Documentation request

[matentzn]

@cmungall

1. Please supply the run.sh file
2. Add three lines of description of what rdf_matcher actually does internally - seems to be more than just label and synonym matching :)

Thanks

[wdduncan]

Something about the docker file is not working right. When I run the commands:

docker run --rm cmungall/rdf_matcher -f tsv -i tests/data/basic.ttl match
docker run -d cmungall/rdf_matcher -f tsv -i tests/data/basic.ttl match
docker run -it cmungall/rdf_matcher -f tsv -i tests/data/basic.ttl match
docker run --rm cmungall/rdf_matcher -p x -f tsv -i tests/data/basic.ttl match

I receive the errors:

docker: Error response from daemon: OCI runtime create failed: container_linux.go:346: starting container process caused "exec: \"-f\": executable file not found in $PATH": unknown.

docker: Error response from daemon: OCI runtime create failed: container_linux.go:346: starting container process caused "exec: \"-p\": executable file not found in $PATH": unknown.

The difference in errors being with I passed a -f or p flag.

I opened and interactive session with the docker container using:

docker run -it cmungall/rdf_matcher /bin/bash

When I run this command runs within /tools directory:

swipl -p library=prolog ./bin/rdfmatch -h

I receive a message about flags to use with Prolog (e.g., --output, --format, etc.)

When I run this command:

swipl -p library=prolog ./bin/rdfmatch -p x -f tsv -i tests/data/basic.ttl match

It returns:

% Loaded "basic.ttl" in 0.00 sec; 153 triples
error(existence_error(procedure,io_utils:opt_if/3),context(io_utils:write_result/2,_22584))

I don't know how to debug this :(

[wdduncan]

@cmungall
Another follow up:
From my command line in the root of the rdf_matcher repo I can run:

swipl -p library=prolog ./bin/rdfmatch -p x -f tsv -i tests/data/basic.ttl match

This starts outputting lines like:

x:eye	y:eye	UBERON:0000970	info(xref-xref,rdf(x:eye,oio:hasDbXref,UBERON:0000970)-rdf(y:eye,oio:hasDbXref,UBERON:0000970),null)
x:eye	z:eye	UBERON:0000970	info(xref-xref,rdf(x:eye,oio:hasDbXref,UBERON:0000970)-rdf(z:eye,oio:hasDbXref,UBERON:0000970),null)
x:eye	y:eye	UBERON:0000970	info(xref-xref,rdf(x:eye,oio:hasDbXref,UBERON:0000970)-rdf(y:eye,oio:hasDbXref,UBERON:0000970),null)
x:eye	y:eye	UBERON:0000970	info(xref-xref,rdf(x:eye,oio:hasDbXref,UBERON:0000970)-rdf(y:eye,oio:hasDbXref,UBERON:0000970),null)

However, although rdfmatch is in my path, I cannot run:

rdfmatch -p x -f tsv -i tests/data/basic.ttl match

This returns:

Warning: /Users/wdduncan/lib/swipl/pack/rdf_matcher/prolog/rdf_matcher.pl:64:
	:- table/1 is built-in.  library(tabling) is deprecated.
% Loaded "basic.ttl" in 0.00 sec; 153 triples
x:appendage	y:appendage	appendag	info(label-label,rdf(x:appendage,rdfs:label,appendage)-rdf(y:appendage,rdfs:label,appendages),stem)
error(existence_error(procedure,add_match_to_graph/3),context(write_result_wrap/2,_58882))

Is there some path setting I need to add so that the necessary modules can be found?

[cmungall]

Added run.sh with d973082

[cmungall]

docker run --rm cmungall/rdf_matcher -f tsv -i tests/data/basic.ttl match

yep, you are passing the -f etc to the docker command. You need to specify the command docker should run. See run.sh

[cmungall]

OK, it looks like you are getting the desired results running directly from swipl

Running outside the repo:

EITHER

1. do a pack_install(rdf_matcher)

This will install from the latest release not github

OR

(this seems horrible but I haven't found a better way of doing this)

cd ~/lib/swipl/pack
ln -s ~/repos/rdf_matcher

The latter way is better if you want to make frequent changes to the rdf_matcher code