app.api.api_v1#

app.api.api_v1.endpoints.acmgseqvar#

async app.api.api_v1.endpoints.acmgseqvar.create_acmgseqvar(acmgseqvar: AcmgSeqVarCreate, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

Create a new ACMG Sequence Variant.

Parameters:: acmgseqvar (dict or schemas.AcmgSeqVarCreate) – ACMG Sequence Variant to create
Returns:: ACMG Sequence Variant
Return type:: dict

async app.api.api_v1.endpoints.acmgseqvar.delete_acmgseqvar(id: str, db: AsyncSession = Depends(get_db))#

Delete a ACMG Sequence Variant by id. Available only for superusers.

Parameters:: id (uuid) – ACMG Sequence Variant id
Returns:: ACMG Sequence Variant
Return type:: dict

async app.api.api_v1.endpoints.acmgseqvar.delete_acmgseqvar_by_user(seqvar: str, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Delete a ACMG Sequence Variant by id.

Parameters:: id (uuid) – ACMG Sequence Variant id
Returns:: ACMG Sequence Variant
Return type:: dict

async app.api.api_v1.endpoints.acmgseqvar.get_acmgseqvar(id: str, db: AsyncSession = Depends(get_db))#

Get a ACMG Sequence Variant by id. Available only for superusers.

Parameters:: id (uuid) – ACMG Sequence Variant id
Returns:: ACMG Sequence Variant
Return type:: dict

async app.api.api_v1.endpoints.acmgseqvar.get_acmgseqvar_by_user(seqvar: str, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Get a ACMG Sequence Variant by id.

Parameters:: id (uuid) – ACMG Sequence Variant id
Returns:: ACMG Sequence Variant
Return type:: dict
Raises:: HTTPException 404 – ACMG Sequence Variant not found
Note:: If user_agent is browser, return 204 Response

async app.api.api_v1.endpoints.acmgseqvar.list_acmgseqvars(skip: int = 0, limit: int = 100, db: AsyncSession = Depends(get_db))#

List all ACMG Sequence Variants. Available only for superusers.

Parameters:

skip (int) – number of ACMG Sequence Variants to skip
limit (int) – maximum number of ACMG Sequence Variants to return

Returns:

list of ACMG Sequence Variants

Return type:

list

async app.api.api_v1.endpoints.acmgseqvar.list_acmgseqvars_by_user(skip: int = 0, limit: int = 100, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

List ACMG Sequence Variants by user.

Returns:: list of ACMG Sequence Variants
Return type:: list

async app.api.api_v1.endpoints.acmgseqvar.update_acmgseqvar(acmgseqvar: AcmgSeqVarUpdate, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

Update a ACMG Sequence Variant.

Parameters:: acmgseqvar (dict or schemas.AcmgSeqVarUpdate) – ACMG Sequence Variant to update
Returns:: ACMG Sequence Variant
Return type:: dict

app.api.api_v1.endpoints.adminmsgs#

async app.api.api_v1.endpoints.adminmsgs.read_adminmsgs(db: AsyncSession = Depends(get_db), skip: int = 0, limit: int = 100) → list[AdminMessageRead]#

Retrieve all admin messages.

Returns:: list of admin messages
Return type:: list

app.api.api_v1.endpoints.auth#

async app.api.api_v1.endpoints.auth.list_oauth2_providers() → list[OAuth2ProviderPublic]#

Retrieve all admin messages.

Returns:: list of admin messages
Return type:: list

app.api.api_v1.endpoints.bookmarks#

async app.api.api_v1.endpoints.bookmarks.create_bookmark(bookmark: BookmarkCreate, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

Create a new bookmark.

Parameters:: bookmark (dict or schemas.BookmarkCreate) – bookmark to create
Returns:: bookmark
Return type:: dict

async app.api.api_v1.endpoints.bookmarks.delete_bookmark(id: str, db: AsyncSession = Depends(get_db))#

Delete a bookmark. Available for superusers and bookmark owners.

Parameters:: id (uuid) – id of the bookmark
Returns:: bookmark which was deleted
Return type:: dict

async app.api.api_v1.endpoints.bookmarks.delete_bookmark_for_user(obj_type: str, obj_id: str, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Delete a bookmark for a current user by obj_type and obj_id.

Parameters:

obj_type (str (enum) - "gene", "seqvar", "strucvar") – type of object to bookmark
obj_id (uuid) – id of object to bookmark

Returns:

bookmark which was deleted

Return type:

dict

Raises:

HTTPException 404 – if bookmark not found

Note:

if user_agent is browser, return 204 Response

async app.api.api_v1.endpoints.bookmarks.get_bookmark(id: str, db: AsyncSession = Depends(get_db))#

Get a bookmark by id. Available only for superusers.

Parameters:: id (uuid) – id of the bookmark
Returns:: bookmark
Return type:: dict

async app.api.api_v1.endpoints.bookmarks.get_bookmark_for_user(obj_type: str, obj_id: str, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Get a bookmark for a current user by obj_type and obj_id.

Parameters:

obj_type (str (enum) - "gene", "seqvar", "strucvar") – type of object to bookmark
obj_id (uuid) – id of object to bookmark

Returns:

bookmark

Return type:

dict

Raises:

HTTPException 404 – if bookmark not found

Note:

if user_agent is browser, return 204

async app.api.api_v1.endpoints.bookmarks.list_bookmarks(skip: int = 0, limit: int = 100, db: AsyncSession = Depends(get_db))#

List all bookmarks. Available only for superusers.

Parameters:

skip (int) – number of bookmarks to skip
limit (int) – maximum number of bookmarks to return

Returns:

list of bookmarks

Return type:

list

async app.api.api_v1.endpoints.bookmarks.list_bookmarks_for_user(skip: int = 0, limit: int = 100, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

List bookmarks for a current user.

Parameters:

skip (int) – number of bookmarks to skip
limit (int) – maximum number of bookmarks to return

Returns:

list of bookmarks

Return type:

list

app.api.api_v1.endpoints.caseinfo#

async app.api.api_v1.endpoints.caseinfo.create_caseinfo(caseinfo: CaseInfoCreate, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

Create a new Case Information.

Parameters:: caseinfo (dict or schemas.CaseInfoCreate) – Case Information to create
Returns:: Case Information
Return type:: dict

async app.api.api_v1.endpoints.caseinfo.delete_caseinfo(id: str, db: AsyncSession = Depends(get_db))#

Delete a Case Information by id. Available only for superusers.

Parameters:: id (uuid) – Case Information id
Returns:: Case Information
Return type:: dict

async app.api.api_v1.endpoints.caseinfo.delete_caseinfo_for_user(db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Delete a Case Information for a current user.

Returns:: Case Information
Return type:: dict

async app.api.api_v1.endpoints.caseinfo.get_caseinfo(id: str, db: AsyncSession = Depends(get_db))#

Get a Case Information by id. Available only for superusers.

Parameters:: id (uuid) – Case Information id
Returns:: Case Information
Return type:: dict

async app.api.api_v1.endpoints.caseinfo.get_caseinfo_for_user(db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Get a Case Information for a current user.

Returns:: Case Information
Return type:: dict

async app.api.api_v1.endpoints.caseinfo.list_caseinfos(skip: int = 0, limit: int = 100, db: AsyncSession = Depends(get_db))#

List all Case Information. Available only for superusers.

Parameters:

skip (int) – number of Case Information to skip
limit (int) – maximum number of Case Information to return

Returns:

list of Case Information

Return type:

list

async app.api.api_v1.endpoints.caseinfo.list_caseinfos_for_user(db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency))#

List all Case Information for a current user.

Returns:: list of Case Information
Return type:: list

async app.api.api_v1.endpoints.caseinfo.update_caseinfo_for_user(caseinfoupdate: CaseInfoUpdate, db: AsyncSession = Depends(get_db), user: User = Depends(current_user_dependency), user_agent: str | None = None)#

Update a Case Information for a current user.

Parameters:: caseinfo (dict or schemas.CaseInfoUpdate) – Case Information to update
Returns:: Case Information
Return type:: dict

app.api.api_v1.endpoints.utils#

app.api.api_v1.endpoints.utils.test_email(email_to: EmailStr) → Any#

Send out a test email.

Parameters:: email_to (str) – email address to send the test email to
Returns:: message
Return type:: dict