diff --git a/docs/source/Af1.rst b/docs/source/Af1.rst index c841ae6d7..145925e7b 100644 --- a/docs/source/Af1.rst +++ b/docs/source/Af1.rst @@ -54,6 +54,7 @@ Sample metadata access plot_samples_bar plot_samples_interactive_map wgs_data_catalog + cohorts SNP data access --------------- diff --git a/docs/source/Ag3.rst b/docs/source/Ag3.rst index 2d9b3ea48..821310e2b 100644 --- a/docs/source/Ag3.rst +++ b/docs/source/Ag3.rst @@ -54,6 +54,7 @@ Sample metadata access plot_samples_bar plot_samples_interactive_map wgs_data_catalog + cohorts SNP data access --------------- diff --git a/malariagen_data/anoph/sample_metadata.py b/malariagen_data/anoph/sample_metadata.py index 10b71ed14..d3b7bc15f 100644 --- a/malariagen_data/anoph/sample_metadata.py +++ b/malariagen_data/anoph/sample_metadata.py @@ -1058,6 +1058,40 @@ def _setup_cohort_queries( return cohort_queries_checked + @check_types + @doc( + summary=""" + Read data for a specific cohort set, including cohort size, + country code, taxon, administrative units name, ISO code, geoBoundaries + shape ID and representative latitude and longitude points. + """, + parameters=dict( + cohort_set=""" + A cohort set name. Accepted values are: + "admin1_month", "admin1_quarter", "admin1_year", + "admin2_month", "admin2_quarter", "admin2_year". + """ + ), + returns="A dataframe of cohort data, one row per cohort.", + ) + def cohorts( + self, + cohort_set: base_params.cohorts, + ) -> pd.DataFrame: + major_version_path = self._major_version_path + cohorts_analysis = self._cohorts_analysis + + path = f"{major_version_path[:2]}_cohorts/cohorts_{cohorts_analysis}/cohorts_{cohort_set}.csv" + + # Read the manifest into a pandas dataframe. + with self.open_file(path) as f: + df_cohorts = pd.read_csv(f, sep=",", na_values="") + + # Ensure all column names are lower case. + df_cohorts.columns = [c.lower() for c in df_cohorts.columns] + + return df_cohorts + def locate_cohorts(*, cohorts, data): # Build cohort dictionary where key=cohort_id, value=loc_coh. diff --git a/tests/anoph/conftest.py b/tests/anoph/conftest.py index 380cac365..ad15f2c0b 100644 --- a/tests/anoph/conftest.py +++ b/tests/anoph/conftest.py @@ -1099,7 +1099,7 @@ def init_config(self): "SITE_ANNOTATIONS_ZARR_PATH": "reference/genome/agamp4/Anopheles-gambiae-PEST_SEQANNOTATION_AgamP4.12.zarr", "DEFAULT_AIM_ANALYSIS": "20220528", "DEFAULT_SITE_FILTERS_ANALYSIS": "dt_20200416", - "DEFAULT_COHORTS_ANALYSIS": "20230223", + "DEFAULT_COHORTS_ANALYSIS": "20230516", "SITE_MASK_IDS": ["gamb_colu_arab", "gamb_colu", "arab"], "PHASING_ANALYSIS_IDS": ["gamb_colu_arab", "gamb_colu", "arab"], "COVERAGE_CALLS_ANALYSIS_IDS": ["gamb_colu", "arab"], @@ -1258,7 +1258,7 @@ def write_metadata(self, release, release_path, sample_set, aim=True, cohorts=Tr / "vo_agam_release" / release_path / "metadata" - / "cohorts_20230223" + / "cohorts_20230516" / sample_set / "samples.cohorts.csv" ) @@ -1268,13 +1268,32 @@ def write_metadata(self, release, release_path, sample_set, aim=True, cohorts=Tr self.bucket_path / release_path / "metadata" - / "cohorts_20230223" + / "cohorts_20230516" / sample_set / "samples.cohorts.csv" ) dst_path.parent.mkdir(parents=True, exist_ok=True) df_coh_ds.to_csv(dst_path, index=False) + # Create cohorts data by sampling from some real files. + src_path = ( + self.fixture_dir + / "vo_agam_release" + / "v3_cohorts" + / "cohorts_20230516" + / "cohorts_admin1_month.csv" + ) + dst_path = ( + self.bucket_path + / "v3_cohorts" + / "cohorts_20230516" + / "cohorts_admin1_month.csv" + ) + dst_path.parent.mkdir(parents=True, exist_ok=True) + with open(src_path, mode="r") as src, open(dst_path, mode="w") as dst: + for line in src.readlines()[:5]: + print(line, file=dst) + # Create data catalog by sampling from some real metadata files. src_path = ( self.fixture_dir diff --git a/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv b/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv deleted file mode 100644 index 3344fe83f..000000000 --- a/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv +++ /dev/null @@ -1,82 +0,0 @@ -sample_id,country,country_ISO,adm1_name,adm1_ISO,adm2_name -AR0047-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0049-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0051-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0061-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0078-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0080-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0084-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0097-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0072-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0094-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0095-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0083-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0093-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0021-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0082-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0008-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0085-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0098-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0092-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0017-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0015-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0019-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0100-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0034-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0086-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0057-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0076-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0042-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0063-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0012-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0087-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0065-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0038-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0089-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0071-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0096-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0088-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0066-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0023-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0020-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0024-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0014-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0079-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0027-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0075-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0077-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0007-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0062-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0060-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0022-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0002-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0059-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0048-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0011-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0009-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0043-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0035-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0074-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0045-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0073-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0004-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0040-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0052-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0064-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0044-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0036-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0001-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0006-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0046-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0070-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0010-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0090-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0054-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0016-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0050-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0069-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0018-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0081-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0013-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0026-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0053-C,Angola,AGO,Luanda,AO-LUA,Luanda diff --git a/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv b/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv new file mode 100644 index 000000000..3d3124dd2 --- /dev/null +++ b/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv @@ -0,0 +1,82 @@ +sample_id,country,country_ISO,country_alpha2,country_alpha3,adm1_name,adm1_ISO,admin1_geoboundaries_shape_id,admin1_representative_longitude,admin1_representative_latitude,adm2_name,admin2_geoboundaries_shape_id,admin2_representative_longitude,admin2_representative_latitude +AR0047-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0049-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0051-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 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+AR0045-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0073-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0004-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0040-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0052-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 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+AR0046-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0070-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0010-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0090-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0054-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0016-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0050-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0069-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0018-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0081-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0013-Cx,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0026-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0053-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 diff --git a/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.cohorts.csv b/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.cohorts.csv similarity index 100% rename from tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.cohorts.csv rename to tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.cohorts.csv diff --git a/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.taxa.csv b/tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.taxa.csv similarity index 100% rename from tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230223/AG1000G-AO/samples.taxa.csv rename to tests/anoph/fixture/missing_metadata/v3/metadata/cohorts_20230516/AG1000G-AO/samples.taxa.csv diff --git a/tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230223/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv b/tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230516/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv similarity index 100% rename from tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230223/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv rename to tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230516/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv index 75588be12..eb54b3456 100644 --- a/tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230223/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv +++ b/tests/anoph/fixture/vo_agam_release/v3.1/metadata/cohorts_20230516/1177-VO-ML-LEHMANN-VMF00004/samples.cohorts.csv @@ -1,7 +1,4 @@ sample_id,country_ISO,adm1_name,adm1_ISO,adm2_name,taxon,cohort_admin1_year,cohort_admin1_month,cohort_admin1_quarter,cohort_admin2_year,cohort_admin2_month,cohort_admin2_quarter -VBS00388-4651STDY7017222,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2012,ML-2_arab_2012_10,ML-2_arab_2012_Q4,ML-2_Banamba_arab_2012,ML-2_Banamba_arab_2012_10,ML-2_Banamba_arab_2012_Q4 -VBS01026-4651STDY7017295,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2014,ML-2_arab_2014_10,ML-2_arab_2014_Q4,ML-2_Banamba_arab_2014,ML-2_Banamba_arab_2014_10,ML-2_Banamba_arab_2014_Q4 -VBS01053-4651STDY7017308,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2014,ML-2_arab_2014_10,ML-2_arab_2014_Q4,ML-2_Banamba_arab_2014,ML-2_Banamba_arab_2014_10,ML-2_Banamba_arab_2014_Q4 VBS00256-4651STDY7017184,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_06,ML-2_colu_2012_Q2,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_06,ML-2_Banamba_colu_2012_Q2 VBS00257-4651STDY7017185,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_06,ML-2_colu_2012_Q2,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_06,ML-2_Banamba_colu_2012_Q2 VBS00259-4651STDY7017186,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_06,ML-2_colu_2012_Q2,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_06,ML-2_Banamba_colu_2012_Q2 @@ -34,6 +31,7 @@ VBS00370-4651STDY7017216,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML- VBS00371-4651STDY7017217,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_10,ML-2_colu_2012_Q4,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_10,ML-2_Banamba_colu_2012_Q4 VBS00373-4651STDY7017218,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_11,ML-2_colu_2012_Q4,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_11,ML-2_Banamba_colu_2012_Q4 VBS00375-4651STDY7017220,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_11,ML-2_colu_2012_Q4,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_11,ML-2_Banamba_colu_2012_Q4 +VBS00388-4651STDY7017222,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2012,ML-2_arab_2012_10,ML-2_arab_2012_Q4,ML-2_Banamba_arab_2012,ML-2_Banamba_arab_2012_10,ML-2_Banamba_arab_2012_Q4 VBS00449-4651STDY7017223,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2012,ML-2_colu_2012_09,ML-2_colu_2012_Q3,ML-2_Banamba_colu_2012,ML-2_Banamba_colu_2012_09,ML-2_Banamba_colu_2012_Q3 VBS00912-4651STDY7017225,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_05,ML-2_colu_2014_Q2,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_05,ML-2_Banamba_colu_2014_Q2 VBS00913-4651STDY7017226,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_05,ML-2_colu_2014_Q2,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_05,ML-2_Banamba_colu_2014_Q2 @@ -100,6 +98,7 @@ VBS01014-4651STDY7017290,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML- VBS01015-4651STDY7017291,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_06,ML-2_colu_2014_Q2,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_06,ML-2_Banamba_colu_2014_Q2 VBS01016-4651STDY7017292,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_06,ML-2_colu_2014_Q2,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_06,ML-2_Banamba_colu_2014_Q2 VBS01018-4651STDY7017293,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 +VBS01026-4651STDY7017295,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2014,ML-2_arab_2014_10,ML-2_arab_2014_Q4,ML-2_Banamba_arab_2014,ML-2_Banamba_arab_2014_10,ML-2_Banamba_arab_2014_Q4 VBS01029-4651STDY7017296,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 VBS01030-4651STDY7017297,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 VBS01031-4651STDY7017298,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 @@ -111,6 +110,7 @@ VBS01048-4651STDY7017304,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML- VBS01049-4651STDY7017305,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 VBS01050-4651STDY7017306,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 VBS01052-4651STDY7017307,MLI,Koulikouro,ML-2,Banamba,gambiae,ML-2_gamb_2014,ML-2_gamb_2014_10,ML-2_gamb_2014_Q4,ML-2_Banamba_gamb_2014,ML-2_Banamba_gamb_2014_10,ML-2_Banamba_gamb_2014_Q4 +VBS01053-4651STDY7017308,MLI,Koulikouro,ML-2,Banamba,arabiensis,ML-2_arab_2014,ML-2_arab_2014_10,ML-2_arab_2014_Q4,ML-2_Banamba_arab_2014,ML-2_Banamba_arab_2014_10,ML-2_Banamba_arab_2014_Q4 VBS01054-4651STDY7017309,MLI,Koulikouro,ML-2,Banamba,gambiae,ML-2_gamb_2014,ML-2_gamb_2014_10,ML-2_gamb_2014_Q4,ML-2_Banamba_gamb_2014,ML-2_Banamba_gamb_2014_10,ML-2_Banamba_gamb_2014_Q4 VBS01055-4651STDY7017310,MLI,Koulikouro,ML-2,Banamba,coluzzii,ML-2_colu_2014,ML-2_colu_2014_10,ML-2_colu_2014_Q4,ML-2_Banamba_colu_2014,ML-2_Banamba_colu_2014_10,ML-2_Banamba_colu_2014_Q4 VBS01056-4651STDY7017311,MLI,Koulikouro,ML-2,Banamba,gambiae,ML-2_gamb_2014,ML-2_gamb_2014_10,ML-2_gamb_2014_Q4,ML-2_Banamba_gamb_2014,ML-2_Banamba_gamb_2014_10,ML-2_Banamba_gamb_2014_Q4 diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv deleted file mode 100644 index 3344fe83f..000000000 --- a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.admin_units.csv +++ /dev/null @@ -1,82 +0,0 @@ -sample_id,country,country_ISO,adm1_name,adm1_ISO,adm2_name -AR0047-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0049-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0051-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0061-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0078-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0080-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0084-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0097-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0072-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0094-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0095-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0083-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0093-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0021-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0082-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0008-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0085-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0098-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0092-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0017-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0015-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0019-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0100-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0034-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0086-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0057-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0076-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0042-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0063-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0012-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0087-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0065-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0038-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0089-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0071-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0096-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0088-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0066-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0023-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0020-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0024-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0014-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0079-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0027-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0075-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0077-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0007-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0062-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0060-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0022-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0002-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0059-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0048-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0011-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0009-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0043-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0035-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0074-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0045-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0073-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0004-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0040-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0052-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0064-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0044-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0036-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0001-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0006-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0046-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0070-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0010-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0090-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0054-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0016-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0050-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0069-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0018-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0081-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0013-Cx,Angola,AGO,Luanda,AO-LUA,Luanda -AR0026-C,Angola,AGO,Luanda,AO-LUA,Luanda -AR0053-C,Angola,AGO,Luanda,AO-LUA,Luanda diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.admin_units.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.admin_units.csv deleted file mode 100644 index 57f244107..000000000 --- a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.admin_units.csv +++ /dev/null @@ -1,182 +0,0 @@ -sample_id,country,country_ISO,adm1_name,adm1_ISO,adm2_name -AB0085-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0086-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0162-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0164-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0165-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0166-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0167-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0169-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0170-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0171-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0172-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0173-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0174-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0175-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0176-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0177-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0178-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0179-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0180-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0197-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0198-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0199-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0200-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0201-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0202-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0203-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0204-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0205-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0206-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0255-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0256-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0257-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0258-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0259-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0260-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0261-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0262-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0263-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0264-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0265-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0266-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0267-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0268-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0269-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0270-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0271-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0272-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0273-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0274-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0275-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0276-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0277-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0278-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0279-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0280-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0281-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0282-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0283-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0284-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0087-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0088-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0089-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0090-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0091-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0092-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0094-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0095-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0096-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0097-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0098-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0099-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0100-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0101-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0103-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0104-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0109-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0110-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0111-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0112-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0113-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0114-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0115-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0116-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0117-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0118-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0119-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0121-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0122-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0123-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0124-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0126-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0127-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0128-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0129-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0130-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0131-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0150-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0151-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0153-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0155-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0157-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0158-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0159-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0160-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0161-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0181-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0182-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0183-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0184-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0185-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0186-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0187-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0188-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0189-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0190-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0191-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0192-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0193-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0194-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0196-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0209-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0210-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0211-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0212-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0132-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0133-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0134-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0135-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0136-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0137-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0138-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0139-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0140-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0142-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0143-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0144-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0145-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0146-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0147-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0148-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0207-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0208-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0213-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0214-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0215-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0216-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0217-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0218-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0219-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0221-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0222-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0223-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0224-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0225-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0226-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0227-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0228-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0229-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0230-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0231-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0232-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0233-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0234-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0235-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0236-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0237-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0238-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0239-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0240-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0241-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0242-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0243-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0244-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0246-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0247-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0248-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0249-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0250-Cx,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0251-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0252-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet -AB0253-C,Burkina Faso,BFA,Hauts-Bassins,BF-09,Houet diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv new file mode 100644 index 000000000..3d3124dd2 --- /dev/null +++ b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.admin_units.csv @@ -0,0 +1,82 @@ +sample_id,country,country_ISO,country_alpha2,country_alpha3,adm1_name,adm1_ISO,admin1_geoboundaries_shape_id,admin1_representative_longitude,admin1_representative_latitude,adm2_name,admin2_geoboundaries_shape_id,admin2_representative_longitude,admin2_representative_latitude +AR0047-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 +AR0049-C,Angola,AGO,AO,AGO,Luanda,AO-LUA,26408823B49174064004395,13.679075010193182,-9.592222213499952,Luanda,91424787B29298874255409,13.263832148325406,-8.834606841953473 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tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.cohorts.csv rename to tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.cohorts.csv diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.taxa.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.taxa.csv similarity index 100% rename from tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-AO/samples.taxa.csv rename to tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-AO/samples.taxa.csv diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.admin_units.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.admin_units.csv new file mode 100644 index 000000000..bbeafef4b --- /dev/null +++ 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Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0270-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0271-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0272-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0273-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0274-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0275-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0276-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0277-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0278-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0279-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0280-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0281-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0282-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0283-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0284-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0132-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0133-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0134-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0135-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0136-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0137-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0138-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0139-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0140-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0142-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0143-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0144-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0145-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0146-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0147-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0148-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0207-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0208-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0213-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0214-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0215-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0216-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0217-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0218-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0219-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0221-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0222-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0223-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0224-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0225-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0226-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0227-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0228-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0229-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0230-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0231-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0232-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0233-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0234-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0235-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0236-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0237-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0238-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0239-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0240-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0241-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0242-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0243-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0244-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0246-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0247-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0248-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0249-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0250-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0251-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0252-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0253-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0087-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0088-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0089-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0090-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0091-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0092-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0094-Cx,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0095-Cx,Burkina 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Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0211-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 +AB0212-C,Burkina Faso,BFA,BF,BFA,Hauts-Bassins,BF-09,92566538B40583601847470,-4.032051209278338,11.38742250200005,Houet,67063806B43041068804188,-4.311665884316067,11.389146701500067 diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.cohorts.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.cohorts.csv similarity index 100% rename from tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.cohorts.csv rename to tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.cohorts.csv diff --git a/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.taxa.csv b/tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.taxa.csv similarity index 100% rename from tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230223/AG1000G-BF-A/samples.taxa.csv rename to tests/anoph/fixture/vo_agam_release/v3/metadata/cohorts_20230516/AG1000G-BF-A/samples.taxa.csv diff --git a/tests/anoph/fixture/vo_agam_release/v3_cohorts/cohorts_20230516/cohorts_admin1_month.csv b/tests/anoph/fixture/vo_agam_release/v3_cohorts/cohorts_20230516/cohorts_admin1_month.csv new file mode 100644 index 000000000..a3e691391 --- /dev/null +++ b/tests/anoph/fixture/vo_agam_release/v3_cohorts/cohorts_20230516/cohorts_admin1_month.csv @@ -0,0 +1,541 @@ +cohort_id,cohort_size,country,country_alpha2,country_alpha3,taxon,year,quarter,month,admin1_name,admin1_iso,admin1_geoboundaries_shape_id,admin1_representative_longitude,admin1_representative_latitude 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+CM-SW_colu_2020_10,23,Cameroon,CM,CMR,coluzzii,2020,4,10,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_colu_2020_11,10,Cameroon,CM,CMR,coluzzii,2020,4,11,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_colu_2020_12,2,Cameroon,CM,CMR,coluzzii,2020,4,12,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_colu_2021_01,2,Cameroon,CM,CMR,coluzzii,2021,1,1,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_colu_2021_02,9,Cameroon,CM,CMR,coluzzii,2021,1,2,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_colu_2021_03,13,Cameroon,CM,CMR,coluzzii,2021,1,3,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_04,9,Cameroon,CM,CMR,gambiae,2020,2,4,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_05,13,Cameroon,CM,CMR,gambiae,2020,2,5,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_06,21,Cameroon,CM,CMR,gambiae,2020,2,6,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_07,15,Cameroon,CM,CMR,gambiae,2020,3,7,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_10,100,Cameroon,CM,CMR,gambiae,2020,4,10,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_11,7,Cameroon,CM,CMR,gambiae,2020,4,11,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2020_12,8,Cameroon,CM,CMR,gambiae,2020,4,12,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2021_02,1,Cameroon,CM,CMR,gambiae,2021,1,2,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_gamb_2021_03,4,Cameroon,CM,CMR,gambiae,2021,1,3,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_mela_2021_01,2,Cameroon,CM,CMR,melas_suspected,2021,1,1,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +CM-SW_mela_2021_02,2,Cameroon,CM,CMR,melas_suspected,2021,1,2,South-West,CM-SW,27767025B15169611165261,9.293015688400509,5.218367651895676 +ET-OR_arab_2020_09,85,Ethiopia,ET,ETH,arabiensis,2020,3,9,Oromia,ET-OR,75662566B49607794683490,40.41471559255447,6.950851765460547 +GA-1_gamb_2000_12,69,Gabon,GA,GAB,gambiae,2000,4,12,Estuaire,GA-1,98808126B35546594440017,10.223578494846954,0.216065871266779 +GA-6_font_2014_11,4,Gabon,GA,GAB,fontenillei,2014,4,11,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2019_04,5,Gabon,GA,GAB,fontenillei,2019,2,4,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2019_07,6,Gabon,GA,GAB,fontenillei,2019,3,7,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2019_09,5,Gabon,GA,GAB,fontenillei,2019,3,9,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2019_11,8,Gabon,GA,GAB,fontenillei,2019,4,11,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2020_02,9,Gabon,GA,GAB,fontenillei,2020,1,2,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_font_2020_06,6,Gabon,GA,GAB,fontenillei,2020,2,6,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GA-6_gamb_2019_09,1,Gabon,GA,GAB,gambiae,2019,3,9,Ogooué-Ivindo,GA-6,98808126B25676054093993,12.711108323828128,0.3374177968255865 +GH-AA_colu_2012_11,14,Ghana,GH,GHA,coluzzii,2012,4,11,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AA_colu_2018_01,27,Ghana,GH,GHA,coluzzii,2018,1,1,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AA_colu_2018_02,241,Ghana,GH,GHA,coluzzii,2018,1,2,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AA_gamb_2012_11,13,Ghana,GH,GHA,gambiae,2012,4,11,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AA_gamb_2017_11,111,Ghana,GH,GHA,gambiae,2017,4,11,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AA_gamb_2017_12,89,Ghana,GH,GHA,gambiae,2017,4,12,Greater Accra Region,GH-AA,69750345B91661082288531,-0.044292361116313,5.75860125 +GH-AH_colu_2018_03,26,Ghana,GH,GHA,coluzzii,2018,1,3,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_colu_2018_10,8,Ghana,GH,GHA,coluzzii,2018,4,10,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_colu_2018_11,221,Ghana,GH,GHA,coluzzii,2018,4,11,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_colu_2018_12,19,Ghana,GH,GHA,coluzzii,2018,4,12,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_gamb_2017_09,198,Ghana,GH,GHA,gambiae,2017,3,9,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_gamb_2018_03,6,Ghana,GH,GHA,gambiae,2018,1,3,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_gamb_2018_10,4,Ghana,GH,GHA,gambiae,2018,4,10,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_gamb_2018_11,52,Ghana,GH,GHA,gambiae,2018,4,11,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-AH_gamb_2018_12,1,Ghana,GH,GHA,gambiae,2018,4,12,Ashanti Region,GH-AH,69750345B92565988218409,-1.6246407578131812,6.73967095 +GH-CP_colu_2012_09,25,Ghana,GH,GHA,coluzzii,2012,3,9,Central Region,GH-CP,69750345B39752153724790,-1.1668126964316936,5.670964250000001 +GH-CP_colu_2018_03,7,Ghana,GH,GHA,coluzzii,2018,1,3,Central Region,GH-CP,69750345B39752153724790,-1.1668126964316936,5.670964250000001 +GH-CP_colu_2018_10,21,Ghana,GH,GHA,coluzzii,2018,4,10,Central Region,GH-CP,69750345B39752153724790,-1.1668126964316936,5.670964250000001 +GH-CP_colu_2018_11,108,Ghana,GH,GHA,coluzzii,2018,4,11,Central Region,GH-CP,69750345B39752153724790,-1.1668126964316936,5.670964250000001 +GH-CP_colu_2018_12,12,Ghana,GH,GHA,coluzzii,2018,4,12,Central Region,GH-CP,69750345B39752153724790,-1.1668126964316936,5.670964250000001 +GH-EP_colu_2012_11,1,Ghana,GH,GHA,coluzzii,2012,4,11,Eastern Region,GH-EP,69750345B54930642926775,-0.4578400483166717,6.45972355 +GH-EP_gamb_2012_11,23,Ghana,GH,GHA,gambiae,2012,4,11,Eastern Region,GH-EP,69750345B54930642926775,-0.4578400483166717,6.45972355 +GH-UE_arab_2016_09,1,Ghana,GH,GHA,arabiensis,2016,3,9,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2016_10,1,Ghana,GH,GHA,arabiensis,2016,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2016_11,1,Ghana,GH,GHA,arabiensis,2016,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2016_12,1,Ghana,GH,GHA,arabiensis,2016,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2017_03,1,Ghana,GH,GHA,arabiensis,2017,1,3,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2017_07,11,Ghana,GH,GHA,arabiensis,2017,3,7,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2017_10,7,Ghana,GH,GHA,arabiensis,2017,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2017_11,4,Ghana,GH,GHA,arabiensis,2017,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2017_12,1,Ghana,GH,GHA,arabiensis,2017,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2018_01,2,Ghana,GH,GHA,arabiensis,2018,1,1,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2018_02,3,Ghana,GH,GHA,arabiensis,2018,1,2,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2018_03,1,Ghana,GH,GHA,arabiensis,2018,1,3,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_arab_2018_08,2,Ghana,GH,GHA,arabiensis,2018,3,8,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2016_09,16,Ghana,GH,GHA,coluzzii,2016,3,9,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2016_10,112,Ghana,GH,GHA,coluzzii,2016,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2016_11,42,Ghana,GH,GHA,coluzzii,2016,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2016_12,34,Ghana,GH,GHA,coluzzii,2016,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_01,6,Ghana,GH,GHA,coluzzii,2017,1,1,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_02,11,Ghana,GH,GHA,coluzzii,2017,1,2,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_03,14,Ghana,GH,GHA,coluzzii,2017,1,3,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_04,42,Ghana,GH,GHA,coluzzii,2017,2,4,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_05,3,Ghana,GH,GHA,coluzzii,2017,2,5,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_06,33,Ghana,GH,GHA,coluzzii,2017,2,6,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_07,164,Ghana,GH,GHA,coluzzii,2017,3,7,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_10,130,Ghana,GH,GHA,coluzzii,2017,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_11,112,Ghana,GH,GHA,coluzzii,2017,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2017_12,42,Ghana,GH,GHA,coluzzii,2017,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_01,5,Ghana,GH,GHA,coluzzii,2018,1,1,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_02,49,Ghana,GH,GHA,coluzzii,2018,1,2,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_03,62,Ghana,GH,GHA,coluzzii,2018,1,3,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_04,135,Ghana,GH,GHA,coluzzii,2018,2,4,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_05,90,Ghana,GH,GHA,coluzzii,2018,2,5,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_06,52,Ghana,GH,GHA,coluzzii,2018,2,6,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_07,51,Ghana,GH,GHA,coluzzii,2018,3,7,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_colu_2018_08,119,Ghana,GH,GHA,coluzzii,2018,3,8,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2016_09,14,Ghana,GH,GHA,gambiae,2016,3,9,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2016_10,6,Ghana,GH,GHA,gambiae,2016,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2016_11,4,Ghana,GH,GHA,gambiae,2016,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2016_12,2,Ghana,GH,GHA,gambiae,2016,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_01,1,Ghana,GH,GHA,gambiae,2017,1,1,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_06,4,Ghana,GH,GHA,gambiae,2017,2,6,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_07,53,Ghana,GH,GHA,gambiae,2017,3,7,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_10,16,Ghana,GH,GHA,gambiae,2017,4,10,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_11,1,Ghana,GH,GHA,gambiae,2017,4,11,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2017_12,1,Ghana,GH,GHA,gambiae,2017,4,12,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2018_03,2,Ghana,GH,GHA,gambiae,2018,1,3,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2018_04,1,Ghana,GH,GHA,gambiae,2018,2,4,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2018_06,2,Ghana,GH,GHA,gambiae,2018,2,6,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2018_07,1,Ghana,GH,GHA,gambiae,2018,3,7,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-UE_gamb_2018_08,3,Ghana,GH,GHA,gambiae,2018,3,8,Upper East Region,GH-UE,69750345B64184297206763,-0.8196590613199154,10.7245907 +GH-WP_colu_2012_08,24,Ghana,GH,GHA,coluzzii,2012,3,8,Western Region,GH-WP,69750345B38025690459934,-2.1020813688018114,5.439712549999999 +GM-L_arab_2001_09,1,"Gambia, The",GM,GMB,arabiensis,2001,3,9,Mansakonko,GM-L,31243875B45830859255282,-15.704203010573202,13.399802025000042 +GM-L_arab_2019_09,6,"Gambia, The",GM,GMB,arabiensis,2019,3,9,Mansakonko,GM-L,31243875B45830859255282,-15.704203010573202,13.399802025000042 +GM-L_gcx2_2006_08,19,"Gambia, The",GM,GMB,gcx2,2006,3,8,Mansakonko,GM-L,31243875B45830859255282,-15.704203010573202,13.399802025000042 +GM-L_gcx2_2019_09,3,"Gambia, The",GM,GMB,gcx2,2019,3,9,Mansakonko,GM-L,31243875B45830859255282,-15.704203010573202,13.399802025000042 +GM-M_arab_2019_09,54,"Gambia, The",GM,GMB,arabiensis,2019,3,9,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_arab_2019_10,12,"Gambia, The",GM,GMB,arabiensis,2019,4,10,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_arab_2019_11,13,"Gambia, The",GM,GMB,arabiensis,2019,4,11,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_arab_2019_12,5,"Gambia, The",GM,GMB,arabiensis,2019,4,12,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gamb_2012_10,2,"Gambia, The",GM,GMB,gambiae,2012,4,10,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gamb_2019_09,1,"Gambia, The",GM,GMB,gambiae,2019,3,9,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gamb_2019_10,1,"Gambia, The",GM,GMB,gambiae,2019,4,10,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gamb_2019_11,1,"Gambia, The",GM,GMB,gambiae,2019,4,11,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gcx1_2019_10,1,"Gambia, The",GM,GMB,gcx1,2019,4,10,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gcx2_2012_10,172,"Gambia, The",GM,GMB,gcx2,2012,4,10,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-M_gcx2_2019_09,27,"Gambia, The",GM,GMB,gcx2,2019,3,9,Janjanbureh,GM-M,31243875B73953417095853,-14.878674602306535,13.522959142000047 +GM-N_arab_2019_10,16,"Gambia, The",GM,GMB,arabiensis,2019,4,10,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx1_2006_08,9,"Gambia, The",GM,GMB,gcx1,2006,3,8,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx1_2011_08,44,"Gambia, The",GM,GMB,gcx1,2011,3,8,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx1_2011_09,8,"Gambia, The",GM,GMB,gcx1,2011,3,9,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx1_2011_10,16,"Gambia, The",GM,GMB,gcx1,2011,4,10,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx2_2006_08,3,"Gambia, The",GM,GMB,gcx2,2006,3,8,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx2_2011_08,2,"Gambia, The",GM,GMB,gcx2,2011,3,8,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-N_gcx2_2011_10,4,"Gambia, The",GM,GMB,gcx2,2011,4,10,Kerewan,GM-N,31243875B27620764341145,-15.734652579233972,13.542233133000051 +GM-U_arab_2019_09,59,"Gambia, The",GM,GMB,arabiensis,2019,3,9,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_arab_2019_10,29,"Gambia, The",GM,GMB,arabiensis,2019,4,10,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_arab_2019_11,6,"Gambia, The",GM,GMB,arabiensis,2019,4,11,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_arab_2019_12,1,"Gambia, The",GM,GMB,arabiensis,2019,4,12,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_gamb_2019_09,10,"Gambia, The",GM,GMB,gambiae,2019,3,9,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_gamb_2019_10,6,"Gambia, The",GM,GMB,gambiae,2019,4,10,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_gcx1_2019_10,1,"Gambia, The",GM,GMB,gcx1,2019,4,10,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_gcx2_2019_09,6,"Gambia, The",GM,GMB,gcx2,2019,3,9,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-U_gcx2_2019_10,1,"Gambia, The",GM,GMB,gcx2,2019,4,10,Basse,GM-U,31243875B15447287102204,-14.297011852172083,13.44776150100006 +GM-W_arab_2019_09,112,"Gambia, The",GM,GMB,arabiensis,2019,3,9,Kanifing,GM-W,31243875B1039529170026,-16.68077902382715,13.436852141000031 +GM-W_gcx1_2019_09,4,"Gambia, The",GM,GMB,gcx1,2019,3,9,Brikama,GM-W,31243875B93952327922203,-16.297963797335903,13.243899169500054 +GN-F_gamb_2012_10,63,Guinea,GN,GIN,gambiae,2012,4,10,Faranah,GN-F,26780975B17934337985358,-10.979918470034464,10.517157 +GN-N_colu_2012_10,11,Guinea,GN,GIN,coluzzii,2012,4,10,Nzerekore,GN-N,26780975B19606696181390,-8.890070091941663,8.391386295000014 +GN-N_gamb_2012_10,63,Guinea,GN,GIN,gambiae,2012,4,10,Nzerekore,GN-N,26780975B19606696181390,-8.890070091941663,8.391386295000014 +GQ-BN_gamb_2002_09,10,Equatorial Guinea,GQ,GNQ,gambiae,2002,3,9,Bioko Norte,GQ-BN,51917635B67588420055426,8.774651307575148,3.64670135 +GW-BM_gcx1_2010,33,Guinea-Bissau,GW,GNB,gcx1,2010,-1,-1,Biombo,GW-BM,76643164B804668395788,-15.79294432700356,11.882051199999989 +GW-BS_gcx1_2010,60,Guinea-Bissau,GW,GNB,gcx1,2010,-1,-1,Bissau,GW-BS,76643164B84090302363721,-15.592690661048358,11.846588549999982 +GW-GA_gamb_2010,8,Guinea-Bissau,GW,GNB,gambiae,2010,-1,-1,Gabu,GW-GA,76643164B54949730536517,-14.176250577969594,12.117035049999991 +KE-08_arab_2017_01,1,Kenya,KE,KEN,arabiensis,2017,1,1,Homa Bay,KE-08,32016919B7435144662741,34.33288381997485,-0.5597141382967834 +KE-14_arab_2007,3,Kenya,KE,KEN,arabiensis,2007,-1,-1,Kilifi,KE-14,32016919B48129662870527,39.662804555634814,-3.151611328250141 +KE-14_arab_2012,10,Kenya,KE,KEN,arabiensis,2012,-1,-1,Kilifi,KE-14,32016919B48129662870527,39.662804555634814,-3.151611328250141 +KE-14_gamb_2000,19,Kenya,KE,KEN,gambiae,2000,-1,-1,Kilifi,KE-14,32016919B48129662870527,39.662804555634814,-3.151611328250141 +KE-14_gcx3_2012,54,Kenya,KE,KEN,gcx3,2012,-1,-1,Kilifi,KE-14,32016919B48129662870527,39.662804555634814,-3.151611328250141 +ML-2_arab_2012_10,1,Mali,ML,MLI,arabiensis,2012,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_arab_2014_09,1,Mali,ML,MLI,arabiensis,2014,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_arab_2014_10,15,Mali,ML,MLI,arabiensis,2014,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_arab_2015_06,1,Mali,ML,MLI,arabiensis,2015,2,6,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_arab_2015_09,2,Mali,ML,MLI,arabiensis,2015,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_arab_2015_10,9,Mali,ML,MLI,arabiensis,2015,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2004_08,11,Mali,ML,MLI,coluzzii,2004,3,8,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2012_06,10,Mali,ML,MLI,coluzzii,2012,2,6,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2012_09,8,Mali,ML,MLI,coluzzii,2012,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2012_10,8,Mali,ML,MLI,coluzzii,2012,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2012_11,2,Mali,ML,MLI,coluzzii,2012,4,11,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2013_08,4,Mali,ML,MLI,coluzzii,2013,3,8,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_05,16,Mali,ML,MLI,coluzzii,2014,2,5,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_06,48,Mali,ML,MLI,coluzzii,2014,2,6,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_08,39,Mali,ML,MLI,coluzzii,2014,3,8,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_09,16,Mali,ML,MLI,coluzzii,2014,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_10,50,Mali,ML,MLI,coluzzii,2014,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_11,3,Mali,ML,MLI,coluzzii,2014,4,11,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2014_12,5,Mali,ML,MLI,coluzzii,2014,4,12,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2015_04,48,Mali,ML,MLI,coluzzii,2015,2,4,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2015_06,49,Mali,ML,MLI,coluzzii,2015,2,6,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2015_07,4,Mali,ML,MLI,coluzzii,2015,3,7,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2015_09,108,Mali,ML,MLI,coluzzii,2015,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_colu_2015_10,33,Mali,ML,MLI,coluzzii,2015,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2004_08,32,Mali,ML,MLI,gambiae,2004,3,8,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2012_09,5,Mali,ML,MLI,gambiae,2012,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2014_08,78,Mali,ML,MLI,gambiae,2014,3,8,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2014_09,2,Mali,ML,MLI,gambiae,2014,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2014_10,15,Mali,ML,MLI,gambiae,2014,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2014_11,17,Mali,ML,MLI,gambiae,2014,4,11,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2014_12,3,Mali,ML,MLI,gambiae,2014,4,12,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2015_09,75,Mali,ML,MLI,gambiae,2015,3,9,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-2_gamb_2015_10,17,Mali,ML,MLI,gambiae,2015,4,10,Koulikouro,ML-2,92416918B5720378388911,-7.617072757441715,13.47885247300005 +ML-3_colu_2012_10,27,Mali,ML,MLI,coluzzii,2012,4,10,Sikasso,ML-3,92416918B11845606031110,-6.862508741717316,11.477565221000049 +ML-3_gamb_2012_10,65,Mali,ML,MLI,gambiae,2012,4,10,Sikasso,ML-3,92416918B11845606031110,-6.862508741717316,11.477565221000049 +ML-4_arab_2004_08,2,Mali,ML,MLI,arabiensis,2004,3,8,Segou,ML-4,92416918B96933474350774,-6.0028816044440525,14.05131584800005 +ML-4_colu_2004_08,25,Mali,ML,MLI,coluzzii,2004,3,8,Segou,ML-4,92416918B96933474350774,-6.0028816044440525,14.05131584800005 +ML-4_colu_2012_03,4,Mali,ML,MLI,coluzzii,2012,1,3,Segou,ML-4,92416918B96933474350774,-6.0028816044440525,14.05131584800005 +ML-4_colu_2012_04,2,Mali,ML,MLI,coluzzii,2012,2,4,Segou,ML-4,92416918B96933474350774,-6.0028816044440525,14.05131584800005 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+ZM-08_gamb_2020_09,20,Zambia,ZM,ZMB,gambiae,2020,3,9,Copperbelt,ZM-08,6923714B61812757118010,27.95617131236294,-13.0788249556133 +ZM-08_gamb_2020_10,46,Zambia,ZM,ZMB,gambiae,2020,4,10,Copperbelt,ZM-08,6923714B61812757118010,27.95617131236294,-13.0788249556133 +ZM-08_gamb_2020_11,30,Zambia,ZM,ZMB,gambiae,2020,4,11,Copperbelt,ZM-08,6923714B61812757118010,27.95617131236294,-13.0788249556133 +ZM-08_gamb_2021_03,20,Zambia,ZM,ZMB,gambiae,2021,1,3,Copperbelt,ZM-08,6923714B61812757118010,27.95617131236294,-13.0788249556133 diff --git a/tests/anoph/test_sample_metadata.py b/tests/anoph/test_sample_metadata.py index 889878c3d..923501b9c 100644 --- a/tests/anoph/test_sample_metadata.py +++ b/tests/anoph/test_sample_metadata.py @@ -33,6 +33,7 @@ def ag3_sim_api(ag3_sim_fixture): "aim_species": object, }, taxon_colors=_ag3.TAXON_COLORS, + cohorts_analysis=ag3_sim_fixture.config["DEFAULT_COHORTS_ANALYSIS"], ) @@ -1016,3 +1017,42 @@ def test_setup_sample_colors_plotly(fixture, api): color_discrete_sequence=None, category_orders=None, ) + + +def cohort_data_expected_columns(): + return { + "cohort_id": "O", + "cohort_size": "i", + "country": "O", + "country_alpha2": "O", + "country_alpha3": "O", + "taxon": "O", + "year": "i", + "quarter": "i", + "month": "i", + "admin1_name": "O", + "admin1_iso": "O", + "admin1_geoboundaries_shape_id": "O", + "admin1_representative_longitude": "f", + "admin1_representative_latitude": "f", + } + + +def validate_cohort_data(df, expected_columns): + # Check column names. + expected_column_names = list(expected_columns.keys()) + assert df.columns.to_list() == expected_column_names + + # Check column types. + for c in df.columns: + assert df[c].dtype.kind == expected_columns[c] + + +@parametrize_with_cases("fixture,api", cases=case_ag3_sim) +def test_cohort_data(fixture, api): + # Set up the test. + cohort_name = "admin1_month" + # Call function to be tested. + df_cohorts = api.cohorts(cohort_name) + # Check output. + validate_cohort_data(df_cohorts, cohort_data_expected_columns()) diff --git a/tests/anopheles_test_data/test_missing_cohorts/ag/v3-config.json b/tests/anopheles_test_data/test_missing_cohorts/ag/v3-config.json index 3bd061b97..913648527 100644 --- a/tests/anopheles_test_data/test_missing_cohorts/ag/v3-config.json +++ b/tests/anopheles_test_data/test_missing_cohorts/ag/v3-config.json @@ -5,5 +5,5 @@ "GENESET_GFF3_PATH": "reference/genome/agamp4/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.12.gff3.gz", "DEFAULT_SPECIES_ANALYSIS": "aim_20220528", "DEFAULT_SITE_FILTERS_ANALYSIS": "dt_20200416", - "DEFAULT_COHORTS_ANALYSIS": "20220608" + "DEFAULT_COHORTS_ANALYSIS": "20230516" }