Skip to content

Commit

Permalink
refactoring
Browse files Browse the repository at this point in the history
  • Loading branch information
@lei0zhou
lei0zhou committed Sep 9, 2024
1 parent f494a98 commit be67008
Show file tree
Hide file tree
Showing 3 changed files with 99 additions and 70 deletions.
125 changes: 77 additions & 48 deletions lib/epiviewpoint/bulk_fhir_parser.ex
View file
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ defmodule EpiViewpoint.BulkFhirParser do
file_content
|> String.split("\n")
|> Stream.map(&String.trim/1)
|> Stream.filter(&filter_empty_lines/1)
|> Stream.filter(&(&1 != ""))
|> Stream.map(&json_to_kindle_schema/1)
|> Enum.to_list()

Expand Down Expand Up @@ -86,23 +86,25 @@ defmodule EpiViewpoint.BulkFhirParser do
{:error, "Unknown resource type: #{unknown_type}"}
end

defp extract_patient(%EpiViewpoint.R4.Patient{
id: caseid,
identifier: [%EpiViewpoint.R4.Identifier{value: person_tid}],
name: [%EpiViewpoint.R4.HumanName{given: [search_firstname], family: search_lastname}],
birth_date: dateofbirth,
gender: sex,
address: [
%EpiViewpoint.R4.Address{
line: [diagaddress_street1],
city: diagaddress_city,
state: diagaddress_state,
postal_code: diagaddress_zip
}
],
telecom: [%EpiViewpoint.R4.ContactPoint{value: phonenumber}],
extension: extensions
}) do
defp extract_patient(%EpiViewpoint.R4.Patient{} = patient) do
%EpiViewpoint.R4.Patient{
id: caseid,
identifier: [%EpiViewpoint.R4.Identifier{value: person_tid}],
name: [%EpiViewpoint.R4.HumanName{given: [search_firstname], family: search_lastname}],
birth_date: dateofbirth,
gender: sex,
address: [
%EpiViewpoint.R4.Address{
line: [diagaddress_street1],
city: diagaddress_city,
state: diagaddress_state,
postal_code: diagaddress_zip
}
],
telecom: [%EpiViewpoint.R4.ContactPoint{value: phonenumber}],
extension: extensions
} = patient

%{
caseid: caseid,
person_tid: person_tid,
Expand All @@ -115,22 +117,24 @@ defmodule EpiViewpoint.BulkFhirParser do
diagaddress_state: diagaddress_state,
diagaddress_zip: diagaddress_zip,
phonenumber: phonenumber,
ethnicity: find_extension(extensions, "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"),
occupation: find_extension(extensions),
race: find_extension(extensions, "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race")
ethnicity: find_extension(extensions, :ethnicity),
occupation: find_extension(extensions, :occupation),
race: find_extension(extensions, :race)
}
end

defp extract_observation(%EpiViewpoint.R4.Observation{
id: lab_result_tid,
subject: %EpiViewpoint.R4.Reference{reference: "Patient/" <> pat_id},
effective_date_time: datecollected,
issued: resultdate,
code: %EpiViewpoint.R4.CodeableConcept{text: testname},
interpretation: [%EpiViewpoint.R4.CodeableConcept{coding: [%EpiViewpoint.R4.Coding{display: result}]}],
performer: [%EpiViewpoint.R4.Reference{reference: "Organization/" <> org_id}],
extension: extensions
}) do
defp extract_observation(%EpiViewpoint.R4.Observation{} = observation) do
%EpiViewpoint.R4.Observation{
id: lab_result_tid,
subject: %EpiViewpoint.R4.Reference{reference: "Patient/" <> pat_id},
effective_date_time: datecollected,
issued: resultdate,
code: %EpiViewpoint.R4.CodeableConcept{text: testname},
interpretation: [%EpiViewpoint.R4.CodeableConcept{coding: [%EpiViewpoint.R4.Coding{display: result}]}],
performer: [%EpiViewpoint.R4.Reference{reference: "Organization/" <> org_id}],
extension: extensions
} = observation

%{
lab_result_tid: lab_result_tid,
pat_id: pat_id,
Expand All @@ -139,31 +143,60 @@ defmodule EpiViewpoint.BulkFhirParser do
testname: testname,
result: result,
org_id: org_id,
datereportedtolhd: find_extension(extensions)
datereportedtolhd: find_extension(extensions, :datereportedtolhd)
}
end

defp extract_organization(%EpiViewpoint.R4.Organization{
id: organization_id,
name: ordering_facility_name
}) do
defp extract_organization(%EpiViewpoint.R4.Organization{} = organization) do
%EpiViewpoint.R4.Organization{
id: organization_id,
name: ordering_facility_name
} = organization

%{
organization_id: organization_id,
ordering_facility_name: ordering_facility_name
}
end

defp find_extension(extensions, url \\ nil) do
Enum.find_value(extensions, fn
defp find_extension(extensions, :race) do
Enum.find_value(extensions, nil, fn
%EpiViewpoint.R4.Extension{
url: "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
extension: [%EpiViewpoint.R4.Extension{url: "ombCategory", value_coding: %EpiViewpoint.R4.Coding{display: value}}, _]
} ->
value

_ ->
nil
end)
end

defp find_extension(extensions, :ethnicity) do
Enum.find_value(extensions, nil, fn
%EpiViewpoint.R4.Extension{
url: ^url,
url: "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
extension: [%EpiViewpoint.R4.Extension{url: "ombCategory", value_coding: %EpiViewpoint.R4.Coding{display: value}}, _]
} ->
value

_ ->
nil
end)
end

defp find_extension(extensions, :occupation) do
Enum.find_value(extensions, nil, fn
%EpiViewpoint.R4.Extension{url: "http://hl7.org/fhir/StructureDefinition/patient-occupation", value_string: value} ->
value

_ ->
nil
end)
end

defp find_extension(extensions, :datereportedtolhd) do
Enum.find_value(extensions, nil, fn
%EpiViewpoint.R4.Extension{url: "http://hl7.org/fhir/StructureDefinition/datereportedtolhd", value_date: value} ->
value

Expand All @@ -183,23 +216,19 @@ defmodule EpiViewpoint.BulkFhirParser do
end

defp merge_resources(observation, patients, organizations) do
patient = Enum.find(patients, &(&1.caseid == observation.pat_id))
organization = Enum.find(organizations, &(&1.organization_id == observation.org_id))
patient = Enum.find(patients, %{}, &(&1.caseid == observation.pat_id))
organization = Enum.find(organizations, %{}, &(&1.organization_id == observation.org_id))

observation
|> Map.merge(patient || %{})
|> Map.merge(organization || %{})
|> Map.merge(patient)
|> Map.merge(organization)
|> Map.drop([:pat_id, :org_id, :organization_id])
end

defp to_map(resources, contents) do
%{file_name: "load.bulk_fhir", contents: contents, list: resources}
end

defp filter_empty_lines(line) do
line != ""
end

defp format_date(date) when is_struct(date, Date), do: Calendar.strftime(date, "%m/%d/%Y")
defp format_date(datetime) when is_struct(datetime, DateTime), do: datetime |> DateTime.to_date() |> format_date()
defp format_date(datetime) when is_struct(datetime, DateTime), do: DateTime.to_date(datetime) |> format_date()
end
4 changes: 2 additions & 2 deletions lib/epiviewpoint_web/controllers/import_controller.ex
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ defmodule EpiViewpointWeb.ImportController do

case result do
{:ok, import_info} ->
{_imported_people, popped_import_info} = import_info |> Map.pop(:imported_people)
{_imported_people, popped_import_info} = Map.pop(import_info, :imported_people)

conn
|> Session.set_last_file_import_info(popped_import_info)
Expand All @@ -50,7 +50,7 @@ defmodule EpiViewpointWeb.ImportController do

case result do
{:ok, import_info} ->
{_imported_people, popped_import_info} = import_info |> Map.pop(:imported_people)
{_imported_people, popped_import_info} = Map.pop(import_info, :imported_people)

conn
|> Session.set_last_file_import_info(popped_import_info)
Expand Down
40 changes: 20 additions & 20 deletions test/epiviewpoint/data_file_test.exs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -218,11 +218,11 @@ defmodule EpiViewpoint.DataFileTest do
}
]

assert {:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{first_name last_name dob sample_date result_date result},
optional: ~w{}
)
{:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{first_name last_name dob sample_date result_date result},
optional: ~w{}
)

assert result == [
%{
Expand Down Expand Up @@ -253,11 +253,11 @@ defmodule EpiViewpoint.DataFileTest do
}
]

assert {:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{column_a},
optional: ~w{column_b}
)
{:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{column_a},
optional: ~w{column_b}
)

assert result == [%{"column_a" => "value_a", "column_b" => "value_b"}]
end
Expand Down Expand Up @@ -288,11 +288,11 @@ defmodule EpiViewpoint.DataFileTest do
}
]

assert {:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{column_a column_b},
optional: ~w{optional_c optional_d}
)
{:ok, result} =
DataFile.read(input, :bulk_fhir, &Function.identity/1,
required: ~w{column_a column_b},
optional: ~w{optional_c optional_d}
)

assert result == [%{"column_a" => "value_a", "column_b" => "value_b", "optional_c" => "value_c"}]
end
Expand All @@ -309,11 +309,11 @@ defmodule EpiViewpoint.DataFileTest do
}
]

assert {:ok, result} =
DataFile.read(input, :bulk_fhir, fn headers -> Enum.map(headers, &String.upcase/1) end,
required: ~w{FIRST_NAME LAST_NAME},
optional: ~w{}
)
{:ok, result} =
DataFile.read(input, :bulk_fhir, fn headers -> Enum.map(headers, &String.upcase/1) end,
required: ~w{FIRST_NAME LAST_NAME},
optional: ~w{}
)

assert result == [
%{
Expand Down

0 comments on commit be67008

Please sign in to comment.