Bug - or improvements to exception handling needed for building prototypes owl

When building prototypes from here:

https://github.com/obophenotype/Pheno_odk_test/tree/master/src/patterns

`dosdp-tools prototype --obo-prefixes --template=. --outfile=../patterns/pattern.owl`

=>

`Exception in thread "main" java.net.MalformedURLException: no protocol: .
at java.net.URL.(URL.java:593)
at java.net.URL.(URL.java:490)
at java.net.URL.(URL.java:439)
at scala.io.Source$.fromURL(Source.scala:131)
at scala.io.Source$.fromURL(Source.scala:126)
at org.monarchinitiative.dosdp.cli.Common.inputDOSDPFrom(Common.scala:50)
at org.monarchinitiative.dosdp.cli.Common.inputDOSDPFrom$(Common.scala:47)
at org.monarchinitiative.dosdp.cli.Prototype$.inputDOSDPFrom(Prototype.scala:14)
at org.monarchinitiative.dosdp.cli.Prototype$.$anonfun$run$5(Prototype.scala:27)
at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:234)
at scala.collection.immutable.HashSet$HashSet1.foreach(HashSet.scala:320)
at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:976)
at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:976)
at scala.collection.TraversableLike.map(TraversableLike.scala:234)
at scala.collection.TraversableLike.map$(TraversableLike.scala:227)
at scala.collection.AbstractSet.scala$collection$SetLike$$super$map(Set.scala:47)
at scala.collection.SetLike.map(SetLike.scala:101)
at scala.collection.SetLike.map$(SetLike.scala:101)
at scala.collection.AbstractSet.map(Set.scala:47)
at org.monarchinitiative.dosdp.cli.Prototype$.run(Prototype.scala:27)
at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1(Main.scala:33)
at org.monarchinitiative.dosdp.cli.Main$.$anonfun$new$1$adapted(Main.scala:33)
at scala.Option.foreach(Option.scala:257)
at org.monarchinitiative.dosdp.cli.Main$.delayedEndpoint$org$monarchinitiative$dosdp$cli$Main$1(Main.scala:33)
at org.monarchinitiative.dosdp.cli.Main$delayedInit$body.apply(Main.scala:29)
at scala.Function0.apply$mcV$sp(Function0.scala:34)
at scala.Function0.apply$mcV$sp$(Function0.scala:34)
at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12)
at scala.App.$anonfun$main$1$adapted(App.scala:76)
at scala.collection.immutable.List.foreach(List.scala:389)
at scala.App.main(App.scala:76)
at scala.App.main$(App.scala:74)
at org.monarchinitiative.dosdp.cli.Main$.main(Main.scala:29)
at org.monarchinitiative.dosdp.cli.Main.main(Main.scala)`

The '.' in the java.net.MalformedURLException seems to refer to the path to templates directory as I get '../patterns' in its place if running from src/ontology/Makefile.

The same command works when running via the Makefile on (or directly on a target) from the ontology_development_kit. The latter has only a single YAML file in src/patterns, so I assume the problem is due to one of the YAML files in `Pheno_odk_test/tree/master/src/patterns` but haven't (yet) tracked down which. If so, it would be great if the command could tell me which one (and what's wrong with it).

Reproduce the prototype command against src/patterns and compare it with the ontology_development_kit Makefile target. Start with org.monarchinitiative.dosdp.cli.Common.inputDOSDPFrom in Common.scala and the Prototype.scala call site, then inspect the YAML files involved. Done means the offending input is identified and the command reports a useful error instead of only a MalformedURLException.

Written by the indexing model from the issue text.