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Merged
eleanorfrajka merged 1 commit into from
Feb 12, 2026
Merged

[DOC] Update metadata + reports #123

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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -10,6 +10,6 @@ authors:
orcid: https://orcid.org/0009-0009-1369-1748
affiliation: University of Hamburg, Bundesstraße 53, 20146 Hamburg, Germany
title: amocatlas
version: 0.1.1
date-released: 2025-04-12
version: 0.3.0
date-released: 2026-02-10
url: https://github.com/AMOCcommunity/amocatlas
23 changes: 13 additions & 10 deletions amocatlas/metadata/arcticgateway.yml
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Expand Up @@ -17,16 +17,19 @@ metadata:
contributor_name: "Hege-Beate Fredriksen, Laura de Steur"
contributor_role: "originator, PI"
contributor_role_vocabulary: "http://vocab.nerc.ac.uk/search_nvs/W08/"
creator_name_overwrite: " "
creator_url_overwrite: " "
creator_email_overwrite: " "
creator_type_overwrite: " "
publisher_name_overwrite: " "
publisher_email_overwrite: " "
institution: " "
contributing_institutions: "Norwegian Polar Institute, Alfred Wegener Institute, Institute for Marine Research, APL-UW"
contributing_institutions_role: "publisher, "

remove_unwanted_attributes:
- creator_institution
- creator_name # if you want to remove this too
- creator_url
- creator_email
- creator_type
- publisher_name
- publisher_email
- publisher_type

files:
Adjusted_fulldepth/BarentsSeaOpening_adjusted_v_fulldepth.nc:
source_url: "https://doi.org/10.21334/NPOLAR.2025.80B69907"
Expand Down Expand Up @@ -103,17 +106,17 @@ files:
description: "Latitude of zonal sections across which freshwater transport is computed."
units: degree_north
standard_name: "latitude"
conservative_temperature:
CT:
long_name: "Cons. Temperature"
description: "Conservative Temperature (TEOS-10)"
units: degree_C
standard_name: sea_water_conservative_temperature
absolute_salinity:
SA:
long_name: "Abs. Salinity"
description: "Absolute Salinity (TEOS-10)"
units: "g kg-1"
standard_name: sea_water_absolute_salinity
northward_velocity:
v:
long_name: "V Velocity"
description: "Northward Velocity component"
units: "m s-1"
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15 changes: 15 additions & 0 deletions amocatlas/metadata/institution_registry.yml
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Expand Up @@ -18,6 +18,21 @@ institutions:
id_url: "https://edmo.seadatanet.org/report/17"
website: "https://noc.ac.uk"

"1224": # NASA JPL
standard_name: "National Aeronautics and Space Administration - Jet Propulsion Laboratory (NASA JPL)"
name_variants:
- "NASA JPL"
- "National Aeronautics and Space Administration, Jet Propulsion Laboratory"
- "National Aeronautics and Space Administration Jet Propulsion Laboratory"
- "NASA Jet Propulsion Laboratory"
- "National Aeronautics and Space Administration (NASA) Jet Propulsion Laboratory"
- "National Aeronautics and Space Administration (NASA) Jet Propulsion Laboratory (JPL)"
- "National Aeronautics and Space Administration JPL"
- "National Aeronautics and Space Administration Jet Propulsion Laboratory (USA)"
country: "USA"
id_url: "https://edmo.seadatanet.org/report/1224"
website: "https://www.jpl.nasa.gov"

"2424": # National Oceanography Centre Liverpool
standard_name: "National Oceanography Centre (Liverpool)"
name_variants:
Expand Down
14 changes: 7 additions & 7 deletions amocatlas/metadata/mocha26n.yml
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Expand Up @@ -24,6 +24,7 @@ files:
variable_mapping:
time: TIME
maxmoc: MOC
moc: STREAMFUNCTION_Z
Q_sum: MHT
Q_ek: MHT_EKMAN
Q_fc: MHT_FC
Expand Down Expand Up @@ -154,17 +155,11 @@ files:
units: Sverdrup
standard_name: ocean_volume_transport_across_line
maxmoc:
long_name: "MOC"
long_name: "MOC_Z"
description: >
time-varying maximum value of MOC streamfunction
units: Sverdrup
standard_name: ocean_meridional_overturning_transport
moc:
long_name: "MOC_Z"
description: >
time-varying MOC streamfunction vs. depth
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
z:
long_name: "Depth"
description: >
Expand Down Expand Up @@ -203,3 +198,8 @@ files:
description: >
corresponding hour of the measurements
standard_name: "Hour"
moc:
long_name: "Streamfunction"
description: "Streamfunction across the Atlantic at 26.5°N"
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
1 change: 1 addition & 0 deletions amocatlas/metadata/noac47n.yml
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Expand Up @@ -10,6 +10,7 @@ metadata:
Wett, Simon; Rhein, Monika; Kieke, Dagmar; Mertens, Christian; Moritz, Martin; Nowitzki, Hannah (2023): Basin-wide AMOC volume transport from the NOAC array at 47°N in the subpolar North Atlantic (1993-2018) [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.959558
featureType: "timeSeries"
time_coverage_start: '1993-01-01'
contributing_institutions: University of Bremen (Germany)
time_coverage_end: '2018-01-01'
contributor_name: "Simon Wett, Monika Rhein"
contributor_role: "originator, PI"
Expand Down
46 changes: 23 additions & 23 deletions amocatlas/metadata/osnap55n.yml
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Expand Up @@ -8,7 +8,7 @@ metadata:
OSNAP data were collected and made freely available by the OSNAP (Overturning in the Subpolar North Atlantic Program) project
and all the national programs that contribute to it (www.o-snap.org).
doi: https://doi.org/10.35090/gatech/70342
license:
license: CC-BY-4.0 # Based on original data location at gatech
Conventions: CF-1.8, ACDD-1.3
time_coverage_start: "2014-08-01"
time_coverage_end: "2020-06-30"
Expand Down Expand Up @@ -74,7 +74,7 @@ files:
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
MOC_EAST_ERR:
long_name: "MOC east uncertainty"
long_name: "MOCeast uncertainty"
description: "Uncertainty in MOC_EAST"
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
Expand All @@ -84,57 +84,57 @@ files:
units: PW
standard_name: northward_ocean_heat_transport
MHT_ALL_ERR:
long_name: "Heat transport uncertainty"
long_name: "MHT uncertainty"
description: "Uncertainty in MHT_ALL"
units: PW
standard_name: northward_ocean_heat_transport
MHT_EAST:
long_name: "Heat transport east"
long_name: "MHTeast"
description: "Meridional heat transport at OSNAP East"
units: PW
standard_name: northward_ocean_heat_transport
MHT_EAST_ERR:
long_name: "Heat transport east uncertainty"
long_name: "MHTeast uncertainty"
description: "Uncertainty in MHT_EAST"
units: PW
standard_name: northward_ocean_heat_transport
MHT_WEST:
long_name: "Heat transport west"
long_name: "MHTwest"
description: "Meridional heat transport at OSNAP West"
units: PW
standard_name: northward_ocean_heat_transport
MHT_WEST_ERR:
long_name: "Heat transport west uncertainty"
long_name: "MHTwest uncertainty"
description: "Uncertainty in MHT_WEST"
units: PW
standard_name: northward_ocean_heat_transport
MFT_ALL:
long_name: "Freshwater transport"
long_name: "MFT"
description: "Meridional freshwater transport across full OSNAP array"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_ALL_ERR:
long_name: "Freshwater transport uncertainty"
long_name: "MFT uncertainty"
description: "Uncertainty in MFT_ALL"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_EAST:
long_name: "Freshwater transport east"
long_name: "MFTeast"
description: "Meridional freshwater transport at OSNAP East"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_EAST_ERR:
long_name: "Freshwater transport east uncertainty"
long_name: "MFTeast uncertainty"
description: "Uncertainty in MFT_EAST"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_WEST:
long_name: "Freshwater transport west"
long_name: "MFTwest"
description: "Meridional freshwater transport at OSNAP West"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_WEST_ERR:
long_name: "Freshwater transport west uncertainty"
long_name: "MFTwest uncertainty"
description: "Uncertainty in MFT_WEST"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
Expand Down Expand Up @@ -186,17 +186,17 @@ files:
description: "Maximum overturning streamfunction across OSNAP East"
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
MOC_SIGMA0_EAST_ERR:
MOC_EAST_ERR:
long_name: "Eastern MOC_sigma0 uncertainty"
description: "Uncertainty in MOC_SIGMA0_EAST"
units: Sverdrup
standard_name: ocean_meridional_overturning_streamfunction
MHT:
MHT_ALL:
long_name: "MHT"
description: "Meridional heat transport across full OSNAP array"
units: PW
standard_name: northward_ocean_heat_transport
MHT_ERR:
MHT_ALL_ERR:
long_name: "MHT uncertainty"
description: "Uncertainty in MHT"
units: PW
Expand All @@ -222,32 +222,32 @@ files:
units: PW
standard_name: northward_ocean_heat_transport
MFT:
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In OSNAP_MOC_MHT_MFT_TimeSeries_201408_202207_2025.nc, variable_mapping indicates the source variable is MFT_ALL (mapped to MFT), and standardise_data() applies original_variable_metadata before renaming. The original_variable_metadata entry is currently keyed as MFT, so it won’t be applied to the source dataset variable and the long_name/attrs may remain missing. Rename this metadata key to MFT_ALL (and keep the attrs the same) so it is applied before the rename.

Suggested change
MFT:
MFT_ALL:

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long_name: "Freshwater trans."
long_name: "MFT"
description: "Meridional freshwater transport across full OSNAP array"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_ERR:
long_name: "Freshwater trans. error"
MFT_ALL_ERR:
long_name: "MFT error"
description: "Uncertainty in MFT"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_WEST:
long_name: "Freshwater trans. west"
long_name: "MFTwest"
description: "Meridional freshwater transport across OSNAP West"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_WEST_ERR:
long_name: "Freshwater trans. west error"
long_name: "MFTwest error"
description: "Uncertainty in MFT_WEST"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_EAST:
long_name: "Freshwater trans. east"
long_name: "MFTeast"
description: "Meridional freshwater transport across OSNAP East"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
MFT_EAST_ERR:
long_name: "Freshwater trans. east error"
long_name: "MFTeast error"
description: "Uncertainty in MFT_EAST"
units: Sverdrup
standard_name: northward_ocean_freshwater_transport
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6 changes: 0 additions & 6 deletions amocatlas/report.py
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Expand Up @@ -1139,12 +1139,6 @@ def generate_array_report(
for ds in datasets:
# Set canonical date_modified to avoid changing every time
ds.attrs["date_modified"] = canonical_date
# Add explanation comment
comment = ds.attrs.get("comment", "")
if comment:
comment += " "
comment += "(Note: date_modified has been set to a canonical value for documentation generation to avoid git churn)"
ds.attrs["comment"] = comment

# Extract and store contributors and institutions
try:
Expand Down
15 changes: 14 additions & 1 deletion amocatlas/standardise.py
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Expand Up @@ -1339,9 +1339,12 @@ def standardise_data(ds: xr.Dataset, file_name: str) -> xr.Dataset:
"standard_name", ""
):
log_debug(f"Converting heat transport variable '{var_name}' from W to PW")
# Preserve all attributes before conversion
original_attrs = ds[var_name].attrs.copy()
# Convert data from watts to petawatts (divide by 10^15)
ds[var_name] = ds[var_name] / 1e15
# Update units attribute
# Restore all attributes and update units
ds[var_name].attrs = original_attrs
ds[var_name].attrs["units"] = "PW"

# If any attributes are blank or value 'n/a', remove them
Expand Down Expand Up @@ -1447,6 +1450,16 @@ def standardise_data(ds: xr.Dataset, file_name: str) -> xr.Dataset:
cleaned.pop(key, None)
log_debug(f"Removed processing directive: '{key}'")

# 4.4) Process remove_unwanted_attributes directive
remove_unwanted = all_yaml_metadata.get("remove_unwanted_attributes", [])
if remove_unwanted:
for attr_name in remove_unwanted:
if attr_name in cleaned:
cleaned.pop(attr_name)
log_debug(f"Removed unwanted attribute: '{attr_name}'")
# Also remove the remove_unwanted_attributes directive itself
cleaned.pop("remove_unwanted_attributes", None)
Comment on lines +1453 to +1461
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remove_unwanted_attributes is applied after _consolidate_contributors(). Since _consolidate_contributors() pops creator_*/publisher_* and folds them into contributor_*, removing those fields afterward won’t prevent them from influencing the consolidated contributor list (e.g., institutional creators/publishers may still appear as contributors). Apply the removals before calling _consolidate_contributors() (e.g., delete the listed keys from merged_attrs/combined first), then drop the directive key so it doesn’t propagate.

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Comment on lines +1453 to +1461
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This introduces new metadata behavior (remove_unwanted_attributes) but there’s no test coverage for it. Add a unit/integration test that constructs attrs/YAML including remove_unwanted_attributes and verifies the listed keys are removed and do not affect contributor consolidation (e.g., creator_name/publisher_name don’t get merged into contributor_name).

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# 5) Standardize date formats and add processing metadata

def standardize_date_format(date_string: str) -> str:
Expand Down
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