Merge pull request #132 from MaRDI4NFDI/stagingv2_header

adjusting the parser to be defusedxml and lxml for xslt transformation

src/swmath2swh/staging_deposit_v2.py

@@ -1,33 +1,49 @@
 from swmath2swh.restApi_software_Json import process_metadata
 from swmath2swh.convertSoftware_from_json_toXml import convert_json_to_xml
+import defusedxml.ElementTree as DET  # Using defusedxml for safe XML parsing
+from defusedxml.lxml import fromstring
 import lxml.etree as ET
 import pandas as pd
 import subprocess
 import time
 import tempfile
 import os
 import requests
-
+import re
+# Load environment variables
 env = os.environ.copy()
 env['SWMATH_USER_DEPOSIT'] = os.getenv('SWMATH_USER_DEPOSIT')
 env['SWMATH_PWD_DEPOSIT'] = os.getenv('SWMATH_PWD_DEPOSIT')
-env['SWMATH_PWD_DEPOSIT'] = os.getenv('SWMATH_PWD_DEPOSIT')
-xsl_filename = '../xslt/software/xslt_SWH_deposit.xslt'
 
+xsl_filename = '../../xslt/software/xslt_SWH_deposit.xslt'
+
+# Fetch XML data
 r = requests.get("https://oai.staging.mardi4nfdi.org/oai/OAIHandler?verb=GetRecord&metadataPrefix=codemeta&identifier=oai:swmath.org:4532")
 xml_str = r.content
-dom = ET.fromstring(xml_str)
+
+dom = DET.fromstring(xml_str)
+
+# Convert the defusedxml-parsed XML to a string for lxml processing
+dom_str = DET.tostring(dom, encoding='unicode')
+
+# Use lxml to parse the XML string for XSLT transformation
+lxml_dom = fromstring(dom_str)
+
+# Perform XSLT transformation using lxml
 xslt = ET.parse(xsl_filename)
 transform = ET.XSLT(xslt)
-newdom = transform(dom)
+newdom = transform(lxml_dom)
 formatted_newdom = ET.tostring(newdom, pretty_print=True, encoding='unicode')
-print(xml_str)
- # Add this before the write statement
+formatted_newdom = re.sub(r'xmlns:ns\d+="[^"]+"', '', formatted_newdom)
+formatted_newdom = re.sub(r'ns\d+:', 'codemeta:', formatted_newdom)
+print(formatted_newdom)
+
 # Write transformed XML to a temporary file
 with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.xml') as temp_file:
     temp_file.write(formatted_newdom)
     temp_filename = temp_file.name
     print(f"Temporary file created: {temp_filename}")
+
 # Format current time for deposit status
 current_time = time.localtime()
 formatted_time = time.strftime("%Y-%m-%d %H:%M:%S", current_time)
@@ -46,4 +62,3 @@
     "--metadata", temp_filename,
     "--format", "json"
 ])
-