config.yaml

---
processes: 10
extractor:
    input_db:
        mongo_db_name: "wos"
        mongo_host: "zebulon"
        mongo_port: 27017
        slave_okay: False
        #mongo_login: "password.yaml"
    output:
        mongodb:
            mongo_db_name: "mdts11"
            mongo_host: "localhost"
            mongo_port: 27017
            slave_okay: False
    filters:
        regexp_content:
            regexp: \bembryolog.+\b|\bembryo(s)?\b|\bembryonic.+\b
            fields:
                - "TI"
                - "AB"
cooccurrences:
    input_db:
        # connection to mongos sharding element
        mongo_db_name: "wos"
        mongo_host: "localhost"
        mongo_port: 30000
        #mongo_login: "password.yaml"
        slave_okay: False
    output:
        mongodb:
            mongo_db_name: "wos_fet"
            mongo_host: "localhost"
            mongo_port: 30000
            #slave_okay: False
            #mongo_login: "password.yaml"
        coocmatrixcsv: "coocmatrix.csv"
        exportwhitelistcsv: "coocwhitelist.csv"
    whitelist:
        path: "FETkeywords-keyphrases.csv"
importer:
    # debugging purposes
    #limit: 10
    whitelist:
        path: "FETkeywords-keyphrases.csv"
    input_path: "/data/tina/Thomson/raw/*"
    output:
#        mongodb:
#            mongo_db_name: "wos_test"
#            mongo_host: "localhost"
#            mongo_port: 27017
#            slave_okay: False
        coocoutput:
            mongo_db_name: "wos_fet"
            mongo_host: "localhost"
            mongo_port: 30000
            output:
                coocmatrixcsv: "coocmatrix.csv"
                exportwhitelistcsv: "coocwhitelist.csv"
#          files:
#            path: "output"
    isi:
        tag_length: 3
        multiline: "--"
        issues:
            key: "UI"
            begin: "UI"
            end: "RE"
            fields:
                UI: ""
                T1: ""
                PW: ""
                GA: ""
                SQ: ""
                PT: ""
                SO: ""
                JI: ""
                J1: ""
                J2: ""
                J9: ""
                CF: ~
                SC: ~
                SN: ""
                SC: ""
                BN: ""
                BS: ""
                PU: ""
                PI: ""
                PA: ""
                VL: ""
                IS: ""
                PY: ""
                PD: ""
                SU: ""
                SI: ""
                PN: ""
                TV: ""
                IL: ""
                LD: ""
                IO: ""
        notices:
            key: "UT"
            begin: "UT"
            end: "EX"
            fields:
                UT: ""
                T9: ""
                T2: ""
                AR: ~
                AU: ~
                RY: ""
                TI: ""
                DT: ""
                DE: ~
                LA: ""
                AB: ""
                AA: ""
                RY: int
            subfields:
                C1:
                    fields:
                        NU: ""
                        NY: ""
                        NF: ""
                        NC : ""
                    end:  "EA"
                CP:
                    fields:
                        '/A': ""
                        '/Y': ""
                        '/W': ""
                        '/N': ""
                        '/C ': ""
                    end:  "EC"
                CR:
                    fields:
                        R9: ""
                        AR: ~
                        '/A': ""
                        '/Y': ""
                        '/W': ""
                        '/I': ""
                        'RS': ""
                        '/V': ""
                    end: "EC"
    filters:
        #regexp_content:
        #    regexp: \bembryolog.+\b|\bembryo(s)?\b|\bembryonic.+\b
        #    fields:
        #        - "TI"
        #        - "AB"
        required_fields:
            - "TI"