How To Create Nested List Of Dictionaries From Xml File In Python

This XML sample represents a sample Metabolite from the HMDB the Serum Metabolites dataset. <

Solution 1:

The problem with the first code snippet is probably reassigning the new dictionary to the variable dict:

newlist = []
for child in metabolites:
    innerlist = []
    dicts = {}
    for subchild in child:
        if subchild.tag=='{http://www.hmdb.ca}accession':
            dicts={"accession":  subchild.text}
        if subchild.tag == '{http://www.hmdb.ca}name':
           # here the old value of dict is overriden with new value
            dicts = {"name": subchild.text}
            innerlist.append(subchild.text)
            print(innerlist)
    newlist.append(dicts)

You should probably use assignment in form dict[key] = value:

newlist = []
for child in metabolites:
    innerlist = []
    dicts = {}
    for subchild in child:
        if subchild.tag=='{http://www.hmdb.ca}accession':
            dicts["accession"] =  subchild.text
        if subchild.tag == '{http://www.hmdb.ca}name':
            dicts["name"] =  subchild.text
            innerlist.append(subchild.text)
            print(innerlist)
    newlist.append(dicts)

Similar problem seems to be also with the second code snippet:

newlist = []
forchildin metabolites:
    dicts = {}
    innerlist = []
    forsubchildin child:
        if subchild.tag == '{http://www.hmdb.ca}synonyms':forsynonymin subchild:
                innerlist.append(synonym.text)
    dicts["synonyms"] = innerlist

    newlist.append(dicts)

But (as it was already pointed out) you could use some more convenient libraries instead of parsing XML manually.

Here is merged script:

newlist = []
for child in metabolites:
    dicts = {}
    innerlist = []
    for subchild in child:
        if subchild.tag=='{http://www.hmdb.ca}accession':
            dicts["accession"] =  subchild.text
        if subchild.tag == '{http://www.hmdb.ca}name':
            dicts["name"] =  subchild.text
        if subchild.tag == '{http://www.hmdb.ca}synonyms':
            for synonym in subchild:
                innerlist.append(synonym.text)
            dicts["synonyms"] = innerlist
    newlist.append(dicts)
   
print(newlist)

It outputs following result:

[{'accession': 'HMDB0000001', 'name': '1-Methylhistidine', 'synonyms': ['(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoic acid', '1-Methylhistidine', 'Pi-methylhistidine', '(2S)-2-amino-3-(1-Methyl-1H-imidazol-4-yl)propanoate', '1 Methylhistidine', '1-Methyl histidine']}]