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Python requirements described in docs to be installed with pip install -r requirements.txt but it appears to be missing

Dear Augusto,

What do you think of integrating the exist questionnaire and clinical report (summary of findings) as one object - in practice it is common to include the results of confirmation with your results (as it might have been a false negative and in this way the clinician can choose to check again further down the line, particularly if better technologies are then available).

As a user it is also very appealing to be able to go to one place to find a summary of case.

Best wishes,
Eik

The final idea is make a public Webserver to facilitate this

Please can we add a field to pass/fail/ambiguous read level support to interpretedGenome

Split this in tasks

Two models to aggregate interpretedGenomes from rare diseases and cancer are needed.

We may want to add a field that has a SNP signature to use for identity checking.

The model is quite completed now thanks to @asosinsky, but it still need to evaluate which fields should be null and the documentation need to be improved

VAF(SNV)=UT_tier1/(DP-FDP)
VAF(indel)=TIR/(TAR+TIR)

Hi Antonio - we appear to be sending the same tier event multiple times - the only unique thing is the "reportEventId"

WNC are condensing these in the UI and are sending all of these back - which we agreed with them as the right thing to do.

Why is GeL generating multiple "reportEventId" when nothing else is different, this is causing the QC team some headaches. If we can fix it on the GeL side that would be awesome

(I believe Omicia and Congenica have raised this in the past too)

@priesgo

Seeing as this field is an array of VariantCall objects, can we please call the field variantCalls (plural) instead of variantCall (singular) ?

This needs to point to the family at a particular time point in the database so that we can ensure consistency between interpretation requests that may go to various interpretation services. This will help reconstruct provenance tracking.

Probably fairly self-explanatory. Encountered whilst validating an InterpretedGenome object.

What is the current recommended way to install the GelReportModels package? Previously I installed using the following steps:

git clone [email protected]:genomicsengland/GelReportModels.git
cd GelReportModels
pip install -r requirements.txt
python build.py --skip-docs --skip-java
pip install . 

But I can't see the requirements.txt file in the latest version (although it is still referenced in the installation instructions in the README and here) .

Can I install using the setup.py script ( python setup.py install)?

Many thanks,
Andy

The Idea will be separate PrimaryFindings and SecondaryFindings

To pull out of the tiering the panels applied and to include it the ClinicalReportRD as part of the methods

The current model has a data structure where the type and subtype is not linked. If there are multiple of either this will not maintain any relationship between the two.

/**
This should be an enumeration when it is well defined
blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.
*/
union {null, array<string>} primaryDiagnosisDisease;

/**
This should be an enumeration when it is well defined
blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.
*/
union {null, array<string>} primaryDiagnosisSubDisease;

Some time the format validation is just not enough, and can be easily tricked, some providers usually take advantage of this using for example empty strings for the required fields.

With a extended method we could cut that behaviour. The proposal is implement a method in ProtocolElement.

could we add this please to interpretation requests

Dear Antonio -

With Alona, we need to review the Cancer interpretation models together and ensure they have everything required to support Hadean interpretation and reporting.

Off the top of my head:

We need to ensure all the cancer metrics are included (Eik to Expand on what these include).

Best wishes,
Eik

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Would it be possible to validate the Tiers returned in the interpretedGenome against the tiers in the interpretationRequest.

In gitlab by @arendon on Jul 19, 2016, 17:54

We need to decide how to report coverage.

also what the content of the gene panels was...
a

This is tricky since AVRO doesn't allow it, but we could use the comments line to do it.

Hi @Antonior26 ,

Apologies in advance if you're not the right contact for this issue but I saw that you were the one that created this latest release. I'm running into the issue below when trying to use the Gel Models in my code.

When running the command 'mvn install' the build fails with the following error:

Traceback (most recent call last): File "C:\Users\aadegunamoo\Documents\Workspace\testing\automation\GelReportModels\build.py", line 11, in <module> import protocols_utils.utils.conversion_tools as conversion_tools File "C:\Users\aadegunamoo\Documents\Workspace\testing\automation\GelReportModels\protocols_utils\utils\conversion_tools.py", line 11, in <module> from protocols_utils.code_generation.process_schemas import SchemaGenerator, ProtocolGenerator File "C:\Users\aadegunamoo\Documents\Workspace\testing\automation\GelReportModels\protocols_utils\code_generation\process_schemas.py", line 19, in <module> import avro.schema ModuleNotFoundError: No module named 'avro'

This issue causes the framework I'm working to fail when importing the gel-models as a maven dependency or when trying to package locally.

GelReportModel7.8.0.log