diff --git a/cada_prio/cli.py b/cada_prio/cli.py index 3c26b08..2b1e257 100644 --- a/cada_prio/cli.py +++ b/cada_prio/cli.py @@ -9,6 +9,7 @@ import cattr import click import logzero +import yaml try: import optuna @@ -140,6 +141,16 @@ def cli_dump_graph( inspection.dump_graph(path_graph, path_hgnc_info, hgnc_to_entrez) +@cli_utils.command("dump-openapi-yaml") +@click.argument("path_out", type=str) +def cli_dump_openapi_yaml(path_out: str): + """Dump OpenAPI YAML file""" + from cada_prio import rest_server + + with open(path_out, "wt") as f: + yaml.dump(rest_server.app.openapi(), f) + + @cli.group("tune") def cli_tune(): """hyperparameter tuning""" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 1db8b20..0000000 --- a/requirements.txt +++ /dev/null @@ -1,13 +0,0 @@ -logzero >=1.7.0, <2.0 -attrs >=22.1.0, <24.0 -cattrs >=22.2.0, <24.0 -click >=8.1.3, <9.0 -toml >=0.10.2, <0.11 -tqdm >=4.0 -pronto >=2.5, <3.0 -networkx -node2vec >=0.4.6, <0.5 -gensim >=4.3.2, <5.0 -uvicorn >=0.23.2 -fastapi >=0.103, <0.105 -python-dotenv >=1.0, <2.0 diff --git a/requirements.txt b/requirements.txt new file mode 120000 index 0000000..2d8105f --- /dev/null +++ b/requirements.txt @@ -0,0 +1 @@ +requirements/base.txt \ No newline at end of file diff --git a/requirements/base.txt b/requirements/base.txt index 1db8b20..4522b29 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -11,3 +11,4 @@ gensim >=4.3.2, <5.0 uvicorn >=0.23.2 fastapi >=0.103, <0.105 python-dotenv >=1.0, <2.0 +pyyaml >=6.0, <7.0 diff --git a/utils/terraform/.gitignore b/utils/terraform/.gitignore deleted file mode 100644 index 5dfe310..0000000 --- a/utils/terraform/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -.terraform* -terraform.tfstate* diff --git a/utils/terraform/main.tf b/utils/terraform/main.tf deleted file mode 100644 index a36f677..0000000 --- a/utils/terraform/main.tf +++ /dev/null @@ -1,19 +0,0 @@ -# Mangement of the GitHub project. - -resource "github_repository" "cada-prio" { - name = "cada-prio" - description = "Re-implementation of the CADA phenotype-based prioritization algorithm" - - has_issues = true - visibility = "public" - - allow_auto_merge = true - allow_rebase_merge = false - allow_merge_commit = false - has_downloads = true - has_discussions = true - delete_branch_on_merge = true - - squash_merge_commit_message = "BLANK" - squash_merge_commit_title = "PR_TITLE" -} diff --git a/utils/terraform/provider.tf b/utils/terraform/provider.tf deleted file mode 100644 index 0349641..0000000 --- a/utils/terraform/provider.tf +++ /dev/null @@ -1 +0,0 @@ -provider "github" {}