From e576957319ff04c25a9b07b9a266741cb46ca54c Mon Sep 17 00:00:00 2001
From: Neli Fonseca <neli@ebi.ac.uk>
Date: Fri, 11 Apr 2025 15:44:16 +0100
Subject: [PATCH] Added script to link publications in europepmc

---
 generate_eupmc_links.py | 145 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 145 insertions(+)
 create mode 100644 generate_eupmc_links.py

diff --git a/generate_eupmc_links.py b/generate_eupmc_links.py
new file mode 100644
index 0000000..e2858a3
--- /dev/null
+++ b/generate_eupmc_links.py
@@ -0,0 +1,145 @@
+import csv
+import logging
+import xml.etree.ElementTree as ET
+from xml.dom import minidom
+from typing import List, Dict
+import argparse
+import configparser
+import os
+from ftplib import FTP
+from pathlib import Path
+import os
+
+
+def setup_logging():
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s [%(levelname)s] %(message)s",
+        handlers=[logging.StreamHandler()]
+    )
+
+
+def read_tsv(file_path: str) -> List[Dict[str, str]]:
+    """Read a TSV file and return a list of dictionaries."""
+    logging.info(f"Reading TSV file: {file_path}")
+    with open(file_path, newline='', encoding='utf-8') as f:
+        reader = csv.DictReader(f, delimiter='\t')
+        return list(reader)
+
+
+def build_xml(data: List[Dict[str, str]]) -> ET.Element:
+    """Build the XML structure from the TSV data."""
+    logging.info("Building XML structure")
+    root = ET.Element("links")
+    for row in data:
+        emdb_id = row["EMDB_ID"]
+        pubmed_id = row["PUBMED_ID"]
+
+        link = ET.SubElement(root, "link", providerId="2057")
+
+        resource = ET.SubElement(link, "resource")
+        ET.SubElement(resource, "title").text = emdb_id
+        ET.SubElement(resource, "url").text = f"https://www.ebi.ac.uk/emdb/{emdb_id}"
+
+        record = ET.SubElement(link, "record")
+        ET.SubElement(record, "source").text = "MED"
+        ET.SubElement(record, "id").text = pubmed_id
+
+    return root
+
+
+def prettify_xml(elem: ET.Element) -> str:
+    """Return a pretty-printed XML string for the Element."""
+    return minidom.parseString(ET.tostring(elem, 'utf-8')).toprettyxml(indent="  ")
+
+
+def write_xml(xml_root: ET.Element, output_file: str) -> None:
+    """Write the XML tree to a file with pretty formatting."""
+    logging.info(f"Writing XML to file: {output_file}")
+    pretty_xml = prettify_xml(xml_root)
+    with open(output_file, "w", encoding='utf-8') as f:
+        f.write(pretty_xml)
+
+
+def upload_file_via_ftp(
+    server: str,
+    username: str,
+    password: str,
+    local_file_path: str,
+    remote_dir: str = ".",
+    remote_filename: str = None
+) -> None:
+    """
+    Upload a file to an FTP server. It uses port 21 by default.
+
+    Args:
+        server (str): FTP server address.
+        username (str): FTP username.
+        password (str): FTP password.
+        local_file_path (str): Path to the local file to upload.
+        remote_dir (str): Remote directory to upload the file to. Default is root.
+        remote_filename (str): Optional name to give the uploaded file. Defaults to same as local file.
+    """
+    if not os.path.exists(local_file_path):
+        logging.error(f"Local file does not exist: {local_file_path}")
+        return
+
+    remote_filename = remote_filename or os.path.basename(local_file_path)
+
+    try:
+        logging.info(f"Connecting to FTP server: {server}")
+        with FTP(server) as ftp:
+            ftp.login(user=username, passwd=password)
+            logging.info(f"Logged in as {username}")
+
+            ftp.cwd(remote_dir)
+            logging.info(f"Changed to remote directory: {remote_dir}")
+
+            with open(local_file_path, "rb") as file:
+                ftp.storbinary(f"STOR {remote_filename}", file)
+                logging.info(f"File uploaded successfully as {remote_filename}")
+    except Exception as e:
+        logging.error(f"FTP upload failed: {e}")
+        return
+
+
+def main():
+    setup_logging()
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-w', '--workDir', type=str, help="Main working directory path .")
+    args = parser.parse_args()
+    base_dir = args.workDir
+
+    input_tsv = os.path.join(base_dir, "tab-files/emdb_pubmed.tab")
+    output_xml = os.path.join(base_dir, "EMDB_linkFile_providerID_2057.xml")
+
+    data = read_tsv(input_tsv)
+    xml_root = build_xml(data)
+    write_xml(xml_root, output_xml)
+
+    logging.info(f"XML file generated: {output_xml}")
+
+    # Upload the XML file to the FTP server
+    logging.info("Uploading XML file to FTP server")
+    config = configparser.ConfigParser()
+    env_file = os.path.join(Path(__file__).parent.absolute(), "config.ini")
+    config.read(env_file)
+    ftp_server = config.get("epmc_ftp", "server")
+    ftp_user = config.get("epmc_ftp", "username")
+    ftp_pass = config.get("epmc_ftp", "password")
+    ftp_dir = config.get("epmc_ftp", "directory")
+
+    upload_file_via_ftp(
+        server=ftp_server,
+        username=ftp_user,
+        password=ftp_pass,
+        local_file_path=output_xml,
+        remote_dir=ftp_dir
+    )
+
+    logging.info("Processing complete.")
+
+
+if __name__ == "__main__":
+    main()