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Merge pull request #76 from hubverse-org/mc/model-info/56
implements [add info about models on viz page #56] by outputting a model_urls options object field that, when present, makes model names links
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‎demo/index.html‎

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</div>
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<script type="module">
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import App from 'https://cdn.jsdelivr.net/gh/reichlab/predtimechart@3.1.2/dist/predtimechart.bundle.js';
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import App from 'https://cdn.jsdelivr.net/gh/reichlab/predtimechart@3.1.3/dist/predtimechart.bundle.js';
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document.predtimechart = App; // for debugging
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function replace_chars(the_string) {

‎src/hub_predtimechart/__init__.py‎

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__version__ = "2.2.1"
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__version__ = "2.2.4"

‎src/hub_predtimechart/generate_options.py‎

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@@ -73,6 +73,18 @@ def get_max_ref_date_or_first_config_ref_date(reference_dates):
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options['models'].sort()
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options['initial_checked_models'] = hub_config.initial_checked_models
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# set `model_urls`
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options['model_urls'] = {}
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for model_id, metadata in hub_config.model_id_to_metadata.items():
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if model_id not in options['models']: # o/w causes a predtimechart validation error
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continue
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host, owner, name = _host_owner_name(hub_config)
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repo_url = f"https://{host}.com/{owner}/{name}"
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# recall that 'file_name' is a custom hub-dashboard-predtimechart field:
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options['model_urls'][model_id] = f"{repo_url}/blob/main/model-metadata/{metadata['file_name']}"
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# add `disclaimer` if present
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if hub_config.disclaimer is not None:
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options['disclaimer'] = hub_config.disclaimer
@@ -81,3 +93,40 @@ def get_max_ref_date_or_first_config_ref_date(reference_dates):
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options['initial_xaxis_range'] = hub_config.initial_xaxis_range if hub_config.initial_xaxis_range else None
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return options
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def _host_owner_name(hub_config):
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"""
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`ptc_options_for_hub()` helper that returns a 3-tuple for `hub_config`'s `repository` section, handling the various
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schemas found in the test hubs
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cases:
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- 'host', 'owner', 'name' (current schema) # flu-metrocast
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- 'host', 'owner', 'repository' # example-complex-forecast-hub, FluSight-forecast-hub
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- 'host', 'url', 'name' # covid19-forecast-hub
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:param hub_config: a HubConfigPtc
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:return: a 3-tuple: (host, owner, name)
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"""
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# validate schema
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admin_repo = hub_config.admin['repository']
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valid_keys = [{'host', 'owner', 'name'},
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{'host', 'owner', 'repository'},
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{'host', 'url', 'name'}]
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admin_repo_keys = set(admin_repo.keys())
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if admin_repo_keys not in valid_keys:
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raise RuntimeError(f"invalid admin repository keys. {admin_repo_keys=}, {valid_keys=}")
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host, owner, name = admin_repo['host'], None, None
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if admin_repo_keys == {'host', 'owner', 'name'}:
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owner = admin_repo['owner']
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name = admin_repo['name']
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elif admin_repo_keys == {'host', 'owner', 'repository'}:
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owner = admin_repo['owner']
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name = admin_repo['repository']
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elif admin_repo_keys == {'host', 'url', 'name'}:
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owner = admin_repo['url'].split('/')[3] # ex: "https://github.com/CDCgov/covid19-forecast-hub"
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name = admin_repo['name']
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else:
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raise RuntimeError(f"invalid admin repository keys. {admin_repo_keys=}")
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return host, owner, name

‎src/hub_predtimechart/hub_config_ptc.py‎

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@@ -82,6 +82,11 @@ def __init__(self, hub_path: Path, ptc_config_file: Path):
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list((self.hub_path / 'model-metadata').glob('*.yaml'))):
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with open(model_metadata_file) as fp:
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model_metadata = yaml.safe_load(fp)
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# add a custom hub-dashboard-predtimechart field to the loaded metadata for functions that need the
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# original file name (which could be .yml OR .yaml)
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model_metadata['file_name'] = model_metadata_file.name
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model_id = f"{model_metadata['team_abbr']}-{model_metadata['model_abbr']}"
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self.model_id_to_metadata[model_id] = model_metadata
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‎tests/expected/FluSight-forecast-hub/predtimechart-options.json‎

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"models": [
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"CADPH-FluCAT_Ensemble", "CEPH-Rtrend_fluH", "CMU-TimeSeries", "CU-ensemble", "FluSight-baseline", "FluSight-ensemble", "GT-FluFNP", "ISU_NiemiLab-NLH", "JHU_CSSE-CSSE_Ensemble", "LUcompUncertLab-chimera", "LosAlamos_NAU-CModel_Flu", "MIGHTE-Nsemble", "MOBS-GLEAM_FLUH", "NIH-Flu_ARIMA", "NU_UCSD-GLEAM_AI_FLUH", "PSI-PROF", "SGroup-RandomForest", "SigSci-CREG", "SigSci-TSENS", "Stevens-GBR", "UGA_flucast-Copycat", "UGA_flucast-INFLAenza", "UGuelph-CompositeCurve", "UGuelphensemble-GRYPHON", "UM-DeepOutbreak", "UMass-flusion", "UMass-trends_ensemble", "UNC_IDD-InfluPaint", "UVAFluX-Ensemble", "VTSanghani-Ensemble", "cfa-flumech", "cfarenewal-cfaepimlight", "fjordhest-ensemble"
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],
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"model_urls": {
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"CADPH-FluCAT_Ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/CADPH-FluCAT_Ensemble.yml",
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"CEPH-Rtrend_fluH": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/CEPH-Rtrend_fluH.yaml",
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"CMU-TimeSeries": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/CMU-TimeSeries.yml",
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"CU-ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/CU-ensemble.yml",
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"FluSight-baseline": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/FluSight-baseline.yml",
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"FluSight-ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/FluSight-ensemble.yml",
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"GT-FluFNP": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/GT-FluFNP.yml",
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"ISU_NiemiLab-NLH": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/ISU_NiemiLab-NLH.yml",
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"JHU_CSSE-CSSE_Ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/JHU_CSSE-CSSE_Ensemble.yml",
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"LUcompUncertLab-chimera": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/LUcompUncertLab-chimera.yml",
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"LosAlamos_NAU-CModel_Flu": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/LosAlamos_NAU-CModel_Flu.yml",
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"MIGHTE-Nsemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/MIGHTE-Nsemble.yml",
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"MOBS-GLEAM_FLUH": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/MOBS-GLEAM_FLUH.yml",
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"NIH-Flu_ARIMA": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/NIH-Flu_ARIMA.yaml",
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"NU_UCSD-GLEAM_AI_FLUH": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/NU_UCSD-GLEAM_AI_FLUH.yml",
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"PSI-PROF": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/PSI-PROF.yml",
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"SGroup-RandomForest": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/SGroup-RandomForest.yml",
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"SigSci-CREG": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/SigSci-CREG.yml",
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"SigSci-TSENS": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/SigSci-TSENS.yml",
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"Stevens-GBR": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/Stevens-GBR.yml",
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"UGA_flucast-Copycat": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UGA_flucast-Copycat.yml",
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"UGA_flucast-INFLAenza": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UGA_flucast-INFLAenza.yml",
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"UGuelph-CompositeCurve": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UGuelph-CompositeCurve.yml",
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"UGuelphensemble-GRYPHON": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UGuelphensemble-GRYPHON.yml",
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"UM-DeepOutbreak": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UM-DeepOutbreak.yml",
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"UMass-flusion": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UMass-flusion.yml",
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"UMass-trends_ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UMass-trends_ensemble.yml",
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"UNC_IDD-InfluPaint": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UNC_IDD-InfluPaint.yml",
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"UVAFluX-Ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/UVAFluX-Ensemble.yml",
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"VTSanghani-Ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/VTSanghani-Ensemble.yml",
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"cfa-flumech": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/cfa-flumech.yml",
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"cfarenewal-cfaepimlight": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/cfarenewal-cfaepimlight.yml",
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"fjordhest-ensemble": "https://github.com/cdcepi/FluSight-forecast-hub/blob/main/model-metadata/fjordhest-ensemble.yml"
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},
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"initial_checked_models": ["FluSight-baseline", "FluSight-ensemble"],
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"disclaimer": "Most forecasts have failed to reliably predict rapid changes in the trends of reported cases and hospitalizations. Due to this limitation, they should not be relied upon for decisions about the possibility or timing of rapid changes in trends.",
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"initial_xaxis_range": null

‎tests/expected/covid19-forecast-hub/predtimechart-options.json‎

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},
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"initial_as_of": "2024-11-09",
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"current_date": "2024-11-09",
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"models": [],
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"model_urls": {
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"UMass-ar6_pooled": "https://github.com/CDCgov/covid19-forecast-hub/blob/main/model-metadata/UMass-ar6_pooled.yml"
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},
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"models": ["UMass-ar6_pooled"],
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"initial_checked_models": [],
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"initial_xaxis_range": null
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}

‎tests/expected/example-complex-forecast-hub/predtimechart-options.json‎

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"initial_as_of": "2022-12-17",
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"current_date": "2022-12-17",
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"models": ["Flusight-baseline", "MOBS-GLEAM_FLUH", "PSI-DICE"],
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"model_urls": {
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"Flusight-baseline": "https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub/blob/main/model-metadata/Flusight-baseline.yml",
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"MOBS-GLEAM_FLUH": "https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub/blob/main/model-metadata/MOBS-GLEAM_FLUH.yml",
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"PSI-DICE": "https://github.com/Infectious-Disease-Modeling-Hubs/example-complex-forecast-hub/blob/main/model-metadata/PSI-DICE.yml"
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},
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"initial_checked_models": ["Flusight-baseline"],
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"disclaimer": "Most forecasts have failed to reliably predict rapid changes in the trends of reported cases and hospitalizations. Due to this limitation, they should not be relied upon for decisions about the possibility or timing of rapid changes in trends.",
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"initial_xaxis_range": null

‎tests/expected/flu-metrocast/predtimechart-options.json‎

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"initial_xaxis_range": null,
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"intervals": ["0%", "50%", "95%"],
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"models": ["epiENGAGE-Copycat", "epiENGAGE-GBQR", "epiENGAGE-INFLAenza", "epiforecasts-dyngam"],
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"model_urls": {
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"epiENGAGE-Copycat": "https://github.com/reichlab/flu-metrocast/blob/main/model-metadata/epiENGAGE-Copycat.yml",
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"epiENGAGE-INFLAenza": "https://github.com/reichlab/flu-metrocast/blob/main/model-metadata/epiENGAGE-INFLAenza.yml",
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"epiENGAGE-GBQR": "https://github.com/reichlab/flu-metrocast/blob/main/model-metadata/epiENGAGE-GBQR.yml",
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"epiforecasts-dyngam": "https://github.com/reichlab/flu-metrocast/blob/main/model-metadata/epiforecasts-dyngam.yml"
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},
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"target_variables": [
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{
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"plot_text": "ED visits due to ILI",

‎tests/hub_predtimechart/test_generate_options.py‎

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import json
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from pathlib import Path
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from hub_predtimechart.generate_options import ptc_options_for_hub
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import pytest
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from hub_predtimechart.generate_options import ptc_options_for_hub, _host_owner_name
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from hub_predtimechart.hub_config_ptc import HubConfigPtc
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exp_options['initial_xaxis_range'] = hub_config.initial_xaxis_range
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act_options = ptc_options_for_hub(hub_config)
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assert act_options == exp_options
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#
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# model_urls tests
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#
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@pytest.mark.parametrize("hub_dir,exp_host_owner_name", [
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('tests/hubs/covid19-forecast-hub',
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('github', 'CDCgov', 'covid19-forecast-hub')),
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('tests/hubs/example-complex-forecast-hub',
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('github', 'Infectious-Disease-Modeling-Hubs', 'example-complex-forecast-hub')),
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('tests/hubs/flu-metrocast',
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('github', 'reichlab', 'flu-metrocast')),
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('tests/hubs/FluSight-forecast-hub',
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('github', 'cdcepi', 'FluSight-forecast-hub'))])
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def test__host_owner_name(hub_dir, exp_host_owner_name):
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hub_dir = Path(hub_dir)
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hub_config = HubConfigPtc(hub_dir, hub_dir / 'hub-config/predtimechart-config.yml')
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assert _host_owner_name(hub_config) == exp_host_owner_name
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def test__host_owner_name_invalid_keys():
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hub_dir = Path('tests/hubs/flu-metrocast')
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hub_config = HubConfigPtc(hub_dir, hub_dir / 'hub-config/predtimechart-config.yml')
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hub_config.admin['repository'] = {'bad-repo': 0}
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with pytest.raises(RuntimeError, match="invalid admin repository keys"):
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_host_owner_name(hub_config)

‎tests/hubs/covid19-forecast-hub/model-metadata/CovidHub-baseline.yaml‎

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team_name: "CovidHub-hub-models"
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team_abbr: "CovidHub"
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model_name: "CovidHub baseline model"
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model_abbr: "baseline"
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model_version: "1.0"
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model_contributors:
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[
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{
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"name": "Covid Hub",
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"affiliation": "Centers for Disease Control and Prevention (CDC)",
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"email": "covidhub@cdc.gov"
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}
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]
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website_url: "https://github.com/CDCgov/covid19-forecast-hub"
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license: "CC-BY-4.0"
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designated_model: false
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methods: "Flat baseline model. The most observed value from the target dataset is the median forward projection. Prospective uncertainty is based on the preceding timeseries."
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data_inputs: "Epiweekly incident COVID-19 hospital admissions from the NHSN Weekly Hospital Respiratory Data dataset,
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https://data.cdc.gov/Public-Health-Surveillance/Weekly-Hospital-Respiratory-Data-HRD-Metrics-by-Ju/mpgq-jmmr/about_data
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"
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methods_long: "Flat baseline model. The most observed value from the target dataset is the median forward projection. Prospective uncertainty is based on the preceding timeseries. This is the standard baseline model used by the COVID-19 Forecast Hub and the FluSight Forecast Hub. It is implemented using the `cdc_baseline_forecaster()` function from the `epipredict` R package. https://cmu-delphi.github.io/epipredict/reference/cdc_baseline_forecaster.html"
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ensemble_of_models: false
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ensemble_of_hub_models: false

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