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more cleanup
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@jsstevenson
jsstevenson committed Dec 11, 2024
1 parent 1de4b0d commit eba9f5c
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Showing 2 changed files with 144 additions and 16 deletions.
158 changes: 143 additions & 15 deletions src/regbot/fetch/clinical_trials.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,25 +19,29 @@


def _get_dt_object(raw_date: str) -> datetime.datetime:
"""Extract datetime object from raw date."""
"""Extract datetime object from raw date.
:param raw_date: raw string from JSON response
:return: structured datetime instance depending on available data
"""
try:
return datetime.datetime.strptime(raw_date, "%Y-%m-%d").replace(
tzinfo=datetime.UTC
)
except ValueError:
pass
try:
return datetime.datetime.strptime(raw_date, "%Y-%m").replace(
tzinfo=datetime.UTC
)
except ValueError:
pass
try:
return datetime.datetime.strptime(raw_date, "%Y").replace(tzinfo=datetime.UTC)
except ValueError as e:
msg = f"Unable to format {raw_date} as YYYY-MM-DD, YYYY-MM, or YYYY"
_logger.error(msg)
raise ValueError(msg) from e
try:
return datetime.datetime.strptime(raw_date, "%Y-%m").replace(
tzinfo=datetime.UTC
)
except ValueError:
try:
return datetime.datetime.strptime(raw_date, "%Y").replace(
tzinfo=datetime.UTC
)
except ValueError as e:
msg = f"Unable to format {raw_date} as YYYY-MM-DD, YYYY-MM, or YYYY"
_logger.error(msg)
raise ValueError(msg) from e


ProtocolIdentification = namedtuple(
Expand Down Expand Up @@ -74,6 +78,15 @@ class AgencyClass(StrEnum):


def _format_protocol_id(id_input: dict) -> ProtocolIdentification:
"""Format ProtocolSection.IdentificationModule
See
* https://clinicaltrials.gov/policy/protocol-definitions#identification
* https://clinicaltrials.gov/data-api/about-api/study-data-structure#IdentificationModule
:param id_input: raw module input
:return: structured output
"""
org_study_id_input = id_input.get("orgStudyIdInfo")
if org_study_id_input:
org_study_id = OrgStudyId(
Expand All @@ -94,7 +107,7 @@ def _format_protocol_id(id_input: dict) -> ProtocolIdentification:
else:
org_study_id, secondary_ids = None, None
return ProtocolIdentification(
nct_id=id_input["nctId"],
nct_id=f"clinicaltrials:{id_input['nctId']}",
nct_id_aliases=id_input.get("nctIdAlias"),
org_id=org_study_id,
secondary_org_ids=secondary_ids,
Expand Down Expand Up @@ -180,6 +193,11 @@ class DateType(StrEnum):


def _format_protocol_status_dates(status_input: dict) -> ProtocolStatusDates:
"""Structure dates from ProtocolSection.StatusModule
:param status_input: StatusModule JSON
:return: structured dates data
"""
if "primaryCompletionDateStruct" in status_input:
primary_completion_date = _get_dt_object(
status_input["primaryCompletionDateStruct"]["date"]
Expand Down Expand Up @@ -231,6 +249,15 @@ def _format_protocol_status_dates(status_input: dict) -> ProtocolStatusDates:


def _format_status(status_input: dict) -> ProtocolStatus:
"""Structure ProtocolSection.StatusModule
See
* https://clinicaltrials.gov/policy/protocol-definitions#status
* https://clinicaltrials.gov/data-api/about-api/study-data-structure#StatusModule
:param status_input: raw StatusModule input
:return: structured data
"""
expanded_access_info_input = status_input.get("expandedAccessInfo")
expanded_access_info = (
ExpandedAccessInfo(
Expand Down Expand Up @@ -264,6 +291,13 @@ def _format_status(status_input: dict) -> ProtocolStatus:


def _format_sponsor_collaborators(spo_collab: dict) -> SponsorCollaborators:
"""Format ProtocolSection.SponsorCollaboratorsModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#SponsorCollaboratorsModule
:param spo_collab: raw JSON
:return: structured output
"""
return SponsorCollaborators(
lead_sponsor_name=spo_collab["leadSponsor"]["name"],
lead_sponsor_class=AgencyClass(spo_collab["leadSponsor"]["class"].lower())
Expand All @@ -285,6 +319,13 @@ def _format_sponsor_collaborators(spo_collab: dict) -> SponsorCollaborators:


def _format_oversight(oversight_input: dict) -> Oversight:
"""Format ProtocolSection.OversightModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#OversightModule
:param oversight_input: raw JSON
:return: structured data
"""
return Oversight(
has_dmc=oversight_input.get("oversightHasDmc"),
is_fda_regulated_drug=oversight_input.get("isFdaRegulatedDrug"),
Expand All @@ -298,6 +339,13 @@ def _format_oversight(oversight_input: dict) -> Oversight:


def _format_description(descr_input: dict) -> Description:
"""Format ProtocolSection.DescriptionModule
see https://clinicaltrials.gov/data-api/about-api/study-data-structure#DescriptionModule
:param descr_input: raw JSON
:return: structured output
"""
return Description(
summary=descr_input.get("briefSummary"),
detailed=descr_input.get("detailedDescription"),
Expand Down Expand Up @@ -363,6 +411,13 @@ class EnrollmentType(StrEnum):


def _format_design(design_input: dict) -> Design:
"""Format ProtocolSection.DesignModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#DesignModule
:param design_input: raw JSON
:return: structured data
"""
enrollment = (
Enrollment(
count=design_input["enrollmentInfo"].get("count"),
Expand Down Expand Up @@ -406,6 +461,13 @@ class InterventionType(StrEnum):


def _format_arms_interventions(arms_ints_input: dict) -> ArmsInterventions:
"""Format ProtocolSection.ArmsInterventionsModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#ArmsInterventionsModule
:param arms_ints_input: raw JSON
:return: structured data
"""
interventions = (
[
Intervention(
Expand All @@ -427,6 +489,13 @@ def _format_arms_interventions(arms_ints_input: dict) -> ArmsInterventions:


def _format_outcomes(outcomes: dict) -> Outcomes:
"""Format ProtocolSection.OutcomesModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#OutcomesModule
:param outcomes: raw JSON
:return: structured data
"""
primary = [
Outcome(
measure=po.get("measure"),
Expand Down Expand Up @@ -461,6 +530,13 @@ class StandardAge(StrEnum):


def _format_eligibility(elig_input: dict) -> Eligibility:
"""Format ProtocolSection.EligibilityModule
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#EligibilityModule
:param elig_input: raw JSON
:return: structured data
"""
return Eligibility(
min_age=elig_input.get("minimumAge"),
max_age=elig_input.get("maximumAge"),
Expand All @@ -487,6 +563,15 @@ class ReferenceType(StrEnum):


def _format_reference(ref_input: dict) -> Reference:
"""Format ProtocolSection.ReferencesModule.reference
See
* https://clinicaltrials.gov/data-api/about-api/study-data-structure#Reference
* https://clinicaltrials.gov/policy/protocol-definitions#RefCitations
:param ref_input: raw JSON
:return: structured data
"""
retraction_pmid, retraction_source = None, None
if "retraction" in ref_input:
retraction = ref_input["retraction"]
Expand Down Expand Up @@ -520,6 +605,15 @@ def _format_reference(ref_input: dict) -> Reference:


def _format_protocol(protocol_input: dict) -> Protocol:
"""Format ProtocolSection
See
* https://clinicaltrials.gov/policy/protocol-definitions
* https://clinicaltrials.gov/data-api/about-api/study-data-structure#protocolSection
:param protocol_input: raw JSON
:return: structured data
"""
conditions = (
ProtocolConditions(
conditions=protocol_input["conditionsModule"].get("conditions"),
Expand Down Expand Up @@ -601,6 +695,9 @@ class EventAssessment(StrEnum):


def _format_event(event_input: dict) -> AdverseEvent:
""":param event_input: raw JSON
:return: Structured data
"""
return AdverseEvent(
term=event_input.get("term"),
organ_system=event_input.get("organSystem"),
Expand All @@ -624,6 +721,15 @@ def _format_event(event_input: dict) -> AdverseEvent:


def _format_adverse_events(aes_input: dict) -> AdverseEvents:
"""Format ResultsSection.AdverseEventsModule
See
* https://clinicaltrials.gov/data-api/about-api/study-data-structure#AdverseEventsModule
* https://clinicaltrials.gov/policy/results-definitions#Result_AdverseEvents
:param aes_input: raw JSON
:return: Structured data
"""
return AdverseEvents(
frequency_threshold=aes_input.get("frequencyThreshold"),
timeframe=aes_input.get("timeFrame"),
Expand All @@ -642,6 +748,13 @@ def _format_adverse_events(aes_input: dict) -> AdverseEvents:


def _format_results(results_input: dict) -> Results:
"""Format ResultsSection
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#resultsSection
:param results_input: raw JSON
:return: structured data
"""
return Results(
adverse_events=_format_adverse_events(results_input["adverseEventsModule"])
if "adverseEventsModule" in results_input
Expand All @@ -654,6 +767,14 @@ def _format_results(results_input: dict) -> Results:


def _format_derived(der_input: dict) -> Derived:
"""Format DerivedSection data
See https://clinicaltrials.gov/data-api/about-api/study-data-structure#DerivedSection
:param der_input: raw JSON
:return: structured data
"""
return Derived(
conditions=[
MeshConcept(id=c.get("id"), term=c.get("term"))
Expand All @@ -668,6 +789,13 @@ def _format_derived(der_input: dict) -> Derived:


def _format_study(study_input: dict) -> Study:
"""Format a raw study JSON object received from the ClinicalTrials.gov API
See https://clinicaltrials.gov/data-api/about-api/study-data-structure
:param study_input: raw JSON
:return: Structured data
"""
return Study(
protocol=_format_protocol(study_input["protocolSection"]),
results=_format_results(study_input["resultsSection"])
Expand Down
2 changes: 1 addition & 1 deletion tests/test_fetch_clinical_trials.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ def test_fetch_clinical_trials(fixtures_dir: Path):
assert results
example = results[2]

assert example.protocol.identification.nct_id == "NCT05386680"
assert example.protocol.identification.nct_id == "clinicaltrials:NCT05386680"
assert example.protocol.identification.org_id.id == "COAV101B12302"
assert (
example.protocol.sponsor_collaborators.lead_sponsor_name
Expand Down

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