Add README.md

README.md

+### Elixibilitas: Quality Metrics tool for Elixir BioTools Registry.
+
+###### Enterprise Java 8 (JEE8) Platform
+Elixibilitas project is strictly adherent to the [JEE8](https://www.jcp.org/en/jsr/detail?id=366) specification.
+The tool is developed and deployed on [WildFly 14.1](http://wildfly.org/) server, 
+but should run on other servers (i.e. [Apache Tomcat](http://tomcat.apache.org/)).
+
+###### MongoDB
+Quality Metrics are stored in [MongoDB](www.mongodb.com)
+
+###### Apache Maven build system
+To simplify build process Elixibilitas uses [Apache Maven](https://maven.apache.org/) build system.
+
+To build Elixibilitas REST application:
+
+Compiling:
+```shell
+>git clone https://gitlab.bsc.es/inb/elixir/tools-platform/elixibilitas/elixibilitas-rest.git
+>cd elixibilitas-rest
+>mvn install
+```
+
+###### REST API
+The REST API is based on [JAX-RS](jcp.org/en/jsr/detail?id=370) API.
+
+> Open API 3.0 (aka Swagger): [https://openebench.bsc.es/monitor/openapi.json](https://openebench.bsc.es/monitor/openapi.json)  
+> Tool JSON Schema: [https://openebench.bsc.es/monitor/tool/tool.json](https://openebench.bsc.es/monitor/tool/tool.json)  
+> Metrics JSON Schema: [https://openebench.bsc.es/monitor/metrics/metrics.json](https://openebench.bsc.es/monitor/metrics/metrics.json)  
+<br/>
+
+The API provides an access to biological tools descriptions:
+```
+https://openebench.bsc.es/monitor/tool/
+```
+> Returns all OpenEBench tools.  
+> The pagination is implemented via the HTTP Range Header (i.g. "Range: tools=10-30").  
+> The response always contains the HTTP Content-Range Header ("Content-Range: tools 10-30/20000").  
+> Alternatively, there are two query parameters: {from} and {to} that may be used instead of the Range Header:  
+>
+> example: [https://openebench.bsc.es/monitor/tool?from=10&to=20](https://openebench.bsc.es/monitor/tool?from=10&to=20) .  
+```
+https://openebench.bsc.es/monitor/tool/{id}
+https://openebench.bsc.es/monitor/tool/{id}/{type}
+https://openebench.bsc.es/monitor/tool/{id}/{type}/{host}
+https://openebench.bsc.es/monitor/tool/{id}/{type}/{host}/{path}
+```
+where:
+- {id} is the prefixed tool id (i.e. "biotools:pmut")
+- {type} is a type of the tool ("web", "app", "cmd", "db", "rest", "soap")
+- {host} is the tool provider which is usually provider's host
+- {path} is a JSON pointer to locate sub-property to return
+
+---
+
+> Note that {id}/{type}/{host} uniquely identify the tool, while omitting the {type} or {host} returns an array of descriptions.  <br/>
+> example 1: [https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org](https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org) .<br/>
+> example 2: [https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org/credits](https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org/credits) .<br/>
+> curl patch tool data example: 
+```
+curl -v -X PATCH -u user:password -H 'Content-Type: application/json' /
+https://openebench.bsc.es/monitor/tool/{id}/description -d '"new description."'
+```
+
+---
+It is also possible to get the list of all tools identifiers providing "Accept: text/uri-list" HTTP header:
+```
+curl -v -H 'Accept: text/uri-list' https://openebench.bsc.es/monitor/tool
+```
+
+Quality Metrics accessed via:
+```
+https://openebench.bsc.es/monitor/metrics/
+https://openebench.bsc.es/monitor/metrics/{id}/{type}/{host}/{path}
+```
+> example 1: [https://openebench.bsc.es/monitor/metrics/biotools:pmut:2017/web/mmb.irbbarcelona.org](https://openebench.bsc.es/monitor/metrics/biotools:pmut:2017/web/mmb.irbbarcelona.org) .<br/>
+> example 2: [https://openebench.bsc.es/monitor/metrics/biotools:pmut:2017/web/mmb.irbbarcelona.org/project/website](https://openebench.bsc.es/monitor/metrics/biotools:pmut:2017/web/mmb.irbbarcelona.org/project/website) .<br/>
+> curl patch metrics data example: 
+```
+curl -v -X PATCH -u user:password -H 'Content-Type: application/json' /
+https://openebench.bsc.es/monitor/metrics/{id}/support/email -d 'true'
+```
+or, what is the same:
+```
+curl -v -X PATCH -u user:password -H 'Content-Type: application/json' /
+https://openebench.bsc.es/monitor/metrics/{id} -d '{"support.email": true}'
+```
+the former patches the json using JSON Patch, while the latter uses mongodb 'upsert' notation.
+
+---
+It is possible to query tools:
+```
+https://openebench.bsc.es/monitor/rest/search?id={id}&{projection}&{text}&{name}&{description}
+```
+where:
+- {id} is the compound tool id (i.e. "pmut", "biotools:pmut", ":pmut:2017")
+- {projection} tools properties to return
+- {text} text to search
+> The method is thought for the client's GUI that may use a pagination mechanism.  
+> The pagination is implemented via the HTTP Range Header (i.g. "Range: tools=10-30").  
+> The response always contains the HTTP Content-Range Header ("Content-Range: tools 10-30/10000").  
+> When pagination is used, the server seponds with 206 Partial Content.  
+> There is also possibility to use query parameters {skip} and {limit} (range 10-30 = skip 10, limit 20).  
+
+<br/>
+
+> The results are grouped by the id and sorted by names.  <br/>
+> example 1: [https://openebench.bsc.es/monitor/rest/search](https://openebench.bsc.es/monitor/rest/search) .<br/>
+> example 2: [https://openebench.bsc.es/monitor/rest/search](https://openebench.bsc.es/monitor/rest/search) .<br/>
+> example 3: [https://openebench.bsc.es/monitor/rest/search?id=pmut](https://openebench.bsc.es/monitor/rest/search?id=pmut) .<br/>
+> example 4: [https://openebench.bsc.es/monitor/rest/search?text=alignment](https://openebench.bsc.es/monitor/rest/search?text=alignment)  .<br/>
+
+---
+
+The METRICS API that aggregates some metrics:
+```
+https://openebench.bsc.es/monitor/rest/metrics/availability/{id}
+```
+> example: [https://openebench.bsc.es/monitor/rest/metrics/availability/trimal](https://openebench.bsc.es/monitor/rest/metrics/availability/trimal) .<br/>
+
+---
+
+The API also provides EDAM descriptions for the tool:
+```
+https://openebench.bsc.es/monitor/rest/edam/tool/
+https://openebench.bsc.es/monitor/rest/edam/tool/{id}/{type}/{host}
+```
+> example: [https://openebench.bsc.es/monitor/rest/edam/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org](https://openebench.bsc.es/monitor/rest/edam/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org) .
+
+or descriptions of the EDAM term itself:
+```
+https://openebench.bsc.es/monitor/rest/edam/description?term={edam id}
+```
+> example: [https://openebench.bsc.es/monitor/rest/edam/description?term=http://edamontology.org/format_3607](https://openebench.bsc.es/monitor/rest/edam/description?term=http://edamontology.org/format_3607) .
+
+There is also full text search over EDAM ontology.
+```
+https://elixir.bsc.es/monitor/rest/edam/search?text={text to search}
+```
+> example: [https://openebench.bsc.es/monitor/rest/edam/search?text=alignment](https://openebench.bsc.es/monitor/rest/edam/search?text=alignment) .
+
+There are simple stat info that can be obtained from the server:
+
+>[https://openebench.bsc.es/monitor/rest/statistics](https://openebench.bsc.es/monitor/rest/statistics) : basic statistics.  
+>[https://openebench.bsc.es/monitor/rest/statistics/total](https://openebench.bsc.es/monitor/rest/statistics/total) : total number of tools.  
+>[https://openebench.bsc.es/monitor/rest/statistics/operational](https://openebench.bsc.es/monitor/rest/statistics/operational) : number of tools those homepage is accessible.
+
+```
+https://openebench.bsc.es/monitor/rest/statistics/{tool_type} : number of tools of particular type ("web", "cmd", etc.)
+```
+> example: [https://openebench.bsc.es/monitor/rest/statistics/cmd](https://openebench.bsc.es/monitor/rest/statistics/cmd) .
+
+All changes are stored in a log collection and could be accessed:
+
+```
+https://openebench.bsc.es/monitor/tools/log/{id}/{type}/{host}/{path}
+https://openebench.bsc.es/monitor/metrics/log/{id}/{type}/{host}/{path}
+```
+> example: [https://openebench.bsc.es/monitor/metrics/log/biotools:pmut:2017/cmd/mmb.irbbarcelona.org/project/website/operational](https://openebench.bsc.es/monitor/metrics/log/biotools:pmut:2017/cmd/mmb.irbbarcelona.org/project/website/operational) .
+
+###### OWL2 Ontology
+There is an ontological view to the OpenEBench tools.
+
+The tools ontology is located at:
+
+> [https://openebench.bsc.es/monitor/tools.owl](https://openebench.bsc.es/monitor/tools.owl)
+
+The tools data may be obtained in OWL2 JSON-LD format for any concrete tool record:<br/>
+> [https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org](https://openebench.bsc.es/monitor/tool/biotools:pmut:2017/web/mmb.irbbarcelona.org)
+
+or for the entire tools collection:<br/>
+> [https://openebench.bsc.es/monitor/tool/](https://openebench.bsc.es/monitor/tool/)
+
+The decision to return JSON or JSON-LD is taken on the HTTP "Accept" header.  
+<br/>
+These URLs may be imported into [Protegé](https://protege.stanford.edu/) tool.  
+**NB:** Entire ontology is very big and exceeds the default Protegé memory settings.