fm-weck 1.5.2__py3-none-any.whl → 1.6.0__py3-none-any.whl

fm_weck/zenodo.py

@@ -0,0 +1,381 @@
+# This file is part of fm-weck: executing fm-tools in containerized environments.
+# https://gitlab.com/sosy-lab/software/fm-weck
+#
+# SPDX-FileCopyrightText: 2024 Dirk Beyer <https://www.sosy-lab.org>
+#
+# SPDX-License-Identifier: Apache-2.0
+import json
+import logging
+import os
+from datetime import datetime
+from pathlib import Path
+
+import httpx
+from dotenv import find_dotenv, load_dotenv, set_key
+from tqdm import tqdm
+
+from fm_weck.config import Config
+from fm_weck.exceptions import ZenodoError
+from fm_weck.image_mgr import ImageMgr
+
+
+class TokenAuth(httpx.Auth):
+    def __init__(self, token: str):
+        self.token = token
+
+    def auth_flow(self, request):
+        request.headers["Authorization"] = f"Bearer {self.token}"
+        yield request
+
+
+class ZenodoSession:
+    def __init__(self, access_token: str | None = None, is_sandbox: bool = False):
+        if is_sandbox:
+            self.base_url = "https://sandbox.zenodo.org/api"
+        else:
+            self.base_url = "https://zenodo.org/api"
+        self.deposit_url = self.base_url + "/deposit/depositions"
+        self.download_url = self.base_url + "/records"
+        self.access_token = access_token
+        if self.access_token is not None:
+            self.client = httpx.Client(auth=TokenAuth(self.access_token))
+        else:
+            self.client = httpx.Client()
+
+    def _require_access_token(self):
+        if self.access_token is None:
+            raise ZenodoError("An API access token is required to interact with the Zenodo API.")
+
+    def publish(self, image_info: tuple):
+        """
+        Publish an image on Zenodo.
+        """
+        self._require_access_token()
+
+        deposition_id = self.upload(image_info)
+        publish_url = self.deposit_url + "/" + deposition_id + "/" + "actions/publish"
+        r = httpx.post(publish_url)
+
+        if r.status_code >= 400:
+            self.delete_deposition(deposition_id)
+            raise ZenodoError(f"Error trying to publish an image: {r.json()['message']}")
+
+        return r.json()["doi"]
+
+    def upload(self, image_info: tuple[str, str, Path]) -> str:
+        """
+        Upload an image to Zenodo and leave it in draft mode (unpublished).
+        """
+        self._require_access_token()
+
+        image_name = image_info[0]
+        image_version = image_info[1]
+        image_path = image_info[2]
+        # Upload the actual file
+        upload_name = image_name + "_" + image_version + ".tar"
+        upload_name = upload_name.replace("/", "-")
+        metadata = self.get_upload_metadata(upload_name, image_version)
+        record_id = self.check_existing_records(metadata)
+        logging.debug(f"Record ID: {record_id}")
+        # Check if we are adding a new version or creating a new record
+        if record_id:
+            r = self.client.post(self.deposit_url + "/" + record_id + "/actions/newversion")
+        else:
+            logging.debug(f"{metadata=}")
+            r = self.client.post(
+                self.deposit_url,
+                json=metadata,
+                headers={"Content-Type": "application/json", "Authorization": f"Bearer {self.access_token}"},
+            )
+
+        if r.status_code >= 400:
+            logging.debug(f"{r.status_code} - {r.text}")
+            raise ZenodoError(f"Error trying to upload the deposition metadata to Zenodo: {r.json()['message']}")
+        bucket_url = r.json()["links"]["bucket"]
+        deposition_id = str(r.json()["id"])
+
+        if record_id:
+            self.prepare_new_version_upload(metadata, deposition_id)
+
+        r = self.upload_with_progress_bar(image_path, upload_name, bucket_url)
+        if r.status_code >= 400:
+            self.delete_deposition(deposition_id)
+            raise ZenodoError(f"Error trying to upload image to Zenodo: {r.json()['message']}")
+
+        return deposition_id
+
+    def upload_with_progress_bar(self, image_path, upload_name, bucket_url):
+        file_size = os.path.getsize(image_path)
+
+        with (
+            open(image_path, "rb") as image,
+            tqdm(total=file_size, unit="B", unit_scale=True, desc="Uploading") as progress_bar,
+        ):
+
+            def file_iterator():
+                chunk_size = 1024 * 1024 * 5  # 5 MB
+                while True:
+                    chunk = image.read(chunk_size)
+                    if not chunk:
+                        break
+                    yield chunk
+                    progress_bar.update(len(chunk))
+
+            r = self.client.put(
+                f"{bucket_url}/{upload_name}",
+                data=file_iterator(),
+                headers={"Content-Length": str(file_size)},
+                timeout=300,
+            )
+
+        return r
+
+    def download(self, doi: str, download_path: str | None, no_progress_bar: bool = False) -> Path:
+        """
+        Download an image from Zenodo using its DOI.
+        """
+        download_url = self.resolve_download_info(doi)
+        image_name = download_url.split("/")[-2] + ".tar"
+        if no_progress_bar:
+            r = self.client.get(download_url)
+            if r.status_code >= 400:
+                raise ZenodoError(f"Error trying to download image: {r.json()['message']}")
+            content = r.content
+        else:
+            content = self.download_with_progress_bar(download_url)
+
+        return self.save_image(image_name, content, download_path)
+
+    def download_with_progress_bar(self, url: str):
+        content = bytearray()
+
+        with self.client.stream("GET", url) as response:
+            response.raise_for_status()
+
+            total_size = int(response.headers.get("Content-Length", 0))
+            chunk_size = 1024 * 1024 * 5  # 5 MB
+
+            with tqdm(total=total_size, unit="B", unit_scale=True, desc="Downloading") as progress_bar:
+                for chunk in response.iter_bytes(chunk_size):
+                    content.extend(chunk)
+                    progress_bar.update(len(chunk))
+
+        return content
+
+    def resolve_download_info(self, doi: str) -> str:
+        """
+        Extract the download URL from the deposition metadata.
+
+        :return: The download URL of the image.
+        """
+        doi_id = doi.split(".")[-1]
+        record_url = self.download_url + "/" + doi_id
+        r = self.client.get(record_url)
+        if r.status_code >= 400:
+            raise ZenodoError(f"Error trying to access the image record: {r.json()['message']}")
+
+        file_name = r.json()["files"][0]["key"]
+
+        return record_url + "/files/" + file_name + "/content"
+
+    def save_image(self, image_name: str, image: bytes, save_path):
+        save_path = Path().cwd() / image_name if not save_path else Path().cwd() / Path(save_path) / image_name
+        save_path.parent.mkdir(parents=True, exist_ok=True)
+        save_path.write_bytes(image)
+        return save_path
+
+    def delete_deposition(self, deposition_id: str):
+        r = self.client.delete(self.deposit_url + "/" + deposition_id)
+        if r.status_code >= 400:
+            raise ZenodoError(f"Error trying to delete a deposition resource from Zenodo: {r.json()['message']}")
+
+    def check_existing_records(self, metadata: dict):
+        """
+        Check if a record with the same name already exists in the depositions.
+        If it exists, prompt whether the image should be uploaded as a new version.
+
+        :return: The deposition ID in case of a positive prompt response, or an empty string.
+        """
+        r = self.client.get(self.deposit_url)
+        if r.status_code >= 400:
+            raise ZenodoError(f"Error trying to access the image record: {r.json()['message']}")
+
+        for record in r.json():
+            if metadata["metadata"]["title"] == record["title"]:
+                while True:
+                    response = (
+                        input(
+                            (
+                                "The record already exists. Do you want to upload this as a new version "
+                                "of the existing record?\n"
+                                "(y)es: upload as a new version of an existing record\n"
+                                "(n)o: create a new record\n"
+                                "(a)bort: cancel the upload\n"
+                            )
+                        )
+                        .strip()
+                        .lower()
+                    )
+
+                    if response == "y":
+                        return str(record["id"])
+                    elif response == "n":
+                        break
+                    elif response == "a":
+                        exit(0)
+        return ""
+
+    def prepare_new_version_upload(self, metadata: dict, deposition_id: str) -> None:
+        """
+        Set up the metadata for the new version and delete the old versions' files from that version.
+        """
+        r = self.client.put(
+            self.deposit_url + "/" + deposition_id,
+            data=json.dumps(metadata),  # type: ignore
+        )
+        if r.status_code >= 400:
+            raise ZenodoError(f"Error trying to upload the new version metadata to Zenodo: {r.json()['message']}")
+
+        for file in r.json()["files"]:
+            r = self.client.delete(
+                self.deposit_url + "/" + deposition_id + "/files/" + file["id"],
+            )
+            if r.status_code >= 400:
+                raise ZenodoError(
+                    f"Error trying to delete old version files from the new version: {r.json()['message']}"
+                )
+
+    def get_upload_metadata(self, image_name: str, image_version: str) -> dict:
+        description = (
+            f"This is an image file.\n"
+            f"<p>In case of manual download, the image can be imported locally using the command: "
+            f"<code>[docker|podman] load --input {image_name}</code></p>"
+        )
+
+        upload_metadata = {
+            "metadata": {
+                "title": image_name,
+                "version": image_version,
+                "upload_type": "software",
+                "creators": [{"name": "fm-weck"}],
+                "publication_date": datetime.now().date().isoformat(),
+                "access_right": "open",
+                "license": "Apache-2.0",
+                "description": description,
+            }
+        }
+        return upload_metadata
+
+
+class ZenodoMgr(object):
+    """
+    Zenodo API manager.
+
+    Args:
+        engine (object): The fm-weck engine object.
+        access_token (str, optional): The access token for authentication with the API. Defaults to None.
+        image (str, optional): The image to be published. Required if no doi is given. Defaults to None.
+        doi (str, optional): The DOI of the image to be pulled. Required if no image is given. Defaults to None.
+
+    Raises:
+        ValueError: If a chosen image is invalid or does not exist.
+    """
+
+    def __init__(
+        self,
+        engine,
+        access_token: str | None,
+        image: str | None,
+        doi: str | None,
+        is_sandbox: bool = False,
+        config: Config | None = None,
+    ):
+        access_token = access_token or ZenodoMgr.load_zenodo_token(config)
+
+        self.session = ZenodoSession(access_token, is_sandbox)
+        self.image = image
+        self.engine = engine
+        if image:
+            self.image_info = ImageMgr().prepare_image_for_zenodo(engine, image)
+        self.doi = doi
+
+    def publish(self):
+        """
+        Publish an image on Zenodo.
+
+        Raises:
+            ZenodoError: If Zenodo API returns an error.
+        """
+        if self.image is None:
+            raise ValueError("No image specified for publishing.")
+        print("Publishing image to Zenodo...")
+        doi = self.session.publish(self.image_info)
+        print("Image successfully published.")
+        ImageMgr().tag_image(self.engine, self.image, doi)
+
+    def push(self):
+        """
+        Upload an image to Zenodo and leave it in draft mode (unpublished).
+
+        Raises:
+            ZenodoError: If Zenodo API returns an error.
+        """
+        if self.image is None:
+            raise ValueError("No image specified for pushing.")
+        logging.info(f"Uploading image to Zenodo... {self.image_info}")
+        self.session.upload(self.image_info)
+        print("Image successfully uploaded.")
+
+    def pull(self, download_path: str | None, force_pull: bool = False):
+        """
+        Download an image from Zenodo using its DOI.
+
+        Raises:
+            ValueError: If no DOI is provided.
+            ZenodoError: If Zenodo API returns an error.
+        """
+        if self.doi:
+            doi = ImageMgr().check_if_doi_exists_locally(self.engine, self.doi)
+        else:
+            raise ValueError("No DOI provided.")
+
+        if not force_pull and not doi:
+            print("Image already exists locally. Pulling aborted.")
+            return
+
+        print("Pulling image from Zenodo...")
+        tar_path = self.session.download(self.doi, download_path)
+        ImageMgr().load_image(self.engine, tar_path, self.doi)
+        print("Image successfully pulled.")
+        tar_path.unlink()
+
+    @staticmethod
+    def save_zenodo_token(config, token):
+        token_path = find_dotenv(filename=".zenodo_token")
+        token_path = Path.cwd() / config.get("defaults").get("token_location") if not token_path else Path(token_path)
+
+        print(f"This action will overwrite the token at: {token_path}\nDo you wish to continue? [y/N]")
+        if input().lower() == "y":
+            load_dotenv(token_path)
+            set_key(token_path, "ZENODO_TOKEN", token)
+            print(f"Token saved to: {token_path}")
+        else:
+            print("Action aborted.")
+
+    @staticmethod
+    def load_zenodo_token(config):
+        """
+        Load the Zenodo token from the Zenodo config file.
+
+        Raises:
+            ZenodoError: If no Zenodo token is found.
+        """
+        token_path = find_dotenv(filename=".zenodo_token")
+        token_path = Path.cwd() / config.get("defaults").get("token_location") if not token_path else Path(token_path)
+        load_dotenv(Path(token_path))
+        token = os.getenv("ZENODO_TOKEN")
+
+        if token:
+            print(f"Using token from: {token_path}\n")
+
+        return token

{fm_weck-1.5.2.dist-info → fm_weck-1.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fm-weck
-Version: 1.5.2
+Version: 1.6.0
 Author-email: Henrik Wachowitz <henrik.wachowitz@ifi.lmu.de>
 Maintainer-email: Henrik Wachowitz <henrik.wachowitz@ifi.lmu.de>
 Classifier: Development Status :: 4 - Beta
@@ -11,6 +11,7 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.10
 Requires-Dist: argcomplete
+Requires-Dist: dotenv
 Requires-Dist: fm-tools>=1.0.0
 Requires-Dist: pyyaml>=6.0
 Requires-Dist: tabulate

fm_weck-1.6.0.dist-info/RECORD

@@ -0,0 +1,188 @@
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