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compbio-UofT / medsavant

MedSavant is a search engine for genetic variants
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MedSavant hangs when it can't access genomesavant.com #321

Open ronammar opened 10 years ago

ronammar commented 10 years ago

Can we add a timeout. Do we even need to go to genomesavant.com? Can it function as a closed system?

mfiume commented 10 years ago

We could theoretically offer an offline version but a better solution is to migrate to a more reliable host.

jvlasblom commented 10 years ago

I'm working now on migrating.

On 14/04/14 02:36 PM, mfiume wrote:

We could theoretically offer an offline version but a better solution is to migrate to a more reliable host.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/321#issuecomment-40401863.

jvlasblom commented 10 years ago

Keeping this issue open to implement a proper offline solution for a future revision. The current version works offline, but doesn't always report the lack of connectivity to the user.

It essentially works offline though, but requires further polish for 1.3.

ronammar commented 10 years ago

It doesn’t work offline yet - Mike had this problem still where when just genomesavant.comhttp://genomesavant.com is inaccessible, it hangs for 10 mins or more. Can we not put a 10 second timeout on it?

On May 12, 2014, at 10:28 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

Keeping this issue open to implement a proper offline solution for a future revision. The current version works offline, but doesn't always report the lack of connectivity to the user.

It essentially works offline though, but requires further polish for 1.3.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911075.

jvlasblom commented 10 years ago

Did you try it? In my tests it works fine offline, although I did not test Apps like discovery. (I replaced 'genomesavant.com' globally with an invalid URL in the client, server, and shared projects)

On 12/05/14 10:42 PM, ronammar wrote:

It doesn’t work offline yet - Mike had this problem still where when just genomesavant.comhttp://genomesavant.com is inaccessible, it hangs for 10 mins or more. Can we not put a 10 second timeout on it?

On May 12, 2014, at 10:28 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

Keeping this issue open to implement a proper offline solution for a future revision. The current version works offline, but doesn't always report the lack of connectivity to the user.

It essentially works offline though, but requires further polish for 1.3.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911075.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911690.

ronammar commented 10 years ago

Mike’s computer failed on Friday because of this. He was running a local VM DB and the internet died midway through our session. Essentially, it’s not that the program works in offline mode, it’s specifically when the DB is up AND the genomesavant.comhttp://genomesavant.com server is inaccessible. If you go completely offline, there is no lag or issue. It’s only if you’re “partially” online (DB but not web server).

On May 12, 2014, at 11:04 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

Did you try it? In my tests it works fine offline, although I did not test Apps like discovery. (I replaced 'genomesavant.comhttp://genomesavant.com' globally with an invalid URL in the client, server, and shared projects)

On 12/05/14 10:42 PM, ronammar wrote:

It doesn’t work offline yet - Mike had this problem still where when just genomesavant.comhttp://genomesavant.comhttp://genomesavant.com is inaccessible, it hangs for 10 mins or more. Can we not put a 10 second timeout on it?

On May 12, 2014, at 10:28 PM, jvlasblom notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Keeping this issue open to implement a proper offline solution for a future revision. The current version works offline, but doesn't always report the lack of connectivity to the user.

It essentially works offline though, but requires further polish for 1.3.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911075.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911690.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42912646.

jvlasblom commented 10 years ago

The program will not work if the DB goes down. (By DB, I assume you mean infobright? Or the perhaps the medsavant server? Doesn't matter -- either way medsavant won't work).

I simulated loss of network connectivity by unplugging the cable, and network timeouts by blocking the port at the firewall. Both cases work as expected, but the latter does take 10 seconds.

The code has a 10s initial timeout (FIRST_TIMEOUT) when fetching version information from genomesavant.com. Subsequent requests will have 1 second timeouts (SUBSEQUENT_TIMEOUT): //... timeoutVal = FIRST_TIMEOUT //... try{ doc = dBuilder.parse(NetworkUtils.openStream(url, timeoutVal, timeoutVal)); }catch(SocketTimeoutException sto){ LOG.info("Timed out after "+timeoutVal+" seconds"); timeoutVal = SUBSEQUENT_TIMEOUT; throw sto; } timeoutVal = FIRST_TIMEOUT;

Where did the hang occur? At login? Did you wait at least 10 seconds? Also, I did not test with any of the 3 Apps (mendel, discovery, or secondary findings)

Jim

On 12/05/14 11:09 PM, ronammar wrote:

Mike’s computer failed on Friday because of this. He was running a local VM DB and the internet died midway through our session. Essentially, it’s not that the program works in offline mode, it’s specifically when the DB is up AND the genomesavant.comhttp://genomesavant.com server is inaccessible. If you go completely offline, there is no lag or issue. It’s only if you’re “partially” online (DB but not web server).

On May 12, 2014, at 11:04 PM, jvlasblom notifications@github.com<mailto:notifications@github.com> wrote:

Did you try it? In my tests it works fine offline, although I did not test Apps like discovery. (I replaced 'genomesavant.comhttp://genomesavant.com' globally with an invalid URL in the client, server, and shared projects)

On 12/05/14 10:42 PM, ronammar wrote:

It doesn’t work offline yet - Mike had this problem still where when just genomesavant.comhttp://genomesavant.comhttp://genomesavant.com is inaccessible, it hangs for 10 mins or more. Can we not put a 10 second timeout on it?

On May 12, 2014, at 10:28 PM, jvlasblom

notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Keeping this issue open to implement a proper offline solution for a future revision. The current version works offline, but doesn't always report the lack of connectivity to the user.

It essentially works offline though, but requires further polish for 1.3.

— Reply to this email directly or view it on

GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911075.

— Reply to this email directly or view it on GitHub

https://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42911690.

— Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42912646.

— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/321#issuecomment-42912905.