Updated the importer to include the new ACMG expected fields along wi…

…th Decision that was missed (#137)
uab-cgds-worthey · Sep 13, 2023 · 1d9e35b · 1d9e35b
1 parent 214eca2
commit 1d9e35b
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Showing 2 changed files with 90 additions and 1 deletion.
diff --git a/backend/src/core/phenotips_importer.py b/backend/src/core/phenotips_importer.py
@@ -76,6 +76,10 @@ def import_analysis_data(self, phenotips_json_data, phenotips_variants, phenotip
  {"type": "section-text", "field": 'Nominator', "value": []},
  {"type": "section-text", "field": 'Participant', "value": []},
  {"type": "section-text", "field": 'Phenotype', "value": []},
+ {"type": "section-text", "field": 'ACMG Classification', "value": []},
+ {"type": "section-text", "field": 'ACMG Classification Criteria', "value": []},
+ {"type": "section-text", "field": 'ACMG Criteria To Add', "value": []},
+ {"type": "section-text", "field": 'Decision', "value": []},
  ]
  }, {
  "header": 'Clinical History', "content": [

diff --git a/etc/fixtures/initial-seed/analyses.json b/etc/fixtures/initial-seed/analyses.json
@@ -54,6 +54,21 @@
  "field": "Phenotype",
  "value": []
  },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
+ "value": []
+ },
  {
  "type": "section-text",
  "field": "Decision",
@@ -275,6 +290,21 @@
  "field": "Phenotype",
  "value": []
  },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
+ "value": []
+ },
  {
  "type": "section-text",
  "field": "Decision",
@@ -487,6 +517,21 @@
  "field": "Phenotype",
  "value": []
  },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
+ "value": []
+ },
  {
  "type": "section-text",
  "field": "Decision",
@@ -711,6 +756,21 @@
  "field": "Phenotype",
  "value": ["Postural instability, delayed gross motor development, generalized hypotonia, generalized hypotonia due to defect at the neuromuscular junction, motor delay, abnormality of the dentate nucleus, abnormality of the periventricular white matter, poor motor coordination, and congenital nystagmus "]
  },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
+ "value": []
+ },
  {
  "type": "section-text",
  "field": "Decision",
@@ -910,6 +970,21 @@
  "field": "Phenotype",
  "value": []
  },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
+ "value": []
+ },
  {
  "type": "section-text",
  "field": "Decision",
@@ -1168,7 +1243,17 @@
  },
  {
  "type": "section-text",
- "field": "Decision",
+ "field": "ACMG Classification",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Classification Criteria",
+ "value": []
+ },
+ {
+ "type": "section-text",
+ "field": "ACMG Criteria To Add",
  "value": []
  },
  {