digitalhub 0.8.0b15__py3-none-any.whl → 0.9.0__py3-none-any.whl

digitalhub/stores/local/store.py

@@ -2,7 +2,9 @@ from __future__ import annotations
 
 import shutil
 from pathlib import Path
+from typing import Any
 
+from digitalhub.readers.api import get_reader_by_object
 from digitalhub.stores._base.store import Store, StoreConfig
 from digitalhub.utils.exceptions import StoreError
 from digitalhub.utils.file_utils import get_file_info_from_local
@@ -28,7 +30,7 @@ class LocalStore(Store):
         self.config = config
 
     ##############################
-    # IO methods
+    # I/O methods
     ##############################
 
     def download(
@@ -59,7 +61,7 @@ class LocalStore(Store):
         """
         raise StoreError("Local store does not support download.")
 
-    def upload(self, src: str | list[str], dst: str | None = None) -> list[tuple[str, str]]:
+    def upload(self, src: str | list[str], dst: str) -> list[tuple[str, str]]:
         """
         Upload an artifact to storage.
 
@@ -70,7 +72,11 @@ class LocalStore(Store):
         """
         raise StoreError("Local store does not support upload.")
 
-    def get_file_info(self, paths: list[str]) -> list[dict]:
+    def get_file_info(
+        self,
+        root: str,
+        paths: list[tuple[str, str]],
+    ) -> list[dict]:
         """
         Method to get file metadata.
 
@@ -189,7 +195,40 @@ class LocalStore(Store):
         return dst
 
     ##############################
-    # Static methods
+    # Datastore methods
+    ##############################
+
+    def write_df(self, df: Any, dst: str, extension: str | None = None, **kwargs) -> str:
+        """
+        Method to write a dataframe to a file. Kwargs are passed to df.to_parquet().
+        If destination is not provided, the dataframe is written to the default
+        store path with generated name.
+
+        Parameters
+        ----------
+        df : Any
+            The dataframe to write.
+        dst : str
+            The destination of the dataframe.
+        **kwargs : dict
+            Keyword arguments.
+
+        Returns
+        -------
+        str
+            Path of written dataframe.
+        """
+        self.store._check_local_dst(dst)
+        self._validate_extension(Path(dst).suffix.removeprefix("."))
+
+        # Write dataframe
+        reader = get_reader_by_object(df)
+        reader.write_df(df, dst, extension=extension, **kwargs)
+
+        return dst
+
+    ##############################
+    # Helper methods
     ##############################
 
     @staticmethod

digitalhub/stores/remote/store.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
+from typing import Any
 
 import requests
 
@@ -25,7 +26,7 @@ class RemoteStore(Store):
         self.config = config
 
     ##############################
-    # IO methods
+    # I/O methods
     ##############################
 
     def download(
@@ -68,7 +69,7 @@ class RemoteStore(Store):
 
         return self._download_file(root, dst, overwrite)
 
-    def upload(self, src: str | list[str], dst: str | None = None) -> list[tuple[str, str]]:
+    def upload(self, src: str | list[str], dst: str) -> list[tuple[str, str]]:
         """
         Upload an artifact to storage.
 
@@ -79,19 +80,44 @@ class RemoteStore(Store):
         """
         raise StoreError("Remote HTTP store does not support upload.")
 
-    def get_file_info(self, paths: list[str]) -> list[dict]:
+    def get_file_info(
+        self,
+        root: str,
+        paths: list[tuple[str, str]],
+    ) -> list[dict]:
         """
         Get file information from HTTP(s) storage.
 
+        Parameters
+        ----------
+        paths : list[str]
+            List of source paths.
+
+        Returns
+        -------
+        list[dict]
+            Returns files metadata.
+        """
+        return []
+
+    ##############################
+    # Datastore methods
+    ##############################
+
+    def write_df(self, df: Any, dst: str, extension: str | None = None, **kwargs) -> str:
+        """
+        Method to write a dataframe to a file. Note that this method is not implemented
+        since the remote store is not meant to write dataframes.
+
         Raises
         ------
         NotImplementedError
             This method is not implemented.
         """
-        raise NotImplementedError("Remote store does not support get_file_info.")
+        raise NotImplementedError("Remote store does not support write_df.")
 
     ##############################
-    # Private helper methods
+    # Helper methods
     ##############################
 
     @staticmethod

digitalhub/stores/s3/store.py

@@ -2,16 +2,18 @@ from __future__ import annotations
 
 from io import BytesIO
 from pathlib import Path
-from typing import Type
+from typing import Any, Type
 from urllib.parse import urlparse
 
 import boto3
 import botocore.client  # pylint: disable=unused-import
 from botocore.exceptions import ClientError
 
+from digitalhub.readers.api import get_reader_by_object
 from digitalhub.stores._base.store import Store, StoreConfig
 from digitalhub.utils.exceptions import StoreError
 from digitalhub.utils.file_utils import get_file_info_from_s3, get_file_mime_type
+from digitalhub.utils.s3_utils import get_bucket_name
 
 # Type aliases
 S3Client = Type["botocore.client.S3"]
@@ -46,7 +48,7 @@ class S3Store(Store):
         self.config = config
 
     ##############################
-    # IO methods
+    # I/O methods
     ##############################
 
     def download(
@@ -75,7 +77,7 @@ class S3Store(Store):
         str
             Destination path of the downloaded artifact.
         """
-        client, bucket = self._check_factory()
+        client, bucket = self._check_factory(root)
 
         # Build destination directory
         if dst.suffix == "":
@@ -125,14 +127,18 @@ class S3Store(Store):
                 return str(Path(dst, trees[0]))
         return str(dst)
 
-    def upload(self, src: str | list[str], dst: str | None = None) -> list[tuple[str, str]]:
+    def upload(
+        self,
+        src: str | list[str],
+        dst: str,
+    ) -> list[tuple[str, str]]:
         """
         Upload an artifact to storage.
 
         Parameters
         ----------
-        src : str
-            List of sources.
+        src : str | list[str]
+            Source(s).
         dst : str
             The destination of the artifact on storage.
 
@@ -141,22 +147,12 @@ class S3Store(Store):
         list[tuple[str, str]]
             Returns the list of destination and source paths of the uploaded artifacts.
         """
-
         # Destination handling
+        key = self._get_key(dst)
 
-        # If no destination is provided, build key from source
-        # Otherwise build key from destination
-        if dst is None:
-            raise StoreError(
-                "Destination must be provided. " + "If source is a list of files or a directory, "
-                "destination must be a partition, e.g. 's3://bucket/partition/', ",
-                "otherwise a destination key, e.g. 's3://bucket/key'",
-            )
-        else:
-            dst = self._get_key(dst)
-
-        # Source handling
-        if not isinstance(src, list):
+        # Source handling (files list, dir or single file)
+        src_is_list = isinstance(src, list)
+        if not src_is_list:
             self._check_local_src(src)
             src_is_dir = Path(src).is_dir()
         else:
@@ -167,21 +163,31 @@ class S3Store(Store):
                 src = src[0]
 
         # If source is a directory, destination must be a partition
-        if (src_is_dir or isinstance(src, list)) and not dst.endswith("/"):
-            raise StoreError("Destination must be a partition if the source is a directory or a list of files.")
+        if (src_is_dir or src_is_list) and not dst.endswith("/"):
+            raise StoreError(
+                "If source is a list of files or a directory, "
+                "destination must be a partition, e.g. 's3://bucket/partition/'"
+            )
+
+        # S3 client
+        client, bucket = self._check_factory(dst)
 
         # Directory
         if src_is_dir:
-            return self._upload_dir(src, dst)
+            return self._upload_dir(src, key, client, bucket)
 
         # List of files
-        elif isinstance(src, list):
-            return self._upload_file_list(src, dst)
+        elif src_is_list:
+            return self._upload_file_list(src, key, client, bucket)
 
         # Single file
-        return self._upload_single_file(src, dst)
+        return self._upload_single_file(src, key, client, bucket)
 
-    def upload_fileobject(self, src: BytesIO, dst: str) -> str:
+    def upload_fileobject(
+        self,
+        src: BytesIO,
+        dst: str,
+    ) -> str:
         """
         Upload an BytesIO to S3 based storage.
 
@@ -190,18 +196,23 @@ class S3Store(Store):
         src : BytesIO
             The source object to be persisted.
         dst : str
-            The destination partition for the artifact.
+            The destination path of the artifact.
 
         Returns
         -------
         str
             S3 key of the uploaded artifact.
         """
-        client, bucket = self._check_factory()
-        self._upload_fileobject(src, dst, client, bucket)
-        return f"s3://{bucket}/{dst}"
+        client, bucket = self._check_factory(dst)
+        key = self._get_key(dst)
+        self._upload_fileobject(src, key, client, bucket)
+        return f"s3://{bucket}/{key}"
 
-    def get_file_info(self, paths: list[tuple[str, str]]) -> list[dict]:
+    def get_file_info(
+        self,
+        root: str,
+        paths: list[tuple[str, str]],
+    ) -> list[dict]:
         """
         Method to get file metadata.
 
@@ -215,7 +226,7 @@ class S3Store(Store):
         list[dict]
             Returns files metadata.
         """
-        client, bucket = self._check_factory()
+        client, bucket = self._check_factory(root)
 
         infos = []
         for i in paths:
@@ -266,7 +277,13 @@ class S3Store(Store):
         # Download file
         client.download_file(bucket, key, dst_pth)
 
-    def _upload_dir(self, src: str, dst: str) -> list[tuple[str, str]]:
+    def _upload_dir(
+        self,
+        src: str,
+        dst: str,
+        client: S3Client,
+        bucket: str,
+    ) -> list[tuple[str, str]]:
         """
         Upload directory to storage.
 
@@ -276,33 +293,40 @@ class S3Store(Store):
             List of sources.
         dst : str
             The destination of the artifact on storage.
+        client : S3Client
+            The S3 client object.
+        bucket : str
+            The name of the S3 bucket.
 
         Returns
         -------
         list[tuple[str, str]]
             Returns the list of destination and source paths of the uploaded artifacts.
         """
-        client, bucket = self._check_factory()
-
+        # Get list of files
         src_pth = Path(src)
         files = [i for i in src_pth.rglob("*") if i.is_file()]
+
+        # Build keys
         keys = []
         for i in files:
-            if src_pth.is_absolute():
-                i = i.relative_to(src_pth)
+            i = i.relative_to(src_pth)
             keys.append(f"{dst}{i}")
 
         # Upload files
         paths = []
-        for i in zip(files, keys):
-            f, k = i
+        for f, k in zip(files, keys):
             self._upload_file(f, k, client, bucket)
-            if src_pth.is_absolute():
-                f = f.relative_to(src_pth)
-            paths.append((k, str(f)))
+            paths.append((k, str(f.relative_to(src_pth))))
         return paths
 
-    def _upload_file_list(self, src: list[str], dst: str) -> list[tuple[str, str]]:
+    def _upload_file_list(
+        self,
+        src: list[str],
+        dst: str,
+        client: S3Client,
+        bucket: str,
+    ) -> list[tuple[str, str]]:
         """
         Upload list of files to storage.
 
@@ -312,13 +336,16 @@ class S3Store(Store):
             List of sources.
         dst : str
             The destination of the artifact on storage.
+        client : S3Client
+            The S3 client object.
+        bucket : str
+            The name of the S3 bucket.
 
         Returns
         -------
         list[tuple[str, str]]
             Returns the list of destination and source paths of the uploaded artifacts.
         """
-        client, bucket = self._check_factory()
         files = src
         keys = []
         for i in files:
@@ -328,13 +355,18 @@ class S3Store(Store):
 
         # Upload files
         paths = []
-        for i in zip(files, keys):
-            f, k = i
+        for f, k in zip(files, keys):
             self._upload_file(f, k, client, bucket)
             paths.append((k, Path(f).name))
         return paths
 
-    def _upload_single_file(self, src: str, dst: str) -> str:
+    def _upload_single_file(
+        self,
+        src: str,
+        dst: str,
+        client: S3Client,
+        bucket: str,
+    ) -> str:
         """
         Upload a single file to storage.
 
@@ -344,14 +376,16 @@ class S3Store(Store):
             List of sources.
         dst : str
             The destination of the artifact on storage.
+        client : S3Client
+            The S3 client object.
+        bucket : str
+            The name of the S3 bucket.
 
         Returns
         -------
         str
             Returns the list of destination and source paths of the uploaded artifacts.
         """
-        client, bucket = self._check_factory()
-
         if dst.endswith("/"):
             dst = f"{dst.removeprefix('/')}{Path(src).name}"
 
@@ -361,7 +395,12 @@ class S3Store(Store):
         return [(dst, name)]
 
     @staticmethod
-    def _upload_file(src: str, key: str, client: S3Client, bucket: str) -> None:
+    def _upload_file(
+        src: str,
+        key: str,
+        client: S3Client,
+        bucket: str,
+    ) -> None:
         """
         Upload a file to S3 based storage. The function checks if the
         bucket is accessible.
@@ -388,7 +427,12 @@ class S3Store(Store):
         client.upload_file(Filename=src, Bucket=bucket, Key=key, ExtraArgs=extra_args)
 
     @staticmethod
-    def _upload_fileobject(fileobj: BytesIO, key: str, client: S3Client, bucket: str) -> None:
+    def _upload_fileobject(
+        fileobj: BytesIO,
+        key: str,
+        client: S3Client,
+        bucket: str,
+    ) -> None:
         """
         Upload a fileobject to S3 based storage. The function checks if the bucket is accessible.
 
@@ -410,10 +454,45 @@ class S3Store(Store):
         client.put_object(Bucket=bucket, Key=key, Body=fileobj.getvalue())
 
     ##############################
-    # Private helper methods
+    # Datastore methods
+    ##############################
+
+    def write_df(
+        self,
+        df: Any,
+        dst: str,
+        extension: str | None = None,
+        **kwargs,
+    ) -> str:
+        """
+        Write a dataframe to S3 based storage. Kwargs are passed to df.to_parquet().
+
+        Parameters
+        ----------
+        df : Any
+            The dataframe.
+        dst : str
+            The destination path on S3 based storage.
+        extension : str
+            The extension of the file.
+        **kwargs : dict
+            Keyword arguments.
+
+        Returns
+        -------
+        str
+            The S3 path where the dataframe was saved.
+        """
+        fileobj = BytesIO()
+        reader = get_reader_by_object(df)
+        reader.write_df(df, fileobj, extension=extension, **kwargs)
+        return self.upload_fileobject(fileobj, dst)
+
+    ##############################
+    # Helper methods
     ##############################
 
-    def _get_bucket(self) -> str:
+    def _get_bucket(self, root: str) -> str:
         """
         Get the name of the S3 bucket from the URI.
 
@@ -422,7 +501,7 @@ class S3Store(Store):
         str
             The name of the S3 bucket.
         """
-        return str(self.config.bucket_name)
+        return get_bucket_name(root)
 
     def _get_client(self) -> S3Client:
         """
@@ -440,7 +519,7 @@ class S3Store(Store):
         }
         return boto3.client("s3", **cfg)
 
-    def _check_factory(self) -> tuple[S3Client, str]:
+    def _check_factory(self, root: str) -> tuple[S3Client, str]:
         """
         Check if the S3 bucket is accessible by sending a head_bucket request.
 
@@ -450,7 +529,7 @@ class S3Store(Store):
             A tuple containing the S3 client object and the name of the S3 bucket.
         """
         client = self._get_client()
-        bucket = self._get_bucket()
+        bucket = self._get_bucket(root)
         self._check_access_to_storage(client, bucket)
         return client, bucket