isis2json: CDS/ISIS to JSON database converter

NOTE: This is Python 2.7 code and this repository is archived.

The isis2json.py is a Python/Jython script to export ISIS (MST+XRF) or ISO-2709 databases to JSON files, optionally compatible with CouchDB and MongoDB.

Running under Jython, both MST+XRF and ISO-2709 files can be read, thanks to the Bruma Java library from BIREME, bundled in the lib/ directory. Running under Python, only ISO-2709 files can be read.

A full description of how this script is used can be found in the paper From ISIS to CouchDB: Databases and Data Models for Bibliographic Records.

Usage

$ ./isis2json.py -h
usage: isis2json.py [-h] [-o OUTPUT.json] [-c] [-m] [-t ISIS_JSON_TYPE]
                    [-q QTY] [-s SKIP] [-i TAG_NUMBER] [-u] [-p PREFIX]
                    [-n] [-k TAG:VALUE]
                    INPUT.(mst|iso)

Convert an ISIS .mst or .iso file to a JSON array

positional arguments:
  INPUT.(mst|iso)     .mst or .iso file to read

optional arguments:
  -h, --help          show this help message and exit
  -o OUTPUT.json, --out OUTPUT.json
                      the file where the JSON output should be written
                        (default: write to stdout)
  -c, --couch         output array within a "docs" item in a JSON document
                        for bulk insert to CouchDB via POST to db/_bulk_docs
  -m, --mongo         output individual records as separate JSON objects,
                        one per line for bulk insert to MongoDB via
                        mongoimport utility
  -t ISIS_JSON_TYPE, --type ISIS_JSON_TYPE
                      ISIS-JSON type, sets field structure:
                        1=string, 2=alist, 3=dict
  -q QTY, --qty QTY   maximum quantity of records to read (default=ALL)
  -s SKIP, --skip SKIP  records to skip from start of .mst (default=0)
  -i TAG_NUMBER, --id TAG_NUMBER
                      generate an "_id" from the given unique TAG field
                        number for each record
  -u, --uuid          generate an "_id" with a random UUID for each record
  -p PREFIX, --prefix PREFIX
                      concatenate prefix to every numeric field tag
                        (ex. 99 becomes "v99")
  -n, --mfn           generate an "_id" from the MFN of each record
                        (available only for .mst input)
  -k TAG:VALUE, --constant TAG:VALUE
                      Include a constant tag:value in every record
                        (ex. -k type:AS)

ISIS-JSON Record Types

There are many ways to represent CDS/ISIS records in JSON [1]. This utility currently exports ISIS-JSON types 1, 2 and 3.

Given an ISIS record with this strcuture:

 2 «538886»
10 «Kanda, Paulo Afonso^1USP^2FMUSP^3CRDC^pBrasil^cSão Paulo^rorg»
10 «Smidth, Magali Taino^1USP^2FMUSP^3CRDC^pBrasil^cSão Paulo^rorg»

Below are the three supported representations of that record in JSON:

ISIS-JSON type 1

{"10":
    ["Kanda, Paulo Afonso^1USP^2FMUSP^3CRDC^pBrasil^cSão Paulo^rorg",
     "Smidth, Magali Taino^1USP^2FMUSP^3CRDC^pBrasil^cSão Paulo^rorg"],
 "2":
    ["538886"]
}

ISIS-JSON type 2

{"10":
    [
        [
            ("_", "Kanda, Paulo Afonso"),
            ("1", "USP"),
            ("2", "FMUSP"),
            ("3", "CRDC"),
            ("p", "Brasil"),
            ("c", "São Paulo"),
            ("r", "org")
        ],
        [
            ("_", "Smidth, Magali Taino"),
            ("1", "USP"),
            ("2", "FMUSP"),
            ("3", "CRDC"),
            ("p", "Brasil"),
            ("c", "São Paulo"),
            ("r", "org")
        ]
    ],
 "2":
    [
        [
            ("_", "538886")
        ]
    ]
}

ISIS-JSON type 3

{"10":
    [
        {
            "_": "Kanda, Paulo Afonso",
            "1": "USP",
            "2": "FMUSP",
            "3": "CRDC",
            "c": "São Paulo",
            "p": "Brasil",
            "r": "org"
        },
        {
            "_": "Smidth, Magali Taino",
            "1": "USP",
            "2": "FMUSP",
            "3": "CRDC",
            "c": "São Paulo",
            "p": "Brasil",
            "r": "org"
        }
    ],
 "2":
    [
        {
            "_": "538886"
        }
    ]
}

Dependencies

Under Python, isis2json.py depends on:

• Python2.6 or 2.7
• argparse.py (bundled; also part of the CPython 2.7 distribution)

Under Jython, isis2json.py depends on:

• Jython 2.5;
• argparse.py (bundled)
• Bruma.jar on the CLASSPATH (bundled);
• jyson-1.0.1.jar on the CLASSPATH (bundled);

Example CLASSPATH:

export CLASSPATH=/home/luciano/lib/Bruma.jar:/home/luciano/lib/jyson-1.0.1.jar

Troubleshooting

SyntaxError on yield fields running isis2json.py under Jython

If you see this:

Traceback (innermost last):
  (no code object) at line 0
  File "./isis2json.py", line 84
        yield fields
            ^
SyntaxError: invalid syntax

You are probably running Jython 2.2, an old version that is packaged with several Linux distributions such as Debian and Ubuntu. To verify, type:

$ jython --version
Jython 2.2.1 on java1.6.0_20

To fix, download and install Jython 2.5 or later from Jython.org.

IMPORT ERROR: Jython 2.5 and Bruma.jar are required to read .mst files

Check if Jython 2.5 or later is installed:

$ jython --version
Jython 2.5.2

If it is not, se issue above. If it is, add the path to Bruma.jar to the CLASSPATH environment variable, or pass it via the jython -J-cp command line option when running isis2json.py, like this:

$ jython -J-cp lib/jyson-1.0.1.jar:lib/Bruma.jar isis2json.py fixtures/LILACS1.mst