start improving dbreaders

cellpy/readers/core.py

@@ -118,6 +118,30 @@ def pickle_protocol(level):
 class BaseDbReader(metaclass=abc.ABCMeta):
     """Base class for database readers."""
 
+    @abc.abstractmethod
+    def from_batch(
+        self, batch_name: str|None=None, 
+        include_key: bool=False, 
+        include_individual_arguments: bool=False,
+        **kwargs: Any
+        ) -> dict:
+        """Get a dictionary with the data from a batch for the journal.
+
+        Args:
+            batch: name of the batch.
+            include_key: include the key (the cell ids).
+            include_individual_arguments: include the individual arguments.
+
+        Returns:
+            dict: dictionary with the data.
+        """
+        pass
+
+
+
+class BaseSimpleDbReader(metaclass=abc.ABCMeta):
+    """Base class for database readers."""
+
     @abc.abstractmethod
     def select_batch(self, batch: str) -> List[int]:
         pass

cellpy/readers/dbreader.py

@@ -35,7 +35,7 @@ def __repr__(self):
         return f"<DbCols: {self.__dict__}>"
 
 
-class Reader(core.BaseDbReader):
+class Reader(core.BaseSimpleDbReader):
     def __init__(
         self,
         db_file=None,

cellpy/readers/json_dbreader.py

@@ -0,0 +1,42 @@
+from typing import Any
+from cellpy.readers.core import BaseDbReader
+import json
+
+
+class BaseJSONReader(BaseDbReader):
+    def __init__(self, json_file: str):
+        self.json_file = json_file
+        self.data = self.load_data()
+
+    def _load_raw_data(self):
+        with open(self.json_file, "r") as f:
+            return json.load(f)
+
+    def load_data(self):
+        return pd.read_json(self.json_file)
+
+
+class BattBaseJSONReader(BaseJSONReader):
+    _version = "1.0.0"
+
+    def from_batch(
+        self,
+        batch_name: str | None = None,
+        project_name: str | None = None,
+        include_key: bool = False,
+        include_individual_arguments: bool = False,
+    ) -> dict:
+        raise NotImplementedError("This method is not implemented for this reader")
+
+
+if __name__ == "__main__":
+    from pathlib import Path
+    import pandas as pd
+
+    pd.set_option("display.max_columns", None)
+
+    local_dir = Path(__file__).parent.parent.parent / "local"
+    json_file = local_dir / "cellpy_journal_table.json"
+    print(json_file.exists())
+    reader = BattBaseJSONReader(json_file)
+    print(reader.from_batch())

cellpy/readers/sql_dbreader.py

@@ -24,7 +24,7 @@
     BATCH_ATTRS_TO_IMPORT_FROM_EXCEL_SQLITE,
     get_headers_journal,
 )
-from cellpy.readers.core import BaseDbReader
+from cellpy.readers.core import BaseSimpleDbReader
 
 # ----------------- USED WHEN CONVERTING FROM EXCEL -----------------
 DB_FILE_EXCEL = prms.Paths.db_filename
@@ -158,7 +158,7 @@ def __str__(self) -> str:
         return f"batch: '{self.name}' (#{self.pk})"
 
 
-class SQLReader(BaseDbReader):
+class SQLReader(BaseSimpleDbReader):
     """A custom database reader for the batch utility in cellpy."""
 
     def __init__(self, db_connection: str = None, batch: str = None, **kwargs) -> None:

cellpy/utils/batch_tools/engines.py

@@ -11,6 +11,7 @@
 import pandas as pd
 
 from cellpy import dbreader
+from cellpy.readers import json_dbreader
 from cellpy.parameters.internal_settings import get_headers_journal, get_headers_summary
 from cellpy.utils.batch_tools import batch_helpers as helper
 
@@ -191,6 +192,15 @@ def simple_db_engine(
         reader = dbreader.Reader()
         logging.debug("No reader provided. Creating one myself.")
 
+    if isinstance(reader, str):
+        match reader:
+            case "simple_excel_reader":
+                reader = dbreader.Reader()
+            case "batbase_json_reader":
+                reader = json_dbreader.BatbaseJSONReader()
+            case _:
+                raise ValueError(f"Invalid reader: {reader}")
+
     if cell_ids is None:
         logging.debug("cell_ids is None")
         pages_dict = reader.from_batch(