Merge pull request #328 from mpsonntag/templates

Add odML templates support

Author: jgrewe

doc/example_odMLs/THGTTG.odml

@@ -2,7 +2,7 @@
 <?xml-stylesheet  type="text/xsl" href="odmlTerms.xsl"?>
 <?xml-stylesheet  type="text/xsl" href="odml.xsl"?>
 <odML version="1.1">
-  <repository>http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml</repository>
+  <repository>https://terminologies.g-node.org/v1.1/terminologies.xml</repository>
   <version>42</version>
   <section>
     <name>TheCrew</name>

doc/example_odMLs/sample_odml.odml

@@ -3,7 +3,7 @@
 <?xml-stylesheet  type="text/xsl" href="odml.xsl"?>
 <odML version="1.1">
   <author>D. N. Adams</author>
-  <repository>http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml</repository>
+  <repository>https://terminologies.g-node.org/v1.1/terminologies.xml</repository>
   <section>
     <property>
       <type>person</type>

doc/example_odMLs/sample_odml.rdf

@@ -83,5 +83,5 @@ odml:d98afe9b-3982-44bf-9373-12aaa4798628 a rdf:Bag ;
         "Tricia Marie McMillan",
         "Zaphod Beeblebrox" .
 
-<https://g-node.org/projects/odml-rdf#7e0e07c7-7501-454e-88e7-cfa072db94c1> a <http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml> .
+<https://g-node.org/projects/odml-rdf#7e0e07c7-7501-454e-88e7-cfa072db94c1> a <https://terminologies.g-node.org/v1.1/terminologies.xml> .
 

doc/example_odMLs/thgttg.py

@@ -25,7 +25,7 @@
 save_to = os.path.join(output_directory, "THGTTG.odml")
 
 
-odmlrepo = 'http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml'
+odmlrepo = 'https://terminologies.g-node.org/v1.1/terminologies.xml'
 
 # CREATE A DOCUMENT
 doc = odml.Document(author="D. N. Adams",

doc/example_rdfs/example_data/drosophila_2.ttl

@@ -643,5 +643,5 @@ odml:fadffec7-6b23-454e-bfd1-9d5884802abb a odml:Property ;
 odml:ff5fb5e5-5104-41c8-ab45-9d8787e7fbdc a rdf:Bag ;
     rdf:li "simpleErg" .
 
-<https://g-node.org/projects/odml-rdf#7517fc3b-a12c-47b3-bfc5-96cc98fefa8a> a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
+<https://g-node.org/projects/odml-rdf#7517fc3b-a12c-47b3-bfc5-96cc98fefa8a> a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
 

doc/example_rdfs/example_data/drosophila_4.ttl

@@ -1352,5 +1352,5 @@ odml:fedefe26-0f36-433f-993d-ad827dcb0a50 a odml:Property ;
     odml:hasUnit "ms" ;
     odml:hasValue <https://g-node.org/projects/odml-rdf#7fe2ea64-262c-4cdd-acd2-4d59c42cd4aa> .
 
-<https://g-node.org/projects/odml-rdf#9cf7f270-eb40-4406-a78b-d5de29fe5879> a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
+<https://g-node.org/projects/odml-rdf#9cf7f270-eb40-4406-a78b-d5de29fe5879> a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
 

doc/example_rdfs/example_data/drosophila_8.ttl

@@ -1351,5 +1351,5 @@ odml:fe6a8363-a5f4-46ed-8eea-b57257d4823b a odml:Property ;
 odml:ff532446-ca25-4092-8abb-302e12344b3b a rdf:Bag ;
     rdf:li "1.0" .
 
-odml:b0d95b14-a12f-4057-aed3-fdd3a6ea5f82 a <http://portal.g-node.org/odml/terminologies/v1.0/terminologies.xml> .
+odml:b0d95b14-a12f-4057-aed3-fdd3a6ea5f82 a <https://terminologies.g-node.org/v1.0/terminologies.xml> .
 

doc/odml_ontology/root-ontology.ttl

@@ -227,7 +227,7 @@ rdf:Seq rdf:type owl:Class ;
       rdfs:subClassOf :Section ;
       rdfs:comment "Description"^^xsd:string ;
       rdfs:label "Cell" ;
-      rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/cell/cell.xml> .
+      rdfs:seeAlso <https://terminologies.g-node.org/v1.0/cell/cell.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#CellProperties
@@ -242,15 +242,15 @@ rdf:Seq rdf:type owl:Class ;
                  rdfs:subClassOf :Section ;
                  rdfs:comment "Description"^^xsd:string ;
                  rdfs:label "DataAcquisition" ;
-                 rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/hardware/daq.xml> .
+                 rdfs:seeAlso <https://terminologies.g-node.org/v1.0/hardware/daq.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Dataset
 :Dataset rdf:type owl:Class ;
          rdfs:subClassOf :Section ;
          rdfs:comment "Description"^^xsd:string ;
          rdfs:label "Dataset" ;
-         rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/dataset/dataset.xml> .
+         rdfs:seeAlso <https://terminologies.g-node.org/v1.0/dataset/dataset.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Document
@@ -298,23 +298,23 @@ rdf:Seq rdf:type owl:Class ;
            rdfs:subClassOf :Section ;
            rdfs:comment "Description"^^xsd:string ;
            rdfs:label "Electrode" ;
-           rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/electrode/electrode.xml> .
+           rdfs:seeAlso <https://terminologies.g-node.org/v1.0/electrode/electrode.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Hardware
 :Hardware rdf:type owl:Class ;
           rdfs:subClassOf :Section ;
           rdfs:comment "Description"^^xsd:string ;
           rdfs:label "Hardware" ;
-          rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/hardware/hardware.xml> .
+          rdfs:seeAlso <https://terminologies.g-node.org/v1.0/hardware/hardware.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#HardwareSettings
 :HardwareSettings rdf:type owl:Class ;
                   rdfs:subClassOf :Section ;
                   rdfs:comment "Description"^^xsd:string ;
                   rdfs:label "HardwareSettings" ;
-                  rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/collection/hardware_settings.xml> .
+                  rdfs:seeAlso <https://terminologies.g-node.org/v1.0/collection/hardware_settings.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Hub
@@ -338,7 +338,7 @@ rdf:Seq rdf:type owl:Class ;
              rdfs:subClassOf :Section ;
              rdfs:comment "Description"^^xsd:string ;
              rdfs:label "Preparation" ;
-             rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/preparation/preparation.xml> .
+             rdfs:seeAlso <https://terminologies.g-node.org/v1.0/preparation/preparation.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Property
@@ -394,7 +394,7 @@ rdf:Seq rdf:type owl:Class ;
            rdfs:subClassOf :Section ;
            rdfs:comment "Description"^^xsd:string ;
            rdfs:label "Recording" ;
-           rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/recording/recording.xml> .
+           rdfs:seeAlso <https://terminologies.g-node.org/v1.0/recording/recording.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Section
@@ -457,23 +457,23 @@ rdf:Seq rdf:type owl:Class ;
        rdfs:subClassOf :Section ;
        rdfs:comment "Description"^^xsd:string ;
        rdfs:label "Setup" ;
-       rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/setup/setup.xml> .
+       rdfs:seeAlso <https://terminologies.g-node.org/v1.0/setup/setup.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Stimulus
 :Stimulus rdf:type owl:Class ;
           rdfs:subClassOf :Section ;
           rdfs:comment "Description of the Stimulus."^^xsd:string ;
           rdfs:label "Stimulus" ;
-          rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/stimulus/stimulus.xml> .
+          rdfs:seeAlso <https://terminologies.g-node.org/v1.0/stimulus/stimulus.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Subject
 :Subject rdf:type owl:Class ;
          rdfs:subClassOf :Section ;
          rdfs:comment "Description"^^xsd:string ;
          rdfs:label "Subject" ;
-         rdfs:seeAlso <http://portal.g-node.org/odml/terminologies/v1.0/subject/subject.xml> .
+         rdfs:seeAlso <https://terminologies.g-node.org/v1.0/subject/subject.xml> .
 
 
 ###  https://g-node.org/projects/odml-rdf#Terminology

doc/tutorial.rst

@@ -71,7 +71,7 @@ The code for the example odML files, which we use within this tutorial is part
 of the documentation package (see doc/example_odMLs/).
 
 A summary of available odML terminologies and templates can be found `here
-<http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml>`_.
+<https://terminologies.g-node.org/v1.1/terminologies.xml>`_.
 
 -------------------------------------------------------------------------------
 
@@ -221,7 +221,7 @@ them to build your own metadata odML file will be described in later chapters.
 Further advanced functions you can use to navigate through your odML files, or to
 create an odML template file, or to make use of common odML terminologies
 provided via `the G-Node repository
-<http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml>`_ can also
+<https://terminologies.g-node.org/v1.1/terminologies.xml>`_ can also
 be found later on in this tutorial.
 
 But now, let us first have a look at the example odML file (THGTTG.odml)!
@@ -289,7 +289,7 @@ Let's check out all attributes with the following commands::
     >>> print(odmlEX.parent)
     None
     >>> print(odmlEX.repository)
-    http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml
+    https://terminologies.g-node.org/v1.1/terminologies.xml
     >>> print(odmlEX.version)
     42
 

docs/data_model.md

@@ -1,19 +1,19 @@
-# odml data model
+# The odML data model
 
-Data exchange requires that also annoations, metadata, are
-exchanged. In oder to allow interoperability we need both a common
+Data exchange requires that annotations, metadata, are also
+shared. In order to allow interoperability both a common
 (meta) data model, the format in which the metadata are exchanged, and
-a common terminology.
+a common terminology are required.
 
 Here, we briefly describe the *odML* data model. It is based on
 the idea of key-value pairs like ``temperature = 26°C``.
 
 The model is as simple as possible while being flexible, allowing
-interoperability, and being customizable. The model defines four
-entities (Property, Section, Value, RootSection) whose relations and
+interoperability, and being customizable. The model defines three
+entities (Property, Section, Document) whose relations and
 elements are shown in the figure below.
 
-![odml_logo](images/erModel.png "odml data model")
+![odml_logo](images/erModel.png "odML data model")
 
 Property and Section are the core entities. A Section contains
 Properties and can further have subsection thus building a tree-like

docs/index.md

@@ -28,13 +28,18 @@ It is a registered research resource with the
 - [odml-ui](https://github.com/g-node/odml-ui "odml-ui - editor for odml metadata files"): Graphical editor
 - [odmlTables](https://github.com/INM-6/python-odmltables) Spreadsheet interface (by INM-6 FZ JÛlich) for odml files.
 
+
 ### Terminologies
 *odML* facilitates and encourages standardization by providing
 [terminologies](https://github.com/G-Node/odml-terminologies). An
 odml-file can be based on such a terminology. In that case one does
 not need to provide definitions since they are part of the linked
 terminology.
 
+Existing terminologies can be browsed and imported from 
+[terminologies.g-node.org](https://terminologies.g-node.org).
+
+
 ### Templates
 Templates are odML documents that can be re-used when collecting the same kind of
 information over the course of multiple identical experiments.
@@ -46,7 +51,10 @@ discussed and shared at the
 
 If you have created your own templates that others might find useful, 
 you are encouraged to share your templates via this repository.
-  
+
+Currently available odML templates can be browsed and imported from
+[templates.g-node.org](https://templates.g-node.org).
+
 
 * * *
 
@@ -67,15 +75,17 @@ pip install odml
 
 ### Python convenience scripts
 
-The Python installation features two convenience commandline scripts.
+The Python installation features multiple convenience commandline scripts.
 
 - `odmlconversion`: Converts odML files of previous file versions into the current one.
 - `odmltordf`: Converts odML files to the supported RDF version of odML.
+- `odmlview`: Render and browse local XML odML files in the webbrowser.
 
-Both scripts provide detailed usage descriptions by adding the help flag to the command.
+All scripts provide detailed usage descriptions by adding the `help` flag to the command.
 
     odmlconversion -h
     odmltordf -h
+    odmlview -h
 
 ### odML - NIX conversion script
 
@@ -90,7 +100,7 @@ You can install the command line script via pip:
 
 
 The script can then be run from the command line and provides a detailed usage
-description by adding the help flag to the command.
+description by adding the `help` flag to the command.
 
 
     nixodmlconverter -h