Multiple VCFs with the same DNA ID

[ronammar]

How do we deal with this? If the DNA ID already exists in the DB, when a new VCF is uploaded, can we tack on a suffix to the ID so that we can store multiple VCFs with the same ID without an internal DNA ID conflict? Is this done already?

[mfiume]

Bumping this. @jvlasblom, can you add a test that adds two files with the same ID (uploading the same file twice will suffice). It should import both, but not create a new patient the second time.

[jvlasblom]

ok, will add it to my test cases.

On Thu, Mar 27, 2014 at 5:45 PM, mfiume notifications@github.com wrote:

Bumping this. Jim, can you add a test that adds two files with the same ID (uploading the same file twice will suffice). It should import both, but not create a new patient the second time.

Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/301#issuecomment-38864796 .

[jvlasblom]

I manually tested and it looks fine: the VCF is imported both times, but there is only one patient in the patient directory.

[ronammar]

What if the same DNA ID represents different patients. For example: GATK outputs “sample” in the standard unifiedgenotyper call when not given a specific sample ID. I think it’s a false assumption that the DNA IDs are uniquely identifying the same patient. Christian didn’t know what a DNA ID was until I showed him, and he’s a knowledgeable user.

On Apr 1, 2014, at 2:40 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

I manually tested and it looks fine: the VCF is imported both times, but there is only one patient in the patient directory.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39242280.

[jvlasblom]

OK, so we'll need to setup the dialog we talked about showing a dropdown, one per VCF per DNA ID, and allow them to select an existing patient or 'New Patient'. If they select 'New Patient', we assign that patient a generated DNA ID by default, but also allow the user to override it. (e.g. a prepopulated JTextField)

Is this a 1.2 issue?

On 01/04/14 02:45 PM, ronammar wrote:

What if the same DNA ID represents different patients. For example: GATK outputs “sample” in the standard unifiedgenotyper call when not given a specific sample ID. I think it’s a false assumption that the DNA IDs are uniquely identifying the same patient. Christian didn’t know what a DNA ID was until I showed him, and he’s a knowledgeable user.

On Apr 1, 2014, at 2:40 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

I manually tested and it looks fine: the VCF is imported both times, but there is only one patient in the patient directory.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39242280.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39242957.

[ronammar]

Yah exactly. 1.3 for sure - this is a big update and we’re on a 1.2 feature freeze.

On Apr 1, 2014, at 2:58 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

OK, so we'll need to setup the dialog we talked about showing a dropdown, one per VCF per DNA ID, and allow them to select an existing patient or 'New Patient'. If they select 'New Patient', we assign that patient a generated DNA ID by default, but also allow the user to override it. (e.g. a prepopulated JTextField)

Is this a 1.2 issue?

On 01/04/14 02:45 PM, ronammar wrote:

What if the same DNA ID represents different patients. For example: GATK outputs “sample” in the standard unifiedgenotyper call when not given a specific sample ID. I think it’s a false assumption that the DNA IDs are uniquely identifying the same patient. Christian didn’t know what a DNA ID was until I showed him, and he’s a knowledgeable user.

On Apr 1, 2014, at 2:40 PM, jvlasblom notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

I manually tested and it looks fine: the VCF is imported both times, but there is only one patient in the patient directory.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39242280.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39242957.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/301#issuecomment-39244428.

[jvlasblom]

Moved to future milestone.

[mfiume]

You can use the new Editable Fields that I made. It allows a field to show text as a JLabel but on click it gets converted to a JTextField for editing. See PatientView.java for use case.