micheldumontier / php-lib Goto Github PK

Need to add the date at which the data files were downloaded.

this will probably cause a level of indirection in the provenance generation from

bio2rdf-dataset-version <-> dataset

to

bio2rdf-dataset-version <-> dataset-version <-> dataset

the pubchem bio2rdf parser needs a pubchembioactivity namespace.

I want to suggest that all literals created using either QuadL (rdfapi.php @ line 133) or QQuadL (rdfapi @ line 171) call SafeLiteral (rdfapi.php @ line 252).

Also SafeLiteral should only create Unicode compliant strings. This can be done using utf8-encode in php (http://php.net/manual/en/function.utf8-encode.php)

enable the control of log messages by setting a configurable filter.

There is a list of namespaces in bio2rdf-webapp that could be used to maintain the information that is currently hardcoded in ns.php.

See the files in the following directory for examples:

https://github.com/bio2rdf/bio2rdf-webapp/tree/develop/src/main/resources/config/namespaces

The schema for these namespace entries is currently generated from java files in queryall, including:

https://github.com/queryall/queryall/blob/develop/queryall-api/src/main/java/org/queryall/api/namespace/NamespaceEntrySchema.java

https://github.com/queryall/queryall/blob/develop/queryall-api/src/main/java/org/queryall/api/namespace/ValidatingNamespaceEntrySchema.java

https://github.com/queryall/queryall/blob/develop/queryall-api/src/main/java/org/queryall/api/namespace/RegexValidatingNamespaceEntrySchema.java

The namespace entry schema may need additions to match the information in ns.php, but in the end it will be easier to maintain these lists in RDF rather than inside of PHP.

I'm using this lib from one of the bio2rdf scripts and I've got an error for PHP not being able to find "application.php". Copying the file from the previous commit (it was deleted in the last one) it worked. May be the file was deleted by mistake?

php-lib needs to offer a configurable directory paths option to remove the need for patches like the following in issue bio2rdf-scripts#150 https://github.com/bio2rdf/bio2rdf-scripts/pull/150.patch :

•   $this->AddParameter('indir',false,null,'/media/twotb/bio2rdf/data/homologene','directory to download files');
  

•   $this->AddParameter('outdir',false,null,'/media/twotb/bio2rdf/n3/gene/','directory to place rdfized files');
  

•   $this->AddParameter('indir',false,null,'/data/download/homologene','directory to download files');
  

•   $this->AddParameter('outdir',false,null,'/data/rdf/homologene/','directory to place rdfized files');
  

abstract more of the common command line options
refactor content out of rdfapi.php
interface with the new registry
offer a simpler set of api calls (describe, triplify)