Merge pull request #1629 from pyiron/read_csv

Inspect csv file without uncompressing `.tar.gz`

pyiron_base/project/archiving/import_archive.py

@@ -1,3 +1,4 @@
+import io
 import os
 import posixpath
 import tarfile
@@ -130,3 +131,29 @@ def get_dataframe(origin_path: str, csv_file_name: str = "export.csv") -> "DataF
         if csv_file_name in files:
             return pandas.read_csv(os.path.join(root, csv_file_name), index_col=0)
     raise FileNotFoundError(f"File: {csv_file_name} was not found.")
+
+
+def inspect_csv(tar_path: str, csv_file: str = "export.csv"):
+    """
+    Inspect the csv file inside a tar archive.
+
+    Args:
+        tar_path (str): Path to the tar archive.
+        csv_file (str): Name of the csv file.
+
+    Returns:
+        pandas.DataFrame: Job table.
+    """
+    with tarfile.open(tar_path, mode="r:gz") as tar:
+        for member in tar.getmembers():
+            # Check if the member is a file and ends with the desired csv file name
+            if member.isfile() and member.name.endswith(f"/{csv_file}"):
+                # Extract the file object
+                extracted_file = tar.extractfile(member)
+
+                if extracted_file:
+                    # Read the file content
+                    return pandas.read_csv(
+                        io.StringIO(extracted_file.read().decode("utf-8")), index_col=0
+                    )
+        raise FileNotFoundError(f"File: {csv_file} in {tar_path} was not found.")

pyiron_base/project/generic.py

@@ -1981,6 +1981,21 @@ def pack(
             df=export_archive.export_database(self.job_table()),
         )
 
+    def unpack_csv(self, tar_path: str):
+        """
+        Import job table from a csv file and copy the content of a project
+        directory from a given path.
+
+        Args:
+            tar_path (str): the relative path of a directory from which the
+                project directory is copied.
+            csv_file (str): the name of the csv file.
+
+        Returns:
+            pandas.DataFrame: job table
+        """
+        return import_archive.inspect_csv(tar_path=tar_path, csv_file="export.csv")
+
     def unpack(self, origin_path, **kwargs):
         """
         by this function, job table is imported from a given csv file,

tests/unit/archiving/test_import.py

@@ -1,7 +1,7 @@
 import os
 import unittest
 from pyiron_base import Project
-from pandas._testing import assert_frame_equal
+import pandas as pd
 from filecmp import dircmp
 from shutil import rmtree, copytree
 import tarfile
@@ -47,6 +47,11 @@ def tearDown(self):
         super().tearDown()
         self.imp_pr.remove_jobs(recursive=True, silently=True)
 
+    def test_inspect(self):
+        df = self.pr.unpack_csv(self.arch_dir_comp + ".tar.gz")
+        self.assertIsInstance(df, pd.DataFrame)
+        self.assertEqual(len(df), 1)
+
     def test_import_csv(self):
         df_original = self.pr.job_table()
         df_import = self.imp_pr.job_table()
@@ -58,7 +63,7 @@ def test_import_csv(self):
         df_original.drop("id", inplace=True, axis=1)
         df_import["hamversion"] = float(df_import["hamversion"])
         df_original["hamversion"] = float(df_original["hamversion"])
-        assert_frame_equal(df_original, df_import)
+        pd._testing.assert_frame_equal(df_original, df_import)
 
     def test_import_compressed(self):
         path_original = self.pr.path
@@ -192,6 +197,7 @@ def test_import_old_tar(self):
             dirs_exist_ok=True,
         )
         pr = Project("old_tar")
+        self.assertRaises(FileNotFoundError, pr.unpack_csv, "test_pack.tar.gz")
         pr.unpack(origin_path="test_pack.tar.gz")
         job = pr.load("toy")
         self.assertEqual(job.job_name, "toy")