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docs(#620): adapt test data
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tamslo authored Sep 27, 2023
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Expand Up @@ -13,10 +13,10 @@ Specific cases that can occur are:
| # | Case | Example (see [test data](#test-data-for-cases-above)) | Handling |
| - | ---- | ----------------------------------------------------- | -------- |
| 1 | A gene in the lab report is not included in CPIC lookups | APOE | Gene is ignored |
| 2 | A gene in the lab report is included in CPIC lookups, but the diplotype is not | CYP2C19 \*1/\*101 | This will be handled manually when pre-processing the data |
| 2 | A gene in the lab report is included in CPIC lookups, but the diplotype is not | CYP2C9 \*1/\*101 | This will be handled manually when pre-processing the data |
| 3 | A gene in the annotations is not included in CPIC lookups | NAT2 | This should also not happen, should adapt FDA crawler to skip such occurrences for now and remove from Anni; such cases will not be included in the lab report (as far as we know) |
| 4 | A gene in the annotations is included in CPIC lookups, but lookup value (phenotype or activity score) is not | Not really present | See case 3 |
| 5 | A gene in annotations (with known lookups) is not included in lab report | CYP2C9 | Currently, the gene is not shown; however, it should be shown with "not tested" |
| 5 | A gene in annotations (with known lookups) is not included in lab report | CYP2C19 | Currently, the gene is not shown; however, it should be shown with "not tested" |

The following table collects which screens are affected by which cases (that
can actually happen).
Expand Down Expand Up @@ -63,7 +63,7 @@ See the example below. User is `test-missing` (Sinai backend) or `unknown-genes`
(HPI backend), password `1234`.

* `CYP2D6`: all good, gene known, diplotype known
* `CYP2C19`: gene known, diplotype unknown (second star allele made up)
* `CYP2C9`: gene known, diplotype unknown (second star allele made up)
* `APOE`: gene not known (also, no guideline in Anni)
* `NAT2`: gene not known (but guideline in Anni; should be no difference to
no guideline in Anni, but for testing)
Expand All @@ -79,7 +79,7 @@ See the example below. User is `test-missing` (Sinai backend) or `unknown-genes`
"allelesTested": "*xN.*3.*4.*5.*6.*8.*9.*10.*14A.*14B.*17.*41"
},
{
"gene": "CYP2C19",
"gene": "CYP2C9",
"resultType": "Diplotype",
"genotype": "*1/*101",
"phenotype": "Intermediate Metabolizer",
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