palimpzest 0.7.21__py3-none-any.whl → 0.8.1__py3-none-any.whl

palimpzest/core/data/{datareaders.py → iter_dataset.py}

@@ -4,69 +4,62 @@ import base64
 import os
 from abc import ABC, abstractmethod
 from io import BytesIO
+from pathlib import Path
 
 import pandas as pd
 from bs4 import BeautifulSoup
+from pydantic import BaseModel
 
 from palimpzest import constants
+from palimpzest.core.data import dataset
 from palimpzest.core.lib.schemas import (
+    AudioFile,
     DefaultSchema,
-    File,
     ImageFile,
     PDFFile,
-    Schema,
     TextFile,
     WebPage,
     XLSFile,
+    create_schema_from_df,
+    create_schema_from_fields,
 )
+from palimpzest.query.operators.logical import BaseScan
 from palimpzest.tools.pdfparser import get_text_from_pdf
 
 
-# First level of abstraction
-class DataReader(ABC):
+####################
+### BASE CLASSES ###
+####################
+class IterDataset(dataset.Dataset, ABC):
     """
-    The `DataReader` is a base class for which may be used to generate data that
-    is processed by PZ.
+    The `IterDataset` is an abstract base class for root `Datasets` whose data is accessed
+    via iteration. Classes which inherit from this class must implement two methods:
 
-    Subclasses of the (abstract) `DataReader` class must implement two methods:
-
-    - `__len__()`: which returns the number of elements in the data source
+    - `__len__()`: which returns the number of elements in the dataset
     - `__getitem__(idx: int)`: which takes in an `idx` and returns the element at that index
     """
 
-    def __init__(self, schema: type[Schema] | list[dict]) -> None:
+    def __init__(self, id: str, schema: type[BaseModel] | list[dict]) -> None:
         """
-            Constructor for the `DataReader` class.
+            Constructor for the `IterDataset` class.
 
             Args:
-                schema (Schema | list[dict]): The output schema of the records returned by the DataReader
+                id (str): a string identifier for the `Dataset`
+                schema (BaseModel | list[dict]): The output schema of the records returned by the `Dataset`
         """
-        # NOTE: _schema attribute currently has to match attribute name in Dataset
-        self._schema = Schema.from_json(schema) if isinstance(schema, list) else schema
-
-    def __eq__(self, __value: object) -> bool:
-        return self.__dict__ == __value.__dict__
-
-    def __str__(self) -> str:
-        return f"{self.__class__.__name__}(schema={self.schema})"
-
-    @property
-    def schema(self) -> Schema:
-        return self._schema
-
-    # NOTE: currently used by optimizer to compute node id for DataReaders
-    def serialize(self) -> dict:
-        return {"schema": self._schema.json_schema()}
+        # compute Schema and call parent constructor
+        schema = create_schema_from_fields(schema) if isinstance(schema, list) else schema
+        super().__init__(sources=None, operator=BaseScan(datasource=self, output_schema=schema), schema=schema, id=id)
 
     @abstractmethod
     def __len__(self) -> int:
-        """Returns the number of items in the data reader."""
+        """Returns the number of items in the `Dataset`."""
         pass
 
     @abstractmethod
     def __getitem__(self, idx: int) -> dict:
         """
-        Returns a single item from the data reader at the given index.
+        Returns a single item from the `Dataset` at the given index.
 
         Args:
             idx (int): The index of the item to return
@@ -74,7 +67,7 @@ class DataReader(ABC):
         Returns:
             dict: A dictionary representing the item at the given index. The dictionary
                   keys (i.e. fields) should match the fields specified in the schema of the
-                  data source, and the values should be the values associated with those fields.
+                  dataset, and the values should be the values associated with those fields.
 
                     # Example return value
                     {"field1": value1, "field2": value2, ...}
@@ -83,111 +76,103 @@ class DataReader(ABC):
         pass
 
 
-# Second level of abstraction
-class DirectoryReader(DataReader):
+class BaseFileDataset(IterDataset):
     """
-    DirectoryReader returns a dictionary for each file in a directory. Each dictionary contains the filename and
-    contents of a single file in the directory.
+    BaseFileDataset is the base class for multiple `IterDatasets` which iterate over
+    different types of files.
     """
 
-    def __init__(self, path: str, schema: Schema) -> None:
+    def __init__(self, path: str, **kwargs) -> None:
         """
-        Constructor for the `DirectoryReader` class.
+        Constructor for the `BaseFileDataset` class.
 
         Args:
-            path (str): The path to the directory
-            schema (Schema): The output schema of the data source
+            path (str): The path to the file
+            kwargs (dict): Keyword arguments containing the `Dataset's` id and file-specific `Schema`
         """
-        assert os.path.isdir(path), f"Path {path} is not a directory"
+        # check that path is a valid file or directory
+        assert os.path.isfile(path) or os.path.isdir(path), f"Path {path} is not a file nor a directory"
 
-        self.filepaths = [
-            os.path.join(path, filename)
-            for filename in sorted(os.listdir(path))
-            if os.path.isfile(os.path.join(path, filename))
-        ]
-        self.path = path
-        super().__init__(schema)
+        # get list of filepaths
+        self.filepaths = []
+        if os.path.isfile(path):
+            self.filepaths = [path]
+        else:
+            self.filepaths = [
+                os.path.join(path, filename)
+                for filename in sorted(os.listdir(path))
+                if os.path.isfile(os.path.join(path, filename))
+            ]
 
-    def serialize(self) -> dict:
-        return {
-            "schema": self.schema.json_schema(),
-            "path": self.path,
-            "source_type": "directory",
-        }
+        # call parent constructor to set id, operator, and schema
+        super().__init__(**kwargs)
 
     def __len__(self) -> int:
         return len(self.filepaths)
 
 
-class FileReader(DataReader):
-    """FileReader returns a single dictionary with the filename and contents of a local file (in bytes)."""
+class BaseFileDirectoryDataset(IterDataset):
+    """
+    BaseFileDirectoryDataset is the base class for multiple `IterDatasets` which iterate over
+    different types of files. This class walks the entire directory tree rooted at `path`.
+    """
 
-    def __init__(self, path: str) -> None:
+    def __init__(self, path: str, **kwargs) -> None:
         """
-        Constructor for the `FileReader` class. The `schema` is set to the default `File` schema.
+        Constructor for the `BaseFileDataset` class.
 
         Args:
             path (str): The path to the file
-        """
-        super().__init__(File)
-        self.filepath = path
-
-    def serialize(self) -> dict:
-        return {
-            "schema": self.schema.json_schema(),
-            "path": self.filepath,
-            "source_type": "file",
-        }
+            kwargs (dict): Keyword arguments containing the `Dataset's` id and file-specific `Schema`
+        """
+        # check that path is a valid file or directory
+        assert os.path.isfile(path) or os.path.isdir(path), f"Path {path} is not a file nor a directory"
+
+        # get list of filepaths
+        self.filepaths = []
+        if os.path.isfile(path):
+            self.filepaths = [path]
+        else:
+            self.filepaths = []
+            for root, _, files in os.walk(path):
+                for file in files:
+                    fp = os.path.join(root, file)
+                    self.filepaths.append(fp)
+            self.filepaths = sorted(self.filepaths)
+
+        # call parent constructor to set id, operator, and schema
+        super().__init__(**kwargs)
 
     def __len__(self) -> int:
-        return 1
-
-    def __getitem__(self, idx: int) -> dict:
-        """
-        Returns a dictionary with the filename and contents of the file.
-
-        Args:
-            idx (int): The index of the item to return. This argument is ignored.
-        
-        Returns:
-            dict: A dictionary with the filename and contents of the file.
-
-            .. code-block:: python
-
-                {
-                    "filename": "path/to/file.txt",
-                    "contents": b"file contents here",
-                }
-        """
-        filename = self.filepath
-        with open(self.filepath, "rb") as f:
-            contents = f.read()
-
-        return {"filename": filename, "contents": contents}
-
+        return len(self.filepaths)
 
-class MemoryReader(DataReader):
+########################
+### CONCRETE CLASSES ###
+########################
+class MemoryDataset(IterDataset):
     """
-    MemoryReader returns one or more dictionaries that reflect the contents of an in-memory Python object `vals`.
+    MemoryDataset returns one or more dictionaries that reflect the contents of an in-memory Python object `vals`.
     If `vals` is not a pd.DataFrame, then the dictionary returned by `__getitem__()` has a single field called "value".
     Otherwise, the dictionary contains the key-value mapping from columns to values for the `idx` row in the dataframe.
 
     TODO(gerardo): Add support for other types of in-memory data structures (he has some code for subclassing
-        MemoryReader on his branch)
+        MemoryDataset on his branch)
     """
 
-    def __init__(self, vals: list | pd.DataFrame) -> None:
+    def __init__(self, id: str, vals: list | pd.DataFrame, schema: type[BaseModel] | list[dict] | None = None) -> None:
         """
-        Constructor for the `MemoryReader` class. The `schema` is set to the default `DefaultSchema` schema.
+        Constructor for the `MemoryDataset` class. The `schema` is set to the default `DefaultSchema` schema.
         If `vals` is a pd.DataFrame, then the schema is set to the schema inferred from the DataFrame.
 
         Args:
-            vals (Any): The in-memory object to use as the data source
+            id (str): a string identifier for the `Dataset`
+            vals (Any): The in-memory data to iterate over
         """
         # if list[dict] --> convert to pd.DataFrame first
         self.vals = pd.DataFrame(vals) if isinstance(vals, list) and all([isinstance(item, dict) for item in vals]) else vals
-        schema = Schema.from_df(self.vals) if isinstance(self.vals, pd.DataFrame) else DefaultSchema
-        super().__init__(schema)
+        if schema is None:
+            schema = create_schema_from_df(self.vals) if isinstance(self.vals, pd.DataFrame) else DefaultSchema
+        super().__init__(id=id, schema=schema)
 
     def __len__(self) -> int:
         return len(self.vals)
@@ -228,20 +213,20 @@ class MemoryReader(DataReader):
         return item
 
 
-# Third level of abstraction
-class HTMLFileDirectoryReader(DirectoryReader):
+class HTMLFileDataset(BaseFileDataset):
     """
-    HTMLFileDirectoryReader returns a dictionary for each HTML file in a directory. Each dictionary contains the
+    HTMLFileDataset returns a dictionary for each HTML file in a directory. Each dictionary contains the
     filename, raw HTML content, and parsed content of a single HTML file in the directory.
     """
-    def __init__(self, path: str) -> None:
+    def __init__(self, id: str, path: str) -> None:
         """
-        Constructor for the `HTMLFileDirectoryReader` class. The `schema` is set to the `WebPage` schema.
+        Constructor for the `HTMLFileDataset` class. The `schema` is set to the `WebPage` schema.
 
         Args:
+            id (str): a string identifier for the `Dataset`
             path (str): The path to the directory
         """
-        super().__init__(path=path, schema=WebPage)
+        super().__init__(path=path, id=id, schema=WebPage)
         assert all([filename.endswith(tuple(constants.HTML_EXTENSIONS)) for filename in self.filepaths])
 
     def _html_to_text_with_links(self, html: str) -> str:
@@ -296,19 +281,20 @@ class HTMLFileDirectoryReader(DirectoryReader):
         return item
 
 
-class ImageFileDirectoryReader(DirectoryReader):
+class ImageFileDataset(BaseFileDataset):
     """
-    ImageFileDirectoryReader returns a dictionary for each image file in a directory. Each dictionary contains the
+    ImageFileDataset returns a dictionary for each image file in a directory. Each dictionary contains the
     filename and the base64 encoded bytes content of a single image file in the directory.
     """
-    def __init__(self, path: str) -> None:
+    def __init__(self, id: str, path: str) -> None:
         """
-        Constructor for the `ImageFileDirectoryReader` class. The `schema` is set to the `ImageFile` schema.
+        Constructor for the `ImageFileDataset` class. The `schema` is set to the `ImageFile` schema.
 
         Args:
+            id (str): a string identifier for the `Dataset`
             path (str): The path to the directory
         """
-        super().__init__(path=path, schema=ImageFile)
+        super().__init__(path=path, id=id, schema=ImageFile)
         assert all([filename.endswith(tuple(constants.IMAGE_EXTENSIONS)) for filename in self.filepaths])
 
     def __getitem__(self, idx: int) -> dict:
@@ -332,33 +318,35 @@ class ImageFileDirectoryReader(DirectoryReader):
         filepath = self.filepaths[idx]
         filename = os.path.basename(filepath)
         with open(filepath, "rb") as f:
-            contents = base64.b64encode(f.read())
+            contents = base64.b64encode(f.read()).decode("utf-8")
 
         return {"filename": filename, "contents": contents}
 
 
-class PDFFileDirectoryReader(DirectoryReader):
+class PDFFileDataset(BaseFileDataset):
     """
-    PDFFileDirectoryReader returns a dictionary for each PDF file in a directory. Each dictionary contains the
+    PDFFileDataset returns a dictionary for each PDF file in a directory. Each dictionary contains the
     filename, raw PDF content, and parsed text content of a single PDF file in the directory.
 
     This class also uses one of a predefined set of PDF processors to extract text content from the PDF files.
     """
     def __init__(
         self,
+        id: str,
         path: str,
         pdfprocessor: str = "pypdf",
         file_cache_dir: str = "/tmp",
     ) -> None:
         """
-        Constructor for the `PDFFileDirectoryReader` class. The `schema` is set to the `PDFFile` schema.
+        Constructor for the `PDFFileDataset` class. The `schema` is set to the `PDFFile` schema.
 
         Args:
+            id (str): a string identifier for the `Dataset`
             path (str): The path to the directory
             pdfprocessor (str): The PDF processor to use for extracting text content from the PDF files
             file_cache_dir (str): The directory to store the temporary files generated during PDF processing
         """
-        super().__init__(path=path, schema=PDFFile)
+        super().__init__(path=path, id=id, schema=PDFFile)
         assert all([filename.endswith(tuple(constants.PDF_EXTENSIONS)) for filename in self.filepaths])
         self.pdfprocessor = pdfprocessor
         self.file_cache_dir = file_cache_dir
@@ -394,19 +382,20 @@ class PDFFileDirectoryReader(DirectoryReader):
         return {"filename": pdf_filename, "contents": pdf_bytes, "text_contents": text_content}
 
 
-class TextFileDirectoryReader(DirectoryReader):
+class TextFileDataset(BaseFileDataset):
     """
-    TextFileDirectoryReader returns a dictionary for each text file in a directory. Each dictionary contains the
+    TextFileDataset returns a dictionary for each text file in a directory. Each dictionary contains the
     filename and contents of a single text file in the directory.
     """
-    def __init__(self, path: str) -> None:
+    def __init__(self, id: str, path: str) -> None:
         """
-        Constructor for the `TextFileDirectoryReader` class. The `schema` is set to the `TextFile` schema.
+        Constructor for the `TextFileDataset` class. The `schema` is set to the `TextFile` schema.
 
         Args:
+            id (str): a string identifier for the `Dataset`
             path (str): The path to the directory
         """
-        super().__init__(path=path, schema=TextFile)
+        super().__init__(path=path, id=id, schema=TextFile)
 
     def __getitem__(self, idx: int) -> dict:
         """
@@ -433,16 +422,16 @@ class TextFileDirectoryReader(DirectoryReader):
         return {"filename": filename, "contents": contents}
 
 
-class XLSFileDirectoryReader(DirectoryReader):
+class XLSFileDataset(BaseFileDataset):
     """
-    XLSFileDirectoryReader returns a dictionary for each XLS file in a directory. Each dictionary contains the
+    XLSFileDataset returns a dictionary for each XLS file in a directory. Each dictionary contains the
     filename, contents, sheet names, and the number of sheets for a single XLS file in the directory.
     """
-    def __init__(self, path: str) -> None:
+    def __init__(self, id: str, path: str) -> None:
         """
-        Constructor for the `XLSFileDirectoryReader` class. The `schema` is set to the `XLSFile` schema.
+        Constructor for the `XLSFileDataset` class. The `schema` is set to the `XLSFile` schema.
         """
-        super().__init__(path=path, schema=XLSFile)
+        super().__init__(path=path, id=id, schema=XLSFile)
         assert all([filename.endswith(tuple(constants.XLS_EXTENSIONS)) for filename in self.filepaths])
 
     def __getitem__(self, idx: int) -> dict:
@@ -478,3 +467,90 @@ class XLSFileDirectoryReader(DirectoryReader):
             "sheet_names": xls.sheet_names,
             "number_sheets": len(xls.sheet_names),
         }
+
+
+class AudioFileDataset(BaseFileDirectoryDataset):
+    """
+    AudioFileDataset returns a dictionary for each audio file in a directory. Each dictionary contains the
+    filename and the base64 encoded bytes content of a single audio file in the directory.
+    """
+    def __init__(self, id: str, path: str) -> None:
+        """
+        Constructor for the `AudioFileDataset` class. The `schema` is set to the `AudioFile` schema.
+
+        Args:
+            id (str): a string identifier for the `Dataset`
+            path (str): The path to the directory
+        """
+        super().__init__(path=path, id=id, schema=AudioFile)
+        assert all([filename.endswith(tuple(constants.AUDIO_EXTENSIONS)) for filename in self.filepaths])
+
+    def __getitem__(self, idx: int) -> dict:
+        """
+        Returns a dictionary with the filename and base64 encoded bytes content of the audio file at the
+        specified `idx`.
+
+        Args:
+            idx (int): The index of the item to return
+
+        Returns:
+            dict: A dictionary with the filename and base64 encoded bytes content of the audio file.
+
+            .. code-block:: python
+
+                {
+                    "filename": "audio.wav",
+                    "contents": b"base64 encoded audio content here",
+                }
+        """
+        filepath = self.filepaths[idx]
+        filename = os.path.basename(filepath)
+        with open(filepath, "rb") as f:
+            contents = base64.b64encode(f.read()).decode("utf-8")
+
+        return {"filename": filename, "contents": contents}
+
+
+def get_local_source(id: str, path: str | Path, **kwargs) -> dataset.Dataset:
+    """Return a `Dataset` for a local file or directory."""
+    if os.path.isfile(path):
+        return TextFileDataset(id, path)
+
+    elif os.path.isdir(path):
+        if all([f.endswith(tuple(constants.IMAGE_EXTENSIONS)) for f in os.listdir(path)]):
+            return ImageFileDataset(id, path)
+
+        elif all([f.endswith(tuple(constants.PDF_EXTENSIONS)) for f in os.listdir(path)]):
+            pdfprocessor = kwargs.get("pdfprocessor", constants.DEFAULT_PDF_PROCESSOR)
+            file_cache_dir = kwargs.get("file_cache_dir", "/tmp")
+            return PDFFileDataset(
+                id=id, path=path, pdfprocessor=pdfprocessor, file_cache_dir=file_cache_dir
+            )
+
+        elif all([f.endswith(tuple(constants.XLS_EXTENSIONS)) for f in os.listdir(path)]):
+            return XLSFileDataset(id, path)
+
+        elif all([f.endswith(tuple(constants.HTML_EXTENSIONS)) for f in os.listdir(path)]):
+            return HTMLFileDataset(id, path)
+
+        else:
+            return TextFileDataset(id, path)
+    else:
+        raise ValueError(f"Path {path} is invalid. Does not point to a file or directory.")
+
+
+def resolve_datasource(id: str, source: str | Path | list | pd.DataFrame, **kwargs) -> dataset.Dataset:
+    """
+    This helper function returns a `Dataset` object based on the `source` type.
+    The returned `Dataset` object is guaranteed to have a schema.
+    """
+    if isinstance(source, (str, Path)):
+        source = get_local_source(id, source, **kwargs)
+
+    elif isinstance(source, (list, pd.DataFrame)):
+        source = MemoryDataset(id=id, vals=source)
+
+    else:
+        raise ValueError(f"Invalid source type: {type(source)}, We only support str, Path, list[dict], and pd.DataFrame")
+
+    return source

palimpzest/core/elements/groupbysig.py

@@ -2,10 +2,12 @@ from __future__ import annotations
 
 from typing import Any
 
-from palimpzest.core.lib.fields import Field
-from palimpzest.core.lib.schemas import OperatorDerivedSchema, Schema
+from pydantic import BaseModel
 
+from palimpzest.core.lib.schemas import create_schema_from_fields
 
+
+# TODO: need to rethink how group bys work
 # signature for a group by aggregate that applies
 # group and aggregation to an input tuple
 class GroupBySig:
@@ -14,12 +16,12 @@ class GroupBySig:
         self.agg_funcs = agg_funcs
         self.agg_fields = agg_fields
 
-    def validate_schema(self, input_schema: Schema) -> tuple[bool, str | None]:
+    def validate_schema(self, input_schema: BaseModel) -> tuple[bool, str | None]:
         for f in self.group_by_fields:
-            if not hasattr(input_schema, f):
+            if f not in input_schema.model_fields:
                 return (False, "Supplied schema has no field " + f)
         for f in self.agg_fields:
-            if not hasattr(input_schema, f):
+            if f not in input_schema.model_fields:
                 return (False, "Supplied schema has no field " + f)
         return (True, None)
 
@@ -48,16 +50,17 @@ class GroupBySig:
             ops.append(self.agg_funcs[i] + "(" + self.agg_fields[i] + ")")
         return ops
 
-    def output_schema(self) -> type[OperatorDerivedSchema]:
+    def output_schema(self) -> type[BaseModel]:
         # the output class varies depending on the group by, so here
         # we dynamically construct this output
-        schema = type("CustomGroupBy", (OperatorDerivedSchema,), {})
-
+        fields = []
         for g in self.group_by_fields:
-            f = Field(desc=g)
-            setattr(schema, g, f)
+            f = {"name": g, "type": Any, "desc": f"Group by field: {g}"}
+            fields.append(f)
+
         ops = self.get_agg_field_names()
         for op in ops:
-            f = Field(desc=op)
-            setattr(schema, op, f)
-        return schema
+            f = {"name": op, "type": Any, "desc": f"Aggregate field: {op}"}
+            fields.append(f)
+
+        return create_schema_from_fields(fields)