diff --git a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml index 7613843dcc6..cac0c8cc3e4 100644 --- a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml +++ b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.meta.yml @@ -6,7 +6,18 @@ definitions: - Global Health - Antibiotics display: - name: << syndrome.capitalize >> + name: << syndrome.capitalize() >> + syndrome: + <%- if syndrome == "BLOOD" %> + bloodstream + <%- elif syndrome == "STOOL" %> + gastrointestinal + <%- elif syndrome == "URINE" %> + urinary tract + <%- elif syndrome == "UROGENITAL" %> + gonorrohea + <% endif %> + # Learn more about the available fields: @@ -19,30 +30,30 @@ tables: who_glass: variables: bcispermillion: - title: Bacteriologically confirmed <> infections per million population + title: Samples tested and confirmed to be {definitions.syndrome} infections per million population unit: "confirmed infections per million" presentation: - title_public: Bacteriologically confirmed <> infections per million population + title_public: Samples tested and confirmed to be {definitions.syndrome} infections per million population totalspecimenisolates: - title: Total specimen isolates of <> infections - unit: "isolates" + title: Total specimens collected of {definitions.syndrome} infections + unit: "specimens" presentation: - title_public: Total specimen isolates of <> infections + title_public: Total specimen collected of {definitions.syndrome} infections isolspermillion: - title: Isolates of <> infections per million population - unit: "isolates per million" + title: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results per million population + unit: "confirmed infections per million" presentation: - title_public: Isolates of <> infections per million population + title_public: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results per million population totalspecimenisolateswithast: - title: Bacterially confirmed <> infections per million population with antibiotic susceptibility test results - unit: "confirmed infections per million" + title: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results + unit: "confirmed infections" presentation: - title_public: Bacterially confirmed <> infections per million population with antibiotic susceptibility test results + title_public: Samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results astresult: - title: Share of bacterial confirmed <> infections with antibiotic susceptibility test results + title: Share of samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results unit: "%" short_unit: "%" display: numDecimalPlaces: 1 presentation: - title_public: Share of bacterial confirmed <> infections with antibiotic susceptibility test results \ No newline at end of file + title_public: Share of samples tested and confirmed to be {definitions.syndrome} infections with antibiotic susceptibility test results \ No newline at end of file diff --git a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py index 9355e6055a2..ced77166136 100644 --- a/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py +++ b/etl/steps/data/garden/antibiotics/2024-10-18/who_glass.py @@ -13,7 +13,7 @@ def run(dest_dir: str) -> None: # # Load meadow dataset. ds_meadow = paths.load_dataset("who_glass") - + # Add population dataset. # Read table from meadow dataset. tb = ds_meadow["who_glass"].reset_index() diff --git a/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc b/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc index 1d9d6f0fd62..2e245ff7341 100644 --- a/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc +++ b/snapshots/antibiotics/2024-10-18/who_glass.zip.dvc @@ -3,7 +3,7 @@ meta: origin: # Data product / Snapshot - title: Global Antimicrobial Resitsance and Use Surveillance System (GLASS) + title: Global Antimicrobial Resistance and Use Surveillance System (GLASS) description: |- GLASS provides a standardized approach to the collection, analysis, interpretation and sharing of data by countries and seeks to actively support capacity building and monitor the status of existing and new national surveillance systems. Furthermore, GLASS promotes a shift from surveillance approaches based solely on laboratory data to a system that includes epidemiological, clinical, and population-level data. GLASS has been conceived to progressively incorporate data from surveillance of AMR in humans, such as monitoring of resistance and the use of antimicrobial medicines, including AMR in the food chain and in the environment. date_published: "2024-09-16" @@ -14,7 +14,7 @@ meta: # Citation producer: World Health Organization citation_full: |- - Global AMR data - Global Antimicrobial Resitsance and Use Surveillance System (GLASS), World Health Organization (2024) + Global AMR data - Global Antimicrobial Resistance and Use Surveillance System (GLASS), World Health Organization (2024) attribution_short: WHO @@ -28,6 +28,6 @@ meta: url: https://www.who.int/about/policies/terms-of-use outs: - - md5: 12d197f03c1dc917f7e27662bd2e581b + - md5: b1c4d820b37417b77214db814348233f size: 55169 path: who_glass.zip diff --git a/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc b/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc index ac012b1fe6c..b52081a7cc3 100644 --- a/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc +++ b/snapshots/antibiotics/2024-10-18/who_glass_by_antibiotic.zip.dvc @@ -3,7 +3,7 @@ meta: origin: # Data product / Snapshot - title: Global Antimicrobial Resitsance and Use Surveillance System (GLASS) - by antibiotic + title: Global Antimicrobial Resistance and Use Surveillance System (GLASS) - by antibiotic description: |- GLASS provides a standardized approach to the collection, analysis, interpretation and sharing of data by countries and seeks to actively support capacity building and monitor the status of existing and new national surveillance systems. Furthermore, GLASS promotes a shift from surveillance approaches based solely on laboratory data to a system that includes epidemiological, clinical, and population-level data. GLASS has been conceived to progressively incorporate data from surveillance of AMR in humans, such as monitoring of resistance and the use of antimicrobial medicines, including AMR in the food chain and in the environment. date_published: "2024-09-16" @@ -14,7 +14,7 @@ meta: # Citation producer: World Health Organization citation_full: |- - Global AMR data - Global Antimicrobial Resitsance and Use Surveillance System (GLASS), World Health Organization (2024) + Global AMR data - Global Antimicrobial Resistance and Use Surveillance System (GLASS), World Health Organization (2024) attribution_short: WHO