Add scripts to add owner fix information to combined manifest.

eol_realign/scripts/make_licenses.py

@@ -0,0 +1,100 @@
+import pandas as pd
+from pathlib import Path
+import argparse
+import sys
+
+# Output of match_owners.py (combined_manifest.csv) should be fed in.
+
+CC_URL = "https://creativecommons.org/"
+
+
+def get_license_url(license_version):
+    """
+    Function to generate the appropriate Creative Commons URL for a given license.
+    All licenses in the media manifest are "cc-XX", a variation on "publicdomain", or "No known copyright restrictions".
+
+    Parameters:
+    -----------
+    license_version - String. License (eg., "cc-by-nc 3.0").
+
+    Returns:
+    --------
+    license_url - String. Creative Commons URL associated with the license_version.
+
+    """
+    # First check for version number and isolate it
+    if "." in license_version:
+        version = license_version.split(sep="-")[-1]
+        license_name = license_version.split(sep="-" + version)[0]
+    else:
+        # No version specified, so default to latest version (4.0)
+        license_name = license_version
+        version = "4.0"
+    # Check which type of license
+    if license_name[:5] == "cc-by":
+        by_x = license_name.split(sep="cc-")[1]
+        license_url = CC_URL + "licenses/" + by_x + "/" + version
+    elif (license_name[:4] == "cc-0") or ("public" in license_name):
+        license_url = CC_URL + "publicdomain/zero/1.0"
+    else:
+        # "No known copyright restrictions"
+        license_url = None
+    return license_url
+
+
+def main(src_csv, dest_dir):
+    # Check CSV compatibility
+    try:
+        print("Reading CSV")
+        df = pd.read_csv(src_csv, low_memory=False)
+    except Exception as e:
+        sys.exit(e)
+
+    # Check for "License Name" or "license_name" column
+    print("Processing data")
+    df_cols = list(df.columns)
+    if "License Name" not in df_cols:
+        if "license_name" not in df_cols:
+            sys.exit("Source CSV does not have a column labeled License Name or license_name.")
+        license_col = "license_name"
+    license_col = "License Name"
+
+    # Check filepath given by user
+    dest_dir_path = Path(dest_dir)
+    if not dest_dir_path.is_absolute():
+        # Use ToL-EDA as reference folder
+        base_path = Path(__file__).parent.parent.resolve()
+        filepath = base_path / dest_dir_path
+    else:
+        filepath = dest_dir_path
+
+    filepath.mkdir(parents=True, exist_ok=True)
+
+    # Add links for licenses to combined manifest
+    print("Getting URLs for licenses")
+    df["license_link"] = df[license_col].apply(get_license_url)
+
+    # Save license file
+    df.to_csv(str(filepath / "combined-manifest-licenses.csv"), index=False)
+
+    # Print counts of licenses for which URL was not resolved
+    print(
+        "Licenses with no URL: \n",
+        df.loc[df["license_link"].isna(), license_col].value_counts(),
+    )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Add license URLs to combined manifest file"
+    )
+    parser.add_argument("input_file", help="Path to the input CSV file")
+    parser.add_argument(
+        "--output_path",
+        default="data",
+        required=False,
+        help="Path to the folder for output license file",
+    )
+    args = parser.parse_args()
+
+    main(args.input_file, args.output_path)

eol_realign/scripts/match_owners.py

@@ -0,0 +1,122 @@
+import pandas as pd
+from tqdm import tqdm
+from pathlib import Path
+import argparse
+import sys
+
+# This file can be used on predicted-catalog or rarespecies-catalog by changing the CATALOG_PATH.
+# It is intended to just add the extra licensing information to the combined manifest
+# Owner fix file: https://huggingface.co/datasets/imageomics/eol/blob/main/owners_info_fix/media_manifest_missing_licenses_jul26_owners.csv
+MANIFEST_PATH = "../data/combined_manifest_with_checksums.csv"
+OWNER_PATH = "../data/media_manifest_missing_licenses_jul26_owners.csv"
+
+
+def get_owners_titles(manifest, owners):
+    """
+    Function to attach owner names and image titles to manifest entries in combined manifest.
+    Fills empty "Copyright Owner" and "Title" values with "not provided".
+
+    Parameters:
+    -----------
+    manifest - DataFrame composed of manifest entries aligned on MD5s from three different manifests,
+                includes columns "md5_combined_manifest", "combined_id_full_manifest".
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+
+    Returns:
+    --------
+    manifest - Media manifest DataFrame with missing owners resolved.
+    """
+    missing_owners = [
+        comb_id
+        for comb_id in list(
+            manifest.loc[manifest["Copyright Owner"].isna(), "combined_id_full_manifest"]
+        )
+    ]
+
+    for comb_id in tqdm(missing_owners):
+        temp = owners.loc[owners.combined_id_owner == comb_id]
+        copyright_owner = temp["Copyright Owner"].values
+        title = temp.title.values
+        manifest.loc[manifest["combined_id_full_manifest"] == comb_id, "Copyright Owner"] = copyright_owner
+        manifest.loc[manifest["combined_id_full_manifest"] == comb_id, "title"] = title
+
+    # Print counts of licenses for which owner info was not resolved
+    print(
+        "Licenses still missing Copyright Owners: \n",
+        manifest.loc[
+            manifest["Copyright Owner"].isna(), "License Name"
+        ].value_counts(),
+    )
+
+    # Fill null "Copyright Owner" and "Title" values with "not provided"
+    manifest["Copyright Owner"].fillna("not provided", inplace=True)
+    manifest["title"].fillna("not provided", inplace=True)
+
+    return manifest
+
+
+def update_owners(manifest, owners, filepath):
+    """
+    Function to fetch and attach the missing owner and title information to EOL catalog entries and save catalog-media file.
+
+    Parameters:
+    -----------
+    manifest - DataFrame composed of manifest entries aligned on MD5s from three different manifests,
+                includes columns "md5_combined_manifest", "combined_id_full_manifest".
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+    """
+    # Need combined IDs for the owner match file
+    # EOL content & page IDs read in as int64
+    owners["combined_id_owner"] = owners["eol_content_id"].astype(str) + "_" + owners["eol_page_id"].astype(str)
+
+    updated_manifest = get_owners_titles(manifest, owners)
+
+    # Save updated combined manifest file to chosen location
+    updated_manifest.to_csv(filepath, index=False)
+
+
+def main(dest_dir):
+    # Read in CSVs
+    try:
+        # Read in media manifest and owner fix CSVs with EOL content and page IDs as type "int64".
+        print("Reading combined media manifest CSV")
+        manifest = pd.read_csv(
+            MANIFEST_PATH,
+            low_memory=False,
+        )
+        print("Reading owner fix CSV")
+        owners = pd.read_csv(
+            OWNER_PATH,
+            dtype={"EOL content ID": "int64", "EOL page ID": "int64"},
+            low_memory=False,
+        )
+    except Exception as e:
+        sys.exit(e)
+
+    # Check filepath given by user
+    dest_dir_path = Path(dest_dir)
+    if not dest_dir_path.is_absolute():
+        # Use ToL-EDA as reference folder
+        base_path = Path(__file__).parent.parent.resolve()
+        filepath = base_path / dest_dir_path
+    else:
+        filepath = dest_dir_path
+
+    filepath.mkdir(parents=True, exist_ok=True)
+
+    # Make and save updated manifest to chosen filepath
+    update_owners(manifest, owners, str(filepath / "combined_manifest.csv"))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Attach missing owner info to combined manifest")
+
+    parser.add_argument(
+        "--output_path",
+        default="data",
+        required=False,
+        help="Path to the folder for output combined manifest file",
+    )
+    args = parser.parse_args()
+
+    main(args.output_path)