Commit eba5bb56 authored by Thomas Huetter's avatar Thomas Huetter
Browse files

workaround: escaping '\', '{' and '}' for dblp and swissprot

parent 03845e51

dblp/dblp_to_bracket.py

+8 −2
Original line number Original line Diff line number Diff line
@@ -15,7 +15,11 @@ class DBLPContentHandler(ContentHandler): 
        d = dict(attributes)

        d = dict(attributes)

        # Sort the attributes by their keys.

        # Sort the attributes by their keys.

        for key, value in sorted(d.items(), key = lambda element : element[0][1]):

        for key, value in sorted(d.items(), key = lambda element : element[0][1]):

            self.bn += "{" + key[1] + "{" + value + "}}"

            self.bn += "{" + key[1].translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "{" + value.translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "}}"





    # Close tag.

    # Close tag.

    def endElementNS(self, name, qname):

    def endElementNS(self, name, qname):
@@ -23,7 +27,9 @@ class DBLPContentHandler(ContentHandler): 




    # Tag content.

    # Tag content.

    def characters(self, data):

    def characters(self, data):

        self.bn += "{" + data + "}"

        self.bn += "{" + data.translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "}"





print("--- Loading DBLP dataset.")

print("--- Loading DBLP dataset.")

swissprot/swissprot_to_bracket.py

+9 −3
Original line number Original line Diff line number Diff line
@@ -15,7 +15,11 @@ class SwissprotContentHandler(ContentHandler): 
        d = dict(attributes)

        d = dict(attributes)

        # Sort the attributes by their keys.

        # Sort the attributes by their keys.

        for key, value in sorted(d.items(), key = lambda element : element[0][1]):

        for key, value in sorted(d.items(), key = lambda element : element[0][1]):

            self.bn += "{" + key[1] + "{" + value + "}}"

            self.bn += "{" + key[1].translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "{" + value.translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "}}"





    # Close tag.

    # Close tag.

    def endElementNS(self, name, qname):

    def endElementNS(self, name, qname):
@@ -23,12 +27,14 @@ class SwissprotContentHandler(ContentHandler): 




    # Tag content.

    # Tag content.

    def characters(self, data):

    def characters(self, data):

        self.bn += "{" + data + "}"

        self.bn += "{" + data.translate(str.maketrans({"{":  r"\{",

                                          "}":  r"\}",

                                          "\\": r"\\"})) + "}"





print("--- Loading Swissprot dataset.")

print("--- Loading Swissprot dataset.")





swissprot_parser = etree.XMLParser(load_dtd=False, remove_blank_text=True)

swissprot_parser = etree.XMLParser(load_dtd=False, remove_blank_text=True)

swissprot_data_tree = etree.parse('uniprot_sprot.xml', dblp_parser)

swissprot_data_tree = etree.parse('uniprot_sprot.xml', swissprot_parser)

root = swissprot_data_tree.getroot()

root = swissprot_data_tree.getroot()





# Output files.

# Output files.