How to extract the path info?

Question

For the following JSON, I'd like to extract something like this ( is a TAB character).

CHROMOSOMESHUMAN11
...
STATUSESnameApproved
...
ATTRIBUTESHGNCHGNC IDgd_hgnc_id
...
ATTRIBUTESEXTERNALNCBI Gene IDmd_eg_idNCBI
...
ORDER_BYHGNC IDgd_hgnc_id
...

I'd like a smart way to extract the path info of this tree structure. Could you anybody show me the best way to do so? Thanks.

{
  "CHROMOSOMES": {
    "HUMAN": [
      {
        "name": "1",
        "value": "1"
      },
      {
        "name": "2",
        "value": "2"
      },
      {
        "name": "3",
        "value": "3"
      },
      {
        "name": "4",
        "value": "4"
      },
      {
        "name": "5",
        "value": "5"
      },
      {
        "name": "6",
        "value": "6"
      },
      {
        "name": "7",
        "value": "7"
      },
      {
        "name": "8",
        "value": "8"
      },
      {
        "name": "9",
        "value": "9"
      },
      {
        "name": "10",
        "value": "10"
      },
      {
        "name": "11",
        "value": "11"
      },
      {
        "name": "12",
        "value": "12"
      },
      {
        "name": "13",
        "value": "13"
      },
      {
        "name": "14",
        "value": "14"
      },
      {
        "name": "15",
        "value": "15"
      },
      {
        "name": "16",
        "value": "16"
      },
      {
        "name": "17",
        "value": "17"
      },
      {
        "name": "18",
        "value": "18"
      },
      {
        "name": "19",
        "value": "19"
      },
      {
        "name": "20",
        "value": "20"
      },
      {
        "name": "21",
        "value": "21"
      },
      {
        "name": "22",
        "value": "22"
      },
      {
        "name": "X",
        "value": "X"
      },
      {
        "name": "Y",
        "value": "Y"
      },
      {
        "name": "reserved loci",
        "value": "reserved"
      },
      {
        "name": "mitochondrial",
        "value": "mito"
      },
      {
        "name": "pseudoautosomal",
        "value": "XandY"
      }
    ]
  },
  "STATUSES": [
    {
      "name": "Approved",
      "value": "Approved"
    },
    {
      "name": "Entry and symbol withdrawn",
      "value": "Entry Withdrawn"
    }
  ],
  "ATTRIBUTES": {
    "HGNC": [
      {
        "name": "HGNC ID",
        "value": "gd_hgnc_id"
      },
      {
        "name": "Approved symbol",
        "value": "gd_app_sym"
      },
      {
        "name": "Approved name",
        "value": "gd_app_name"
      },
      {
        "name": "Status",
        "value": "gd_status"
      },
      {
        "name": "Locus type",
        "value": "gd_locus_type"
      },
      {
        "name": "Locus group",
        "value": "gd_locus_group"
      },
      {
        "name": "Previous symbols",
        "value": "gd_prev_sym"
      },
      {
        "name": "Previous name",
        "value": "gd_prev_name"
      },
      {
        "name": "Synonyms",
        "value": "gd_aliases"
      },
      {
        "name": "Name synonyms",
        "value": "gd_name_aliases"
      },
      {
        "name": "Chromosome",
        "value": "gd_pub_chrom_map"
      },
      {
        "name": "Date approved",
        "value": "gd_date2app_or_res"
      },
      {
        "name": "Date modified",
        "value": "gd_date_mod"
      },
      {
        "name": "Date symbol changed",
        "value": "gd_date_sym_change"
      },
      {
        "name": "Date name changed",
        "value": "gd_date_name_change"
      },
      {
        "name": "Accession numbers",
        "value": "gd_pub_acc_ids"
      },
      {
        "name": "Enzyme IDs",
        "value": "gd_enz_ids"
      },
      {
        "name": "NCBI Gene ID",
        "value": "gd_pub_eg_id"
      },
      {
        "name": "Ensembl gene ID",
        "value": "gd_pub_ensembl_id"
      },
      {
        "name": "Mouse genome database ID",
        "value": "gd_mgd_id"
      },
      {
        "name": "Specialist database links",
        "value": "gd_other_ids"
      },
      {
        "name": "Specialist database IDs",
        "value": "gd_other_ids_list"
      },
      {
        "name": "Pubmed IDs",
        "value": "gd_pubmed_ids"
      },
      {
        "name": "RefSeq IDs",
        "value": "gd_pub_refseq_ids"
      },
      {
        "name": "Gene group ID",
        "value": "family.id"
      },
      {
        "name": "Gene group name",
        "value": "family.name"
      },
      {
        "name": "CCDS IDs",
        "value": "gd_ccds_ids"
      },
      {
        "name": "Vega IDs",
        "value": "gd_vega_ids"
      },
      {
        "name": "Locus specific databases",
        "value": "gd_lsdb_links"
      }
    ],
    "EXTERNAL": [
      {
        "name": "NCBI Gene ID",
        "source": "NCBI",
        "value": "md_eg_id"
      },
      {
        "name": "OMIM ID",
        "source": "OMIM",
        "value": "md_mim_id"
      },
      {
        "name": "RefSeq",
        "source": "NCBI",
        "value": "md_refseq_id"
      },
      {
        "name": "UniProt ID",
        "source": "UniProt",
        "value": "md_prot_id"
      },
      {
        "name": "Ensembl ID",
        "source": "Ensembl",
        "value": "md_ensembl_id"
      },
      {
        "name": "Vega ID",
        "source": "Vega",
        "value": "md_vega_id"
      },
      {
        "name": "UCSC ID",
        "source": "UCSC",
        "value": "md_ucsc_id"
      },
      {
        "name": "Mouse genome database ID",
        "source": "MGI",
        "value": "md_mgd_id"
      },
      {
        "name": "Rat genome database ID",
        "source": "RGD",
        "value": "md_rgd_id"
      },
      {
        "name": "LNCipedia",
        "source": "LNCipedia",
        "value": "md_lncipedia"
      },
      {
        "name": "GtRNAdb",
        "source": "GtRNAdb",
        "value": "md_gtrnadb"
      }
    ]
  },
  "ORDER_BY": [
    {
      "name": "HGNC ID",
      "value": "gd_hgnc_id"
    },
    {
      "name": "Approved symbol",
      "value": "gd_app_sym_sort"
    },
    {
      "name": "Approved name",
      "value": "gd_app_name"
    },
    {
      "name": "Status",
      "value": "gd_status"
    },
    {
      "name": "Locus type",
      "value": "gd_locus_type"
    },
    {
      "name": "Locus group",
      "value": "gd_locus_group"
    },
    {
      "name": "Previous symbols",
      "value": "gd_prev_sym"
    },
    {
      "name": "Previous name",
      "value": "gd_prev_name"
    },
    {
      "name": "Synonyms",
      "value": "gd_aliases"
    },
    {
      "name": "Name synonyms",
      "value": "gd_name_aliases"
    },
    {
      "name": "Chromosome",
      "value": "gd_pub_chrom_map_sort"
    },
    {
      "name": "Date approved",
      "value": "gd_date2app_or_res"
    },
    {
      "name": "Date modified",
      "value": "gd_date_mod"
    },
    {
      "name": "Date symbol changed",
      "value": "gd_date_sym_change"
    },
    {
      "name": "Date name changed",
      "value": "gd_date_name_change"
    },
    {
      "name": "Accession numbers",
      "value": "gd_pub_acc_ids"
    },
    {
      "name": "Enzyme IDs",
      "value": "gd_enz_ids"
    },
    {
      "name": "NCBI Gene ID",
      "value": "gd_pub_eg_id"
    },
    {
      "name": "Ensembl gene ID",
      "value": "gd_pub_ensembl_id"
    },
    {
      "name": "Mouse genome database ID",
      "value": "gd_mgd_id"
    },
    {
      "name": "Specialist database links",
      "value": "gd_other_ids"
    },
    {
      "name": "Specialist database IDs",
      "value": "gd_other_ids_list"
    },
    {
      "name": "Pubmed IDs",
      "value": "gd_pubmed_ids"
    },
    {
      "name": "RefSeq IDs",
      "value": "gd_pub_refseq_ids"
    },
    {
      "name": "Gene group ID",
      "value": "family.id"
    },
    {
      "name": "Gene group name",
      "value": "family.name"
    },
    {
      "name": "CCDS IDs",
      "value": "gd_ccds_ids"
    },
    {
      "name": "Vega IDs",
      "value": "gd_vega_ids"
    },
    {
      "name": "Locus specific databases",
      "value": "gd_lsdb_links"
    },
    {
      "name": "NCBI Gene ID (supplied by NCBI)",
      "value": "md_eg_id"
    },
    {
      "name": "OMIM ID (supplied by OMIM)",
      "value": "md_mim_id"
    },
    {
      "name": "RefSeq (supplied by NCBI)",
      "value": "md_refseq_id"
    },
    {
      "name": "UniProt ID (supplied by UniProt)",
      "value": "md_prot_id"
    },
    {
      "name": "Ensembl ID (supplied by Ensembl)",
      "value": "md_ensembl_id"
    },
    {
      "name": "Vega ID (supplied by Vega)",
      "value": "md_vega_id"
    },
    {
      "name": "UCSC ID (supplied by UCSC)",
      "value": "md_ucsc_id"
    },
    {
      "name": "Mouse genome database ID (supplied by MGI)",
      "value": "md_mgd_id"
    },
    {
      "name": "Rat genome database ID (supplied by RGD)",
      "value": "md_rgd_id"
    },
    {
      "name": "LNCipedia ID (supplied by LNCipedia)",
      "value": "md_lncipedia"
    },
    {
      "name": "GtRNAdb ID (supplied by GtRNAdb)",
      "value": "md_gtrnadb"
    }
  ],
  "OUTPUT": [
    "Text",
    "Make URL for text"
  ]
}

user_997358 · Answer

I'd like a smart way to extract the path info of this tree structure.

paths is your friend.

Given certain irregularities in the input, the exact requirements are not always clear, but the following might be what you are looking for and even if not, it would be easy to tweak in accordance with your detailed requirements.

totsv.jq

def s: map(select(type=="string"));

paths as $p
| getpath($p) 
| if type == "object" and has("name")
  then ($p|s) + [.name, .value, (.source // empty)]
  elif type == "array" and .[0] == "Text" then ($p|s) + .
  else empty
  end
| @tsv

Invocation

jq -crf totsv.jq chromosomes.json

Selection from output

CHROMOSOMES HUMAN   1   1
CHROMOSOMES HUMAN   2   2
...
STATUSES    Approved    Approved
STATUSES    Entry and symbol withdrawn  Entry Withdrawn
ATTRIBUTES  HGNC    HGNC ID gd_hgnc_id
...
ORDER_BY    GtRNAdb ID (supplied by GtRNAdb)    md_gtrnadb
OUTPUT  Text    Make URL for text

For future reference

Rather than give a very long sample input, it would be better to give a small sample that is tightly woven with detailed requirements.

How to extract the path info?

1 Answers

totsv.jq

Invocation

Selection from output

For future reference