gdcParseMetadata error

[Liripo]

gdcParseMetadata error

> metaMatrix.RNA <- gdcParseMetadata(metafile = "./metadata.cart.2020-05-08.json")
Error in vapply(seq_len(nSam), function(i) metadata[[i]]$cases[[1]]$samples[[1]]$submitter_id,  : 
  值的长度必需为1，
 但FUN(X[[1]])结果的长度却是0

The metadata.cart.2020-05-08.json file head is

[{
  "file_id": "ccf08842-c001-43be-b2c4-7a37499dcd18", 
  "associated_entities": [
    {
      "entity_submitter_id": "TCGA-71-6725-01A-11R-1858-07", 
      "entity_id": "9680a78d-59ab-4cf0-bd92-e6ecbc640e04", 
      "entity_type": "aliquot", 
      "case_id": "4b7cd595-e7f9-45a8-b736-a8c7c42d9539"
    }
  ], 
  "state": "released", 
  "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
  "file_name": "5d420937-4d97-4f04-9ce9-754054261d97.htseq.counts.gz", 
  "experimental_strategy": "RNA-Seq", 
  "access": "open", 
  "data_format": "TXT", 
  "data_type": "Gene Expression Quantification", 
  "data_category": "Transcriptome Profiling", 
  "analysis": {
    "analysis_id": "390fff89-0e17-41c2-b0c5-2de8124271f0", 
    "input_files": [
      {
        "file_id": "745f6641-f01a-4c42-9883-f36872514020", 
        "state": "released", 
        "updated_datetime": "2018-11-15T21:12:37.513272-06:00", 
        "data_category": "Sequencing Reads", 
        "created_datetime": "2016-05-27T22:03:53.926564-05:00", 
        "file_name": "792a9dd3-28b5-42f5-aa23-e64f47995f9a_gdc_realn_rehead.bam", 
        "experimental_strategy": "RNA-Seq", 
        "access": "controlled", 
        "data_format": "BAM", 
        "data_type": "Aligned Reads", 
        "submitter_id": "792a9dd3-28b5-42f5-aa23-e64f47995f9a", 
        "md5sum": "d95c94ce0b5f02e70c6e7df27dc7d478", 
        "file_size": 10602206295, 
        "platform": "Illumina"
      }
    ], 
    "workflow_link": "https://github.com/NCI-GDC/htseq-cwl", 
    "updated_datetime": "2018-09-06T21:10:41.393019-05:00", 
    "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
    "created_datetime": "2016-05-29T10:24:46.178710-05:00", 
    "state": "released", 
    "workflow_version": "v1", 
    "workflow_type": "HTSeq - Counts"
  }, 
  "md5sum": "f8b64783717da58198a723cfa52f0723", 
  "file_size": 254695
}

[jiangzh-coder]

i met the same problem, hopefully auther will answer !

[Oxalin]

I'm getting the same error. Did you find a workaround or a solution?

[Oxalin]

So 3 years later, here I am again. Last time, I took another approach at the time to achieve my goals.

But once again, I faced the same problem: the metadata.json file format I'm working with is not the one expected by gdcParseMetadata(). I digged deeper this time and here are my observations.

The metadata.json dowloaded from the GDC portail can be of at least two different formats, depending on the requested data: repository or cohort. The cohort and the repository metadata file differ in their structure and don't provide the same information.

The current gdcParseMetadata() seems to be supporting the cohort metadata format, but not the repository one.

So I coded a different parser for the repository metadata json file, inspired by a suggestion that had been made by someone who had encountered the same problem. I'm willing to make this code available in the main branch if the current project is still alive.