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mcwdsi / dron

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ODK 1.4 migration #12

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

This PR contains a lot of updates from ODK 1.4 migration. If anything goes wrong (which it shouldn't, but because Dron is big I cant exclude the possibility), I will fix it!

hoganwr commented 1 year ago

The build process is getting stuck. It won't go past here:

dron.Makefile:24: warning: overriding recipe for target 'dron-lite.owl' Makefile:627: warning: ignoring old recipe for target 'dron-lite.owl' echo "ODK Makefile version: v1.4 (this is the version of the ODK with which this Makefile was generated, \ not the version of the ODK you are running)" &&\ echo "ROBOT version (ODK): " && robot --catalog catalog-v001.xml --version ODK Makefile version: v1.4 (this is the version of the ODK with which this Makefile was generated, not the version of the ODK you are running) ROBOT version (ODK): ROBOT version 1.9.3 robot --catalog catalog-v001.xml convert --input dron-edit.owl --format ofn --output tmp/dron-preprocess.owl robot --catalog catalog-v001.xml reason --input tmp/dron-preprocess.owl --reasoner ELK --equivalent-classes-allowed asserted-only \ --exclude-tautologies structural --output test.owl && rm test.owl

matentzn commented 1 year ago

On the server, or on the local machine? How large is the servers available main memory? This will be the deciding factor here!

matentzn commented 1 year ago

(should be at least 32GB)

hoganwr commented 1 year ago

it's an AWS large instance. Don't know exact number but think it's 64GB but for sure at least 32GB.

On Mon, Feb 20, 2023 at 5:39 AM Nico Matentzoglu @.***> wrote:

(should be at least 32GB)

— Reply to this email directly, view it on GitHub https://github.com/ufbmi/dron/pull/12#issuecomment-1436723240, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJR55VPEWMXZ55ZRRD6RVLWYNCU3ANCNFSM6AAAAAAVBBCSWY . You are receiving this because you commented.Message ID: @.***>

hoganwr commented 1 year ago

I'm checking on this. I was under the impression that the instance I'm working on is a huge one with 64GB RAM. It appears as though that either we downsized it, or there is another instance and I've got them confused. This is on me to sort out at the moment. Many apologies.

On Mon, Feb 20, 2023 at 7:34 AM Bill Hogan @.***> wrote:

it's an AWS large instance. Don't know exact number but think it's 64GB but for sure at least 32GB.

On Mon, Feb 20, 2023 at 5:39 AM Nico Matentzoglu @.***> wrote:

(should be at least 32GB)

— Reply to this email directly, view it on GitHub https://github.com/ufbmi/dron/pull/12#issuecomment-1436723240, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJR55VPEWMXZ55ZRRD6RVLWYNCU3ANCNFSM6AAAAAAVBBCSWY . You are receiving this because you commented.Message ID: @.***>

hoganwr commented 1 year ago

Ok I got the process to run to completion.

Problem: the ChEBI import is broken. All the chebi classes show up at the top level under owl:Thing.

matentzn commented 1 year ago

Anything in the log files to go on?

hoganwr commented 1 year ago

Sorry for taking so long to respond. I think the issue was that I tested it out on the main branch instead of a release branch. I've just run the process again and the problem did not recur. The only difference being this time I ran it on a release branch. It looks good. I will merge the pull request