remove bedms, for now

pepkit · Dec 4, 2024 · 040fe92 · 040fe92
1 parent 4c700a2
commit 040fe92
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Showing 5 changed files with 72 additions and 73 deletions.
diff --git a/pephub/routers/api/v1/namespace.py b/pephub/routers/api/v1/namespace.py
@@ -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()
 
@@ -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
diff --git a/pephub/routers/api/v1/project.py b/pephub/routers/api/v1/project.py
@@ -62,7 +62,7 @@
 )
 from .helpers import verify_updated_project
 
-from bedms import AttrStandardizer
+# from bedms import AttrStandardizer
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -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)
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -16,4 +16,4 @@ fastembed
 numpy<2.0.0
 slowapi
 cachetools>=4.2.4
-bedms>=0.2.0
+# bedms>=0.2.0
diff --git a/web/src/components/modals/standardize-metadata.tsx b/web/src/components/modals/standardize-metadata.tsx
@@ -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) => {
@@ -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>
               )}

diff --git a/web/src/components/project/project-page-header-bar.tsx b/web/src/components/project/project-page-header-bar.tsx
@@ -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'];
@@ -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>
@@ -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)}>