Adds manifest verification warning message to the load_one_app script

nschwertner commented 12 years ago

This should do it, but we should test it a bit.

jmandel commented 12 years ago

I don't see how this works without init.py in common. On May 23, 2012 7:35 PM, "nschwertner" < reply@reply.github.com> wrote:

This should do it, but we should test it a bit.

Reply to this email directly or view it on GitHub: https://github.com/chb/smart_server/pull/21#issuecomment-5889432

nschwertner commented 12 years ago

That's not a problem. There is an init.py in the smart_common/rdf directory, which I symlinked as needed. Works on my VM.

nschwertner commented 12 years ago

It looks like we are not using the python client at the smart_server level. Only the modules in the common package are being used in the following scripts:

load_tools/load_one_patient.py smart/lib/i2b2_export.py smart/lib/utils.py smart/lib/wiki_apidocs.py smart/models/accounts.py smart/models/ontology_url_patterns.py smart/models/rdf_rest_operations.py smart/models/record_object.py smart/models/records.py smart/plugins/record_proxy_backend.py smart/triplestore/base.py smart/triplestore/triplestore.py smart/views/smarthacks.py structured_product_label/models.py

I am thinking of dropping the python client altogether from the smart_server, now that the shared code is in the smart_common module and updating these files accordingly.

jmandel commented 12 years ago

symlinking gets messy fast! I'm seeing two different checkouts of smart_common:

smart_server/client/smart_common
smart_server/common

And symlinks from:

smart_server/smart/schema
smart_server/smart/client/common

Right now smart_server only needs smart_common. It doesn't use smart_client at all, except to access the common subdir:

~/smart/smart_server$ grep -r "smart.client" * | grep -v common
[no output]

I would propose:

Remove the smart_client submodule from smart_server
Remove all symlinks
Add __init__.py to smart_common
Update code in smart_server to use appropriate paths.
Update README.md to use git clone --recursive

The files referenced in 4 are:

~/smart/smart_server$ grep -ril "smart.client.common" *
load_tools/load_one_patient.py
smart/triplestore/triplestore.py
smart/triplestore/base.py
smart/plugins/record_proxy_backend.py
smart/models/ontology_url_patterns.py
smart/models/records.py
smart/models/record_object.py
smart/models/accounts.py
smart/models/rdf_rest_operations.py
smart/views/smarthacks.py
smart/lib/wiki_apidocs.py
smart/lib/i2b2_export.py
smart/lib/utils.py
structured_product_label/models.py

nschwertner commented 12 years ago

Great minds think alike. ;) Already on it! :)

nschwertner commented 12 years ago

Ok, I think we are good. I updated smart_server (manifest_verify branch), smart_sample_patients (dev branch), and smart_sample_apps (dev branch). Tested everything on a VM and it works fine. Please verify and merge with the dev branch, if it looks good to you.

jmandel commented 12 years ago

`smart_sample_apps` has

redundant modules (smart_client and smart_common).
static/framework/smart/scripts/build.py referring to "../../../../../smart_server/smart/document_processing/schema/smart.owl"
api_verify/main.py has its own copy of the ontology (and refers to APP_PATH + '/data/smart.owl' x4)

`smart_sample_patients`

bin/ontology_service.py refers to "(SMART_SERVER_PATH + 'smart/document_processing/schema/smart.owl"

nschwertner commented 12 years ago

All right, I fixed all of the above and retested on the VM. Looks good.

I think we are done with this surgery. Let's close it up. Hopefully, no scalpels or bandages left inside. ;)

smart-classic / smart_server