Add script to match EOL citation data and missing owners to catalog.

scripts/match_owners.py

@@ -0,0 +1,215 @@
+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.
+CATALOG_PATH = "data/catalog.csv"
+LICENSE_COLS = ["treeoflife_id", "eol_content_id", "eol_page_id"]
+EXPECTED_COLS = [
+    "EOL content ID",
+    "EOL page ID",
+    "Medium Source URL",
+    "EOL Full-Size Copy URL",
+    "License Name",
+    "Copyright Owner",
+]
+
+
+def merge_dfs(df, media):
+    """
+    Function to process and merge the ToL catalog with the media manifest.
+
+    Parameters:
+    -----------
+    df - DataFrame composed of catalog entries, includes columns "treeoflife_id", "eol_content_id", and "eol_page_id".
+    media - DataFrame of EOL media manifest with EXPECTED_COLS.
+
+    Returns:
+    --------
+    cat_media - DataFrame with media manifest information attached to treeoflife_ids in catalog.
+
+    """
+    # Reduce to just EOL entries
+    eol_df = df.loc[df["eol_content_id"].notna()].copy()
+    eol_df = eol_df[LICENSE_COLS]
+
+    # Set content and page ID types to int64
+    eol_df = eol_df.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+    # Rename media versions to match (already int64)
+    media.rename(
+        columns={"EOL content ID": "eol_content_id", "EOL page ID": "eol_page_id"},
+        inplace=True,
+    )
+
+    # Merge dataframes on EOL content and page IDs
+    cat_media = pd.merge(
+        eol_df, media, how="inner", left_on=LICENSE_COLS[1:], right_on=LICENSE_COLS[1:]
+    )
+
+    return cat_media
+
+
+def merge_owners(cat_media, owners):
+    """
+    Function to process and merge the owner fix DataFrame with cat_media for owner matching.
+
+    Parameters:
+    -----------
+    cat_media - DataFrame with media manifest information attached to treeoflife_ids in catalog.
+    owners - DataFrame of media manifest entries that had missing owners, updated with their information.
+
+    Returns:
+    --------
+    cat_owners - DataFrame with media manifest information from missing owners attached to treeoflife_ids.
+
+    """
+    # Rename owner EOL content and page IDs to match cat_media (already int64)
+    owners.rename(
+        columns={"EOL content ID": "eol_content_id", "EOL page ID": "eol_page_id"},
+        inplace=True,
+    )
+    # Set columns to merge on
+    merge_cols = list(owners.columns)[:5]
+    cat_owners = pd.merge(
+        cat_media, owners, how="inner", left_on=merge_cols, right_on=merge_cols
+    )
+
+    return cat_owners
+
+
+def get_owners_titles(cat_media, cat_owners):
+    """
+    Function to attach owner names and image titles to catalog entries in cat_media.
+    Fills empty "Copyright Owner" and "Title" values with "not provided".
+
+    Parameters:
+    -----------
+    cat_media - DataFrame with media manifest information attached to treeoflife_ids in catalog.
+    cat_owners - DataFrame with media manifest information from missing owners attached to treeoflife_ids.
+
+    Returns:
+    --------
+    cat_media - DataFrame with media manifest information attached to treeoflife_ids in catalog with missing owners resolved.
+    """
+    missing_owners = [
+        tol_id
+        for tol_id in list(
+            cat_media.loc[cat_media["Copyright Owner"].isna(), "treeoflife_id"]
+        )
+    ]
+    for tol_id in tqdm(missing_owners):
+        temp = cat_owners.loc[cat_owners.treeoflife_id == tol_id]
+        copyright_owner = temp["Copyright Owner_y"].values
+        title = temp.title.values
+        cat_media.loc[
+            cat_media["treeoflife_id"] == tol_id, "Copyright Owner"
+        ] = copyright_owner
+        cat_media.loc[cat_media["treeoflife_id"] == tol_id, "title"] = title
+
+    # Print counts of licenses for which owner info was not resolved
+    print(
+        "Licenses still missing Copyright Owners: \n",
+        cat_media.loc[
+            cat_media["Copyright Owner"].isna(), "License Name"
+        ].value_counts(),
+    )
+
+    # Fill null "Copyright Owner" and "Title" values with "not provided"
+    cat_media["Copyright Owner"].fillna("not provided", inplace=True)
+    cat_media["title"].fillna("not provided", inplace=True)
+
+    return cat_media
+
+
+def update_owners(df, media, owners, filepath):
+    """
+    Function to fetch and attach the missing owner and title information to EOL catalog entries and save catalog-media file.
+
+    Parameters:
+    -----------
+    df - DataFrame composed of catalog entries.
+    media - DataFrame of EOL media manifest.
+    owners - DataFrame of media manifest entries that had missing owners, updated with their information.
+    """
+    cat_media = merge_dfs(df, media)
+    cat_owners = merge_owners(cat_media, owners)
+    cat_media = get_owners_titles(cat_media, cat_owners)
+
+    # Save updated catalog media file to chosen location
+    cat_media.to_csv(filepath, index=False)
+
+
+def main(media_csv, owner_csv, dest_dir):
+    # Check CSV compatibility
+    try:
+        print("Reading catalog CSV")
+        df = pd.read_csv(CATALOG_PATH, low_memory=False)
+
+        # Read in media manifest and owner fix CSVs with EOL content and page IDs as type "int64".
+        print("Reading media manifest CSV")
+        media = pd.read_csv(
+            media_csv,
+            dtype={"EOL content ID": "int64", "EOL page ID": "int64"},
+            low_memory=False,
+        )
+        print("Reading owner fix CSV")
+        owners = pd.read_csv(
+            owner_csv,
+            dtype={"EOL content ID": "int64", "EOL page ID": "int64"},
+            low_memory=False,
+        )
+    except Exception as e:
+        sys.exit(e)
+
+    # Check for columns
+    print("Processing data")
+    missing_media_cols = []
+    missing_owner_cols = []
+    for col in EXPECTED_COLS:
+        if col not in list(media.columns):
+            missing_media_cols.append(col)
+        if col not in list(owners.columns):
+            missing_owner_cols.append(col)
+    if len(missing_media_cols) > 0:
+        sys.exit(f"Media CSV does not have {missing_media_cols} columns.")
+    if len(missing_owner_cols) > 0:
+        sys.exit(f"Owners CSV does not have {missing_owner_cols} columns.")
+
+    # If split column included, remove "train_small" entries as they are duplicates from "train".
+    if "split" in list(df.columns):
+        df = df.loc[df.split != "train_small"]
+
+    # 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(df, media, owners, str(filepath / "catalog-media.csv"))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Attach missing owner info to catalog")
+    parser.add_argument(
+        "-m", "--media_input_file", help="Path to the media manifest input CSV file"
+    )
+    parser.add_argument(
+        "-o", "--owner_input_file", help="Path to the owner fix input CSV file"
+    )
+    parser.add_argument(
+        "--output_path",
+        default="data",
+        required=False,
+        help="Path to the folder for output visualization files",
+    )
+    args = parser.parse_args()
+
+    main(args.media_input_file, args.owner_input_file, args.output_path)