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PR from forked work #2

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f5cb22c
copied README.md from RSV-scenario-modeling-hub repo
kjsato Nov 29, 2023
b97962f
added model-metadata/team2-modelb.yaml with some modification for test
kjsato Nov 29, 2023
82f4280
added model-output/team2-modelb/2023-11-12-team2-modelb.parquet for test
kjsato Nov 29, 2023
42a24cc
copied model-output/README.md from rsv-scenario-modeling-hub repo
kjsato Nov 29, 2023
8eb2dff
modified tasks.json not to show lexical error in origin_date{optional}
kjsato Nov 29, 2023
34d0140
modified team2-modelb.yaml to comply with the current rsv-scenario-mo…
kjsato Nov 29, 2023
0f787f3
modified model-metadata-schema-json to comply with the current rsv-sc…
kjsato Nov 29, 2023
4b54f21
added validate-submission.yaml in .github/workflows
kjsato Nov 29, 2023
cefa945
modified model-metadata-schema.json to add some licenses on enum
kjsato Nov 30, 2023
3b35332
moved model-metadata/team2-modelb.yaml to teamsam-modelple.yaml
kjsato Dec 1, 2023
d028f80
added 2023-11-12-teamsam-modelple.parquet as a sample
kjsato Dec 1, 2023
eda045f
added 2023-11-12-teamsam-modelple.parquet again for testing
kjsato Dec 1, 2023
7515531
added 2023-11-12-teamsam-modelple.parquet for testing
kjsato Dec 1, 2023
c616b0b
deleted model-metadata/team2-modelb.yaml related
kjsato Dec 1, 2023
c5b9e2c
modified validate-submission.yaml to ref 'mod-delete-alert'
kjsato Dec 2, 2023
4a3bc04
Merge remote-tracking branch 'origin/main' into main-submission-test
kjsato Dec 2, 2023
cbc9ae0
Merge pull request #1 from kjsato/main-submission-test
kjsato Dec 2, 2023
12f2c8e
Download truth data file from RSV repo
github-actions[bot] Dec 4, 2023
04f8354
modified to add copy new files section in validate-submission.yaml
kjsato Dec 4, 2023
7e00774
added README.me and two scripts in the rsv-scenrio-modeling-hub/targe…
kjsato Dec 5, 2023
2264a67
modified tasks.json with
kjsato Dec 6, 2023
1ccb82c
modified a test parquet comformed with tasks.json
kjsato Dec 6, 2023
e4c4a35
modified validate-submission.yaml in pushing the data into another repo
kjsato Dec 6, 2023
c970765
modified validate-submission.yaml not to use ref="mod-delete-alert" b…
kjsato Dec 6, 2023
cb3b40e
modified two columns which should not be in the file
kjsato Dec 6, 2023
ff691e5
revert submission_due end to 2
kjsato Dec 6, 2023
6093eea
added 2023-11-19-teamsam-modelple.parquet for test
kjsato Dec 6, 2023
6028f0b
deleted 2023-11-12-teamsam-modelple.parquet because of an error in va…
kjsato Dec 6, 2023
1064ab9
modified tasks.json to enlarge the submission window - end to 100
kjsato Dec 7, 2023
6b18452
Merge branch 'main' of github.com:kjsato/rsv-forecast-hub
kjsato Dec 7, 2023
369e164
changed 2023-11-19-teamsam-modelple.parquet for test to eliminate dub…
kjsato Dec 8, 2023
fe83552
added 2023-11-26-teamsam-modelple.parquet for test
kjsato Dec 8, 2023
914e508
deleted 2023-11-19-teamsam-modelple.parquet not to avoid validtion fa…
kjsato Dec 8, 2023
c77c2a6
Merge remote-tracking branch 'origin/main' into main-submission-test
kjsato Dec 8, 2023
58e0e9c
addded 2023-11-19-teamsam-modelple.parquet again to try avoiding hubV…
kjsato Dec 8, 2023
289b518
modified the sections after validations in validate-submission.yaml
kjsato Dec 8, 2023
509b68b
Download truth data file from RSV repo
github-actions[bot] Dec 11, 2023
d23a227
modified Comit and push new files section in validate-submission.yaml
kjsato Dec 12, 2023
7d4b374
added 'fetch-depth: 2' in checkout section in validate-submission.yaml
kjsato Dec 12, 2023
eaacd52
deleted unnecessary files
kjsato Dec 13, 2023
908a008
deleted unnecessary files
kjsato Dec 13, 2023
e212884
deleted model-output/.DS_Store
kjsato Dec 13, 2023
866699f
added fetch-depth: on checkout in validate-submission.yaml
kjsato Dec 13, 2023
2ea9e0c
Merge remote-tracking branch 'upstream/main' into main-submission-test
kjsato Dec 13, 2023
552e655
Merge branch 'main' of github.com:kjsato/rsv-forecast-hub into main-s…
kjsato Dec 13, 2023
6d3822f
Merge pull request #4 from kjsato/main-submission-test
kjsato Dec 13, 2023
2ab283e
Merge branch 'main' into main
kjsato Dec 13, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/validate-submission.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ jobs:
if: success()
uses: actions/checkout@v2
with:
repository: HpokinsIDD/rsv-forecast-hub_data
repository: HopkinsIDD/rsv-forecast-hub_data
token: ${{ secrets.KJ3_PAT }}
path: ./rsv-forecast-hub_data
fetch-depth: 2
Expand Down
150 changes: 147 additions & 3 deletions model-metadata/README.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,149 @@
# Model metadata
# Model Metadata

This folder should contain metadata files for the models submitting to the hub, following the recommended [model metadata guidelines in our documentation](https://hubdocs.readthedocs.io/en/latest/format/model-metadata.html).
This folder contains metadata files for each team-models submitting to the
RSV Scenario Modeling Hub.

Since some metadata fields may be specific to this hub, creators of the hub are encouraged to modify the template model metadata file so that it is a valid model metadata file for your project.
Each model is required to have metadata in yaml format and should contains
required information and be stored in a team-model specific sub-directory.

----

## Subdirectory

Each sub-directory within the [model-metadata/](./) directory has the
format:

team-model

where

- `team` is the abbraviated teamname (`team_abbr`) and
- `model` is the abbreviated name of your model (`model_abbr`).

Both team and model should be less than 15 characters, and not include
hyphens nor spaces.

The `team-model` should correspond to the `team-model` sub-directory in the
associated model-output folder containing the associated projections.

----

## Required information

### `team_name`

The name of your team that is less than 50 characters, no spaces.
Will be displayed online.

### `model_name`

The name of your model that is less than 50 characters, no spaces.
Will be displayed online.

### Abbreviation

#### `model_abbr`

An abbreviated name for your model that is less than 30 alphanumeric characters.

#### `team_abbr`

An abbreviated name for your team that is less than 30 alphanumeric characters.

#### Team-model name and filename

The team-model abbreviation used in all the file names must be in the
format of `[team_abbr]-[model_abbr]`, where each of the `[team_abbr]` and
`[model_abbr]` are text strings that are each less than 15 alphanumeric
characters that do not include a hyphen or whitespace.

Note that this is a uniquely identifying field in our system, so please choose
this name carefully, as it may not be changed once defined. The model
abbreviation will be displayed online.

### `model_contributors`

A list of all individuals involved in the forecasting effort,
affiliations, and email address.

At least one contributor needs to have a valid email address. All email
addresses provided will be added to an email distribution list for model
contributors.

The syntax of this field should be

```yaml
[
{
"name": "Smith J",
"affiliation": "Affiliation",
"email": "user@address"
},
{
"name": "Smith S",
"affiliation": "Affiliation"
},
{
"name": "Smith C",
"affiliation": "Affiliation",
"email": "user3@address"
}
]
```
### `website_url`

A url to a website that has additional data about your model.
We encourage teams to submit the most user-friendly version of your
model, e.g. a dashboard, or similar, that displays your model scenarios.

If you have additionally a data repository where you store scenarios and other
model code, please include that in your methods section below.

If you only have a more technical site, e.g. github repo, please include that
link here. Will be displayed online.

### `model_version`

A version number or date in YYYY-MM-DD format, to designate the version of
the model used for submitted model projections.
Will be displayed online.

### `methods`

A brief description of your methodology that is less than 200 characters.
Will be displayed online.

### `license`

We encourage teams to submit as a "cc-by-4.0" to allow the broadest possible
uses including private vaccine production
(which would be excluded by the "cc-by-nc-4.0" license).

Alternatively, add the name and URL of the license used, as in `cc-by-4.0, https://creativecommons.org/licenses/by/4.0/`
Or, add the value `LICENSE.txt`, if a LICENSE.txt file was added within the folder.

Will be displayed online.

## Optional

### `team_funding`

Acknowledgement of funding source, by name of funding agency, grant title,
and grant number.

### `data_inputs`

A brief description of the data sources used to inform the model, using as much
as possible standard terminology that includes a source name and the type of
data, such as `CDC RSV-NET`, etc.

### `methods_long`

A long description of your methodology.

### `citation`

A bibliographic citation to a paper, website, or other object that people
can go to to find out more about the model, in the style used by PubMed,
as
`"Smith J, Smith S, Smith C. MyModel is the best model. Nature. 2020 Aug. doi: 10.1038/s12345-678-90123-45."`
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