add edamfu code tests

notes:
- disregard python code
- important parts are EDAM files:
  - tests/EDAM_dev.owl -> raw EDAM file
  - tests/EDAM_dev.robot.owl -> raw EDAM file loaded/saved with robot
  - tests/edamontology.org.owl -> raw EDAM file loaded/saved with WebProtégé
  - tests/edamontology.org.robot.owl -> -> raw EDAM file loaded/saved with WebProtégé then robot

edamfu/edamfu/core.py

@@ -0,0 +1,23 @@
+import shutil
+import tempfile
+
+from edamfu.tree import reorder_root, add_comments
+
+from edamfu.utils import (
+    escape_irrelevant_xml_entities_in_text,
+    unescape_irrelevant_xml_entities_in_text,
+    prettify_xml,
+)
+
+
+def reformat(input_file_path, output_file_path):
+    temp_edam_file = tempfile.NamedTemporaryFile(delete=False)
+    temp_edam_file.close()
+    shutil.copy2(input_file_path, temp_edam_file.name)
+    escape_irrelevant_xml_entities_in_text(temp_edam_file.name)
+    reorder_root(temp_edam_file.name)
+    add_comments(temp_edam_file.name)
+    unescape_irrelevant_xml_entities_in_text(temp_edam_file.name)
+    prettify_xml(temp_edam_file.name)
+    shutil.copy2(temp_edam_file.name, output_file_path)
+    return output_file_path

edamfu/edamfu/reorder.py

@@ -0,0 +1,11 @@
+import shutil
+from edamfu.core import reformat
+
+# Input file:
+xml_file_path = (
+    "/home/hmenager/edamfu/tests/EDAM_dev.owl"  # Replace with the path to your XML file
+)
+# Processed file
+sorted_path = "/home/hmenager/edamfu/tests/EDAM_dev.processed.owl"
+
+reformat(xml_file_path, sorted_path)

edamfu/edamfu/reorder_lxml.py

@@ -0,0 +1,122 @@
+from lxml import etree
+import re
+from copy import copy
+
+def get_element_sort_key(elem, order_mapping):
+    first_key = order_mapping.get(elem.tag, {}).get("element_order", 0)
+    if elem.tag == "{http://www.w3.org/2002/07/owl#}Class":
+        secondary_key = elem.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about")
+    elif elem.tag == "{http://www.w3.org/2002/07/owl#}Axiom":
+        annotated_source = elem.find("{http://www.w3.org/2002/07/owl#}annotatedSource")
+        secondary_key = annotated_source.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}resource") if annotated_source is not None else "zzz"
+    else:
+        secondary_key = "zzz"
+    return (first_key, secondary_key)
+
+
+## A
+##  C
+##   C1
+##   C2
+##  B
+##   B1
+##   B2
+def reorder_elements(element, order_mapping):
+    ## element=A
+    sorted_elements = sorted(element, key=lambda elem: get_element_sort_key(elem, order_mapping))
+    ## element=A, sorted_elements=[B,C]
+    new_element = etree.Element(element.tag, attrib=element.attrib)
+    if element.text:
+        new_element.text = etree.CDATA(element.text)
+    for child in sorted_elements:
+        child = reorder_elements(child, order_mapping)
+    new_element.extend(sorted_elements)
+    print(new_element.tag, len(new_element.getchildren()))
+    ontology = new_element.iter("{http://www.w3.org/2002/07/owl#}Ontology")
+    return new_element
+
+def add_comments(xml_file_path):
+    tree = etree.parse(xml_file_path)
+    root = tree.getroot()
+    for class_element in root.findall("{http://www.w3.org/2002/07/owl#}*"):
+        class_uri = class_element.get("{http://www.w3.org/1999/02/22-rdf-syntax-ns#}about")
+        root.insert(list(root).index(class_element), etree.Comment(f" {class_uri} "))
+    with open(xml_file_path, "wb") as f:
+        tree.write(f, encoding="utf-8", xml_declaration=True)
+    print(f"Comments added to '{xml_file_path}'.")
+
+
+def reorder_root(xml_file_path, order_mapping, namespaces):
+    # etree.register_namespace(None, "http://edamontology.org/")
+    # etree.register_namespace("dc", "http://purl.org/dc/elements/1.1/")
+    # etree.register_namespace("dcterms", "http://purl.org/dc/terms/")
+    # etree.register_namespace("owl", "http://www.w3.org/2002/07/owl#")
+    # etree.register_namespace("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#")
+    # etree.register_namespace("skos", "http://www.w3.org/2004/02/skos/core#")
+    # etree.register_namespace("xml", "http://www.w3.org/XML/1998/namespace")
+    # etree.register_namespace("xsd", "http://www.w3.org/2001/XMLSchema#")
+    # etree.register_namespace("doap", "http://usefulinc.com/ns/doap#")
+    # etree.register_namespace("foaf", "http://xmlns.com/foaf/0.1/")
+    # etree.register_namespace("rdfs", "http://www.w3.org/2000/01/rdf-schema#")
+    # etree.register_namespace("oboInOwl", "http://www.geneontology.org/formats/oboInOwl#")
+    # etree.register_namespace("oboLegacy", "http://purl.obolibrary.org/obo/")
+
+    tree = etree.parse(xml_file_path, parser=etree.XMLParser(resolve_entities=False, remove_comments=True))
+    root = tree.getroot()
+    etree.strip_elements(root, etree.Comment, with_tail=True)
+    new_root = reorder_elements(root, order_mapping)
+    ontology = new_root.iter("{http://www.w3.org/2002/07/owl#}Ontology")
+    for el in ontology:
+        print("##", el)
+
+    #escape_special_characters(new_root)
+
+    sorted_path = "/home/hmenager/edamfu/tests/EDAM_dev.sorted-lxml.owl"
+
+    with open(sorted_path, "wb") as f:
+        f.write(etree.tostring(new_root, xml_declaration=True))
+
+    print(f"XML elements reordered and saved to '{sorted_path}'.")
+    return sorted_path
+
+def prettify_xml(file_path):
+    with open(file_path, 'r') as file:
+        file_content = file.read()
+    modified_content = file_content.replace('" />', '"/>')
+    modified_content = modified_content.replace('--><', '-->\n\n    <')
+    modified_content = modified_content.replace('>\n    \n\n\n    \n\n    <!--', '>\n    \n\n\n    <!--')
+    with open(file_path, 'w') as file:
+        file.write(modified_content)
+    print(f"XML prettified in '{file_path}'.")
+
+# Example usage:
+xml_file_path = "/home/hmenager/edamfu/tests/EDAM_dev.owl"  # Replace with the path to your XML file
+
+order_mapping = {
+    "{http://www.w3.org/2002/07/owl#}Ontology": {
+        "element_order": 1,
+        "attribute_order": {etree.QName("http://example.com/ns1", "attribute1"): 1},
+    },
+    "{http://www.w3.org/2002/07/owl#}AnnotationProperty": {
+        "element_order": 2,
+        "attribute_order": {etree.QName("http://example.com/ns1", "attribute1"): 1},
+    },
+    "{http://www.w3.org/2002/07/owl#}ObjectProperty": {
+        "element_order": 3,
+        "attribute_order": {etree.QName("http://example.com/ns1", "attribute1"): 1},
+    },
+    "{http://www.w3.org/2002/07/owl#}Axiom": {
+        "element_order": 4,
+        "attribute_order": {etree.QName("http://example.com/ns1", "attribute1"): 1},
+    },
+    "{http://www.w3.org/2002/07/owl#}Class": {
+        "element_order": 4,
+        "attribute_order": {etree.QName("http://example.com/ns1", "attribute1"): 1},
+    },
+}
+
+namespaces = {"prefix1": "http://example.com/ns1", "prefix2": "http://example.com/ns2"}
+
+sorted_path = reorder_root(xml_file_path, order_mapping, namespaces)
+#add_comments(sorted_path)
+#prettify_xml(sorted_path)