_config, 'params': ['configs'], 'identifier': '4001'},
{'rule': check_measurement_technology_types, 'params': ['investigation_df_dict', 'configs'], 'identifier': '4002'},
{'rule': check_investigation_against_config, 'params': ['investigation_df_dict', 'configs'], 'identifier': '4003'},
{'rule': load_config, 'params': ['configs', 'no_config'], 'identifier': '4001'},
{'rule': check_measurement_technology_types, 'params': ['investigation_df_dict', 'configs', 'no_config'], 'identifier': '4002'},
{'rule': check_investigation_against_config, 'params': ['investigation_df_dict', 'configs', 'no_config'], 'identifier': '4003'},

# copies
{'rule': check_table_files_read, 'params': ['investigation_df_dict', 'dir_context'], 'identifier': '0008'},
Expand All @@ -58,22 +58,22 @@

STUDY_RULES_MAPPING = [

{'rule': check_unit_field, 'params': ['study_sample_table', 'config'], 'identifier': '1099'},
{'rule': check_unit_field, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '1099'},

{
'rule': check_ontology_fields,
'params': ['study_sample_table', 'config', 'term_source_refs'],
'params': ['study_sample_table', 'config', 'term_source_refs', 'no_config'],
'identifier': '3010'
},

{'rule': check_required_fields, 'params': ['study_sample_table', 'config'], 'identifier': '4003'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4003'},
{'rule': check_factor_value_presence, 'params': ['study_sample_table'], 'identifier': '4007'},
{
'rule': check_protocol_fields,
'params': ['study_sample_table', 'config', 'protocol_names_and_types'],
'params': ['study_sample_table', 'config', 'protocol_names_and_types', 'no_config'],
'identifier': '4009'
},
{'rule': check_field_values, 'params': ['study_sample_table', 'config'], 'identifier': '4011'},
{'rule': check_field_values, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4011'},
{'rule': load_table_checks, 'params': ['study_sample_table', 'study_filename'], 'identifier': '4014'},

{
Expand All @@ -83,30 +83,30 @@
},

# copies
{'rule': check_required_fields, 'params': ['study_sample_table', 'config'], 'identifier': '4008'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config'], 'identifier': '4010'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4008'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4010'},
]

ASSAY_RULES_MAPPING = [
{'rule': check_sample_names, 'params': ['study_sample_table', 'assay_tables'], 'identifier': '0000'},

{'rule': check_unit_field, 'params': ['assay_table', 'config'], 'identifier': '1099'},
{'rule': check_unit_field, 'params': ['assay_table', 'config', 'no_config'], 'identifier': '1099'},

{'rule': check_ontology_fields, 'params': ['assay_table', 'config', 'term_source_refs'], 'identifier': '3010'},
{'rule': check_ontology_fields, 'params': ['assay_table', 'config', 'term_source_refs', 'no_config'], 'identifier': '3010'},

{'rule': check_required_fields, 'params': ['assay_table', 'config'], 'identifier': '4003'},
{'rule': check_required_fields, 'params': ['assay_table', 'config', 'no_config'], 'identifier': '4003'},
{'rule': check_factor_value_presence, 'params': ['assay_table'], 'identifier': '4007'},
{
'rule': check_protocol_fields,
'params': ['assay_table', 'config', 'protocol_names_and_types'],
'params': ['assay_table', 'config', 'protocol_names_and_types', 'no_config'],
'identifier': '4009'
},
{'rule': check_field_values, 'params': ['assay_table', 'config'], 'identifier': '4011'},
{'rule': check_field_values, 'params': ['assay_table', 'config', 'no_config'], 'identifier': '4011'},
{'rule': load_table_checks, 'params': ['assay_table', 'assay_filename'], 'identifier': '4014'},

# copies
{'rule': check_required_fields, 'params': ['study_sample_table', 'config'], 'identifier': '4008'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config'], 'identifier': '4010'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4008'},
{'rule': check_required_fields, 'params': ['study_sample_table', 'config', 'no_config'], 'identifier': '4010'},

{
'rule': check_study_groups,
Expand Down
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