Merge pull request #53 from OCHA-DAP/main

HDXDSYS-1318  Simplify poverty rate HAPI pipeline to read from global…

Author: ccataalin

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [0.10.36] = 2025-01-30
+
+### Changed
+
+- Row functions in Admins use HXL tags instead of headers
+- Poverty rate columns updated
+
 ## [0.10.35] = 2025-01-27
 
 ### Changed

pyproject.toml

@@ -39,7 +39,7 @@ dependencies = [
     "hdx-python-country>= 3.8.7",
     "hdx-python-database[postgresql]>= 1.3.4",
     "hdx-python-scraper>= 2.5.5",
-    "hdx-python-utilities>= 3.8.2",
+    "hdx-python-utilities>= 3.8.3",
     "libhxl",
     "sqlalchemy"
 ]

requirements.txt

@@ -69,7 +69,7 @@ hdx-python-database==1.3.4
     # via hapi-pipelines (pyproject.toml)
 hdx-python-scraper==2.5.5
     # via hapi-pipelines (pyproject.toml)
-hdx-python-utilities==3.8.2
+hdx-python-utilities==3.8.3
     # via
     #   hapi-pipelines (pyproject.toml)
     #   hdx-python-api
@@ -295,7 +295,7 @@ xlrd3==1.1.0
     # via libhxl
 xlsx2csv==0.8.4
     # via hdx-python-utilities
-xlsxwriter==3.2.1
+xlsxwriter==3.2.2
     # via tableschema-to-template
 xlwt==1.3.0
     # via hdx-python-utilities

src/hapi/pipelines/database/admins.py

@@ -26,7 +26,7 @@
 
 
 class Admins(BaseUploader):
-    admin_name_regex = re.compile(r"Admin (\d) Name")
+    admin_name_regex = re.compile(r"#adm(\d)\+name")
 
     def __init__(
         self,
@@ -202,29 +202,77 @@ def get_admin2_ref(
         return ref
 
     @classmethod
-    def get_max_admin_from_headers(cls, headers) -> int:
+    def get_max_admin_from_hxltags(cls, hxltag_to_header: Dict) -> int:
         max_admin_level = 0
-        for header in headers:
-            match = cls.admin_name_regex.match(header)
+        for hxltag in hxltag_to_header:
+            match = cls.admin_name_regex.match(hxltag)
             if match:
                 admin_level = int(match.group(1))
                 if admin_level > max_admin_level:
                     max_admin_level = admin_level
         return max_admin_level
 
     @staticmethod
-    def get_admin_level_from_row(row: Dict, max_admin_level: int) -> int:
+    def get_admin_level_from_row(
+        hxltag_to_header: Dict,
+        row: Dict,
+        max_admin_level: int,
+    ) -> int:
         for i in range(max_admin_level, 0, -1):
-            admin_name = row.get(f"Admin {i} Name")
+            admin_name = row.get(hxltag_to_header[f"#adm{i}+name"])
             if admin_name:
                 return i
         return 0
 
+    def get_admin1_ref_from_row(
+        self,
+        hxltag_to_header: Dict,
+        row: Dict,
+        dataset_name: str,
+        pipeline: str,
+        admin_level: int,
+    ) -> Optional[int]:
+        if admin_level == 1:
+            admin_code = row[hxltag_to_header["#adm1+code"]]
+            if admin_code:
+                admin1_ref = self.get_admin1_ref(
+                    "adminone",
+                    admin_code,
+                    dataset_name,
+                    pipeline,
+                    self._error_handler,
+                )
+                if admin1_ref:
+                    return admin1_ref
+            admin_code = get_admin1_to_location_connector_code(
+                row[hxltag_to_header["#country+code"]]
+            )
+            return self.get_admin1_ref(
+                "adminone",
+                admin_code,
+                dataset_name,
+                pipeline,
+                self._error_handler,
+            )
+        if admin_level == 0:
+            return self.get_admin1_ref(
+                "national",
+                row[hxltag_to_header["#country+code"]],
+                dataset_name,
+                pipeline,
+                self._error_handler,
+            )
+
     def get_admin2_ref_from_row(
-        self, row: Dict, dataset_name: str, pipeline: str, admin_level: int
+        self,
+        hxltag_to_header: Dict,
+        row: Dict,
+        dataset_name: str,
+        pipeline: str,
+        admin_level: int,
     ) -> Optional[int]:
         if admin_level == 2:
-            admin_code = row["Admin 2 PCode"]
+            admin_code = row[hxltag_to_header["#adm2+code"]]
             if admin_code:
                 admin2_ref = self.get_admin2_ref(
                     "admintwo",
@@ -235,7 +283,7 @@ def get_admin2_ref_from_row(
                 )
                 if admin2_ref:
                     return admin2_ref
-            admin_code = row["Admin 1 PCode"]
+            admin_code = row[hxltag_to_header["#adm1+code"]]
             if admin_code:
                 admin_code = get_admin2_to_admin1_connector_code(admin_code)
                 admin2_ref = self.get_admin2_ref(
@@ -248,7 +296,7 @@ def get_admin2_ref_from_row(
                 if admin2_ref:
                     return admin2_ref
             admin_code = get_admin2_to_location_connector_code(
-                row["Country ISO3"]
+                row[hxltag_to_header["#country+code"]]
             )
             return self.get_admin2_ref(
                 "admintwo",
@@ -258,7 +306,7 @@ def get_admin2_ref_from_row(
                 self._error_handler,
             )
         if admin_level == 1:
-            admin_code = row["Admin 1 PCode"]
+            admin_code = row[hxltag_to_header["#adm1+code"]]
             if admin_code:
                 admin2_ref = self.get_admin2_ref(
                     "adminone",
@@ -270,7 +318,7 @@ def get_admin2_ref_from_row(
                 if admin2_ref:
                     return admin2_ref
             admin_code = get_admin1_to_location_connector_code(
-                row["Country ISO3"]
+                row[hxltag_to_header["#country+code"]]
             )
             return self.get_admin2_ref(
                 "adminone",
@@ -282,7 +330,7 @@ def get_admin2_ref_from_row(
         if admin_level == 0:
             return self.get_admin2_ref(
                 "national",
-                row["Country ISO3"],
+                row[hxltag_to_header["#country+code"]],
                 dataset_name,
                 pipeline,
                 self._error_handler,

src/hapi/pipelines/database/humanitarian_needs.py

@@ -6,6 +6,7 @@
 from hapi_schema.db_humanitarian_needs import DBHumanitarianNeeds
 from hdx.api.configuration import Configuration
 from hdx.scraper.framework.utilities.reader import Read
+from hdx.utilities.dictandlist import invert_dictionary
 from hdx.utilities.text import get_numeric_if_possible
 from sqlalchemy.orm import Session
 
@@ -47,23 +48,27 @@ def populate(self) -> None:
             time_period_end = datetime(year, 12, 31, 23, 59, 59)
             url = resource["url"]
             headers, rows = reader.get_tabular_rows(url, dict_form=True)
-            max_admin_level = self._admins.get_max_admin_from_headers(headers)
+            hxltag_to_header = invert_dictionary(next(rows))
+            max_admin_level = self._admins.get_max_admin_from_hxltags(
+                hxltag_to_header
+            )
             # Admin 1 PCode,Admin 2 PCode,Sector,Gender,Age Group,Disabled,Population Group,Population,In Need,Targeted,Affected,Reached
             for row in rows:
                 error = row.get("Error")
                 if error:
                     continue
-                countryiso3 = row["Country ISO3"]
-                if countryiso3 == "#country+code":  # ignore HXL row
-                    continue
                 admin_level = self._admins.get_admin_level_from_row(
-                    row, max_admin_level
+                    hxltag_to_header, row, max_admin_level
                 )
                 # Can't handle higher admin levels
                 if admin_level > 2:
                     continue
                 admin2_ref = self._admins.get_admin2_ref_from_row(
-                    row, dataset_name, "HumanitarianNeeds", admin_level
+                    hxltag_to_header,
+                    row,
+                    dataset_name,
+                    "HumanitarianNeeds",
+                    admin_level,
                 )
                 if not admin2_ref:
                     continue

src/hapi/pipelines/database/operational_presence.py

@@ -7,6 +7,7 @@
 from hdx.api.utilities.hdx_error_handler import HDXErrorHandler
 from hdx.scraper.framework.utilities.reader import Read
 from hdx.utilities.dateparse import parse_date
+from hdx.utilities.dictandlist import invert_dictionary
 from sqlalchemy.orm import Session
 
 from ..utilities.batch_populate import batch_populate
@@ -42,23 +43,23 @@ def populate(self) -> None:
         resource = dataset.get_resource()
         url = resource["url"]
         headers, rows = reader.get_tabular_rows(url, dict_form=True)
-        max_admin_level = self._admins.get_max_admin_from_headers(headers)
+        hxltag_to_header = invert_dictionary(next(rows))
+        max_admin_level = self._admins.get_max_admin_from_hxltags(
+            hxltag_to_header
+        )
         resources_to_ignore = []
         operational_presence_rows = []
         # Country ISO3,Admin 1 PCode,Admin 1 Name,Admin 2 PCode,Admin 2 Name,Admin 3 PCode,Admin 3 Name,Org Name,Org Acronym,Org Type,Sector,Start Date,End Date,Resource Id
         for row in rows:
             resource_id = row["Resource Id"]
             if resource_id in resources_to_ignore:
                 continue
-            countryiso3 = row["Country ISO3"]
             dataset_id = row["Dataset Id"]
-            if dataset_id[0] == "#":
-                continue
             dataset_name = self._metadata.get_dataset_name(dataset_id)
             if not dataset_name:
                 dataset_name = dataset_id
             admin_level = self._admins.get_admin_level_from_row(
-                row, max_admin_level
+                hxltag_to_header, row, max_admin_level
             )
             actual_admin_level = admin_level
             # Higher admin levels treat as admin 2
@@ -68,10 +69,16 @@ def populate(self) -> None:
             else:
                 error_when_duplicate = True
             admin2_ref = self._admins.get_admin2_ref_from_row(
-                row, dataset_name, "OperationalPresence", admin_level
+                hxltag_to_header,
+                row,
+                dataset_name,
+                "OperationalPresence",
+                admin_level,
             )
             if not admin2_ref:
                 continue
+
+            countryiso3 = row["Country ISO3"]
             provider_admin1_name = get_provider_name(row, "Admin 1 Name")
             provider_admin2_name = get_provider_name(row, "Admin 2 Name")
 

src/hapi/pipelines/database/poverty_rate.py

@@ -8,13 +8,12 @@
 from hdx.api.utilities.hdx_error_handler import HDXErrorHandler
 from hdx.scraper.framework.utilities.reader import Read
 from hdx.utilities.dateparse import parse_date
-from hdx.utilities.dictandlist import dict_of_lists_add
+from hdx.utilities.dictandlist import dict_of_lists_add, invert_dictionary
 from hdx.utilities.text import get_numeric_if_possible
 from sqlalchemy.orm import Session
 
 from ..utilities.provider_admin_names import get_provider_name
 from . import admins
-from .admins import get_admin1_to_location_connector_code
 from .base_uploader import BaseUploader
 from .metadata import Metadata
 
@@ -36,29 +35,6 @@ def __init__(
         self._configuration = configuration
         self._error_handler = error_handler
 
-    def get_admin1_ref(self, row, dataset_name):
-        countryiso3 = row["country_code"]
-        if countryiso3 == "#country+code":  # ignore HXL row
-            return None
-        admin_code = row["admin1_code"]
-        if admin_code:
-            admin_level = "adminone"
-        else:
-            admin1_name = row["admin1_name"]
-            if admin1_name:
-                admin_level = "adminone"
-                admin_code = get_admin1_to_location_connector_code(countryiso3)
-            else:
-                admin_level = "national"
-                admin_code = countryiso3
-        return self._admins.get_admin1_ref(
-            admin_level,
-            admin_code,
-            dataset_name,
-            "PovertyRate",
-            self._error_handler,
-        )
-
     def populate(self) -> None:
         logger.info("Populating poverty rate table")
         reader = Read.get_reader("hdx")
@@ -69,9 +45,9 @@ def populate(self) -> None:
         null_values_by_iso3 = {}
 
         def get_value(row: Dict, in_col: str) -> float:
-            countryiso3 = row["country_code"]
+            countryiso3 = row["Country ISO3"]
             value = row[in_col]
-            admin_name = row["admin1_name"]
+            admin_name = row["Admin 1 Name"]
             if not admin_name:
                 admin_name = countryiso3
             if value is None:
@@ -84,18 +60,24 @@ def get_value(row: Dict, in_col: str) -> float:
             resource_id = resource["id"]
             self._metadata.add_resource(dataset_id, resource)
             url = resource["url"]
-            _, rows = reader.get_tabular_rows(url, dict_form=True)
-
-            # country_code,admin1_code,admin1_name,mpi,headcount_ratio,intensity_of_deprivation,vulnerable_to_poverty,in_severe_poverty,reference_period_start,reference_period_end
+            header, rows = reader.get_tabular_rows(url, dict_form=True)
+            hxltag_to_header = invert_dictionary(next(rows))
             for row in rows:
-                admin1_ref = self.get_admin1_ref(row, dataset_name)
+                admin_level = self._admins.get_admin_level_from_row(
+                    hxltag_to_header, row, 1
+                )
+                admin1_ref = self._admins.get_admin1_ref_from_row(
+                    hxltag_to_header,
+                    row,
+                    dataset_name,
+                    "PovertyRate",
+                    admin_level,
+                )
                 if not admin1_ref:
                     continue
-                provider_admin1_name = get_provider_name(row, "admin1_name")
-                reference_period_start = parse_date(
-                    row["reference_period_start"]
-                )
-                reference_period_end = parse_date(row["reference_period_end"])
+                provider_admin1_name = get_provider_name(row, "Admin 1 Name")
+                reference_period_start = parse_date(row["Start Date"])
+                reference_period_end = parse_date(row["End Date"])
                 key = (
                     admin1_ref,
                     provider_admin1_name,
@@ -118,15 +100,15 @@ def get_value(row: Dict, in_col: str) -> float:
                     provider_admin1_name=provider_admin1_name,
                     reference_period_start=reference_period_start,
                     reference_period_end=reference_period_end,
-                    mpi=get_value(row, "mpi"),
-                    headcount_ratio=get_value(row, "headcount_ratio"),
+                    mpi=get_value(row, "MPI"),
+                    headcount_ratio=get_value(row, "Headcount Ratio"),
                     intensity_of_deprivation=get_value(
-                        row, "intensity_of_deprivation"
+                        row, "Intensity of Deprivation"
                     ),
                     vulnerable_to_poverty=get_value(
-                        row, "vulnerable_to_poverty"
+                        row, "Vulnerable to Poverty"
                     ),
-                    in_severe_poverty=get_value(row, "in_severe_poverty"),
+                    in_severe_poverty=get_value(row, "In Severe Poverty"),
                 )
                 self._session.add(row)
         self._session.commit()

tests/fixtures/input/download-global-mpi-trends.csv

@@ -1,4 +1,4 @@
-country_code,admin1_code,admin1_name,mpi,headcount_ratio,intensity_of_deprivation,vulnerable_to_poverty,in_severe_poverty,reference_period_start,reference_period_end
+Country ISO3,Admin 1 PCode,Admin 1 Name,MPI,Headcount Ratio,Intensity of Deprivation,Vulnerable to Poverty,In Severe Poverty,Start Date,End Date
 #country+code,#adm1+code,#adm1+name,#indicator+mpi,#indicator+headcount_ratio,#indicator+intensity_of_deprivation,#indicator+vulnerable_to_poverty,#indicator+in_severe_poverty,#date+start,#date+end
 AFG,,,0.2342396091002832,46.93584855784794,49.90633306897293,27.381337677259033,20.80265720520784,2015-01-01 00:00:00+00:00,2016-12-31 00:00:00+00:00
 AFG,,,0.2683302947167732,52.177907473390185,51.42603598153431,26.33666305841249,25.971520762600047,2022-01-01 00:00:00+00:00,2023-12-31 00:00:00+00:00