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Remove bedms temporarily #406

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merged 2 commits into from
Dec 4, 2024
Merged

Remove bedms temporarily #406

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040fe92
remove bedms, for now
nleroy917 Dec 4, 2024
62997ed
bump version
nleroy917 Dec 4, 2024
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2 changes: 1 addition & 1 deletion pephub/_version.py
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
__version__ = "0.14.2"
__version__ = "0.14.3"
14 changes: 7 additions & 7 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 bedms.const import AVAILABLE_SCHEMAS
# from bedms.const import AVAILABLE_SCHEMAS

load_dotenv()

Expand Down Expand Up @@ -459,10 +459,10 @@ async def get_archive(namespace: str, agent: PEPDatabaseAgent = Depends(get_db))
return result


@namespace.get(
"/standardizer-schemas",
summary="Get all available schemas from BEDMS",
)
async def get_schemas(namespace: str, agent: PEPDatabaseAgent = Depends(get_db)):
# @namespace.get(
# "/standardizer-schemas",
# summary="Get all available schemas from BEDMS",
# )
# async def get_schemas(namespace: str, agent: PEPDatabaseAgent = Depends(get_db)):

return AVAILABLE_SCHEMAS
# return AVAILABLE_SCHEMAS
102 changes: 51 additions & 51 deletions pephub/routers/api/v1/project.py
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Expand Up @@ -62,7 +62,7 @@
)
from .helpers import verify_updated_project

from bedms import AttrStandardizer
# from bedms import AttrStandardizer

_LOGGER = logging.getLogger(__name__)

Expand Down Expand Up @@ -1180,53 +1180,53 @@ def delete_full_history(
)


@project.post(
"/standardize",
summary="Standardize PEP metadata column headers",
response_model=StandardizerResponse,
)
async def get_standardized_cols(
pep: dict = Depends(get_project),
schema: str = "",
):
"""
Standardize PEP metadata column headers using BEDms.

:param pep: PEP string to be standardized
:param schema: Schema for AttrStandardizer

:return dict: Standardized results
"""

if schema == "" or schema not in ["ENCODE", "BEDBASE", "FAIRTRACKS"]:
raise HTTPException(
status_code=404,
detail="Schema not available! Available schemas are ENCODE, BEDBASE and FAIRTRACKS.",
)

if len(pep["_sample_dict"]) > MAX_STANDARDIZED_PROJECT_SIZE:
# raise HTTPException(
# status_code=400,
# detail=f"Project is too large. Cannot standardize. "
# f"Limit is {MAX_STANDARDIZED_PROJECT_SIZE} samples.",
# )
prj = peppy.Project.from_dict(
{
"_config": pep["_config"],
"_sample_dict": pep["_sample_dict"][:50],
}
)
else:
prj = peppy.Project.from_dict(pep)
model = AttrStandardizer(repo_id=BEDMS_REPO_URL, model_name=schema.lower())

try:
results = model.standardize(pep=prj)
except Exception as e:
_LOGGER.error(f"Error standardizing PEP. {e}")
raise HTTPException(
status_code=400,
detail=f"Error standardizing PEP.",
)

return StandardizerResponse(results=results)
# @project.post(
# "/standardize",
# summary="Standardize PEP metadata column headers",
# response_model=StandardizerResponse,
# )
# async def get_standardized_cols(
# pep: dict = Depends(get_project),
# schema: str = "",
# ):
# """
# Standardize PEP metadata column headers using BEDms.

# :param pep: PEP string to be standardized
# :param schema: Schema for AttrStandardizer

# :return dict: Standardized results
# """

# if schema == "" or schema not in ["ENCODE", "BEDBASE", "FAIRTRACKS"]:
# raise HTTPException(
# status_code=404,
# detail="Schema not available! Available schemas are ENCODE, BEDBASE and FAIRTRACKS.",
# )

# if len(pep["_sample_dict"]) > MAX_STANDARDIZED_PROJECT_SIZE:
# # raise HTTPException(
# # status_code=400,
# # detail=f"Project is too large. Cannot standardize. "
# # f"Limit is {MAX_STANDARDIZED_PROJECT_SIZE} samples.",
# # )
# prj = peppy.Project.from_dict(
# {
# "_config": pep["_config"],
# "_sample_dict": pep["_sample_dict"][:50],
# }
# )
# else:
# prj = peppy.Project.from_dict(pep)
# model = AttrStandardizer(repo_id=BEDMS_REPO_URL, model_name=schema.lower())

# try:
# results = model.standardize(pep=prj)
# except Exception as e:
# _LOGGER.error(f"Error standardizing PEP. {e}")
# raise HTTPException(
# status_code=400,
# detail=f"Error standardizing PEP.",
# )

# return StandardizerResponse(results=results)
2 changes: 1 addition & 1 deletion requirements/requirements-all.txt
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Expand Up @@ -16,4 +16,4 @@ fastembed
numpy<2.0.0
slowapi
cachetools>=4.2.4
bedms>=0.2.0
# bedms>=0.2.0
10 changes: 5 additions & 5 deletions web/src/components/modals/standardize-metadata.tsx
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Expand Up @@ -228,7 +228,7 @@ export const StandardizeMetadataModal = (props: Props) => {
}),
}}
// @ts-ignore
options={schemaOptions?.map(option => ({ value: option, label: option }))}
options={schemaOptions?.map((option) => ({ value: option, label: option }))}
defaultValue={selectedOption}
value={selectedOption}
onChange={(selectedOption) => {
Expand All @@ -252,11 +252,11 @@ export const StandardizeMetadataModal = (props: Props) => {
</form>

{maxColsExceeded && (
<div className='row'>
<p className='text-sm mt-3 mb-1'>
<div className="row">
<p className="text-sm mt-3 mb-1">
<strong>Note: </strong>
Your project has nine or more columns.
Due to server constraints, standardization of nine or more columns on PEPhub may take some time. Please be patient.
Your project has nine or more columns. Due to server constraints, standardization of nine or more
columns on PEPhub may take some time. Please be patient.
</p>
</div>
)}
Expand Down
17 changes: 8 additions & 9 deletions web/src/components/project/project-page-header-bar.tsx
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Expand Up @@ -13,14 +13,14 @@ import { useAddStar } from '../../hooks/mutations/useAddStar';
import { useRemoveStar } from '../../hooks/mutations/useRemoveStar';
import { useNamespaceStars } from '../../hooks/queries/useNamespaceStars';
import { useProjectAnnotation } from '../../hooks/queries/useProjectAnnotation';
import { useSampleTable } from '../../hooks/queries/useSampleTable';
import { useStandardizeModalStore } from '../../hooks/stores/useStandardizeModalStore';
import { copyToClipboard, getOS, numberWithCommas } from '../../utils/etc';
import { canEdit } from '../../utils/permissions';
import { downloadZip } from '../../utils/project';
import { ProjectHistoryModal } from '../modals/project-history';
import { ProjectHeaderBarPlaceholder } from './placeholders/project-header-bar-placeholder';
import { ProjectStars } from './project-stars'
import { useStandardizeModalStore } from '../../hooks/stores/useStandardizeModalStore'
import { useSampleTable } from '../../hooks/queries/useSampleTable'
import { ProjectStars } from './project-stars';

type Props = {
sampleTable: ReturnType<typeof useSampleTable>['data'];
Expand Down Expand Up @@ -146,10 +146,9 @@ export const ProjectHeaderBar = (props: Props) => {
</button>
</div>
</div>
{projectInfo && !isLoading ?
{projectInfo && !isLoading ? (
<ProjectStars project={projectInfo} isStarred={isStarred} starNumber={projectInfo.stars_number} />
: null
}
) : null}
<Dropdown>
<Dropdown.Toggle size="sm" variant="dark">
<i className="bi bi-gear-fill me-1"></i>
Expand Down Expand Up @@ -204,13 +203,13 @@ export const ProjectHeaderBar = (props: Props) => {
{!projectInfo.pop && (
<>
<Dropdown.Item onClick={() => setShowProjectHistoryModal(true)}>
<i className="me-1 bi bi-stopwatch" />
<i className="me-1 bi bi-stopwatch" />
History
</Dropdown.Item>
<Dropdown.Item onClick={() => setShowStandardizeMetadataModal(true)}>
{/* <Dropdown.Item onClick={() => setShowStandardizeMetadataModal(true)}>
<i className="me-1 bi bi-magic"></i>
Standardize
</Dropdown.Item>
</Dropdown.Item> */}
</>
)}
<Dropdown.Item className="text-danger" onClick={() => setShowDeletePEPModal(true)}>
Expand Down
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