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update standardizer after bedms deployment
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sanghoonio committed Sep 16, 2024
1 parent 52bf105 commit 8cf8ed0
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Showing 3 changed files with 5 additions and 8 deletions.
9 changes: 3 additions & 6 deletions pephub/routers/api/v1/namespace.py
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Expand Up @@ -42,7 +42,7 @@
from ....helpers import parse_user_file_upload, split_upload_files_on_init_file
from ...models import FavoriteRequest, ProjectJsonRequest, ProjectRawModel

from attribute_standardizer import AttrStandardizer
from bedms.const import AVAILABLE_SCHEMAS

load_dotenv()

Expand Down Expand Up @@ -462,11 +462,8 @@ async def get_archive(namespace: str, agent: PEPDatabaseAgent = Depends(get_db))

@namespace.get(
"/standardizer_schemas",
summary="Get metadata of all archived files of all projects in the namespace",
summary="Get all available schemas from BEDMS",
)
async def get_schemas(namespace: str, agent: PEPDatabaseAgent = Depends(get_db)):

model = AttrStandardizer("ENCODE")
schemas = model.get_available_schemas()

return schemas
return AVAILABLE_SCHEMAS
2 changes: 1 addition & 1 deletion pephub/routers/api/v1/project.py
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Expand Up @@ -57,7 +57,7 @@
)
from .helpers import verify_updated_project

from attribute_standardizer import AttrStandardizer
from bedms import AttrStandardizer

_LOGGER = logging.getLogger(__name__)

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2 changes: 1 addition & 1 deletion web/src/components/modals/standardize-metadata.tsx
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Expand Up @@ -202,7 +202,7 @@ export const StandardizeMetadataModal = (props: Props) => {
<i className="bi bi-x-lg"></i>
</button>
<p className="text-sm mt-1 mb-3">
Use the metadata standardizer powered by BEDms to bring consistency across metadata columns in all of your
Use the metadata standardizer powered by BEDMS to bring consistency across metadata columns in all of your
projects. After choosing a standardizer schema below, compare predicted suggestions (confidence indicated in
parenthesis) and choose whether to keep or discard them. Column contents are not modified by the
standardizer. After accepting the changes, save your project for them to take effect.
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