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["standard"], version = "^0.115.0"} sqlmodel = "^0.0.22" sqlalchemy = "^2.0.36" +bagit = "^1.8.1" [tool.poetry.group.dev.dependencies] diff --git a/src/api/main.py b/src/api/main.py index d06920a..a19fa9e 100644 --- a/src/api/main.py +++ b/src/api/main.py @@ -10,6 +10,7 @@ from sqlalchemy.exc import IntegrityError from sqlmodel import Session, SQLModel, create_engine, select +from api.manifests import generate_manifest from api.security import ApiKey, validate_api_key, validate_permissions from models.member import Member from models.person import Person @@ -107,6 +108,9 @@ async def set_drive_info( for drive in input_project.services.research_drive ] project.research_drives = drives + for drive in drives: + drive.manifest = generate_manifest(drive.name) + # Add the validated services and members into the project project.members = members # Upsert the project. session.merge(project) @@ -155,6 +159,14 @@ async def get_drive_info( status_code=404, detail=f"No Projects associated with {drive_id} in local database", ) + + manifest = drive_found.manifest.manifest + if manifest is None: + raise HTTPException( + status_code=404, + detail=f"Manifest not available for {drive_id}", + ) + return { "drive_id": drive_id, "ro_crate": "TODO: Make RO-Crate from: " + str(projects), diff --git a/src/api/manifests.py b/src/api/manifests.py new file mode 100644 index 0000000..cb0c23f --- /dev/null +++ b/src/api/manifests.py @@ -0,0 +1,71 @@ +"""Scripts for generating file manifests +""" + +import multiprocessing +import os +from pathlib import Path +from typing import Dict, Generator + +import bagit + +from models.manifest import Manifest + +PROCESSES = max(multiprocessing.cpu_count() - 2, 1) +DEFAULT_CHECKSUM = "sha512" + + +def _sorted_walk(data_dir: str) -> Generator[str, None, None]: + for dirpath, dirnames, filenames in os.walk(data_dir): + filenames.sort() + dirnames.sort() + for fn in filenames: + path = os.path.join(dirpath, fn) + yield path + + +def _encode_filename(s: str) -> str: + s = s.replace("\r", "%0D") + s = s.replace("\n", "%0A") + return s + + +def genertate_filelist(drive_path: Path) -> str: + """Generate a list of all the files in a path separated by newlines. + Sorts on filenames and dirnames to mirror bagit process. + """ + if PROCESSES > 1: + with multiprocessing.Pool(processes=PROCESSES) as pool: + filenames = pool.map(_encode_filename, _sorted_walk(drive_path.as_posix())) + # pool.close() + # pool.join() + else: + filenames = [_encode_filename(i) for i in _sorted_walk(drive_path.as_posix())] + return "\n".join(filenames) + + +def generate_manifest(drive_id: str) -> Manifest: + """Generate a manifest from a drive ID. + in future provide logic for a service account to mount a research drive. + Currently generate a mockup from a test directory. + """ + # mount drive based on ID + # use service account to mount drive to mountpoint + _ = f"//files.auckland.ac.nz/research/{drive_id}" + mountpoint = Path("tests/restst000000001-testing") + manifest = genertate_filelist(mountpoint) + return Manifest(manifest=manifest) + + +def bag_directory(drive_path: Path, bag_info: Dict[str, str]) -> None: + """Create a bagit bag from a given directory + + Args: + drive_path (Path): the path to the directory to bag + bag_info (Dict[str,str]): a dictionary documenting ownership of the bag + """ + _ = bagit.make_bag( + bag_dir=drive_path.as_posix(), + bag_info=bag_info, + processes=PROCESSES, + checksums=DEFAULT_CHECKSUM, + ) diff --git a/src/models/manifest.py b/src/models/manifest.py new file mode 100644 index 0000000..612d780 --- /dev/null +++ b/src/models/manifest.py @@ -0,0 +1,30 @@ +"""sql models for storing maninfests +""" + +from typing import TYPE_CHECKING + +from sqlmodel import Field, Relationship, SQLModel + +if TYPE_CHECKING: + from models.services import ResearchDriveService + + +class ManifestDriveLink(SQLModel, table=True): + """Linking table between research drive service and a manifest of files""" + + manifest_id: int | None = Field( + default=None, foreign_key="manifest.id", primary_key=True + ) + research_drive_id: int | None = Field( + default=None, foreign_key="researchdriveservice.id", primary_key=True + ) + + +class Manifest(SQLModel, table=True): + """SQL model for storing simple file manifests""" + + id: int = Field(primary_key=True) + manifest: str + research_drive: "ResearchDriveService" = Relationship( + link_model=ManifestDriveLink, back_populates="manifest" + ) diff --git a/src/models/services.py b/src/models/services.py index e2c215b..9df4a3d 100644 --- a/src/models/services.py +++ b/src/models/services.py @@ -5,6 +5,8 @@ from sqlmodel import Field, Relationship, SQLModel +from models.manifest import Manifest, ManifestDriveLink + if TYPE_CHECKING: from models.project import Project diff --git a/tests/restst000000001-testing/data/cleaned/file.a b/tests/restst000000001-testing/data/cleaned/file.a new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/data/cleaned/file.b b/tests/restst000000001-testing/data/cleaned/file.b new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/data/cleaned/file.c b/tests/restst000000001-testing/data/cleaned/file.c new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/data/raw/file.a b/tests/restst000000001-testing/data/raw/file.a new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/data/raw/file.b b/tests/restst000000001-testing/data/raw/file.b new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/data/raw/file.c b/tests/restst000000001-testing/data/raw/file.c new file mode 100644 index 0000000..e69de29 diff --git a/tests/restst000000001-testing/thesis/docs/publication.txt b/tests/restst000000001-testing/thesis/docs/publication.txt new file mode 100644 index 0000000..e69de29 From 2b87b42413a88bf38c479b6e71fa63526edc12af Mon Sep 17 00:00:00 2001 From: JloveUOA Date: Tue, 26 Nov 2024 09:35:26 +1300 Subject: [PATCH 2/4] restore manifest generation after rebase --- src/api/main.py | 3 ++- src/models/services.py | 5 ++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/src/api/main.py b/src/api/main.py index a19fa9e..748b58a 100644 --- a/src/api/main.py +++ b/src/api/main.py @@ -170,5 +170,6 @@ async def get_drive_info( return { "drive_id": drive_id, "ro_crate": "TODO: Make RO-Crate from: " + str(projects), - "manifest": "TODO: Make Manifest", + + "manifest": manifest, } diff --git a/src/models/services.py b/src/models/services.py index 9df4a3d..a16c6cb 100644 --- a/src/models/services.py +++ b/src/models/services.py @@ -24,7 +24,7 @@ class ResearchDriveProjectLink(SQLModel, table=True): class ResearchDriveService(SQLModel, table=True): """Object describing a research drive service.""" - + allocated_gb: float date: datetime first_day: datetime @@ -37,6 +37,9 @@ class ResearchDriveService(SQLModel, table=True): projects: list["Project"] = Relationship( link_model=ResearchDriveProjectLink, back_populates="research_drives" ) + manifest: Manifest = Relationship( + link_model=ManifestDriveLink, back_populates="research_drive" + ) class InputServices(SQLModel): From 2b1181056ac0d2216db3300cb6d973335377ef68 Mon Sep 17 00:00:00 2001 From: JloveUOA Date: Tue, 26 Nov 2024 09:36:16 +1300 Subject: [PATCH 3/4] re-lint manifest models --- src/api/main.py | 1 - src/models/services.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/api/main.py b/src/api/main.py index 748b58a..9d92810 100644 --- a/src/api/main.py +++ b/src/api/main.py @@ -170,6 +170,5 @@ async def get_drive_info( return { "drive_id": drive_id, "ro_crate": "TODO: Make RO-Crate from: " + str(projects), - "manifest": manifest, } diff --git a/src/models/services.py b/src/models/services.py index a16c6cb..9176304 100644 --- a/src/models/services.py +++ b/src/models/services.py @@ -24,7 +24,7 @@ class ResearchDriveProjectLink(SQLModel, table=True): class ResearchDriveService(SQLModel, table=True): """Object describing a research drive service.""" - + allocated_gb: float date: datetime first_day: datetime From 37dd9421bfbfe338fe4704cf5e99fbffbfc3abaf Mon Sep 17 00:00:00 2001 From: JloveUOA Date: Tue, 26 Nov 2024 12:00:57 +1300 Subject: [PATCH 4/4] seperate request for manifest --- src/api/main.py | 30 +++++++++++++++++++++++++++--- 1 file changed, 27 insertions(+), 3 deletions(-) diff --git a/src/api/main.py b/src/api/main.py index 9d92810..6cae3bf 100644 --- a/src/api/main.py +++ b/src/api/main.py @@ -143,16 +143,17 @@ async def get_drive_info( """Retrieve information about the specified Research Drive.""" validate_permissions("GET", api_key) - code_query = select(ResearchDriveService).where( ResearchDriveService.name == drive_id ) drive_found = session.exec(code_query).first() + if drive_found is None: raise HTTPException( status_code=404, detail=f"Research Drive ID {drive_id} not found in local database.", ) + projects = drive_found.projects if len(projects) == 0: raise HTTPException( @@ -160,7 +161,32 @@ async def get_drive_info( detail=f"No Projects associated with {drive_id} in local database", ) + return { + "drive_id": drive_id, + "ro_crate": "TODO: Make RO-Crate from: " + str(projects), + } + + +@app.get(ENDPOINT_PREFIX + "/resdrivemanifest") +async def get_drive_manifest( + drive_id: ResearchDriveID, + session: SessionDep, + api_key: ApiKey = Security(validate_api_key), +) -> dict[str, str]: + """Retrieve a manifest from a research drive that has been loaded into the backend""" + validate_permissions("GET", api_key) + code_query = select(ResearchDriveService).where( + ResearchDriveService.name == drive_id + ) + drive_found = session.exec(code_query).first() + + if drive_found is None: + raise HTTPException( + status_code=404, + detail=f"Research Drive ID {drive_id} not found in local database.", + ) manifest = drive_found.manifest.manifest + if manifest is None: raise HTTPException( status_code=404, @@ -168,7 +194,5 @@ async def get_drive_info( ) return { - "drive_id": drive_id, - "ro_crate": "TODO: Make RO-Crate from: " + str(projects), "manifest": manifest, }