From 99ee58ae15aed7a32f1df8c1c418249e1d2147ca Mon Sep 17 00:00:00 2001 From: Harpo Date: Tue, 10 Oct 2023 16:56:26 -0400 Subject: [PATCH 01/17] Fixes MediaFilesGuidsField, combines usage (#170) --- chowda/fields.py | 19 ++++++++++++++----- chowda/views.py | 24 +++--------------------- 2 files changed, 17 insertions(+), 26 deletions(-) diff --git a/chowda/fields.py b/chowda/fields.py index 8ac45f27..237b9ca4 100644 --- a/chowda/fields.py +++ b/chowda/fields.py @@ -11,10 +11,17 @@ @dataclass class MediaFilesGuidsField(TextAreaField): - """A field that displays a list of MediaFile GUIDs as html links""" - - render_function_key: str = 'media_file_guid_links' + """A field that displays a list of MediaFile GUIDs + Edit view: Textarea with GUIDs as strings + List view: Comma separated list of GUID Links + Detail view: Datatable with GUID links + """ + + id = 'media_file_guids' + label: str = 'Media Files' + display_template: str = 'displays/collection_media_files.html' form_template: str = 'forms/media_file_guids_textarea.html' + render_function_key: str = 'media_file_guid_links' async def parse_form_data( self, request: Request, form_data: FormData, action: RequestAction @@ -26,7 +33,9 @@ async def serialize_value( self, request: Request, value: Any, action: RequestAction ) -> Any: """Maps a Collection's MediaFile objects to a list of GUIDs""" - return [media_file.guid for media_file in value] + if request.state.action in (RequestAction.EDIT, RequestAction.LIST): + return [media_file.guid for media_file in value] + return value @dataclass @@ -127,7 +136,7 @@ async def parse_obj(self, request: Request, obj: Any) -> Any: class BatchUnstartedGuids(BaseField): """GUIDs in a batch that have not yet started""" - name: str = 'batch_unstarted_guids' + id: str = 'batch_unstarted_guids' read_only: bool = True label: str = 'Unstarted GUIDs' exclude_from_create: bool = True diff --git a/chowda/views.py b/chowda/views.py index a7519dcd..274ae80e 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -102,20 +102,7 @@ class CollectionView(ClammerModelView): 'description', MediaFileCount(), # 'media_files', # default view - MediaFilesGuidsField( - 'media_files', - id='media_file_guids', - label='GUIDs', - exclude_from_detail=True, - ), - BaseField( - 'media_files', - display_template='displays/collection_media_files.html', - label='Media Files', - exclude_from_edit=True, - exclude_from_create=True, - exclude_from_list=True, - ), + MediaFilesGuidsField('media_files', label='GUIDs'), ] async def validate(self, request: Request, data: Dict[str, Any]): @@ -208,13 +195,8 @@ class BatchView(ClammerModelView): BatchPercentCompleted(), BatchPercentSuccessful(), BatchUnstartedGuidsCount(), - BatchUnstartedGuids(), - MediaFilesGuidsField( - 'media_files', - id='media_file_guids', - label='GUIDs', - exclude_from_detail=True, - ), + BatchUnstartedGuids('media_files'), + MediaFilesGuidsField('media_files', exclude_from_detail=True), BatchMetaflowRunDisplayField(), ] From 21c124d2591f1f1e177832b45967bc92fe7330fa Mon Sep 17 00:00:00 2001 From: Harpo Date: Wed, 11 Oct 2023 13:15:18 -0400 Subject: [PATCH 02/17] =?UTF-8?q?=F0=9F=93=84=20Page=20title=20(#162)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Uses starlette-admin fork:dev branch * Adds Clammer permission to PipelineView --------- Co-authored-by: Andrew Myers --- chowda/views.py | 16 +++- pdm.lock | 234 ++++++++++++++++++++++++++---------------------- 2 files changed, 142 insertions(+), 108 deletions(-) diff --git a/chowda/views.py b/chowda/views.py index 274ae80e..d30d15cd 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -10,6 +10,7 @@ from starlette.responses import Response from starlette.templating import Jinja2Templates from starlette_admin import CustomView, action +from starlette_admin._types import RequestAction from starlette_admin.contrib.sqlmodel import ModelView from starlette_admin.exceptions import ActionFailed from starlette_admin.fields import BaseField @@ -59,6 +60,17 @@ class ChowdaModelView(ModelView): 'fixedHeader': True, } + def title(self, request: Request) -> str: + if request.state.action == RequestAction.LIST: + return self.label + if request.state.action == RequestAction.DETAIL: + return f'{self.label} - {request.path_params["pk"]}' + if request.state.action == RequestAction.EDIT: + return f'{self.label} - Edit {request.path_params["pk"]}' + if request.state.action == RequestAction.CREATE: + return f'{self.label} - Create' + return None + class ClammerModelView(ChowdaModelView): """Base Clammer permissions for all protected views""" @@ -368,7 +380,7 @@ class ClamsAppView(ClammerModelView): fields: ClassVar[list[Any]] = ['name', 'endpoint', 'description', 'pipelines'] -class PipelineView(AdminModelView): +class PipelineView(ClammerModelView): fields: ClassVar[list[Any]] = ['name', 'description', 'clams_apps'] def is_accessible(self, request: Request) -> bool: @@ -391,9 +403,11 @@ async def render(self, request: Request, templates: Jinja2Templates) -> Response sync_disabled = datetime.now() - history[0]['created_at'] < timedelta( minutes=15 ) + title = self.title(request) return templates.TemplateResponse( 'dashboard.html', { + 'title' if title else None: title, 'request': request, 'user': user, 'sync_history': history, diff --git a/pdm.lock b/pdm.lock index 58c652a6..cca429b1 100644 --- a/pdm.lock +++ b/pdm.lock @@ -202,7 +202,7 @@ summary = "The AWS SDK for Python" dependencies = [ "botocore<1.32.0,>=1.31.59", "jmespath<2.0.0,>=0.7.1", - "s3transfer<0.8.0,>=0.7.0", + "s3transfer<0.7.0,>=0.6.0", ] files = [ {file = "boto3-1.28.59-py3-none-any.whl", hash = "sha256:7623b52c135becf145f762a9cc4203a1fb30055bb1cc7a254f82e5f7954d44a1"}, @@ -732,12 +732,12 @@ files = [ [[package]] name = "dnspython" -version = "2.4.2" +version = "2.4.1" requires_python = ">=3.8,<4.0" summary = "DNS toolkit" files = [ - {file = "dnspython-2.4.2-py3-none-any.whl", hash = "sha256:57c6fbaaeaaf39c891292012060beb141791735dbb4004798328fc2c467402d8"}, - {file = "dnspython-2.4.2.tar.gz", hash = "sha256:8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984"}, + {file = "dnspython-2.4.1-py3-none-any.whl", hash = "sha256:5b7488477388b8c0b70a8ce93b227c5603bc7b77f1565afe8e729c36c51447d7"}, + {file = "dnspython-2.4.1.tar.gz", hash = "sha256:c33971c79af5be968bb897e95c2448e11a645ee84d93b265ce0b7aabe5dfdca8"}, ] [[package]] @@ -1168,15 +1168,15 @@ files = [ [[package]] name = "griffe" -version = "0.36.2" +version = "0.32.3" requires_python = ">=3.8" summary = "Signatures for entire Python programs. 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"pydantic[email]~=1.10", "sonyci~=0.1", "psycopg2~=2.9", - "metaflow~=2.9", + "metaflow~=2.10", "alembic~=1.12", "python-dotenv~=1.0", "authlib~=1.2", @@ -52,7 +52,7 @@ test = [ "trio~=0.22", ] locust = [ - "locust~=2.16", + "locust~=2.17", "pydantic-factories~=1.17", ] development = [ From b47611d9e8ec6ab013581a21b98d380808cfe56e Mon Sep 17 00:00:00 2001 From: Harpo Date: Wed, 11 Oct 2023 15:34:11 -0400 Subject: [PATCH 04/17] =?UTF-8?q?=E2=8C=9B=20Expires=20all=20(#172)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Fixes guid validation: session.expire_all() * Changes SonyCiAsset.id to Optional to fix validation * Protects percent complete fields from zero division --- chowda/app.py | 2 +- chowda/fields.py | 4 ++-- chowda/models.py | 2 +- chowda/utils.py | 7 +++++-- chowda/views.py | 1 + 5 files changed, 10 insertions(+), 6 deletions(-) diff --git a/chowda/app.py b/chowda/app.py index 636f62d6..3b03a526 100644 --- a/chowda/app.py +++ b/chowda/app.py @@ -70,7 +70,7 @@ admin.add_view(MediaFileView(MediaFile, icon='fa fa-file-video')) admin.add_view(SonyCiAssetView(SonyCiAsset, icon='fa fa-file-video')) admin.add_view(CollectionView(Collection, icon='fa fa-folder')) -admin.add_view(BatchView(Batch, icon='fa fa-folder', label='Batches')) +admin.add_view(BatchView(Batch, icon='fa fa-folder')) admin.add_view(ClamsAppView(ClamsApp, icon='fa fa-box')) admin.add_view(PipelineView(Pipeline, icon='fa fa-boxes-stacked')) admin.add_view(UserView(User, icon='fa fa-users')) diff --git a/chowda/fields.py b/chowda/fields.py index 237b9ca4..46ecb299 100644 --- a/chowda/fields.py +++ b/chowda/fields.py @@ -111,7 +111,7 @@ class BatchPercentCompleted(BaseField): async def parse_obj(self, request: Request, obj: Any) -> Any: runs = [run.finished for run in obj.metaflow_runs] - if runs: + if runs and obj.media_files: return f'{runs.count(True) / len(obj.media_files):.1%}' return None @@ -127,7 +127,7 @@ class BatchPercentSuccessful(BaseField): async def parse_obj(self, request: Request, obj: Any) -> Any: runs = [run.successful for run in obj.metaflow_runs] - if runs: + if runs and obj.media_files: return f'{runs.count(True) / len(obj.media_files):.1%}' return None diff --git a/chowda/models.py b/chowda/models.py index a5b544f7..236a8dec 100644 --- a/chowda/models.py +++ b/chowda/models.py @@ -148,7 +148,7 @@ class SonyCiAssetThumbnail(SQLModel): class SonyCiAsset(SQLModel, table=True): __tablename__ = 'sonyci_assets' - id: str = Field(primary_key=True, index=True) + id: Optional[str] = Field(primary_key=True, index=True, default=None) name: str = Field(index=True) size: int = Field(index=True, sa_column=Column(postgresql.BIGINT)) type: MediaType = Field(sa_column=Column(Enum(MediaType))) diff --git a/chowda/utils.py b/chowda/utils.py index ac81ca96..0f2b0535 100644 --- a/chowda/utils.py +++ b/chowda/utils.py @@ -2,7 +2,6 @@ from pydantic import BaseModel from sqlalchemy.dialects.postgresql import insert - from starlette.requests import Request @@ -57,12 +56,16 @@ def validate_media_file_guids(request: Request, data: Dict[str, Any]): relate to Batch and Collection objects. """ from sqlmodel import Session, select + from starlette_admin.exceptions import FormValidationError + from chowda.db import engine from chowda.models import MediaFile - from starlette_admin.exceptions import FormValidationError media_files = [] + # Clear the session to avoid conflicts with session instances used by the API + request.state.session.expire_all() + with Session(engine) as db: # Get all MediaFiles objects for the GUIDs in data['media_files'] media_files = db.exec( diff --git a/chowda/views.py b/chowda/views.py index d30d15cd..af3552f7 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -184,6 +184,7 @@ async def create_multiple_batches(self, request: Request, pks: List[Any]) -> str class BatchView(ClammerModelView): + label: ClassVar[str] = 'Batches' exclude_fields_from_create: ClassVar[list[Any]] = [Batch.id] exclude_fields_from_edit: ClassVar[list[Any]] = [Batch.id] exclude_fields_from_list: ClassVar[list[Any]] = [Batch.media_files] From 8931f0431b143757d5c15177ac99fa8d352e4a9c Mon Sep 17 00:00:00 2001 From: Harpo Date: Wed, 18 Oct 2023 14:54:36 -0400 Subject: [PATCH 05/17] =?UTF-8?q?=F0=9F=8F=9E=20`MMIF`=20source=20=20(#168?= =?UTF-8?q?)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adds new_mmif checkbox to start batch form * Adds MMIF model - WIP * Fixes MediaType Enum names to match values * Adds MMIF: MediaFile, Batch relationships * Migrates models: 1 MediaFile => Many SonyCiAssets * Adds input_mmifs, output_mmifs to batch * Filters MediaFile Ingest for video+audio only * Refactors start batch event with input_mmifs * Adds migration file * Migrates to many MMIF.input_mmifs * Switches back to jowilf/starlette-admin * Adds indices to improve ingest performance * Includes mmifs table in migration * Fixes index error, uess new_mmif as name * Fixes review notes * Fixes permission by adding audience to OAuth --- chowda/app.py | 3 + chowda/auth/oauth.py | 8 +- chowda/flows/ingest.py | 32 +++-- chowda/models.py | 122 ++++++++++++++---- chowda/views.py | 63 +++++++-- migrations/versions/65237fddcce3_mmifs.py | 104 +++++++++++++++ .../6a71376e4001_removes_mmif_json.py | 37 ++++++ pdm.lock | 16 +-- pyproject.toml | 2 +- 9 files changed, 332 insertions(+), 55 deletions(-) create mode 100644 migrations/versions/65237fddcce3_mmifs.py create mode 100644 migrations/versions/6a71376e4001_removes_mmif_json.py diff --git a/chowda/app.py b/chowda/app.py index 3b03a526..0f9573e7 100644 --- a/chowda/app.py +++ b/chowda/app.py @@ -16,6 +16,7 @@ from chowda.config import SECRET, STATIC_DIR, TEMPLATES_DIR from chowda.db import engine from chowda.models import ( + MMIF, Batch, ClamsApp, Collection, @@ -33,6 +34,7 @@ DashboardView, MediaFileView, MetaflowRunView, + MMIFView, PipelineView, SonyCiAssetView, UserView, @@ -75,6 +77,7 @@ admin.add_view(PipelineView(Pipeline, icon='fa fa-boxes-stacked')) admin.add_view(UserView(User, icon='fa fa-users')) admin.add_view(MetaflowRunView(MetaflowRun, icon='fa fa-person-running')) +admin.add_view(MMIFView(MMIF, icon='fa fa-person-running')) # Mount admin to app diff --git a/chowda/auth/oauth.py b/chowda/auth/oauth.py index c39f58fb..1bb870b2 100644 --- a/chowda/auth/oauth.py +++ b/chowda/auth/oauth.py @@ -9,7 +9,12 @@ from starlette_admin import BaseAdmin from starlette_admin.auth import AdminUser, AuthMiddleware, AuthProvider -from chowda.config import AUTH0_CLIENT_ID, AUTH0_CLIENT_SECRET, AUTH0_DOMAIN +from chowda.config import ( + API_AUDIENCE, + AUTH0_CLIENT_ID, + AUTH0_CLIENT_SECRET, + AUTH0_DOMAIN, +) oauth = OAuth() oauth.register( @@ -20,6 +25,7 @@ 'scope': 'openid profile email', }, server_metadata_url=f'https://{AUTH0_DOMAIN}/.well-known/openid-configuration', + authorize_params={'audience': API_AUDIENCE}, ) diff --git a/chowda/flows/ingest.py b/chowda/flows/ingest.py index 73b1aa4b..10792352 100644 --- a/chowda/flows/ingest.py +++ b/chowda/flows/ingest.py @@ -1,6 +1,9 @@ from metaflow import FlowSpec, secrets, step, trigger from chowda.log import log +from chowda.models import MediaType + +media_types = {MediaType('Video'), MediaType('Audio')} @trigger(event='sync') @@ -66,32 +69,35 @@ def batch_ingest_page(self, n): from chowda.models import MediaFile, SonyCiAsset from chowda.utils import upsert - with Session(engine) as session: - batch = self.get_batch(n) - media = [SonyCiAsset(**asset) for asset in batch] - results = [] + batch = self.get_batch(n) + media = [SonyCiAsset(**asset) for asset in batch] + results = [] + + with Session(engine) as db: for asset in media: - results.append(session.execute(upsert(SonyCiAsset, asset, ['id']))) - # If it's a GUID - if search('^cpb-aacip-', asset.name): + results.append(db.execute(upsert(SonyCiAsset, asset, ['id']))) + # If it's a video or audio, and starts with cpb-aacip-* + if asset.type in media_types and search('^cpb-aacip-', asset.name): + # It's a MediaFile! # Extract the GUID name guid = split(r'_|\.|-dupe', asset.name)[0] # Check for existing MediaFile - media_file = session.exec( + media_file = db.exec( select(MediaFile).where(MediaFile.guid == guid) ).first() if not media_file: # Create a new MediaFile with the new guid media_file = MediaFile(guid=guid) - ci_asset = session.get(SonyCiAsset, asset.id) + # Get the SonyCiAsset we just saved to the db + ci_asset = db.get(SonyCiAsset, asset.id) # Add the asset to the existing MediaFile media_file.assets.append(ci_asset) - session.add(media_file) + db.add(media_file) result = sum([r.rowcount for r in results]) - session.commit() - log.success(f'Ingested page {n} with {result} assets') - return result + db.commit() + log.success(f'Ingested page {n} with {result} assets') + return result if __name__ == '__main__': diff --git a/chowda/models.py b/chowda/models.py index 236a8dec..300665b6 100644 --- a/chowda/models.py +++ b/chowda/models.py @@ -29,8 +29,19 @@ class AppStatus(enum.Enum): class MediaType(enum.Enum): - video = 'Video' - audio = 'Audio' + """Media type enum + Type of Media: video or audio. + This is not the same as the format of the media file. + + # FIXME: + Enum class attributes are the values that are stored in the database. + The value of the class attribute is the value returned by SonyCi (for validation) + But starlette-admin + SQLAlchemy send the value to the db, not the name. + Therefore, we need to Capatalize the name to make it match the db value. + """ + + Video = 'Video' + Audio = 'Audio' class ThumbnailType(enum.Enum): @@ -64,28 +75,31 @@ async def __admin_repr__(self, request: Request): class MediaFileCollectionLink(SQLModel, table=True): media_file_id: Optional[str] = Field( - default=None, foreign_key='media_files.guid', primary_key=True + default=None, foreign_key='media_files.guid', primary_key=True, index=True ) collection_id: Optional[int] = Field( - default=None, foreign_key='collections.id', primary_key=True + default=None, foreign_key='collections.id', primary_key=True, index=True ) class MediaFileBatchLink(SQLModel, table=True): media_file_id: Optional[str] = Field( - default=None, foreign_key='media_files.guid', primary_key=True + default=None, foreign_key='media_files.guid', primary_key=True, index=True ) batch_id: Optional[int] = Field( - default=None, foreign_key='batches.id', primary_key=True + default=None, foreign_key='batches.id', primary_key=True, index=True + ) + source_mmif_id: Optional[int] = Field( + default=None, foreign_key='mmifs.id', index=True ) -class MediaFileSonyCiAssetLink(SQLModel, table=True): - media_file_id: Optional[str] = Field( - default=None, foreign_key='media_files.guid', primary_key=True +class MMIFBatchInputLink(SQLModel, table=True): + mmif_id: Optional[int] = Field( + default=None, foreign_key='mmifs.id', primary_key=True, index=True ) - sonyci_asset_id: Optional[str] = Field( - default=None, foreign_key='sonyci_assets.id', primary_key=True + batch_id: Optional[int] = Field( + default=None, foreign_key='batches.id', primary_key=True, index=True ) @@ -98,14 +112,13 @@ class MediaFile(SQLModel, table=True): collections: List of Collections batches: List of Batches metaflow_runs: List of MetaflowRuns + mmifs: List of MMIFs """ __tablename__ = 'media_files' guid: Optional[str] = Field(primary_key=True, default=None, index=True) - mmif_json: Dict[str, Any] = Field(sa_column=Column(JSON), default=None) - assets: List['SonyCiAsset'] = Relationship( - back_populates='media_files', link_model=MediaFileSonyCiAssetLink - ) + mmifs: List['MMIF'] = Relationship(back_populates='media_file') + assets: List['SonyCiAsset'] = Relationship(back_populates='media_files') collections: List['Collection'] = Relationship( back_populates='media_files', link_model=MediaFileCollectionLink ) @@ -156,9 +169,10 @@ class SonyCiAsset(SQLModel, table=True): thumbnails: Optional[List[Dict[str, Any]]] = Field( sa_column=Column(postgresql.ARRAY(JSON)), default=None ) - media_files: List[MediaFile] = Relationship( - back_populates='assets', link_model=MediaFileSonyCiAssetLink + media_file_id: Optional[str] = Field( + default=None, foreign_key='media_files.guid', index=True ) + media_files: Optional[MediaFile] = Relationship(back_populates='assets') @property def thumbnails_by_type(self): @@ -194,6 +208,17 @@ class Batch(SQLModel, table=True): media_files: List[MediaFile] = Relationship( back_populates='batches', link_model=MediaFileBatchLink ) + output_mmifs: List['MMIF'] = Relationship( + back_populates='batch_output', + sa_relationship_kwargs={ + "primaryjoin": "Batch.id==MMIF.batch_output_id", + }, + ) + + input_mmifs: List['MMIF'] = Relationship( + back_populates='batch_inputs', + link_model=MMIFBatchInputLink, + ) metaflow_runs: List['MetaflowRun'] = Relationship(back_populates='batch') def unstarted_guids(self) -> set: @@ -211,10 +236,10 @@ async def __admin_select2_repr__(self, request: Request) -> str: class ClamsAppPipelineLink(SQLModel, table=True): clams_app_id: Optional[int] = Field( - default=None, foreign_key='clams_apps.id', primary_key=True + default=None, foreign_key='clams_apps.id', primary_key=True, index=True ) pipeline_id: Optional[int] = Field( - default=None, foreign_key='pipelines.id', primary_key=True + default=None, foreign_key='pipelines.id', primary_key=True, index=True ) @@ -237,7 +262,7 @@ async def __admin_select2_repr__(self, request: Request): class Pipeline(SQLModel, table=True): __tablename__ = 'pipelines' - id: Optional[int] = Field(primary_key=True, default=None) + id: Optional[int] = Field(primary_key=True, default=None, index=True) name: str description: str clams_apps: List[ClamsApp] = Relationship( @@ -254,11 +279,13 @@ async def __admin_select2_repr__(self, request: Request) -> str: class MetaflowRun(SQLModel, table=True): __tablename__ = 'metaflow_runs' - id: Optional[str] = Field(primary_key=True, default=None) + id: Optional[str] = Field(primary_key=True, default=None, index=True) pathspec: str - batch_id: Optional[int] = Field(default=None, foreign_key='batches.id') + batch_id: Optional[int] = Field(default=None, foreign_key='batches.id', index=True) batch: Optional[Batch] = Relationship(back_populates='metaflow_runs') - media_file_id: Optional[str] = Field(default=None, foreign_key='media_files.guid') + media_file_id: Optional[str] = Field( + default=None, foreign_key='media_files.guid', index=True + ) media_file: Optional[MediaFile] = Relationship(back_populates='metaflow_runs') created_at: Optional[datetime] = Field( sa_column=Column(DateTime(timezone=True), default=datetime.utcnow) @@ -271,8 +298,57 @@ class MetaflowRun(SQLModel, table=True): current_step: Optional[str] = Field(default=None) current_task: Optional[str] = Field(default=None) + mmif: Optional['MMIF'] = Relationship(back_populates='metaflow_run') + @property def source(self): # TODO: is setting namespace to None the right way to go here? namespace(None) return Run(self.pathspec) + + +class MMIF(SQLModel, table=True): + """MMIF model + + Attributes: + id: Primary key + created_at: Creation timestamp + media_file_id: GUID + media_file: MediaFile + metaflow_run_id: MetaflowRun ID + metaflow_run: MetaflowRun + batch_output: Batch that generated this MMIF + batch_inputs: Batch that uses this as an input + """ + + __tablename__ = 'mmifs' + id: Optional[int] = Field(primary_key=True, default=None, index=True) + created_at: Optional[datetime] = Field( + sa_column=Column(DateTime(timezone=True), default=datetime.utcnow) + ) + media_file_id: Optional[str] = Field( + default=None, foreign_key='media_files.guid', index=True + ) + media_file: Optional[MediaFile] = Relationship(back_populates='mmifs') + metaflow_run_id: Optional[str] = Field(default=None, foreign_key='metaflow_runs.id') + metaflow_run: Optional[MetaflowRun] = Relationship(back_populates='mmif') + batch_output_id: Optional[int] = Field(default=None, foreign_key='batches.id') + batch_output: Optional[Batch] = Relationship( + back_populates='output_mmifs', + sa_relationship_kwargs={ + "primaryjoin": "MMIF.batch_output_id==Batch.id", + }, + ) + batch_inputs: List[Batch] = Relationship( + back_populates='input_mmifs', + link_model=MMIFBatchInputLink, + ) + + mmif_location: Optional[str] = Field(default=None) + + async def __admin_repr__(self, request: Request): + return f'{self.metaflow_run.batch.name}' if self.metaflow_run else self.id + + async def __admin_select2_repr__(self, request: Request) -> str: + text = self.metaflow_run.batch.name if self.metaflow_run else self.id + return f'{text}' diff --git a/chowda/views.py b/chowda/views.py index af3552f7..4fcc1e3e 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -4,6 +4,7 @@ from metaflow import Flow from metaflow.exception import MetaflowNotFound from metaflow.integrations import ArgoEvent +from multipart.exceptions import MultipartParseError from sqlmodel import Session, select from starlette.datastructures import FormData from starlette.requests import Request @@ -208,9 +209,11 @@ class BatchView(ClammerModelView): BatchPercentCompleted(), BatchPercentSuccessful(), BatchUnstartedGuidsCount(), + 'input_mmifs', BatchUnstartedGuids('media_files'), MediaFilesGuidsField('media_files', exclude_from_detail=True), BatchMetaflowRunDisplayField(), + 'output_mmifs', ] async def validate(self, request: Request, data: Dict[str, Any]): @@ -234,9 +237,22 @@ async def is_action_allowed(self, request: Request, name: str) -> bool: action_btn_class='btn-outline-success', submit_btn_text='Yep', submit_btn_class='btn-success', + form=""" +
+ + + +
+ """, ) async def start_batches(self, request: Request, pks: List[Any]) -> str: """Starts a Batch by sending a message to the Argo Event Bus""" + try: + data: FormData = await request.form() + except MultipartParseError as parse_error: + raise ActionFailed('Error parsing form') from parse_error + + new_mmif = data.get('new_mmif') == 'on' try: with Session(engine) as db: for batch_id in pks: @@ -244,15 +260,30 @@ async def start_batches(self, request: Request, pks: List[Any]) -> str: pipeline = ','.join( [app.endpoint for app in batch.pipeline.clams_apps] ) + mmifs = { + mmif.media_file_id: mmif.mmif_location + for mmif in batch.input_mmifs + } + mmif_guids = set(mmifs.keys()) for media_file in batch.media_files: - ArgoEvent( - 'pipeline', - payload={ - 'batch_id': batch_id, - 'guid': media_file.guid, - 'pipeline': pipeline, - }, - ).publish(ignore_errors=False) + payload = { + 'batch_id': batch_id, + 'guid': media_file.guid, + 'pipeline': pipeline, + } + if new_mmif: + payload['mmif_location'] = '' + elif media_file.guid in mmif_guids: + # Prefer the Batch's MMIF if specified + payload['mmif_location'] = mmifs[media_file.guid] + elif media_file.mmifs: + # If there is an MMIF in the MediaFile's MMIFs + payload['mmif_location'] = media_file.mmifs[ + -1 + ].mmif_location + ArgoEvent('pipeline', payload=payload).publish( + ignore_errors=False + ) except Exception as error: raise ActionFailed(f'{error!s}') from error @@ -332,8 +363,10 @@ class MediaFileView(ClammerModelView): 'batches', 'assets', BaseField('mmif_json', display_template='displays/media_file_mmif_json.html'), + 'mmifs', + 'metaflow_runs', ] - exclude_fields_from_list: ClassVar[list[str]] = ['mmif_json'] + exclude_fields_from_list: ClassVar[list[str]] = ['mmif_json', 'mmifs'] page_size_options: ClassVar[list[int]] = [10, 25, 100, 500, 2000, 10000] def can_create(self, request: Request) -> bool: @@ -438,3 +471,15 @@ def can_create(self, request: Request) -> bool: class MetaflowRunView(AdminModelView): form_include_pk: ClassVar[bool] = True + + +class MMIFView(ChowdaModelView): + label: ClassVar[str] = 'MMIFs' + fields: ClassVar[List[Any]] = [ + 'media_file', + 'batch_inputs', + 'batch_output', + 'metaflow_run', + 'mmif_location', + 'created_at', + ] diff --git a/migrations/versions/65237fddcce3_mmifs.py b/migrations/versions/65237fddcce3_mmifs.py new file mode 100644 index 00000000..d06e4349 --- /dev/null +++ b/migrations/versions/65237fddcce3_mmifs.py @@ -0,0 +1,104 @@ +"""MMIFs + +Revision ID: 65237fddcce3 +Revises: 42a163f0faec +Create Date: 2023-10-13 14:58:07.011114 + +""" +from alembic import op +import sqlalchemy as sa +import sqlmodel +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision = '65237fddcce3' +down_revision = '42a163f0faec' +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('mmifs', + sa.Column('created_at', sa.DateTime(timezone=True), nullable=True), + sa.Column('mmif_json', sa.JSON(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('media_file_id', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('metaflow_run_id', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('batch_output_id', sa.Integer(), nullable=True), + sa.Column('mmif_location', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.ForeignKeyConstraint(['batch_output_id'], ['batches.id'], ), + sa.ForeignKeyConstraint(['media_file_id'], ['media_files.guid'], ), + sa.ForeignKeyConstraint(['metaflow_run_id'], ['metaflow_runs.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_index(op.f('ix_mmifs_id'), 'mmifs', ['id'], unique=False) + op.create_index(op.f('ix_mmifs_media_file_id'), 'mmifs', ['media_file_id'], unique=False) + op.create_table('mmifbatchinputlink', + sa.Column('mmif_id', sa.Integer(), nullable=False), + sa.Column('batch_id', sa.Integer(), nullable=False), + sa.ForeignKeyConstraint(['batch_id'], ['batches.id'], ), + sa.ForeignKeyConstraint(['mmif_id'], ['mmifs.id'], ), + sa.PrimaryKeyConstraint('mmif_id', 'batch_id') + ) + op.create_index(op.f('ix_mmifbatchinputlink_batch_id'), 'mmifbatchinputlink', ['batch_id'], unique=False) + op.create_index(op.f('ix_mmifbatchinputlink_mmif_id'), 'mmifbatchinputlink', ['mmif_id'], unique=False) + op.drop_table('mediafilesonyciassetlink') + op.create_index(op.f('ix_clamsapppipelinelink_clams_app_id'), 'clamsapppipelinelink', ['clams_app_id'], unique=False) + op.create_index(op.f('ix_clamsapppipelinelink_pipeline_id'), 'clamsapppipelinelink', ['pipeline_id'], unique=False) + op.create_index(op.f('ix_mediafilebatchlink_batch_id'), 'mediafilebatchlink', ['batch_id'], unique=False) + op.create_index(op.f('ix_mediafilebatchlink_media_file_id'), 'mediafilebatchlink', ['media_file_id'], unique=False) + op.create_index(op.f('ix_mediafilecollectionlink_collection_id'), 'mediafilecollectionlink', ['collection_id'], unique=False) + op.create_index(op.f('ix_mediafilecollectionlink_media_file_id'), 'mediafilecollectionlink', ['media_file_id'], unique=False) + op.alter_column('metaflow_runs', 'finished_at', + existing_type=postgresql.TIMESTAMP(), + type_=sa.DateTime(timezone=True), + existing_nullable=True) + op.create_index(op.f('ix_metaflow_runs_batch_id'), 'metaflow_runs', ['batch_id'], unique=False) + op.create_index(op.f('ix_metaflow_runs_id'), 'metaflow_runs', ['id'], unique=False) + op.create_index(op.f('ix_metaflow_runs_media_file_id'), 'metaflow_runs', ['media_file_id'], unique=False) + op.create_index(op.f('ix_pipelines_id'), 'pipelines', ['id'], unique=False) + op.add_column('sonyci_assets', sa.Column('media_file_id', sqlmodel.sql.sqltypes.AutoString(), nullable=True)) + op.create_index(op.f('ix_sonyci_assets_media_file_id'), 'sonyci_assets', ['media_file_id'], unique=False) + op.create_foreign_key(None, 'sonyci_assets', 'media_files', ['media_file_id'], ['guid']) + # ### end Alembic commands ### + + op.execute("ALTER TYPE mediatype RENAME VALUE 'video' TO 'Video';") + op.execute("ALTER TYPE mediatype RENAME VALUE 'audio' TO 'Audio';") + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + # op.drop_constraint(None, 'sonyci_assets', type_='foreignkey') + op.drop_index(op.f('ix_sonyci_assets_media_file_id'), table_name='sonyci_assets') + op.drop_column('sonyci_assets', 'media_file_id') + op.drop_index(op.f('ix_pipelines_id'), table_name='pipelines') + op.drop_index(op.f('ix_metaflow_runs_media_file_id'), table_name='metaflow_runs') + op.drop_index(op.f('ix_metaflow_runs_id'), table_name='metaflow_runs') + op.drop_index(op.f('ix_metaflow_runs_batch_id'), table_name='metaflow_runs') + op.alter_column('metaflow_runs', 'finished_at', + existing_type=sa.DateTime(timezone=True), + type_=postgresql.TIMESTAMP(), + existing_nullable=True) + op.drop_index(op.f('ix_mediafilecollectionlink_media_file_id'), table_name='mediafilecollectionlink') + op.drop_index(op.f('ix_mediafilecollectionlink_collection_id'), table_name='mediafilecollectionlink') + op.drop_index(op.f('ix_mediafilebatchlink_media_file_id'), table_name='mediafilebatchlink') + op.drop_index(op.f('ix_mediafilebatchlink_batch_id'), table_name='mediafilebatchlink') + op.drop_index(op.f('ix_clamsapppipelinelink_pipeline_id'), table_name='clamsapppipelinelink') + op.drop_index(op.f('ix_clamsapppipelinelink_clams_app_id'), table_name='clamsapppipelinelink') + op.create_table('mediafilesonyciassetlink', + sa.Column('media_file_id', sa.VARCHAR(), autoincrement=False, nullable=False), + sa.Column('sonyci_asset_id', sa.VARCHAR(), autoincrement=False, nullable=False), + sa.ForeignKeyConstraint(['media_file_id'], ['media_files.guid'], name='mediafilesonyciassetlink_media_file_id_fkey'), + sa.ForeignKeyConstraint(['sonyci_asset_id'], ['sonyci_assets.id'], name='mediafilesonyciassetlink_sonyci_asset_id_fkey'), + sa.PrimaryKeyConstraint('media_file_id', 'sonyci_asset_id', name='mediafilesonyciassetlink_pkey') + ) + op.drop_index(op.f('ix_mmifbatchinputlink_mmif_id'), table_name='mmifbatchinputlink') + op.drop_index(op.f('ix_mmifbatchinputlink_batch_id'), table_name='mmifbatchinputlink') + op.drop_table('mmifbatchinputlink') + op.drop_index(op.f('ix_mmifs_media_file_id'), table_name='mmifs') + op.drop_index(op.f('ix_mmifs_id'), table_name='mmifs') + op.drop_table('mmifs') + # ### end Alembic commands ### + + op.execute("ALTER TYPE mediatype RENAME VALUE 'Video' TO 'video';") + op.execute("ALTER TYPE mediatype RENAME VALUE 'Audio' TO 'audio';") \ No newline at end of file diff --git a/migrations/versions/6a71376e4001_removes_mmif_json.py b/migrations/versions/6a71376e4001_removes_mmif_json.py new file mode 100644 index 00000000..802114a5 --- /dev/null +++ b/migrations/versions/6a71376e4001_removes_mmif_json.py @@ -0,0 +1,37 @@ +"""Removes mmif_json + +Revision ID: 6a71376e4001 +Revises: 65237fddcce3 +Create Date: 2023-10-16 15:26:35.973058 + +""" +from alembic import op +import sqlalchemy as sa +import sqlmodel +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision = '6a71376e4001' +down_revision = '65237fddcce3' +branch_labels = None +depends_on = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('media_files', 'mmif_json') + op.add_column('mediafilebatchlink', sa.Column('source_mmif_id', sa.Integer(), nullable=True)) + op.create_index(op.f('ix_mediafilebatchlink_source_mmif_id'), 'mediafilebatchlink', ['source_mmif_id'], unique=False) + op.create_foreign_key(None, 'mediafilebatchlink', 'mmifs', ['source_mmif_id'], ['id']) + op.drop_column('mmifs', 'mmif_json') + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('mmifs', sa.Column('mmif_json', postgresql.JSON(astext_type=sa.Text()), autoincrement=False, nullable=True)) + op.drop_constraint(None, 'mediafilebatchlink', type_='foreignkey') + op.drop_index(op.f('ix_mediafilebatchlink_source_mmif_id'), table_name='mediafilebatchlink') + op.drop_column('mediafilebatchlink', 'source_mmif_id') + op.add_column('media_files', sa.Column('mmif_json', postgresql.JSON(astext_type=sa.Text()), autoincrement=False, nullable=True)) + # ### end Alembic commands ### diff --git a/pdm.lock b/pdm.lock index 6a0078da..1259606e 100644 --- a/pdm.lock +++ b/pdm.lock @@ -6,7 +6,7 @@ groups = ["default", "ci", "dev", "development", "docs", "locust", "production", cross_platform = true static_urls = false lock_version = "4.3" -content_hash = "sha256:39cdf5f81aaae22323b182d0717477cf17735ec2dc4f9e3f35b267a56236abbe" +content_hash = "sha256:5a6ceb4becede446d306ddf9f7b9acd3627add0be4a43abf7a7ba16255bcbd83" [[package]] name = "alembic" @@ -202,7 +202,7 @@ summary = "The AWS SDK for Python" dependencies = [ "botocore<1.32.0,>=1.31.62", "jmespath<2.0.0,>=0.7.1", - "s3transfer<0.7.0,>=0.6.0", + "s3transfer<0.8.0,>=0.7.0", ] files = [ {file = "boto3-1.28.62-py3-none-any.whl", hash = "sha256:0dfa2fc96ccafce4feb23044d6cba8b25075ad428a0c450d369d099c6a1059d2"}, @@ -3166,15 +3166,15 @@ files = [ [[package]] name = "s3transfer" -version = "0.6.2" +version = "0.7.0" requires_python = ">= 3.7" summary = "An Amazon S3 Transfer Manager" dependencies = [ "botocore<2.0a.0,>=1.12.36", ] files = [ - {file = "s3transfer-0.6.2-py3-none-any.whl", hash = "sha256:b014be3a8a2aab98cfe1abc7229cc5a9a0cf05eb9c1f2b86b230fd8df3f78084"}, - {file = "s3transfer-0.6.2.tar.gz", hash = "sha256:cab66d3380cca3e70939ef2255d01cd8aece6a4907a9528740f668c4b0611861"}, + {file = "s3transfer-0.7.0-py3-none-any.whl", hash = "sha256:10d6923c6359175f264811ef4bf6161a3156ce8e350e705396a7557d6293c33a"}, + {file = "s3transfer-0.7.0.tar.gz", hash = "sha256:fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e"}, ] [[package]] @@ -3346,9 +3346,9 @@ files = [ name = "starlette-admin" version = "0.11.2" requires_python = ">=3.8" -git = "https://github.com/WGBH-MLA/starlette-admin.git" -ref = "detail-actions" -revision = "a3fe3f27cc66217eb2901d079dcdf5f2d859b2f2" +git = "https://github.com/jowilf/starlette-admin.git" +ref = "main" +revision = "855a71ccf7b7a4fa6ccd3026a9bf593eccb18d7c" summary = "Fast, beautiful and extensible administrative interface framework for Starlette/FastApi applications" dependencies = [ "jinja2<4,>=3", diff --git a/pyproject.toml b/pyproject.toml index 5276a236..18a89031 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ description = 'A CLAMS processing application' authors = [{ name = 'WGBH-MLA', email = 'ryan_harbert@wgbh.org' }] dependencies = [ "fastapi~=0.103", - "starlette-admin @ git+https://github.com/WGBH-MLA/starlette-admin.git@dev", + "starlette-admin @ git+https://github.com/jowilf/starlette-admin.git@main", "sqlmodel~=0.0", "pydantic[email]~=1.10", "sonyci~=0.1", From c648f637d246964cfd6ed32398c02c69f8176327 Mon Sep 17 00:00:00 2001 From: Andrew Myers Date: Wed, 25 Oct 2023 14:28:05 -0400 Subject: [PATCH 06/17] =?UTF-8?q?=F0=9F=94=8F=20Requires=20valid=20access?= =?UTF-8?q?=20tokens=20for=20API=20calls=20(#173)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Requires valid access tokens for API calls * Adds a dependency function called `permissions` that allows API endpoints to require specific permissions. * A permissions is a combination of an action and a resource type, delimited by a colon, for instance "read:messages". * The permissions() dependency function takes a single permission string, or a list of them. * POST /api/events/ now requiress "create:event" permission * POST /api/sony_ci/sync now requires "sync:sony_ci" permission * The "permissions" dependency can be added to any API endpoint like this: `@app.get('/users/', dependencies=[Depends(permissions('read:users'))])` * The "permissions" dependency in turn depends on a verified access token, which is verified by fetching the unverified access token from the HTTP request header and verifying it with the well-known public key provided by Auth0. * NOTE: for testing, the verified access token dependency is overridden to avoid depending on live connection with Auth0 for tests. * Adds tests for testing the authentication and authorization dependencies of the API endpoints. * The testing pattern involves a factory for generating a fake access tokens with whatever permissions the test is concerned with testing. Also: * Removes unused launch config for tests. Use vscode pytest settings instead. * Changes param name from allow_redirects to follow_redirects to fix deprecation warning * Adds git-guardian cache dir to git ignore * Adds constants to config used for verifying access token and specifying the authorization 'audience'. * Renames admin_user dependency to to 'get_admin_user' for consistency. * Renames get_user to get_oauth_user for specificity -- i.e. not a User model from the Chowda db. * Adds pyjwt for dealing with Javascript Web Tokens (jwt). * Removes test for api calls to create batches - not needed. * Removes .env files from revision, but leaves a sample template: '.env.sample'. * Prefixes all env vars and constants having to do with Auth0 with "AUTH0_" for consistency. * Sets test db used in github CI workflow to use name 'chowda' and default port 5432. Closes #153. --------- Co-authored-by: Harpo Harbert --- .env.development | 1 - .env.sample | 13 + .env.test | 1 - .github/workflows/CI.yml | 5 +- .gitignore | 7 +- .vscode/launch.json | 14 - chowda/app.py | 9 +- chowda/auth/oauth.py | 4 +- chowda/auth/utils.py | 132 +++++- chowda/config.py | 6 +- chowda/routers/dashboard.py | 6 +- chowda/routers/events.py | 42 +- chowda/routers/sony_ci.py | 8 +- chowda/views.py | 22 +- pdm.lock | 802 ++++++++++++++++++---------------- pyproject.toml | 1 + tests/conftest.py | 59 +++ tests/routers/test_events.py | 104 +++++ tests/routers/test_sony_ci.py | 62 ++- tests/test_app.py | 4 +- tests/test_batches.py | 57 --- 21 files changed, 835 insertions(+), 524 deletions(-) delete mode 100644 .env.development create mode 100644 .env.sample delete mode 100644 .env.test create mode 100644 tests/routers/test_events.py delete mode 100644 tests/test_batches.py diff --git a/.env.development b/.env.development deleted file mode 100644 index 4ec96ff8..00000000 --- a/.env.development +++ /dev/null @@ -1 +0,0 @@ -DB_URL='postgresql://postgres:postgres@localhost:5432/chowda-development' diff --git a/.env.sample b/.env.sample new file mode 100644 index 00000000..587370db --- /dev/null +++ b/.env.sample @@ -0,0 +1,13 @@ +# Postgres URL for Chowda DB. +# Format: postgresql://{user}:{password}@{host}:{port}/{database} +DB_URL='' + +# Env vars beginning with "AUTH0_" are used for authentication and authorization with Auth0. +# These values can be obtained by logging into our Auth0 account. +AUTH0_DOMAIN='' +AUTH0_CLIENT_ID='' +AUTH0_CLIENT_SECRET='' +AUTH0_API_AUDIENCE='' + +# Secret value for securing session data using SessionMiddleware +CHOWDA_SECRET='' diff --git a/.env.test b/.env.test deleted file mode 100644 index 02ceb49a..00000000 --- a/.env.test +++ /dev/null @@ -1 +0,0 @@ -DB_URL='postgresql://postgres:postgres@localhost:5432/chowda-test' diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 59eb015f..22e290dd 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -2,9 +2,6 @@ name: 🧪 Integration Tests on: [push, pull_request, workflow_dispatch] -env: - DB_URL: postgresql://postgres:postgres@postgres:5432/chowda-test - jobs: tests: name: ⚗️ Application Tests @@ -13,7 +10,7 @@ jobs: with: pdm_args: -G test,ci pytest_args: -n auto --nbmake -ra -s - pg_db: chowda-test + pg_db: chowda lint: name: 👕 Lint diff --git a/.gitignore b/.gitignore index 4db66c1c..93226767 100644 --- a/.gitignore +++ b/.gitignore @@ -23,4 +23,9 @@ ci.toml # Metaflow generated files metaflow.s3.* -.metaflow \ No newline at end of file +.metaflow + +.cache_ggshield + +.env.* +!.env.sample diff --git a/.vscode/launch.json b/.vscode/launch.json index ad34829f..1d0549be 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -18,20 +18,6 @@ "jinja": false, "justMyCode": false }, - { - "name": "Chowda: tests", - "type": "python", - "request": "launch", - "cwd": "${workspaceFolder}", - "module": "pytest", - "args": [ - "-v", - "-n", - "auto" - ], - "jinja": false, - "justMyCode": false - }, { "name": "Metaflow: Run", "type": "python", diff --git a/chowda/app.py b/chowda/app.py index 0f9573e7..3381eeb1 100644 --- a/chowda/app.py +++ b/chowda/app.py @@ -2,7 +2,7 @@ Main Chowda application""" -from fastapi import FastAPI +from fastapi import Depends, FastAPI from fastapi.staticfiles import StaticFiles from starlette.middleware import Middleware from starlette.middleware.sessions import SessionMiddleware @@ -13,6 +13,7 @@ from chowda.admin import Admin from chowda.api import api from chowda.auth import OAuthProvider +from chowda.auth.utils import get_admin_user, verified_access_token from chowda.config import SECRET, STATIC_DIR, TEMPLATES_DIR from chowda.db import engine from chowda.models import ( @@ -53,8 +54,10 @@ ) app.mount('/static', StaticFiles(directory=STATIC_DIR), name='static') -app.include_router(api, prefix='/api') -app.include_router(dashboard, prefix='/dashboard') +app.include_router(api, prefix='/api', dependencies=[Depends(verified_access_token)]) +app.include_router( + dashboard, prefix='/dashboard', dependencies=[Depends(get_admin_user)] +) # Create admin diff --git a/chowda/auth/oauth.py b/chowda/auth/oauth.py index 1bb870b2..b9cb9231 100644 --- a/chowda/auth/oauth.py +++ b/chowda/auth/oauth.py @@ -10,7 +10,7 @@ from starlette_admin.auth import AdminUser, AuthMiddleware, AuthProvider from chowda.config import ( - API_AUDIENCE, + AUTH0_API_AUDIENCE, AUTH0_CLIENT_ID, AUTH0_CLIENT_SECRET, AUTH0_DOMAIN, @@ -25,7 +25,7 @@ 'scope': 'openid profile email', }, server_metadata_url=f'https://{AUTH0_DOMAIN}/.well-known/openid-configuration', - authorize_params={'audience': API_AUDIENCE}, + authorize_params={'audience': AUTH0_API_AUDIENCE}, ) diff --git a/chowda/auth/utils.py b/chowda/auth/utils.py index 6165e8c7..a40c02a7 100644 --- a/chowda/auth/utils.py +++ b/chowda/auth/utils.py @@ -1,17 +1,35 @@ -from typing import Annotated +from typing import Annotated, List, Set from fastapi import Depends, HTTPException, Request, status from pydantic import BaseModel, Field -from chowda.config import API_AUDIENCE +from chowda.config import AUTH0_API_AUDIENCE, AUTH0_JWKS_URL + +unauthorized_redirect = HTTPException( + status_code=status.HTTP_303_SEE_OTHER, + detail='Not Authorized', + headers={'Location': '/admin'}, +) + +unauthorized = HTTPException( + status_code=status.HTTP_401_UNAUTHORIZED, + detail='Not Authorized', +) -class UserToken(BaseModel): +class OAuthAccessToken(BaseModel): + """OAuth Authorization token""" + + sub: str + permissions: List[str] = [] + + +class OAuthUser(BaseModel): """ID Token model for authorization.""" name: str email: str | None = None - roles: set[str] = Field(set(), alias=f'{API_AUDIENCE}/roles') + roles: set[str] = Field(set(), alias=f'{AUTH0_API_AUDIENCE}/roles') @property def is_admin(self) -> bool: @@ -24,29 +42,107 @@ def is_clammer(self) -> bool: return 'clammer' in self.roles -unauthorized = HTTPException( - status_code=status.HTTP_303_SEE_OTHER, - detail='Not Authorized', - headers={'Location': '/admin'}, -) - - -def get_user(request: Request) -> UserToken: +def get_oauth_user(request: Request) -> OAuthUser: """Get the user token from the session.""" user = request.session.get('user', None) if not user: request.session['error'] = 'Not Logged In' - raise unauthorized - return UserToken(**user) + raise unauthorized_redirect + return OAuthUser(**user) -def admin_user( - request: Request, user: Annotated[UserToken, Depends(get_user)] -) -> UserToken: +def get_admin_user( + request: Request, user: Annotated[OAuthUser, Depends(get_oauth_user)] +) -> OAuthUser: """Check if the user has the admin role using FastAPI Depends. If not, sets a session error and raises an HTTPException.""" if not user.is_admin: request.session['error'] = 'Not Authorized' - raise unauthorized + raise unauthorized_redirect return user + + +def unverified_access_token(request: Request) -> str: + """Extract and return the unverified access token from the Authorization header. + Raises an HTTPUnauthorizedException if the header is missing or malformed.""" + auth_header = request.headers.get('Authorization', None) + + if not auth_header: + raise HTTPException(status_code=401, detail="Missing Authorization header") + if not auth_header.startswith('Bearer '): + raise HTTPException( + status_code=401, + detail="Bearer token malformed or missing in Authorization header", + ) + + # Return the access token from the Authorization header, + # i.e. the string without the "Bearer " prefix + return auth_header.replace('Bearer ', '') + + +def jwt_signing_key( + unverified_access_token: Annotated[str, Depends(unverified_access_token)] +) -> str: + """Get the JWT signing key from the JWKS URL.""" + from jwt import PyJWKClient + + jwks_client = PyJWKClient(AUTH0_JWKS_URL) + try: + signing_key = jwks_client.get_signing_key_from_jwt(unverified_access_token) + return signing_key.key + + except Exception as exc: + raise HTTPException( + status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc) + ) from exc + + +def verified_access_token( + request: Request, + unverified_access_token: Annotated[str, Depends(unverified_access_token)], + jwt_signing_key: Annotated[str, Depends(jwt_signing_key)], +) -> OAuthAccessToken: + """Decodes and verifies an access token. If any exceptions occur, an + HTTPUnauthorizedException is raised from the original exception.""" + from jwt import decode + + try: + decoded_token = decode( + unverified_access_token, + jwt_signing_key, + algorithms=['RS256', 'HS256'], + audience='https://chowda.wgbh-mla.org/api', + ) + return OAuthAccessToken(**decoded_token) + + except Exception as exc: + raise HTTPException( + status_code=status.HTTP_401_UNAUTHORIZED, detail=str(exc) + ) from exc + + +def permissions(permissions: str | List[str] | Set[str]) -> None: + """Dependency function to check if token has required permissions. + + Args: + permissions (str, List, Set): Required permissions. Can be a str, list, or set. + Examples: + @app.get('/users/', dependencies=[Depends(permissions('read:users'))]) + """ + if isinstance(permissions, (str, list)): + permissions: set = {permissions} + + def _permissions( + token: Annotated[OAuthAccessToken, Depends(verified_access_token)], + ) -> None: + """Verify token has all required permissions, or raise a 403 Forbidden exception + with the missing permissions in the detail message.""" + missing_permissions = permissions - set(token.permissions) + if missing_permissions: + raise HTTPException( + status_code=status.HTTP_403_FORBIDDEN, + detail=f'Missing required permissions: {missing_permissions}', + ) + + return _permissions diff --git a/chowda/config.py b/chowda/config.py index 831e33eb..6a58dd07 100644 --- a/chowda/config.py +++ b/chowda/config.py @@ -16,7 +16,9 @@ AUTH0_CLIENT_ID = environ.get('AUTH0_CLIENT_ID') AUTH0_CLIENT_SECRET = environ.get('AUTH0_CLIENT_SECRET') AUTH0_DOMAIN = environ.get('AUTH0_DOMAIN') +AUTH0_JWKS_URL = f'https://{AUTH0_DOMAIN}/.well-known/jwks.json' +AUTH0_API_AUDIENCE = environ.get( + 'AUTH0_API_AUDIENCE', 'https://chowda.wgbh-mla.org/api' +) SECRET = environ.get('CHOWDA_SECRET') - -API_AUDIENCE = environ.get('API_AUDIENCE', 'https://chowda.wgbh-mla.org/api') diff --git a/chowda/routers/dashboard.py b/chowda/routers/dashboard.py index 990b14fd..6a340fce 100644 --- a/chowda/routers/dashboard.py +++ b/chowda/routers/dashboard.py @@ -1,10 +1,8 @@ -from fastapi import APIRouter, Depends, Request, status +from fastapi import APIRouter, Request, status from metaflow.integrations import ArgoEvent from starlette.responses import RedirectResponse, Response -from chowda.auth.utils import admin_user - -dashboard = APIRouter(dependencies=[Depends(admin_user)]) +dashboard = APIRouter() @dashboard.post('/sync') diff --git a/chowda/routers/events.py b/chowda/routers/events.py index 33ea3694..779c26c2 100644 --- a/chowda/routers/events.py +++ b/chowda/routers/events.py @@ -1,36 +1,54 @@ -from json import loads +from json import JSONDecodeError, loads -from fastapi import APIRouter, HTTPException +from fastapi import APIRouter, Depends, HTTPException, status from metaflow import Run, namespace from sqlmodel import Session +from chowda.auth.utils import permissions from chowda.db import engine from chowda.models import MetaflowRun events = APIRouter() -@events.post('/') -def event(event: dict): +@events.post('/', dependencies=[Depends(permissions('create:event'))]) +async def event(event: dict): """Receive an event from Argo Events.""" print('Chowda event received', event) - if not event.get('body'): - raise HTTPException(400, 'No body') - body = loads(event['body']) - if body['name'] == 'pipeline': + body = event.get('body') + if not body: + raise HTTPException( + status.HTTP_400_BAD_REQUEST, + 'Argo Event must include a `body` key as a string', + ) + try: + body = loads(event['body']) + except JSONDecodeError as e: + raise HTTPException( + status.HTTP_400_BAD_REQUEST, 'Argo Event body must be valid JSON' + ) from e + name = body.get('name') + if not name: + raise HTTPException( + status.HTTP_400_BAD_REQUEST, + "Argo Event body string must include a `name` key", + ) + if name == 'pipeline': print('new pipeline event!') # FIXME: Ideally, we would add the run to the database here, # but the run_id won't be minted until metaflow gets this event. # For now, we can continue creating the db row inside the running flow, # then update metaflow status events, as they come in. - return + return None if body['name'].startswith('metaflow.Pipeline'): print('Found event!', body['name']) payload = body['payload'] with Session(engine) as db: row = db.get(MetaflowRun, payload['run_id']) if not row: - raise HTTPException(404, 'MetaflowRun row not found!') + raise HTTPException( + status.HTTP_404_NOT_FOUND, 'MetaflowRun row not found!' + ) namespace(None) run = Run(f"{payload['flow_name']}/{payload['run_id']}") row.finished = run.finished @@ -41,5 +59,5 @@ def event(event: dict): db.add(row) db.commit() print('Successfully updated MetaflowRun row!', row) - return - raise HTTPException(400, 'Unknown event') + return None + return 'Event successfully processed, but did not match known event' diff --git a/chowda/routers/sony_ci.py b/chowda/routers/sony_ci.py index 82d0ff99..fce321a0 100644 --- a/chowda/routers/sony_ci.py +++ b/chowda/routers/sony_ci.py @@ -1,9 +1,11 @@ from datetime import datetime -from fastapi import APIRouter, HTTPException +from fastapi import APIRouter, Depends, HTTPException from metaflow.integrations import ArgoEvent from pydantic import BaseModel +from chowda.auth.utils import permissions + sony_ci = APIRouter() @@ -11,7 +13,9 @@ class SyncResponse(BaseModel): started_at: datetime -@sony_ci.post('/sync', tags=['sync']) +@sony_ci.post( + '/sync', tags=['sync'], dependencies=[Depends(permissions('sync:sonyci'))] +) async def sony_ci_sync() -> SyncResponse: try: ArgoEvent('sync').publish(ignore_errors=False) diff --git a/chowda/views.py b/chowda/views.py index 4fcc1e3e..88c7d360 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -16,7 +16,7 @@ from starlette_admin.exceptions import ActionFailed from starlette_admin.fields import BaseField -from chowda.auth.utils import get_user +from chowda.auth.utils import get_oauth_user from chowda.db import engine from chowda.fields import ( BatchMetaflowRunDisplayField, @@ -77,30 +77,30 @@ class ClammerModelView(ChowdaModelView): """Base Clammer permissions for all protected views""" def can_create(self, request: Request) -> bool: - return get_user(request).is_clammer + return get_oauth_user(request).is_clammer def can_delete(self, request: Request) -> bool: - return get_user(request).is_clammer + return get_oauth_user(request).is_clammer def can_edit(self, request: Request) -> bool: - return get_user(request).is_clammer + return get_oauth_user(request).is_clammer class AdminModelView(ClammerModelView): """Base Admin permissions for all protected views""" def is_accessible(self, request: Request) -> bool: - user = get_user(request) + user = get_oauth_user(request) return user.is_admin or user.is_clammer def can_create(self, request: Request) -> bool: - return get_user(request).is_admin + return get_oauth_user(request).is_admin def can_delete(self, request: Request) -> bool: - return get_user(request).is_admin + return get_oauth_user(request).is_admin def can_edit(self, request: Request) -> bool: - return get_user(request).is_admin + return get_oauth_user(request).is_admin class CollectionView(ClammerModelView): @@ -220,7 +220,7 @@ async def validate(self, request: Request, data: Dict[str, Any]): validate_media_file_guids(request, data) async def is_action_allowed(self, request: Request, name: str) -> bool: - user = get_user(request) + user = get_oauth_user(request) if name == 'start_batches': return user.is_clammer if name == 'duplicate_batches': @@ -370,7 +370,7 @@ class MediaFileView(ClammerModelView): page_size_options: ClassVar[list[int]] = [10, 25, 100, 500, 2000, 10000] def can_create(self, request: Request) -> bool: - return get_user(request).is_admin + return get_oauth_user(request).is_admin @action( name='create_new_batch', @@ -433,7 +433,7 @@ def sync_history(self) -> Dict[str, Any]: async def render(self, request: Request, templates: Jinja2Templates) -> Response: history = self.sync_history() - user = get_user(request) + user = get_oauth_user(request) sync_disabled = datetime.now() - history[0]['created_at'] < timedelta( minutes=15 ) diff --git a/pdm.lock b/pdm.lock index 1259606e..c6a2c02b 100644 --- a/pdm.lock +++ b/pdm.lock @@ -6,7 +6,7 @@ groups = ["default", "ci", "dev", "development", "docs", "locust", "production", cross_platform = true static_urls = false lock_version = "4.3" -content_hash = "sha256:5a6ceb4becede446d306ddf9f7b9acd3627add0be4a43abf7a7ba16255bcbd83" +content_hash = "sha256:c8e8833b4bcc08bb605c048514e64748d998bb42a17559cb662e29d9b8e4e1ac" [[package]] name = "alembic" @@ -133,7 +133,7 @@ files = [ [[package]] name = "black" -version = "23.9.1" +version = "23.10.0" requires_python = ">=3.8" summary = "The uncompromising code formatter." dependencies = [ @@ -146,28 +146,24 @@ dependencies = [ "typing-extensions>=4.0.1; python_version < \"3.11\"", ] files = [ - 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json import dumps, loads from json.decoder import JSONDecodeError from os import environ, path +from typing import List, Optional, Type +import jwt +from fastapi.testclient import TestClient +from httpx import AsyncClient from pytest import fixture +from chowda.app import app +from chowda.auth.utils import jwt_signing_key +from chowda.config import AUTH0_API_AUDIENCE + # Set CHOWDA_ENV env var to 'test' always. This serves as a flag for anywhere else in # the application where we need to detect whether we are running tests or not. environ['CHOWDA_ENV'] = 'test' @@ -53,3 +61,54 @@ def vcr_config(request): # Replace secrets in response body 'before_record_response': clean_response, } + + +@fixture +def async_client(request): + return AsyncClient(app=app, base_url='http://test') + + +@fixture +def client(request): + return TestClient(app) + + +def fake_signing_key() -> str: + """ + Returns a fake secret key with which to encode/decode JWTS. This is a + regular function, not a fixture, because it is used as a FastAPI dependency + override, which will throw an error if it tries to call a fixture directly. + """ + + return 'FAKE SECRET KEY' + + +@fixture +def fake_access_token() -> Type[callable]: + """ + Returns a factory for generating fake access tokens for testing. + """ + + def _fake_access_token( + permissions: Optional[List[str]] = None, algorithm: str = 'HS256' + ) -> str: + if permissions is None: + permissions = [] + jwt_decoded = { + 'permissions': permissions, + 'aud': AUTH0_API_AUDIENCE, + 'sub': 'fake-api-subject', + } + return jwt.encode(jwt_decoded, fake_signing_key(), algorithm=algorithm) + + return _fake_access_token + + +# Override FastAPI dependency for jwt_signing_key to use the same fake signing key we +# use for encoding the JWT. +# NOTE: for testing we us a the synchronous HS256 algorithm which uses the same key for +# encoding and decoding, but in production we may use the asynchronous RS256 algorithm +# which uses a public/private key. We can do this only because the logic that does the +# decoding attempts algorithms, first RS256 then HS256. +# See also chowda.auth.utils.validated_access_token. +app.dependency_overrides[jwt_signing_key] = fake_signing_key diff --git a/tests/routers/test_events.py b/tests/routers/test_events.py new file mode 100644 index 00000000..4148555c --- /dev/null +++ b/tests/routers/test_events.py @@ -0,0 +1,104 @@ +import json +from json import dumps + +import pytest +from fastapi import status +from httpx import AsyncClient + + +@pytest.fixture +def event(): + body = {'name': 'pipeline'} + return {'body': dumps(body)} + + +@pytest.mark.asyncio +async def test_events(event: dict, async_client: AsyncClient, fake_access_token: str): + async with async_client as ac: + bearer_token = fake_access_token(permissions=["create:event"]) + response = await ac.post( + '/api/event/', + json=event, + follow_redirects=True, + headers={'Authorization': f'Bearer {bearer_token}'}, + ) + + assert response.status_code == 200 + + +@pytest.mark.asyncio +async def test_events_missing_auth_header(event: dict, async_client: AsyncClient): + async with async_client as ac: + response = await ac.post('/api/event/', json=event, follow_redirects=True) + + assert response.status_code == status.HTTP_401_UNAUTHORIZED + error = json.loads(response.text) + assert error['detail'] == 'Missing Authorization header' + + +@pytest.mark.asyncio +async def test_events_malformed_auth_header(event: dict, async_client: AsyncClient): + async with async_client as ac: + response = await ac.post( + '/api/event/', + json=event, + follow_redirects=True, + headers={'Authorization': 'not a bearer token'}, + ) + + assert response.status_code == status.HTTP_401_UNAUTHORIZED + error = json.loads(response.text) + assert ( + error['detail'] == 'Bearer token malformed or missing in Authorization header' + ) + + +@pytest.mark.asyncio +async def test_events_invalid_bearer_token(event: dict, async_client: AsyncClient): + async with async_client as ac: + response = await ac.post( + '/api/event/', + json=event, + follow_redirects=True, + headers={'Authorization': 'Bearer N0t.AR3al.TOKeN'}, + ) + + assert response.status_code == status.HTTP_401_UNAUTHORIZED + error = json.loads(response.text) + assert 'Invalid header string' in error['detail'] + + +@pytest.mark.asyncio +async def test_events_valid_unauthorized_bearer_token( + event: dict, async_client: AsyncClient +): + async with async_client as ac: + response = await ac.post( + '/api/event/', + json=event, + follow_redirects=True, + headers={ + 'Authorization': 'Bearer eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJzdWIiOiIxMjM0NTY3ODkwIiwibmFtZSI6IkpvaG4gRG9lIiwiaWF0IjoxNTE2MjM5MDIyfQ.SflKxwRJSMeKKF2QT4fwpMeJf36POk6yJV_adQssw5c' # noqa E501 + }, + ) + + assert response.status_code == status.HTTP_401_UNAUTHORIZED + error = json.loads(response.text) + assert error['detail'] == 'Signature verification failed' + + +@pytest.mark.asyncio +async def test_events_without_permission( + event: dict, async_client: AsyncClient, fake_access_token: str +): + async with async_client as ac: + response = await ac.post( + '/api/event/', + json=event, + follow_redirects=True, + headers={ + 'Authorization': f'Bearer {fake_access_token(permissions=["wrong"])}' + }, + ) + + assert response.status_code == status.HTTP_403_FORBIDDEN diff --git a/tests/routers/test_sony_ci.py b/tests/routers/test_sony_ci.py index b07fcd80..6d6157d6 100644 --- a/tests/routers/test_sony_ci.py +++ b/tests/routers/test_sony_ci.py @@ -1,20 +1,17 @@ +from typing import Type + import pytest from httpx import AsyncClient - -from chowda.app import app - -from chowda.routers.sony_ci import SyncResponse - from metaflow.plugins.argo.argo_events import ArgoEventException +from pytest_mock import MockerFixture - -@pytest.fixture -def async_client(request): - return AsyncClient(app=app, base_url='http://test') +from chowda.routers.sony_ci import SyncResponse -@pytest.mark.anyio -async def test_sony_ci_sync(mocker, async_client): +@pytest.mark.asyncio +async def test_sony_ci_sync( + mocker: MockerFixture, async_client: AsyncClient, fake_access_token: Type[callable] +): mocker.patch( 'metaflow.integrations.ArgoEvent.publish', autospec=True, @@ -22,14 +19,43 @@ async def test_sony_ci_sync(mocker, async_client): ) async with async_client as ac: - response = await ac.post('/api/sony_ci/sync') + bearer_token = fake_access_token(permissions=['sync:sonyci']) + response = await ac.post( + '/api/sony_ci/sync', + headers={'Authorization': f'Bearer {bearer_token}'}, + ) assert response.status_code == 200 assert SyncResponse(**response.json()) -@pytest.mark.anyio -async def test_sony_ci_sync_fail(mocker, async_client): +@pytest.mark.asyncio +async def test_sony_ci_sync_no_permission( + mocker: MockerFixture, async_client: AsyncClient, fake_access_token: Type[callable] +): + mocker.patch( + 'metaflow.integrations.ArgoEvent.publish', + autospec=True, + side_effect=ArgoEventException('Mocked exception'), + ) + + async with async_client as ac: + bearer_token = fake_access_token(permissions=['wrong_permission:sonyci']) + response = await ac.post( + '/api/sony_ci/sync', headers={'Authorization': f'Bearer {bearer_token}'} + ) + + assert response.status_code == 403 + response_json = response.json() + error = response_json['detail'] + assert 'Missing required permissions:' in error + assert "{'sync:sonyci'}" in error + + +@pytest.mark.asyncio +async def test_sony_ci_sync_fail( + mocker: MockerFixture, async_client: AsyncClient, fake_access_token: Type[callable] +): mocker.patch( 'metaflow.integrations.ArgoEvent.publish', autospec=True, @@ -37,7 +63,13 @@ async def test_sony_ci_sync_fail(mocker, async_client): ) async with async_client as ac: - response = await ac.post('/api/sony_ci/sync') + bearer_token = fake_access_token(permissions=['sync:sonyci']) + response = await ac.post( + '/api/sony_ci/sync', + headers={ + 'Authorization': f'Bearer {bearer_token}', + }, + ) assert response.status_code == 500 response_json = response.json() diff --git a/tests/test_app.py b/tests/test_app.py index fb994be6..2170a474 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -7,13 +7,13 @@ def test_get_admin_home(): """GET / returns a Redirect response""" - response = client.get('/', allow_redirects=False) + response = client.get('/', follow_redirects=False) assert response.status_code == 200, 'Home page did not display sucessfully' def test_get_admin_redirect(): """GET /admin returns a Redirect response""" - response = client.get('/admin/', allow_redirects=False) + response = client.get('/admin/', follow_redirects=False) assert response.status_code == 303, 'Home page did not redirect sucessfully' assert ( '/admin/login?next=' in response.headers['location'] diff --git a/tests/test_batches.py b/tests/test_batches.py deleted file mode 100644 index 1a271afb..00000000 --- a/tests/test_batches.py +++ /dev/null @@ -1,57 +0,0 @@ -from fastapi import FastAPI -from fastapi.testclient import TestClient -from httpx import AsyncClient -from pytest import fixture, mark -from pytest_asyncio import fixture as async_fixture -from sqlmodel import Session, select - -from chowda.db import engine -from chowda.models import Batch - - -@fixture -def app(): - from chowda.app import app - - return app - - -@fixture -def client(app: FastAPI): - return TestClient(app) - - -@async_fixture -async def async_client(app: FastAPI): - async with AsyncClient(app=app, base_url='http://testserver') as c: - yield c - - -@fixture -def session(): - return Session(engine) - - -@fixture -def unsaved_batch(): - from tests.factories import BatchFactory - - return BatchFactory.build() - - -@mark.anyio -@mark.skip("Redirecting due to user being unauthenticated in tests") -async def test_create_batch( - async_client: AsyncClient, - session: Session, - unsaved_batch: Batch, -): - response = await async_client.post( - '/admin/batch/create', - data=unsaved_batch.dict(), - follow_redirects=False, - ) - assert response.status_code == 303 - stmt = select(Batch).where(Batch.name == unsaved_batch.name) - batch = session.execute(stmt).scalar_one() - assert batch is not None From c6cfce7771c355934dfe21ed542a39ad19c7a00c Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 25 Oct 2023 12:56:47 -0700 Subject: [PATCH 07/17] =?UTF-8?q?=F0=9F=A4=96=20Update=20dependencies=20(#?= =?UTF-8?q?177)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Harpo Harbert --- .gitguardian.yaml | 5 + pdm.lock | 532 +++++++++++++++++++++++----------------------- pyproject.toml | 10 +- 3 files changed, 275 insertions(+), 272 deletions(-) create mode 100644 .gitguardian.yaml diff --git a/.gitguardian.yaml b/.gitguardian.yaml new file mode 100644 index 00000000..3c3b9a12 --- /dev/null +++ b/.gitguardian.yaml @@ -0,0 +1,5 @@ +secret: + ignored-matches: + - 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description = 'A CLAMS processing application' authors = [{ name = 'WGBH-MLA', email = 'ryan_harbert@wgbh.org' }] dependencies = [ - "fastapi~=0.103", + "fastapi~=0.104", "starlette-admin @ git+https://github.com/jowilf/starlette-admin.git@main", "sqlmodel~=0.0", "pydantic[email]~=1.10", @@ -48,7 +48,7 @@ test = [ "vcrpy~=5.1", "pytest-vcr~=1.0", "urllib3~=1.26", - "pytest-mock~=3.11", + "pytest-mock~=3.12", "pytest-asyncio~=0.21", "trio~=0.22", ] @@ -104,9 +104,9 @@ includes = [] [tool.pdm.dev-dependencies] dev = [ "uvicorn~=0.23", - "black~=23.9", - "ruff~=0.0", - "pre-commit~=3.4", + "black~=23.10", + "ruff~=0.1", + "pre-commit~=3.5", ] docs = [ "mkdocs~=1.5", From 154ff05fc3eee24e8a6efd2c96e66b90ea591ba2 Mon Sep 17 00:00:00 2001 From: Harpo Date: Fri, 27 Oct 2023 12:35:48 -0400 Subject: [PATCH 08/17] =?UTF-8?q?=E2=9E=95=20Add=20MMIF=20to=20batch=20(#1?= =?UTF-8?q?81)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adds mmif batch actions * Improves labels for MMIFView batch fields * Validates selected MMIFs for duplicates --- chowda/models.py | 12 +++++- chowda/utils.py | 16 ++++++- chowda/views.py | 110 ++++++++++++++++++++++++++++++++++++++++++++--- 3 files changed, 128 insertions(+), 10 deletions(-) diff --git a/chowda/models.py b/chowda/models.py index 300665b6..c6091e48 100644 --- a/chowda/models.py +++ b/chowda/models.py @@ -347,8 +347,16 @@ class MMIF(SQLModel, table=True): mmif_location: Optional[str] = Field(default=None) async def __admin_repr__(self, request: Request): - return f'{self.metaflow_run.batch.name}' if self.metaflow_run else self.id + return ( + f'{self.metaflow_run.batch.name}' + if self.metaflow_run and self.metaflow_run.batch + else self.id + ) async def __admin_select2_repr__(self, request: Request) -> str: - text = self.metaflow_run.batch.name if self.metaflow_run else self.id + text = ( + self.metaflow_run.batch.name + if self.metaflow_run and self.metaflow_run.batch + else self.id + ) return f'{text}' diff --git a/chowda/utils.py b/chowda/utils.py index 0f2b0535..d8ae8f6a 100644 --- a/chowda/utils.py +++ b/chowda/utils.py @@ -1,4 +1,4 @@ -from typing import Any, Dict +from typing import Any, Dict, List, Set from pydantic import BaseModel from sqlalchemy.dialects.postgresql import insert @@ -92,3 +92,17 @@ def validate_media_file_guids(request: Request, data: Dict[str, Any]): # to a parent object when that MediaFile is already there. for media_file in data['media_files']: request.state.session.add(media_file) + + +def get_duplicates(values: List[Any]) -> Set[Any]: + """Return a set of duplicate values in a list, or an empty set if there are none. + + NOTE: This is a fast approach that does not preserve order, but runs in O(n)""" + unique: Set = set() + duplicates: Set = set() + for v in values: + if v not in unique: + unique.add(v) + else: + duplicates.add(v) + return duplicates diff --git a/chowda/views.py b/chowda/views.py index 88c7d360..88c694dc 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -1,5 +1,5 @@ from datetime import datetime, timedelta -from typing import Any, ClassVar, Dict, List +from typing import Any, ClassVar, Dict, List, Set from metaflow import Flow from metaflow.exception import MetaflowNotFound @@ -14,7 +14,7 @@ from starlette_admin._types import RequestAction from starlette_admin.contrib.sqlmodel import ModelView from starlette_admin.exceptions import ActionFailed -from starlette_admin.fields import BaseField +from starlette_admin.fields import BaseField, HasMany, HasOne from chowda.auth.utils import get_oauth_user from chowda.db import engine @@ -28,8 +28,8 @@ MediaFilesGuidsField, SonyCiAssetThumbnail, ) -from chowda.models import Batch, Collection, MediaFile -from chowda.utils import validate_media_file_guids +from chowda.models import MMIF, Batch, Collection, MediaFile +from chowda.utils import get_duplicates, validate_media_file_guids from templates import filters # noqa: F401 @@ -362,7 +362,6 @@ class MediaFileView(ClammerModelView): 'collections', 'batches', 'assets', - BaseField('mmif_json', display_template='displays/media_file_mmif_json.html'), 'mmifs', 'metaflow_runs', ] @@ -477,9 +476,106 @@ class MMIFView(ChowdaModelView): label: ClassVar[str] = 'MMIFs' fields: ClassVar[List[Any]] = [ 'media_file', - 'batch_inputs', - 'batch_output', + HasMany('batch_inputs', identity='batch', label='Input to Batches'), + HasOne('batch_output', identity='batch', label='Generated from Batch'), 'metaflow_run', 'mmif_location', 'created_at', ] + actions: ClassVar[List[str]] = ['add_to_new_batch', 'add_to_existing_batch'] + + @action( + name='add_to_new_batch', + text='Add to New Batch', + confirmation='Create a Batch from these MMIFs?', + action_btn_class='btn-ghost-primary', + submit_btn_text="Aye, Capt'n!", + form=""" +
+
+ + +
+
+ """, + ) + async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: + try: + data: FormData = await request.form() + with Session(engine) as db: + mmifs: List[MMIF] = db.exec(select(MMIF).where(MMIF.id.in_(pks))).all() + media_files: List[MediaFile] = [mmif.media_file for mmif in mmifs] + guids: List[str] = [media_file.guid for media_file in media_files] + duplicates: Set = get_duplicates(guids) + if duplicates: + raise ActionFailed( + f'{len(duplicates)} duplicate Media File{"s" if len(duplicates) > 1 else ""} found:
' # noqa: E501 + + '
'.join(duplicates) + ) + + batch = Batch( + name=data.get("batch_name"), + description=data.get("batch_description"), + input_mmifs=mmifs, + media_files=media_files, + ) + db.add(batch) + db.commit() + + return f"Batch of {len(pks)} MMIFs created" + except Exception as error: + raise ActionFailed(f'{error!s}') from error + + @action( + name='add_to_existing_batch', + text='Add to Existing Batch', + confirmation='Which batch should these be added to?', + action_btn_class='btn-ghost-primary', + submit_btn_text="Make it so!", + form=""" +
+
+ +
+
+ """, + ) + async def add_to_existing_batch(self, request: Request, pks: List[Any]) -> str: + try: + data: FormData = await request.form() + with Session(engine) as db: + mmifs: List[MMIF] = db.exec(select(MMIF).where(MMIF.id.in_(pks))).all() + batch: Batch = db.get(Batch, data.get("batch_id")) + batch.input_mmifs += mmifs + media_files: List[MediaFile] = [mmif.media_file for mmif in mmifs] + + # Check for duplicate Media Files in selection + guids: List[str] = [media_file.guid for media_file in media_files] + duplicates: Set = get_duplicates(guids) + if duplicates: + raise ActionFailed( + f'{len(duplicates)} duplicate Media File{"s" if len(duplicates) > 1 else ""} found in selection:
' # noqa: E501 + + '
'.join(duplicates) + ) + # Check batch input_mmifs for other MMIFs linked to these MediaFiles + existing_batch_mmif_guids: Set[str] = { + mmif.media_file.guid for mmif in batch.input_mmifs + } + existing_media_files = existing_batch_mmif_guids.intersection(guids) + if existing_media_files: + s = 's' if len(existing_media_files) > 1 else '' + raise ActionFailed( + f'{len(existing_media_files)} Media File{s} already exist{"" if s else "s"} in Batch {batch.id}:
' # noqa: E501 + + '
'.join(existing_media_files) + ) + + batch.media_files += media_files + + db.commit() + + return f"Added {len(pks)} MMIFs to Batch {batch.id}" + except Exception as error: + raise ActionFailed(f'{error!s}') from error From fb696c4b8c6703e705cbc1978cfad2b26c0416e8 Mon Sep 17 00:00:00 2001 From: Harpo Date: Fri, 27 Oct 2023 14:22:14 -0400 Subject: [PATCH 09/17] =?UTF-8?q?=F0=9F=8E=B1=20Fields:=20`Finished`,=20`S?= =?UTF-8?q?uccessful`=20(#184)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adds custom bool fields for Finished, Successful * Simplifies js render logic --- chowda/fields.py | 26 +++++++++++++++++++++++++- chowda/routers/events.py | 3 ++- chowda/views.py | 15 +++++++++++++++ static/js/custom-render.js | 27 +++++++++++++++++++++++++++ templates/displays/finished.html | 9 +++++++++ templates/displays/successful.html | 9 +++++++++ 6 files changed, 87 insertions(+), 2 deletions(-) create mode 100644 templates/displays/finished.html create mode 100644 templates/displays/successful.html diff --git a/chowda/fields.py b/chowda/fields.py index 46ecb299..40923e9f 100644 --- a/chowda/fields.py +++ b/chowda/fields.py @@ -4,7 +4,7 @@ from starlette.datastructures import FormData from starlette.requests import Request from starlette_admin._types import RequestAction -from starlette_admin.fields import BaseField, IntegerField, TextAreaField +from starlette_admin.fields import BaseField, BooleanField, IntegerField, TextAreaField from chowda.models import MediaFile @@ -161,3 +161,27 @@ class BatchUnstartedGuidsCount(IntegerField): async def parse_obj(self, request: Request, obj: Any) -> Any: return len(obj.unstarted_guids()) + + +@dataclass +class FinishedField(BooleanField): + """A field that displays a boolean value for the 'Finished' property. + + True: Green check + False: Grey clock""" + + display_template: str = 'displays/finished.html' + render_function_key: str = 'finished' + + +@dataclass +class SuccessfulField(BooleanField): + """A field that displays a boolean value for the 'Successful' property. + + True: Green check circle + False: Red X circle + None: Blank + """ + + display_template: str = 'displays/successful.html' + render_function_key: str = 'successful' diff --git a/chowda/routers/events.py b/chowda/routers/events.py index 779c26c2..53464108 100644 --- a/chowda/routers/events.py +++ b/chowda/routers/events.py @@ -53,7 +53,8 @@ async def event(event: dict): run = Run(f"{payload['flow_name']}/{payload['run_id']}") row.finished = run.finished row.finished_at = run.finished_at - row.successful = run.successful + if row.finished: + row.successful = run.successful row.current_step = payload['step_name'] row.current_task = payload['task_id'] db.add(row) diff --git a/chowda/views.py b/chowda/views.py index 88c694dc..6f8f8c6d 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -24,9 +24,11 @@ BatchPercentSuccessful, BatchUnstartedGuids, BatchUnstartedGuidsCount, + FinishedField, MediaFileCount, MediaFilesGuidsField, SonyCiAssetThumbnail, + SuccessfulField, ) from chowda.models import MMIF, Batch, Collection, MediaFile from chowda.utils import get_duplicates, validate_media_file_guids @@ -471,6 +473,19 @@ def can_create(self, request: Request) -> bool: class MetaflowRunView(AdminModelView): form_include_pk: ClassVar[bool] = True + fields: ClassVar[list[Any]] = [ + 'id', + 'pathspec', + 'batch', + 'mmif', + 'media_file', + 'created_at', + FinishedField('finished'), + SuccessfulField('successful'), + 'current_step', + 'current_task', + ] + class MMIFView(ChowdaModelView): label: ClassVar[str] = 'MMIFs' diff --git a/static/js/custom-render.js b/static/js/custom-render.js index c068cc48..820bd0bb 100644 --- a/static/js/custom-render.js +++ b/static/js/custom-render.js @@ -5,6 +5,7 @@ Object.assign(render, { guid => ` ${guid} ` ) }, + media_file_count: function render(data, type, full, meta, fieldOptions) { // Render a count of media files return data.length @@ -21,4 +22,30 @@ Object.assign(render, { ? `` : null }, + + finished: function render(data, type, full, meta, fieldOptions) { + if (data == null) return null_column(); + data = Array.isArray(data) ? data : [data]; + if (data.length == 0) return empty_column(); + return `
${data + .map((d) => + d === true + ? `
` + : `
` + ) + .join("")}
`; + }, + + successful: function render(data, type, full, meta, fieldOptions) { + if (data == null) return null_column(); + data = Array.isArray(data) ? data : [data]; + if (data.length == 0) return empty_column(); + return `
${data + .map((d) => + d === true + ? `
` + : `
` + ) + .join("")}
`; + }, }) diff --git a/templates/displays/finished.html b/templates/displays/finished.html new file mode 100644 index 00000000..5c5100e6 --- /dev/null +++ b/templates/displays/finished.html @@ -0,0 +1,9 @@ +{% if data %} + + + +{% else %} + + + +{% endif %} diff --git a/templates/displays/successful.html b/templates/displays/successful.html new file mode 100644 index 00000000..98b9d393 --- /dev/null +++ b/templates/displays/successful.html @@ -0,0 +1,9 @@ +{% if data %} + + + +{% elif data != None %} + + + +{% endif %} From c92e9d91d840f3006ecff4ddfd93f1757db52e32 Mon Sep 17 00:00:00 2001 From: Harpo Date: Thu, 16 Nov 2023 09:17:07 -0800 Subject: [PATCH 10/17] =?UTF-8?q?=E2=9B=93=EF=B8=8F=20Metaflow=20links=20(?= =?UTF-8?q?#185)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adds metaflow link fields * Reuses fields in batch_metaflow_runs --- chowda/fields.py | 46 ++++++++++++- chowda/views.py | 9 ++- static/js/custom-render.js | 19 +++--- templates/displays/batch_metaflow_runs.html | 68 ++++++++++--------- templates/displays/metaflow_link_field.html | 4 ++ .../metaflow_pathspec_link_field.html | 4 ++ 6 files changed, 105 insertions(+), 45 deletions(-) create mode 100644 templates/displays/metaflow_link_field.html create mode 100644 templates/displays/metaflow_pathspec_link_field.html diff --git a/chowda/fields.py b/chowda/fields.py index 40923e9f..fd13c034 100644 --- a/chowda/fields.py +++ b/chowda/fields.py @@ -4,7 +4,13 @@ from starlette.datastructures import FormData from starlette.requests import Request from starlette_admin._types import RequestAction -from starlette_admin.fields import BaseField, BooleanField, IntegerField, TextAreaField +from starlette_admin.fields import ( + BaseField, + BooleanField, + IntegerField, + StringField, + TextAreaField, +) from chowda.models import MediaFile @@ -167,7 +173,7 @@ async def parse_obj(self, request: Request, obj: Any) -> Any: class FinishedField(BooleanField): """A field that displays a boolean value for the 'Finished' property. - True: Green check + True: Green check False: Grey clock""" display_template: str = 'displays/finished.html' @@ -185,3 +191,39 @@ class SuccessfulField(BooleanField): display_template: str = 'displays/successful.html' render_function_key: str = 'successful' + + +@dataclass +class MetaflowPathspecLinkField(StringField): + """A field that displays a link to the metaflow pathspec in Mario""" + + display_template: str = 'displays/metaflow_pathspec_link_field.html' + + render_function_key: str = 'metaflow_pathspec_link' + + async def parse_obj(self, request: Request, obj: Any) -> Any: + return f'https://mario.wgbh-mla.org/{obj.pathspec}' + + +@dataclass +class MetaflowLinkField(StringField): + """A field that displays a link to a metaflow step or task in Mario""" + + display_template: str = 'displays/metaflow_link_field.html' + render_function_key: str = 'metaflow_link' + + +@dataclass +class MetaflowStepLinkField(MetaflowLinkField): + """A field that displays a link to the metaflow step in Mario""" + + async def parse_obj(self, request: Request, obj: Any) -> Any: + return f'https://mario.wgbh-mla.org/{obj.pathspec}/{obj.current_step}' + + +@dataclass +class MetaflowTaskLinkField(MetaflowLinkField): + """A field that displays a link to the metaflow task in Mario""" + + async def parse_obj(self, request: Request, obj: Any) -> Any: + return f'https://mario.wgbh-mla.org/{obj.pathspec}/{obj.current_step}/{obj.current_task}' diff --git a/chowda/views.py b/chowda/views.py index 6f8f8c6d..d54b6c21 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -27,6 +27,9 @@ FinishedField, MediaFileCount, MediaFilesGuidsField, + MetaflowPathspecLinkField, + MetaflowStepLinkField, + MetaflowTaskLinkField, SonyCiAssetThumbnail, SuccessfulField, ) @@ -475,15 +478,15 @@ class MetaflowRunView(AdminModelView): fields: ClassVar[list[Any]] = [ 'id', - 'pathspec', + MetaflowPathspecLinkField('pathspec'), 'batch', 'mmif', 'media_file', 'created_at', FinishedField('finished'), SuccessfulField('successful'), - 'current_step', - 'current_task', + MetaflowStepLinkField('current_step'), + MetaflowTaskLinkField('current_task'), ] diff --git a/static/js/custom-render.js b/static/js/custom-render.js index 820bd0bb..f2ae695c 100644 --- a/static/js/custom-render.js +++ b/static/js/custom-render.js @@ -11,13 +11,7 @@ Object.assign(render, { return data.length }, - sony_ci_asset_thumbnail: function render( - data, - type, - full, - meta, - fieldOptions - ) { + sony_ci_asset_thumbnail: function render(data, type, full, meta, fieldOptions) { return data ? `` : null @@ -35,7 +29,6 @@ Object.assign(render, { ) .join("")}`; }, - successful: function render(data, type, full, meta, fieldOptions) { if (data == null) return null_column(); data = Array.isArray(data) ? data : [data]; @@ -48,4 +41,14 @@ Object.assign(render, { ) .join("")}`; }, + + metaflow_pathspec_link: function render(data, type, full, meta, fieldOptions) { + return `${data.split('https://mario.wgbh-mla.org/')[1]} + `; + }, + + metaflow_link: function render(data, type, full, meta, fieldOptions) { + return `${data.split('/').pop()} + `; + }, }) diff --git a/templates/displays/batch_metaflow_runs.html b/templates/displays/batch_metaflow_runs.html index 88afb6e4..b26cff95 100644 --- a/templates/displays/batch_metaflow_runs.html +++ b/templates/displays/batch_metaflow_runs.html @@ -5,6 +5,7 @@ > + Run ID GUID Metaflow Run Current step @@ -15,55 +16,58 @@ - {% for media_file_row in data %} + {% for metaflow_run in data %} + {{media_file_row.media_file_id }} + href="../../metaflow-run/detail/{{ metaflow_run.id }}" + >{{ metaflow_run.id }} - + - {{ media_file_row.pathspec }} - + class="m-1 py-1 px-2 badge bg-blue-lt lead" + href="../../media-file/detail/{{ metaflow_run.media_file_id }}" + >{{ metaflow_run.media_file_id }} + - {% if media_file_row.current_task %} {{ media_file_row.current_step }} {% - endif %} + {% with data = 'https://mario.wgbh-mla.org/' + metaflow_run.pathspec %} + {% include 'displays/metaflow_pathspec_link_field.html' %} + {% endwith %} + - {% if media_file_row.current_task %} - - {{ media_file_row.current_task }} - - + {% if metaflow_run.current_step %} + {% with data = 'https://mario.wgbh-mla.org/' + metaflow_run.pathspec +'/' + metaflow_run.current_step %} + {% include 'displays/metaflow_link_field.html' %} + {% endwith %} + {% endif %} + + + + {% if metaflow_run.current_task %} + {% with data = 'https://mario.wgbh-mla.org/' + metaflow_run.pathspec +'/' + metaflow_run.current_step + '/' + metaflow_run.current_task %} + {% include 'displays/metaflow_link_field.html' %} + {% endwith %} {% endif %} - {{ media_file_row.finished_at }} + + {{ metaflow_run.finished_at }} + - + {% with data = metaflow_run.finished %} + {% include 'displays/finished.html' %} + {% endwith %} - + + {% with data = metaflow_run.successful %} + {% include 'displays/successful.html' %} + {% endwith %} {% endfor %} diff --git a/templates/displays/metaflow_link_field.html b/templates/displays/metaflow_link_field.html new file mode 100644 index 00000000..616a94a0 --- /dev/null +++ b/templates/displays/metaflow_link_field.html @@ -0,0 +1,4 @@ + + {{ data.split('/') | last }} + + \ No newline at end of file diff --git a/templates/displays/metaflow_pathspec_link_field.html b/templates/displays/metaflow_pathspec_link_field.html new file mode 100644 index 00000000..dcc071b0 --- /dev/null +++ b/templates/displays/metaflow_pathspec_link_field.html @@ -0,0 +1,4 @@ + + {{ data.split('https://mario.wgbh-mla.org/')[1] }} + + \ No newline at end of file From 3f3bb7f07a2586a6e25a8a01f012a8e69709b9c9 Mon Sep 17 00:00:00 2001 From: Andrew Myers Date: Fri, 17 Nov 2023 09:28:16 -0500 Subject: [PATCH 11/17] =?UTF-8?q?=F0=9F=93=A9=20MMIF=20Download=20(#182)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Adds an action to Batch view for downloading MMIF from S3 * Adds specs to check for permissions. * Still do do: * DRY up specs * Parameterize tmp directory name for MMIF downloads so we can set it to a shared volume guranteed to have enough size. * Use metaflow FlowSpec for larger MMIF export --- .dockerignore | 3 +- Dockerfile | 25 +- chowda/config.py | 2 + chowda/models.py | 2 +- chowda/views.py | 104 +++- pdm.lock | 1069 ++++++++++++++++++----------------- pyproject.toml | 2 +- tests/conftest.py | 36 +- tests/test_app.py | 8 +- tests/test_batch_actions.py | 76 +++ 10 files changed, 768 insertions(+), 559 deletions(-) create mode 100644 tests/test_batch_actions.py diff --git a/.dockerignore b/.dockerignore index 8e532402..c1b047c8 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1 +1,2 @@ -.pdm.toml \ No newline at end of file +.pdm.toml +__pycache__ diff --git a/Dockerfile b/Dockerfile index 7930ec81..76a15ebf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,11 @@ ########################### # 'base' build stage, common to all build stages ########################### -FROM python:3.11 as base +FROM python:3.11-slim as base # Set working dir to /app, where all Chowda code lives. WORKDIR /app -RUN pip install -U pip +RUN pip install -U pip pdm # Copy app code to container COPY pyproject.toml pdm.lock README.md ./ @@ -20,8 +20,6 @@ COPY migrations migrations # 'dev' build stage ########################### FROM base as dev -# Install PDM dependency manager -RUN pip install pdm # Configure pdm to instal dependencies into ./__pypyackages__/ RUN pdm config python.use_venv false # Configure python to use pep582 with local __pypyackages__ @@ -59,11 +57,24 @@ CMD poetry run locust ########################### # 'production' build stage ############################ -FROM base as production -RUN pip install .[production] +FROM base as build +# build-essential libpq-dev python3-dev +RUN apt update && apt install -y gcc libpq-dev git +RUN pdm install -G production -COPY static static +FROM python:3.11-slim as production +WORKDIR /app + +RUN apt update && apt install -y libpq-dev +RUN apt-get autoremove -y \ + && apt-get clean -y \ + && rm -rf /var/lib/apt/lists/* +COPY --from=build /app/ /app/ COPY templates templates +COPY static static + ENV CHOWDA_ENV=production +ENV PATH=$PATH:/app/.venv/bin/ +EXPOSE 8000 CMD gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker diff --git a/chowda/config.py b/chowda/config.py index 6a58dd07..fea63259 100644 --- a/chowda/config.py +++ b/chowda/config.py @@ -22,3 +22,5 @@ ) SECRET = environ.get('CHOWDA_SECRET') + +MMIF_S3_BUCKET_NAME = environ.get('MMIF_S3_BUCKET_NAME', 'clams-mmif') diff --git a/chowda/models.py b/chowda/models.py index c6091e48..401cf97d 100644 --- a/chowda/models.py +++ b/chowda/models.py @@ -163,7 +163,7 @@ class SonyCiAsset(SQLModel, table=True): __tablename__ = 'sonyci_assets' id: Optional[str] = Field(primary_key=True, index=True, default=None) name: str = Field(index=True) - size: int = Field(index=True, sa_column=Column(postgresql.BIGINT)) + size: int = Field(sa_column=Column(postgresql.BIGINT)) type: MediaType = Field(sa_column=Column(Enum(MediaType))) format: Optional[str] = Field(default=None, index=True) thumbnails: Optional[List[Dict[str, Any]]] = Field( diff --git a/chowda/views.py b/chowda/views.py index d54b6c21..a4c87e1b 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -1,6 +1,7 @@ from datetime import datetime, timedelta from typing import Any, ClassVar, Dict, List, Set +from fastapi import status from metaflow import Flow from metaflow.exception import MetaflowNotFound from metaflow.integrations import ArgoEvent @@ -8,7 +9,7 @@ from sqlmodel import Session, select from starlette.datastructures import FormData from starlette.requests import Request -from starlette.responses import Response +from starlette.responses import RedirectResponse, Response from starlette.templating import Jinja2Templates from starlette_admin import CustomView, action from starlette_admin._types import RequestAction @@ -203,6 +204,7 @@ class BatchView(ClammerModelView): 'start_batches', 'duplicate_batches', 'combine_batches', + 'download_mmif', ] fields: ClassVar[list[Any]] = [ @@ -232,6 +234,8 @@ async def is_action_allowed(self, request: Request, name: str) -> bool: return user.is_clammer or user.is_admin if name == 'combine_batches': return user.is_clammer or user.is_admin + if name == 'download_mmif': + return user.is_clammer or user.is_admin return await super().is_action_allowed(request, name) @action( @@ -356,6 +360,86 @@ async def combine_batches(self, request: Request, pks: List[Any]) -> str: # Display Success message return f'Combined {len(pks)} Batch(es)' + @action( + name='download_mmif', + text='Download MMIF', + confirmation='Download all MMIF JSON for these Batches?', + icon_class='fa fa-download', + submit_btn_text='Gimme the MMIF!', + submit_btn_class='btn-outline-primary', + custom_response=True, + ) + async def download_mmif(self, request: Request, pks: List[Any]) -> str: + """Create a new batch from the selected batch""" + import zipfile + from tempfile import TemporaryDirectory + + import boto3 + + from chowda.config import MMIF_S3_BUCKET_NAME + + try: + with Session(engine) as db: + # Get all of the MMIF S3 locations from the database. + batches = db.exec(select(Batch).where(Batch.id.in_(pks))).all() + all_mmif_locations = [ + mmif.mmif_location + for batch in batches + for mmif in batch.output_mmifs + ] + + # Download files from S3 + s3 = boto3.client('s3') + downloaded_mmif_files = [] + tmp_dir = TemporaryDirectory() + download_errors = {} + for mmif_location in all_mmif_locations: + mmif_tmp_location = f'{tmp_dir.name}/{mmif_location.split("/")[-1]}' + try: + s3.download_file( + MMIF_S3_BUCKET_NAME, mmif_location, mmif_tmp_location + ) + downloaded_mmif_files.append(mmif_tmp_location) + except Exception as ex: + # TODO: log errors and notify user of them + download_errors[mmif_location] = ex + + # Create zip archive + import io + from datetime import datetime + + from starlette.responses import StreamingResponse + + current_datetime = datetime.now().strftime('%Y-%m-%d_%H%M%S') + # TODO: include batch count, or names in the download file name? + zip_filename = f'chowda_mmif_download.{current_datetime}.zip' + zip_buffer = io.BytesIO() + with zipfile.ZipFile(zip_buffer, 'w') as zip: + for downloaded_mmif_file in downloaded_mmif_files: + filename = downloaded_mmif_file.split('/')[-1] + zip.write(downloaded_mmif_file, arcname=filename) + + # Reset buffer to beginning of stream + zip_buffer.seek(0) + + # Send download response + return StreamingResponse( + zip_buffer, + headers={ + 'Content-Disposition': f'attachment; filename="{zip_filename}"' + }, + media_type='application/zip', + ) + except Exception as error: + # TODO: pop 'error' out of session and display with javascript + # dangrerAlert() when admin/batch/list renders. + # See statics/js/alerts.js from starlette-admin. + request.session['error'] = f'{error!s}' + return RedirectResponse( + request.url_for('admin:list', identity='batch'), + status_code=status.HTTP_303_SEE_OTHER, + ) + class MediaFileView(ClammerModelView): pk_attr: str = 'guid' @@ -400,14 +484,14 @@ async def create_new_batch(self, request: Request, pks: List[Any]) -> str: ).all() data: FormData = await request.form() batch = Batch( - name=data.get("batch_name"), - description=data.get("batch_description"), + name=data.get('batch_name'), + description=data.get('batch_description'), media_files=media_files, ) db.add(batch) db.commit() - return f"Batch of {len(pks)} Media Files created" + return f'Batch of {len(pks)} Media Files created' class UserView(AdminModelView): @@ -534,15 +618,15 @@ async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: ) batch = Batch( - name=data.get("batch_name"), - description=data.get("batch_description"), + name=data.get('batch_name'), + description=data.get('batch_description'), input_mmifs=mmifs, media_files=media_files, ) db.add(batch) db.commit() - return f"Batch of {len(pks)} MMIFs created" + return f'Batch of {len(pks)} MMIFs created' except Exception as error: raise ActionFailed(f'{error!s}') from error @@ -551,7 +635,7 @@ async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: text='Add to Existing Batch', confirmation='Which batch should these be added to?', action_btn_class='btn-ghost-primary', - submit_btn_text="Make it so!", + submit_btn_text='Make it so!', form="""
@@ -566,7 +650,7 @@ async def add_to_existing_batch(self, request: Request, pks: List[Any]) -> str: data: FormData = await request.form() with Session(engine) as db: mmifs: List[MMIF] = db.exec(select(MMIF).where(MMIF.id.in_(pks))).all() - batch: Batch = db.get(Batch, data.get("batch_id")) + batch: Batch = db.get(Batch, data.get('batch_id')) batch.input_mmifs += mmifs media_files: List[MediaFile] = [mmif.media_file for mmif in mmifs] @@ -594,6 +678,6 @@ async def add_to_existing_batch(self, request: Request, pks: List[Any]) -> str: db.commit() - return f"Added {len(pks)} MMIFs to Batch {batch.id}" + return f'Added {len(pks)} MMIFs to Batch {batch.id}' except Exception as error: raise ActionFailed(f'{error!s}') from error diff --git a/pdm.lock b/pdm.lock index 9cb52229..5c0ffbb3 100644 --- a/pdm.lock +++ b/pdm.lock @@ -3,14 +3,13 @@ [metadata] groups = ["default", "ci", "dev", "development", "docs", "locust", "production", "test"] -cross_platform = true -static_urls = false -lock_version = "4.3" -content_hash = "sha256:d59d877919bc132c806d5be4dc7a433f34b169709e83eb0bebcf3909975855e1" +strategy = ["cross_platform"] +lock_version = "4.4" +content_hash = "sha256:20b9fadc15c708aea48e9e01526b336df33f3171b0ca7fefa383073a4a070883" [[package]] name = "alembic" -version = "1.12.0" +version = "1.12.1" requires_python = ">=3.7" summary = "A database migration tool for SQLAlchemy." dependencies = [ @@ -21,8 +20,8 @@ dependencies = [ "typing-extensions>=4", ] files = [ - 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jwt_signing_key -from chowda.config import AUTH0_API_AUDIENCE +from starlette.requests import Request # Set CHOWDA_ENV env var to 'test' always. This serves as a flag for anywhere else in # the application where we need to detect whether we are running tests or not. environ['CHOWDA_ENV'] = 'test' -# This import must come *after* setting CHOWDA_ENV to 'test' above. +from chowda.app import app # noqa: E402 +from chowda.auth.utils import jwt_signing_key # noqa: E402 +from chowda.config import AUTH0_API_AUDIENCE # noqa: E402 from chowda.db import init_db # noqa: E402 # Set CI_CONFIG to use ./test/ci.test.toml *only* if it's not already set. We need to be @@ -112,3 +112,29 @@ def _fake_access_token( # decoding attempts algorithms, first RS256 then HS256. # See also chowda.auth.utils.validated_access_token. app.dependency_overrides[jwt_signing_key] = fake_signing_key + + +"""Create some test routes for setting session data.""" +test_router = APIRouter() + + +@test_router.get('/session') +def get_session_data(request: Request): + return request.session + + +@test_router.post('/session') +async def add_session_data(request: Request): + new_session_data = await request.json() + request.session.update(new_session_data) + return request.session + + +@test_router.put('/session') +async def set_session_data(request: Request): + new_session_data = await request.json() + request.session = new_session_data + return request.session + + +app.mount('/test', test_router) diff --git a/tests/test_app.py b/tests/test_app.py index 2170a474..c45d4c75 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -1,17 +1,13 @@ from fastapi.testclient import TestClient -from chowda.app import app -client = TestClient(app) - - -def test_get_admin_home(): +def test_get_admin_home(client: TestClient): """GET / returns a Redirect response""" response = client.get('/', follow_redirects=False) assert response.status_code == 200, 'Home page did not display sucessfully' -def test_get_admin_redirect(): +def test_get_admin_redirect(client: TestClient): """GET /admin returns a Redirect response""" response = client.get('/admin/', follow_redirects=False) assert response.status_code == 303, 'Home page did not redirect sucessfully' diff --git a/tests/test_batch_actions.py b/tests/test_batch_actions.py new file mode 100644 index 00000000..f74e87f7 --- /dev/null +++ b/tests/test_batch_actions.py @@ -0,0 +1,76 @@ +import pytest +from httpx import AsyncClient + +from chowda.config import AUTH0_API_AUDIENCE + + +@pytest.mark.asyncio +async def test_download_mmif_as_clammer(async_client: AsyncClient): + async with async_client as ac: + await ac.post( + "/test/session", + json={ + "user": { + "name": "test user", + f"{AUTH0_API_AUDIENCE}/roles": ["clammer"], + } + }, + ) + response = await ac.get( + "/admin/api/batch/action", + params={"pks": [2, 3], "name": "download_mmif"}, + ) + assert response.status_code == 200 + + +@pytest.mark.asyncio +async def test_download_mmif_as_admin(async_client: AsyncClient): + async with async_client as ac: + await ac.post( + "/test/session", + json={ + "user": { + "name": "test user", + f"{AUTH0_API_AUDIENCE}/roles": ["admin"], + } + }, + ) + response = await ac.get( + "/admin/api/batch/action", + params={"pks": [2, 3], "name": "download_mmif"}, + ) + assert response.status_code == 200 + + +@pytest.mark.asyncio +async def test_download_mmif_unauthenticated(async_client: AsyncClient): + """Assumes no user is in the session; responds with 401 Unauthorized.""" + async with async_client as ac: + response = await ac.get( + "/admin/api/batch/action", + params={"pks": [2, 3], "name": "download_mmif"}, + ) + assert response.status_code == 303 + + +@pytest.mark.asyncio +async def test_download_mmif_insufficient_role(async_client: AsyncClient): + async with async_client as ac: + await ac.post( + "/test/session", + json={ + "user": { + "name": "test user", + f"{AUTH0_API_AUDIENCE}/roles": ["peon"], + } + }, + ) + + response = await ac.get( + "/admin/api/batch/action", + params={"pks": [2, 3], "name": "download_mmif"}, + ) + # NOTE: should probably be a 403 Forbidden, but BaseAdmin.handle_action + # returns a 400 + assert response.status_code == 400 + assert response.json()['msg'] == 'Forbidden' From a223795aed1963b2f51b64068c8ec672f1c92697 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 17 Nov 2023 08:52:23 -0800 Subject: [PATCH 12/17] =?UTF-8?q?=F0=9F=A4=96=20Update=20dependencies=20(#?= =?UTF-8?q?186)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Harpo Harbert --- pdm.lock | 327 ++++++++++++++++++++++++++----------------------- pyproject.toml | 18 +-- 2 files changed, 180 insertions(+), 165 deletions(-) diff --git a/pdm.lock b/pdm.lock index 5c0ffbb3..905a4113 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "ci", "dev", "development", "docs", "locust", "production", "test"] strategy = ["cross_platform"] lock_version = "4.4" -content_hash = "sha256:20b9fadc15c708aea48e9e01526b336df33f3171b0ca7fefa383073a4a070883" +content_hash = "sha256:e4c62e1e35f16cf401d06d4c6dcb780833b8b936677e34f801955260bb830383" [[package]] name = "alembic" @@ -192,22 +192,22 @@ files = [ [[package]] name = "boto3" -version = "1.28.85" +version = "1.29.2" requires_python = ">= 3.7" summary = "The AWS SDK for Python" dependencies = [ - "botocore<1.32.0,>=1.31.85", + "botocore<1.33.0,>=1.32.2", "jmespath<2.0.0,>=0.7.1", "s3transfer<0.8.0,>=0.7.0", ] files = [ - {file = "boto3-1.28.85-py3-none-any.whl", hash = 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[[package]] @@ -3341,11 +3356,11 @@ files = [ [[package]] name = "starlette-admin" -version = "0.12.1" +version = "0.12.2" requires_python = ">=3.8" git = "https://github.com/wgbh-mla/starlette-admin.git" ref = "actions-btn" -revision = "7c6e88420240804c5de9639ea65d44e4f0c8f7ef" +revision = "933af3775f03ae08d6e005e91ae27d0369541e61" summary = "Fast, beautiful and extensible administrative interface framework for Starlette/FastApi applications" dependencies = [ "jinja2<4,>=3", @@ -3701,11 +3716,11 @@ files = [ [[package]] name = "wcwidth" -version = "0.2.9" +version = "0.2.10" summary = "Measures the displayed width of unicode strings in a terminal" files = [ - {file = "wcwidth-0.2.9-py2.py3-none-any.whl", hash = "sha256:9a929bd8380f6cd9571a968a9c8f4353ca58d7cd812a4822bba831f8d685b223"}, - {file = "wcwidth-0.2.9.tar.gz", hash = "sha256:a675d1a4a2d24ef67096a04b85b02deeecd8e226f57b5e3a72dbb9ed99d27da8"}, + {file = "wcwidth-0.2.10-py2.py3-none-any.whl", hash = "sha256:aec5179002dd0f0d40c456026e74a729661c9d468e1ed64405e3a6c2176ca36f"}, + {file = "wcwidth-0.2.10.tar.gz", hash = "sha256:390c7454101092a6a5e43baad8f83de615463af459201709556b6e4b1c861f97"}, ] [[package]] diff --git a/pyproject.toml b/pyproject.toml index 7b1c5b80..b605d111 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ dependencies = [ "itsdangerous~=2.1", "httpx~=0.25", "rich~=13.6", - "pyjwt>=2.8.0", + "pyjwt~=2.8", ] requires-python = '>=3.8.1,<4.0' readme = 'README.md' @@ -34,7 +34,7 @@ repository = 'https://github.com/WGBH-MLA/chowda' [project.optional-dependencies] production = [ - "uvicorn[standard]~=0.23", + "uvicorn[standard]~=0.24", "gunicorn~=21.2", ] test = [ @@ -42,7 +42,7 @@ test = [ "pytest~=7.4", "pytest-cov~=4.1", "pytest-sugar~=0.9", - "pytest-xdist~=3.3", + "pytest-xdist~=3.4", "httpx~=0.25", "nbmake~=1.4", "vcrpy~=5.1", @@ -50,10 +50,10 @@ test = [ "urllib3~=1.26", "pytest-mock~=3.12", "pytest-asyncio~=0.21", - "trio~=0.22", + "trio~=0.23", ] locust = [ - "locust~=2.17", + "locust~=2.18", "pydantic-factories~=1.17", ] development = [ @@ -103,8 +103,8 @@ includes = [] [tool.pdm.dev-dependencies] dev = [ - "uvicorn~=0.23", - "black~=23.10", + "uvicorn~=0.24", + "black~=23.11", "ruff~=0.1", "pre-commit~=3.5", ] @@ -112,8 +112,8 @@ docs = [ "mkdocs~=1.5", "mkdocs-material~=9.4", "mkdocs-git-revision-date-localized-plugin~=1.2", - "mike~=1.1", - "mkdocstrings[python]~=0.23", + "mike~=2.0", + "mkdocstrings[python]~=0.24", "mkdocs-jupyter~=0.24", ] ci = [ From 46c19bd0af6f23beb63133300b092e48811d0928 Mon Sep 17 00:00:00 2001 From: Harpo Date: Fri, 17 Nov 2023 13:02:03 -0800 Subject: [PATCH 13/17] =?UTF-8?q?=F0=9F=8E=AC=20Row=20actions=20(#188)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Converts collections create_batch to row_action * Converts rest of actions * Uses official starlette-admin as dependency * Better row actions choices for views --- chowda/utils.py | 36 +++++++++ chowda/views.py | 191 +++++++++++++++++++++++++++++++++++++++++------- pdm.lock | 9 ++- pyproject.toml | 2 +- 4 files changed, 205 insertions(+), 33 deletions(-) diff --git a/chowda/utils.py b/chowda/utils.py index d8ae8f6a..48ef336c 100644 --- a/chowda/utils.py +++ b/chowda/utils.py @@ -106,3 +106,39 @@ def get_duplicates(values: List[Any]) -> Set[Any]: else: duplicates.add(v) return duplicates + + +YES = [ + 'Yes!', + 'Aye!', + 'Aye aye!', + 'Aye aye, Captain!', + "Aye aye, Capt'n!", + 'YAAASS!!!', + 'Yup!', + 'Yuppers!', + 'Yup yup!', + 'Yup yup yup!', + 'Do it!', + 'Make it so!', + 'Absolutley!', + 'Sure!', + 'Sure thing!', + 'You bet!', + 'You betcha!', + 'Certainly', + 'Of course!', + 'Definitely!', + 'Affirmative!', + 'Indubitably!', + 'Without a doubt!', + 'By all means!', + 'Without question!', +] + + +def yes() -> str: + """Return a random 'yes' string""" + from random import choice + + return choice(YES) diff --git a/chowda/views.py b/chowda/views.py index a4c87e1b..05158083 100644 --- a/chowda/views.py +++ b/chowda/views.py @@ -11,7 +11,7 @@ from starlette.requests import Request from starlette.responses import RedirectResponse, Response from starlette.templating import Jinja2Templates -from starlette_admin import CustomView, action +from starlette_admin import CustomView, action, row_action from starlette_admin._types import RequestAction from starlette_admin.contrib.sqlmodel import ModelView from starlette_admin.exceptions import ActionFailed @@ -35,7 +35,7 @@ SuccessfulField, ) from chowda.models import MMIF, Batch, Collection, MediaFile -from chowda.utils import get_duplicates, validate_media_file_guids +from chowda.utils import get_duplicates, validate_media_file_guids, yes from templates import filters # noqa: F401 @@ -115,7 +115,7 @@ class CollectionView(ClammerModelView): exclude_actions_from_detail: ClassVar[list[Any]] = ['create_multiple_batches'] actions: ClassVar[list[Any]] = ['create_batch', 'create_multiple_batches'] - + row_actions: ClassVar[list[Any]] = ['view', 'edit', 'create_batch'] fields: ClassVar[list[Any]] = [ 'name', 'description', @@ -127,15 +127,27 @@ class CollectionView(ClammerModelView): async def validate(self, request: Request, data: Dict[str, Any]): validate_media_file_guids(request, data) + @row_action( + name='create_batch', + text='Create Batch', + confirmation='Create a Batch from this Collection?', + action_btn_class='btn-ghost-primary', + submit_btn_text=yes(), + icon_class='fa-regular fa-square-plus', + ) @action( name='create_batch', text='Create Batch', confirmation='Create a single Batch from these Collections?', - action_btn_class='btn-ghost-primary', - submit_btn_text='Yep', + submit_btn_text=yes(), + icon_class='fa-regular fa-square-plus', ) - async def create_batch(self, request: Request, pks: List[Any]) -> str: + async def create_batch( + self, request: Request, pks: list[int | str] | int | str + ) -> str: """Create a new batch from the combined collections""" + if not isinstance(pks, list): + pks = [pks] try: with Session(engine) as db: collections = db.exec( @@ -162,9 +174,8 @@ async def create_batch(self, request: Request, pks: List[Any]) -> str: name='create_multiple_batches', text='Create multiple Batches', confirmation='Create multiple Batches from these Collections?', - action_btn_class='btn-ghost-primary', icon_class='fa-solid fa-square-plus', - submit_btn_text='Yep', + submit_btn_text=yes(), ) async def create_multiple_batches(self, request: Request, pks: List[Any]) -> str: """Create multiple batches from the collections""" @@ -206,6 +217,13 @@ class BatchView(ClammerModelView): 'combine_batches', 'download_mmif', ] + row_actions: ClassVar[list[Any]] = [ + 'view', + 'edit', + 'duplicate_batch', + 'start_batch', + 'download_mmif', + ] fields: ClassVar[list[Any]] = [ 'id', @@ -238,13 +256,28 @@ async def is_action_allowed(self, request: Request, name: str) -> bool: return user.is_clammer or user.is_admin return await super().is_action_allowed(request, name) + @row_action( + name='start_batch', + text='Start', + confirmation='This might cost money. Are you sure?', + icon_class='fa fa-play', + action_btn_class='btn-outline-success', + submit_btn_text=yes(), + submit_btn_class='btn-success', + form=""" + + + + + + """, + ) @action( name='start_batches', text='Start', confirmation='This might cost money. Are you sure?', icon_class='fa fa-play', - action_btn_class='btn-outline-success', - submit_btn_text='Yep', + submit_btn_text=yes(), submit_btn_class='btn-success', form="""
@@ -254,8 +287,12 @@ async def is_action_allowed(self, request: Request, name: str) -> bool:
""", ) - async def start_batches(self, request: Request, pks: List[Any]) -> str: + async def start_batches( + self, request: Request, pks: list[int | str] | int | str + ) -> str: """Starts a Batch by sending a message to the Argo Event Bus""" + if not isinstance(pks, list): + pks = [pks] try: data: FormData = await request.form() except MultipartParseError as parse_error: @@ -300,16 +337,30 @@ async def start_batches(self, request: Request, pks: List[Any]) -> str: # Display Success message return f'Started {len(pks)} Batch(es)' + @row_action( + name='duplicate_batch', + text='Duplicate', + confirmation='Duplicate this Batch?', + action_btn_class='btn-ghost', + icon_class='fa fa-copy', + submit_btn_text=yes(), + submit_btn_class='btn-outline-primary', + exclude_from_list=True, + ) @action( name='duplicate_batches', text='Duplicate', confirmation='Duplicate all selected Batches?', icon_class='fa fa-copy', - submit_btn_text='Indeed!', + submit_btn_text=yes(), submit_btn_class='btn-outline-primary', ) - async def duplicate_batches(self, request: Request, pks: List[Any]) -> str: + async def duplicate_batches( + self, request: Request, pks: list[int | str] | int | str + ) -> str: """Create a new batch from the selected batch""" + if not isinstance(pks, list): + pks = [pks] try: with Session(engine) as db: for batch_id in pks: @@ -333,8 +384,7 @@ async def duplicate_batches(self, request: Request, pks: List[Any]) -> str: text='Combine', confirmation='Combine all selected Batches into a new Batch?', icon_class='fa fa-compress', - action_btn_class='btn-ghost', - submit_btn_text='Heck yeah!', + submit_btn_text=yes(), submit_btn_class='btn-outline-primary', ) async def combine_batches(self, request: Request, pks: List[Any]) -> str: @@ -360,18 +410,33 @@ async def combine_batches(self, request: Request, pks: List[Any]) -> str: # Display Success message return f'Combined {len(pks)} Batch(es)' + @row_action( + name='download_mmif', + text='Download MMIF', + confirmation='Download all MMIF JSON for this Batch?', + icon_class='fa fa-download', + submit_btn_text=yes() + ' Gimme the MMIF!', + submit_btn_class='btn-outline-primary', + custom_response=True, + action_btn_class='btn-ghost', + ) @action( name='download_mmif', text='Download MMIF', confirmation='Download all MMIF JSON for these Batches?', icon_class='fa fa-download', - submit_btn_text='Gimme the MMIF!', + submit_btn_text=yes() + ' Gimme ALL the MMIF!', submit_btn_class='btn-outline-primary', custom_response=True, ) - async def download_mmif(self, request: Request, pks: List[Any]) -> str: + async def download_mmif( + self, request: Request, pks: list[int | str] | int | str + ) -> str: """Create a new batch from the selected batch""" import zipfile + + if not isinstance(pks, list): + pks = [pks] from tempfile import TemporaryDirectory import boto3 @@ -445,6 +510,7 @@ class MediaFileView(ClammerModelView): pk_attr: str = 'guid' actions: ClassVar[List[str]] = ['create_new_batch'] + row_actions: ClassVar[List[str]] = ['view', 'edit', 'create_new_batch'] fields: ClassVar[list[str]] = [ 'guid', @@ -460,12 +526,30 @@ class MediaFileView(ClammerModelView): def can_create(self, request: Request) -> bool: return get_oauth_user(request).is_admin + @row_action( + name='create_new_batch', + text='Create Batch', + confirmation='Create a Batch from this Media File?', + action_btn_class='btn-ghost-primary', + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), + form=""" +
+
+ + +
+
+ """, + ) @action( name='create_new_batch', text='Create Batch', confirmation='Create a Batch from these Media Files?', - action_btn_class='btn-ghost-primary', - submit_btn_text='Yasss!', + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), form="""
@@ -477,7 +561,12 @@ def can_create(self, request: Request) -> bool: """, ) - async def create_new_batch(self, request: Request, pks: List[Any]) -> str: + async def create_new_batch( + self, request: Request, pks: list[int | str] | int | str + ) -> str: + """Create a new batch from the selected media files""" + if not isinstance(pks, list): + pks = [pks] with Session(engine) as db: media_files = db.exec( select(MediaFile).where(MediaFile.guid.in_(pks)) @@ -549,6 +638,7 @@ class SonyCiAssetView(AdminModelView): 'format', 'media_files', ] + row_actions: ClassVar[list[Any]] = ['view', 'edit'] page_size_options: ClassVar[list[int]] = [10, 25, 100, 500, 2000, 10000] @@ -586,12 +676,31 @@ class MMIFView(ChowdaModelView): ] actions: ClassVar[List[str]] = ['add_to_new_batch', 'add_to_existing_batch'] + @row_action( + name='add_to_new_batch', + text='Add to New Batch', + confirmation='Create a Batch from this MMIF?', + action_btn_class='btn-ghost-primary', + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), + exclude_from_list=True, + form=""" +
+
+ + +
+
+ """, + ) @action( name='add_to_new_batch', text='Add to New Batch', confirmation='Create a Batch from these MMIFs?', - action_btn_class='btn-ghost-primary', - submit_btn_text="Aye, Capt'n!", + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), form="""
@@ -603,7 +712,12 @@ class MMIFView(ChowdaModelView): """, ) - async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: + async def add_to_new_batch( + self, request: Request, pks: list[int | str] | int | str + ) -> str: + """Create a new batch from the selected media files""" + if not isinstance(pks, list): + pks = [pks] try: data: FormData = await request.form() with Session(engine) as db: @@ -630,12 +744,29 @@ async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: except Exception as error: raise ActionFailed(f'{error!s}') from error + @row_action( + name='add_to_existing_batch', + text='Add to Existing Batch', + confirmation='Which batch should this be added to?', + action_btn_class='btn-ghost-primary', + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), + exclude_from_list=True, + form=""" +
+
+ +
+
+ """, + ) @action( name='add_to_existing_batch', text='Add to Existing Batch', confirmation='Which batch should these be added to?', - action_btn_class='btn-ghost-primary', - submit_btn_text='Make it so!', + icon_class='fa-regular fa-square-plus', + submit_btn_text=yes(), form="""
@@ -645,13 +776,17 @@ async def add_to_new_batch(self, request: Request, pks: List[Any]) -> str: """, ) - async def add_to_existing_batch(self, request: Request, pks: List[Any]) -> str: + async def add_to_existing_batch( + self, request: Request, pks: list[int | str] | int | str + ) -> str: + """Add MMIFs to an existing batch""" + if not isinstance(pks, list): + pks = [pks] try: data: FormData = await request.form() with Session(engine) as db: mmifs: List[MMIF] = db.exec(select(MMIF).where(MMIF.id.in_(pks))).all() batch: Batch = db.get(Batch, data.get('batch_id')) - batch.input_mmifs += mmifs media_files: List[MediaFile] = [mmif.media_file for mmif in mmifs] # Check for duplicate Media Files in selection @@ -673,7 +808,7 @@ async def add_to_existing_batch(self, request: Request, pks: List[Any]) -> str: f'{len(existing_media_files)} Media File{s} already exist{"" if s else "s"} in Batch {batch.id}:
' # noqa: E501 + '
'.join(existing_media_files) ) - + batch.input_mmifs += mmifs batch.media_files += media_files db.commit() diff --git a/pdm.lock b/pdm.lock index 905a4113..3cbcccb1 100644 --- a/pdm.lock +++ b/pdm.lock @@ -5,7 +5,7 @@ groups = ["default", "ci", "dev", "development", "docs", "locust", "production", "test"] strategy = ["cross_platform"] lock_version = "4.4" -content_hash = "sha256:e4c62e1e35f16cf401d06d4c6dcb780833b8b936677e34f801955260bb830383" +content_hash = "sha256:5709dc0797a602e0975a7f9708f16f7f82f3724c3a4b0832c410d46079ccbc3f" [[package]] name = "alembic" @@ -3358,15 +3358,16 @@ files = [ name = "starlette-admin" version = "0.12.2" requires_python = ">=3.8" -git = "https://github.com/wgbh-mla/starlette-admin.git" -ref = "actions-btn" -revision = "933af3775f03ae08d6e005e91ae27d0369541e61" summary = "Fast, beautiful and extensible administrative interface framework for Starlette/FastApi applications" dependencies = [ "jinja2<4,>=3", "python-multipart", "starlette", ] +files = [ + {file = "starlette_admin-0.12.2-py3-none-any.whl", hash = "sha256:25bf5ddd2af8d2f6b3bec3e5c16c883e810274ce35eee9cc27c6242bea7a6a34"}, + {file = "starlette_admin-0.12.2.tar.gz", hash = "sha256:b8da375ff5e2ce0f6e1407977b23f4c147e1cb69b2b4abe07f96714e4c59b7f0"}, +] [[package]] name = "termcolor" diff --git a/pyproject.toml b/pyproject.toml index b605d111..cce59ba8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ description = 'A CLAMS processing application' authors = [{ name = 'WGBH-MLA', email = 'ryan_harbert@wgbh.org' }] dependencies = [ "fastapi~=0.104", - "starlette-admin @ git+https://github.com/wgbh-mla/starlette-admin.git@actions-btn", + "starlette-admin~=0.12", "sqlmodel~=0.0", "pydantic[email]~=1.10", "sonyci~=0.1", From 422eae8b50b9a6ad90b196cdb091c9e7ed6c139e Mon Sep 17 00:00:00 2001 From: Harpo Date: Thu, 18 Jan 2024 12:36:53 -0800 Subject: [PATCH 14/17] Activates venv in production image (#190) --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 76a15ebf..efdb9f02 100644 --- a/Dockerfile +++ b/Dockerfile @@ -77,4 +77,4 @@ ENV CHOWDA_ENV=production ENV PATH=$PATH:/app/.venv/bin/ EXPOSE 8000 -CMD gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker +CMD . .venv/bin/activate && gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker From 669af5d14908683c945d6a01c74c37e03ffe8503 Mon Sep 17 00:00:00 2001 From: Harpo Date: Fri, 19 Jan 2024 12:34:34 -0500 Subject: [PATCH 15/17] Adds venv to start of PATH (#191) --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index efdb9f02..bda4ba48 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,7 +25,7 @@ RUN pdm config python.use_venv false # Configure python to use pep582 with local __pypyackages__ ENV PYTHONPATH=/usr/local/lib/python3.11/site-packages/pdm/pep582 # Add local packages to $PATH -ENV PATH=$PATH:/app/__pypackages__/3.11/bin/ +ENV PATH=/app/__pypackages__/3.11/bin/:$PATH # Install dev dependencies with pdm RUN pdm install -G dev @@ -74,7 +74,7 @@ COPY templates templates COPY static static ENV CHOWDA_ENV=production -ENV PATH=$PATH:/app/.venv/bin/ +ENV PATH=/app/.venv/bin/:$PATH EXPOSE 8000 -CMD . .venv/bin/activate && gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker +CMD gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker From bc0dafdb5a763d2da331be7f1a3fbb0ce7591faf Mon Sep 17 00:00:00 2001 From: Harpo Date: Wed, 21 Feb 2024 11:28:39 -0800 Subject: [PATCH 16/17] Adds pip to venv (#192) --- Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index bda4ba48..a327ce80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,8 +58,10 @@ CMD poetry run locust # 'production' build stage ############################ FROM base as build -# build-essential libpq-dev python3-dev RUN apt update && apt install -y gcc libpq-dev git + +RUN pdm config venv.with_pip True + RUN pdm install -G production FROM python:3.11-slim as production From ea0c1802819200ac1ec3222fadfe29c4ef6be464 Mon Sep 17 00:00:00 2001 From: Harpo Date: Wed, 21 Feb 2024 14:01:54 -0800 Subject: [PATCH 17/17] =?UTF-8?q?=F0=9F=8D=BC=20Ensure=20pip=20(#195)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Installs pip into .venv python * Black format with new version --- Dockerfile | 12 +++++++++--- chowda/fields.py | 12 ++++++------ 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index a327ce80..b84fa8cd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -55,15 +55,20 @@ CMD poetry run locust ########################### -# 'production' build stage +# 'base' build stage for production ############################ FROM base as build RUN apt update && apt install -y gcc libpq-dev git RUN pdm config venv.with_pip True - RUN pdm install -G production +# Install pip into the virtual environment +RUN /app/.venv/bin/python -m ensurepip + +########################### +# 'production' final production image +############################ FROM python:3.11-slim as production WORKDIR /app @@ -76,7 +81,8 @@ COPY templates templates COPY static static ENV CHOWDA_ENV=production -ENV PATH=/app/.venv/bin/:$PATH +ENV PATH="/app/.venv/bin:$PATH" EXPOSE 8000 + CMD gunicorn chowda.app:app -b 0.0.0.0:8000 -w 2 --worker-class uvicorn.workers.UvicornWorker diff --git a/chowda/fields.py b/chowda/fields.py index fd13c034..e872a2b2 100644 --- a/chowda/fields.py +++ b/chowda/fields.py @@ -95,12 +95,12 @@ async def serialize_value( return [ { **run, - 'finished_at': run['finished_at'].isoformat() - if run.get('finished_at') - else None, - 'created_at': run['created_at'].isoformat() - if run.get('created_at') - else None, + 'finished_at': ( + run['finished_at'].isoformat() if run.get('finished_at') else None + ), + 'created_at': ( + run['created_at'].isoformat() if run.get('created_at') else None + ), } for run in value ]