Answers.Body: <p>When I visit the <code>cases_endpt</code> page you linked <a href="https://api.gdc.cancer.gov/cases" rel="nofollow noreferrer">directly</a> on Firefox v88, I get a filterable JSON file. Looking for &quot;type&quot; only comes up with &quot;disease_type&quot;, not sample or analyte:</p>
  <pre><code>data    
   hits   
    0 
     disease_type &quot;Adenomas and Adenocarcinomas&quot;
    1 
     disease_type &quot;Ductal and Lobular Neoplasms&quot;
    2 
     disease_type &quot;Ductal and Lobular Neoplasms&quot;
    3 
     disease_type &quot;Adenomas and Adenocarcinomas&quot;
    4 
     disease_type &quot;Squamous Cell Neoplasms&quot;
    5 
     disease_type &quot;Adenomas and Adenocarcinomas&quot;
    6 
     disease_type &quot;Squamous Cell Neoplasms&quot;
    7 
     disease_type &quot;Adenomas and Adenocarcinomas&quot;
    8 
     disease_type &quot;Squamous Cell Neoplasms&quot;
    9 
     disease_type &quot;Ductal and Lobular Neoplasms&quot;
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-19T12:02:40.067Z
Answers.LastActivityDate: 2021-06-19T12:02:40.067Z
Answers.UserDisplayName: gringer
Body: <p>I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to show up in the tsv file? I have tried altering what I pass as a field (towards the top of the code), or adding a different filter, but nothing seems to change what shows up in the tsv file. Any help is appreciated!</p>
  <pre><code>import requests
  import json
  
  cases_endpt = &quot;https://api.gdc.cancer.gov/cases&quot;
  
  # The 'fields' parameter is passed as a comma-separated string of single names.
  fields = [
      &quot;sample_ids&quot;,
      &quot;submitter_sample_ids&quot;,
      &quot;files.cases.sample_ids&quot;,
      &quot;files.cases.submitter_sample_ids&quot;,
      &quot;files.cases.samples.sample_id&quot;,
      &quot;files.cases.samples.sample_type&quot;,
      &quot;files.cases.samples.sample_type_id&quot;,
      &quot;files.cases.samples.submitter_id&quot;,
      &quot;samples.sample_id&quot;,
      &quot;samples.sample_type&quot;,
      &quot;samples.sample_type_id&quot;,
      &quot;tissue_source_site.bcr_id&quot;,
      &quot;tissue_source_site.code&quot;,
      &quot;tissue_source_site.name&quot;,
      &quot;tissue_source_site.project&quot;,
      &quot;tissue_source_site.tissue_source_site_id&quot;,
      &quot;diagnoses.classification_of_tumor&quot;,
      &quot;diagnoses.tumor_stage&quot;,
      &quot;diagnoses.tumor_grade&quot;,
      &quot;files.cases.diagnoses.tumor_grade&quot;,
      &quot;files.cases.diagnoses.tumor_stage&quot;,
      &quot;files.cases.diagnoses.classification_of_tumor&quot;,
      &quot;files.cases.samples.tumor_code&quot;,
      &quot;files.cases.samples.tumor_code_id&quot;,
      &quot;files.cases.samples.tumor_descriptor&quot;,
      &quot;files.cases.samples.portions.slides.percent_tumor_cells&quot;,
      &quot;files.cases.samples.portions.slides.percent_tumor_nuclei&quot;,
      &quot;samples.tumor_code&quot;,
      &quot;samples.tumor_code_id&quot;,
      &quot;samples.tumor_descriptor&quot;,
      &quot;samples.portions.slides.percent_tumor_cells&quot;,
      &quot;samples.portions.slides.percent_tumor_nuclei&quot;,
      &quot;files.cases.samples.oct_embedded&quot;,
      &quot;samples.oct_embedded&quot;,
      &quot;files.cases.samples.intermediate_dimension&quot;,
      &quot;files.cases.samples.longest_dimension&quot;,
      &quot;files.cases.samples.shortest_dimension&quot;,
      &quot;samples.intermediate_dimension&quot;,
      &quot;samples.longest_dimension&quot;,
      &quot;samples.shortest_dimension&quot;,
      &quot;files.cases.samples.portions.is_ffpe&quot;,
      &quot;samples.is_ffpe&quot;,
      &quot;samples.portions.is_ffpe&quot;,
      &quot;files.cases.samples.pathology_report_uuid&quot;,
      &quot;samples.pathology_report_uuid&quot;,
      &quot;exposures.weight&quot;,
      &quot;files.cases.exposures.weight&quot;,
      &quot;files.cases.samples.current_weight&quot;,
      &quot;files.cases.samples.initial_weight&quot;,
      &quot;files.cases.samples.portions.weight&quot;,
      &quot;samples.current_weight&quot;,
      &quot;samples.initial_weight&quot;,
      &quot;samples.portions.weight&quot;,
      &quot;files.cases.samples.composition&quot;,
      &quot;samples.composition&quot;,
      &quot;files.cases.samples.freezing_method&quot;,
      &quot;files.cases.samples.time_between_clamping_and_freezing&quot;,
      &quot;files.cases.samples.time_between_excision_and_freezing&quot;,
      &quot;samples.freezing_method&quot;,
      &quot;samples.time_between_clamping_and_freezing&quot;,
      &quot;samples.time_between_excision_and_freezing&quot;,
      &quot;files.cases.samples.days_to_sample_procurement&quot;,
      &quot;samples.days_to_sample_procurement&quot;,
      &quot;files.cases.samples.preservation_method&quot;,
      &quot;samples.preservation_method&quot;,
      &quot;samples.days_to_collection&quot;,
      &quot;files.cases.samples.days_to_collection&quot;,
      &quot;files.cases.samples.portions.analytes.analyte_type&quot;,
      &quot;files.cases.samples.portions.analytes.analyte_type_id&quot;,
      &quot;files.cases.samples.portions.analytes.aliquots.analyte_type&quot;,
      &quot;files.cases.samples.portions.analytes.aliquots.analyte_type_id&quot;,
      &quot;samples.portions.analytes.analyte_type&quot;,
      &quot;samples.portions.analytes.analyte_type_id&quot;,
      &quot;samples.portions.analytes.aliquots.analyte_type&quot;,
      &quot;samples.portions.analytes.aliquots.analyte_type_id&quot;,
      ]
  
  fields = ','.join(fields)
  
  filters = {
      &quot;op&quot;: &quot;in&quot;,
      &quot;content&quot;: {&quot;field&quot;: &quot;cases.project.project_id&quot;,
                  &quot;value&quot;: [&quot;TCGA-BRCA&quot;]},
  }
  
  params = {&quot;filters&quot;: json.dumps(filters),
            &quot;format&quot;: &quot;TSV&quot;,
            &quot;size&quot;: &quot;12000&quot;}
  
  response = requests.get(cases_endpt, params=params)
  content = str(response.content, &quot;utf-8&quot;)
  
  with open(&quot;addingsampletype5.tsv&quot;, &quot;w&quot;) as file:
      file.write(content)
  </code></pre>
  
Tags: <data-retrieval><api><python>
Title: querying gdc metadata issues with resulting fields
ThreadText: # querying gdc metadata issues with resulting fields
  
  (Asked by: username_0 on 2021-06-17)
  
  I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to show up in the tsv file? I have tried altering what I pass as a field (towards the top of the code), or adding a different filter, but nothing seems to change what shows up in the tsv file. Any help is appreciated!
  
  ```
  import requests
  import json
  
  cases_endpt = "https://api.gdc.cancer.gov/cases"
  
  # The 'fields' parameter is passed as a comma-separated string of single names.
  fields = [
      "sample_ids",
      "submitter_sample_ids",
      "files.cases.sample_ids",
      "files.cases.submitter_sample_ids",
      "files.cases.samples.sample_id",
      "files.cases.samples.sample_type",
      "files.cases.samples.sample_type_id",
      "files.cases.samples.submitter_id",
      "samples.sample_id",
      "samples.sample_type",
      "samples.sample_type_id",
      "tissue_source_site.bcr_id",
      "tissue_source_site.code",
      "tissue_source_site.name",
      "tissue_source_site.project",
      "tissue_source_site.tissue_source_site_id",
      "diagnoses.classification_of_tumor",
      "diagnoses.tumor_stage",
      "diagnoses.tumor_grade",
      "files.cases.diagnoses.tumor_grade",
      "files.cases.diagnoses.tumor_stage",
      "files.cases.diagnoses.classification_of_tumor",
      "files.cases.samples.tumor_code",
      "files.cases.samples.tumor_code_id",
      "files.cases.samples.tumor_descriptor",
      "files.cases.samples.portions.slides.percent_tumor_cells",
      "files.cases.samples.portions.slides.percent_tumor_nuclei",
      "samples.tumor_code",
      "samples.tumor_code_id",
      "samples.tumor_descriptor",
      "samples.portions.slides.percent_tumor_cells",
      "samples.portions.slides.percent_tumor_nuclei",
      "files.cases.samples.oct_embedded",
      "samples.oct_embedded",
      "files.cases.samples.intermediate_dimension",
      "files.cases.samples.longest_dimension",
      "files.cases.samples.shortest_dimension",
      "samples.intermediate_dimension",
      "samples.longest_dimension",
      "samples.shortest_dimension",
      "files.cases.samples.portions.is_ffpe",
      "samples.is_ffpe",
      "samples.portions.is_ffpe",
      "files.cases.samples.pathology_report_uuid",
      "samples.pathology_report_uuid",
      "exposures.weight",
      "files.cases.exposures.weight",
      "files.cases.samples.current_weight",
      "files.cases.samples.initial_weight",
      "files.cases.samples.portions.weight",
      "samples.current_weight",
      "samples.initial_weight",
      "samples.portions.weight",
      "files.cases.samples.composition",
      "samples.composition",
      "files.cases.samples.freezing_method",
      "files.cases.samples.time_between_clamping_and_freezing",
      "files.cases.samples.time_between_excision_and_freezing",
      "samples.freezing_method",
      "samples.time_between_clamping_and_freezing",
      "samples.time_between_excision_and_freezing",
      "files.cases.samples.days_to_sample_procurement",
      "samples.days_to_sample_procurement",
      "files.cases.samples.preservation_method",
      "samples.preservation_method",
      "samples.days_to_collection",
      "files.cases.samples.days_to_collection",
      "files.cases.samples.portions.analytes.analyte_type",
      "files.cases.samples.portions.analytes.analyte_type_id",
      "files.cases.samples.portions.analytes.aliquots.analyte_type",
      "files.cases.samples.portions.analytes.aliquots.analyte_type_id",
      "samples.portions.analytes.analyte_type",
      "samples.portions.analytes.analyte_type_id",
      "samples.portions.analytes.aliquots.analyte_type",
      "samples.portions.analytes.aliquots.analyte_type_id",
      ]
  
  fields = ','.join(fields)
  
  filters = {
      "op": "in",
      "content": {"field": "cases.project.project_id",
                  "value": ["TCGA-BRCA"]},
  }
  
  params = {"filters": json.dumps(filters),
            "format": "TSV",
            "size": "12000"}
  
  response = requests.get(cases_endpt, params=params)
  content = str(response.content, "utf-8")
  
  with open("addingsampletype5.tsv", "w") as file:
      file.write(content)
  
  ```
  
  **Tags:** data-retrieval, api, python
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-06-19. Score: 0
  
  When I visit the `cases_endpt` page you linked [directly](https://api.gdc.cancer.gov/cases) on Firefox v88, I get a filterable JSON file. Looking for "type" only comes up with "disease\_type", not sample or analyte:
  
  ```
  data    
   hits   
    0 
     disease_type "Adenomas and Adenocarcinomas"
    1 
     disease_type "Ductal and Lobular Neoplasms"
    2 
     disease_type "Ductal and Lobular Neoplasms"
    3 
     disease_type "Adenomas and Adenocarcinomas"
    4 
     disease_type "Squamous Cell Neoplasms"
    5 
     disease_type "Adenomas and Adenocarcinomas"
    6 
     disease_type "Squamous Cell Neoplasms"
    7 
     disease_type "Adenomas and Adenocarcinomas"
    8 
     disease_type "Squamous Cell Neoplasms"
    9 
     disease_type "Ductal and Lobular Neoplasms"
  
  ```
  
  
  ---
  
  