[Tutor] Python Help: Converting a text file into a specified format

[Peter Otten]

Vazquez, Juliana Mary wrote:

> Your task is to process each record in a file named “punned_result.txt
> (see attached) and convert it into the following format:
> 
> –[2] Brandt, Mary D; London, Jack E. “Health Informatics Standards: A
> User’s Guide.” Journal of AHIMA 71, no. 4 (2000): 39-43.
> 
> 1.    You are required to list all the author names [last_name, first_name
> initial]
> 
> 2.    The content in the quotation is the title of the article
> 
> 3.    Here [2] is the order of the record, 71 is the volume, 4 is the
> issue number, 2000 is the year of publication, and 39-43 is the start and
> end pages of the article in that issue of the journal.
> 
> Hints:
> 
> –You may want to use if/elif/else structure inside a while statement to
> test the first two characters in each line so that you can determine
> whether you need the info in that line or not.

Uh -- that seems to be a rather hard problem to solve with just if and 
while.

> Please help me work through this problem!

Start small and write a script that breaks your input data into individual 
records. These seem to be separated by empty lines. For now you can build a 
list of lists where each publication record is one of the inner lists:

[ 
   ["PMID- 32203977", ...],
   ["PMID- 32203970", ...],
   ...
]

When you have that working (in the process you may need to ask here again) 
you can split the inner lists into 
(key, [value1, value2, ...]) pairs. Note how the value part consists of a 
list because one key (example: FAU (which is "full author" according to 
https://www.nlm.nih.gov/bsd/mms/medlineelements.html) will occur once for 
every author of a publication. A Python dict is well-suited for that data 
(look at the dict.setdefault() method, or collections.defaultdict).
Example dict:


{'AD': ['Department of Cardiovascular, Endocrine-Metabolic Diseases '
        'and Aging, IstitutoSuperiore di Sanita, Rome, Italy.',
        'Department of Infectious Diseases, Istituto Superiore di '
        'Sanita, Rome, Italy.',
        'Office of the President, Istituto Superiore di Sanita, Rome, '
        'Italy.'],
 'AID': ['2763667 [pii]', '10.1001/jama.2020.4683 [doi]'],
 'AU': ['Onder G', 'Rezza G', 'Brusaferro S'],
 'CRDT': ['2020/03/24 06:00'],
 'DEP': ['20200323'],
 'DP': ['2020 Mar 23'],
 'EDAT': ['2020/03/24 06:00'],
 'FAU': ['Onder, Graziano', 'Rezza, Giovanni', 'Brusaferro, Silvio'],
 'IS': ['1538-3598 (Electronic)', '0098-7484 (Linking)'],
 'JID': ['7501160'],
 'JT': ['JAMA'],
 'LA': ['eng'],
 'LID': ['10.1001/jama.2020.4683 [doi]'],
 'LR': ['20200323'],
 'MHDA': ['2020/03/24 06:00'],
 'OWN': ['NLM'],
 'PHST': ['2020/03/24 06:00 [entrez]',
          '2020/03/24 06:00 [pubmed]',
          '2020/03/24 06:00 [medline]'],
 'PL': ['United States'],
 'PMID': ['32203977'],
 'PST': ['aheadofprint'],
 'PT': ['Journal Article'],
 'SB': ['AIM', 'IM'],
 'SO': ['JAMA. 2020 Mar 23. pii: 2763667. doi: '
        '10.1001/jama.2020.4683.'],
 'STAT': ['Publisher'],
 'TA': ['JAMA'],
 'TI': ['Case-Fatality Rate and Characteristics of Patients Dying in '
        'Relation to COVID-19 in Italy.']}


Once you have your data in the format above the next step is to print it as 
requested -- and to come up with a way to cope with missing information 
(example: some of the publications do not provide an author).

Some final tweaks (like extracting the year from the publication date), and 
you are there.