Issue 209 ability to save visualisation as package and mint doi for package

[jasensch]

Contains two commits from the ANUPhylolink fork:

Increment the version in build.gradle to be 0.7.0-SNAPSHOT as agreed with Temi;
Updated README.md file to reflect the latest instructions to set up a local development environment;
Moved groovy files to their defined package (their compiled bytecode ends up in the defined package and not the current folder in the built war), to fix Errors messages detected by the Groovy Plug-in for Eclipse;
Updated the defined packaged of ChartController.groovy to match the folder it is currently in ... there was no direct reference to this class and calling code in UrlMappings.groovy (in a different package) uses controller: 'chart' to refer to the ChartController, so changing the defined package is not expected to cause any issues;
In build.gradle added a pathingJar to address gradle/gradle#1989;

Issue 209: Ability to save visualisation as package and mint DOI for package (#209);
Issue 210: Ability to list 'expert/DOI' visualisation packages (via visualisation name) and allow user to select one to display (use) (#210);

• More user friendly message shown to an unauthenticated user trying to access a visualisation (that is not a demonstration visualisation), as apart from demonstration visualisations, to view a visualisation the user must now be authenticated.
• added a "Metadata" tab to capture the fields to create an expert visualisation that will form a permanent digital object identifier (doi) reference (not shown for demonstration visualisations)
• the Metadata tab requires an occurrence data set to be selected before a doi visualisation can be created. A Character data set is optional.
• parse the Species names from the tree and show on the metadata tab, prepopulate the Genus field from the first word (based on the first space or underscore) in the Species names.
• On the Characters tab, and at the point in the existing application when characters are associated with the visualisation, show a characters section on the Metadata tab. This characters section will have 2 mandatory fields for each trait: description and classification (one of: continuous, integer, discrete, or categorical)
• On the metadata tab allow the Character trait metadata to be loaded from a csv as an alternative to doing the data entry manually
• Allow the saving of data on the metadata tab, without having all mandatory information provided. However, when a workflow action is attempted, all mandatory information is still validated that it has been provided.
• added a workflow (see /documentation/visualisation_workflow_status_diagram) to allow the approval and feedback on visualisations. During the workflow, all workflow administrators (
  currently identified by having the PHYLOLINK_ADMIN role) are emailed when an author requests approval (they are also sent a For your information email when the visualisation is handled by someone else). The visualisation author is emailed when the visualisation is "Approve and Publish" or "Revision Required" by a Workflow Admin.
• Prevent the removal of data sets (occurrences and character traits) that are associated with a visualisation that is Published.
• Prevent the editing of tree metadata by a phylolink admin, if the tree is associated with a Published visualisation
• On the characters tab fixed current production behaviour when a file is uploaded that has no species that overlap with the tree, as the uploaded file is set to be the selected characters, but on reload any characters that do not overlap with the tree are filtered out, so the previously selected characters is changed to the first characters file available, which wasn't selected by the user.
• On the characters tab fixed current production behaviour, when the current character file is removed another characters file would be selected if there was one in the dropdown , (both on the screen and when reloaded), now the Choose option is selected
• When adding a character to the tree (on the Characters tab), the character metadata description is shown, if it exists
• On the Start Phylolink page, alert if there are any visualisations that require the attention of the logged on user (which are those in status of "Revision Required" for authors and "Requested Approval" for Workflow Admins, with a link to the list of the visualisations
• On the Start Phylolink page, add an option to view Published visualisations in reverse chronological order that they were published
• On the Published visualisations page, implement the text phrase search filter (where each word (limited to the first 5) in the search phrase must exist (case insensitive) in at least one of the following visualisation fields: title, genus, species, created by, doi)
• Moved sample csv files from src/main/webapp to src/main/resources/public so they are packaged in the JAR (see https://gsp.grails.org/latest/guide/resources.html) that is run in non-development environments, to fix the 404 errors currently in production;
• Updated README.md for receiving emails in local environments, change nameindexes to match production which is 20171012, fix for web2py restart issues in the vagrant container;
• New parameters in /data/phylolink/config/phylolink-config.properties (ones that are commented out show their default values):
  alaDoiUrl = https://doi-test.ala.org.au
  alaDoiUrl_webservice_apiKey = secret_key_value
  #doi.author = Atlas Of Living Australia
  #doi.provider = ANDS
  #doi.description = ALA phylolink visualisation
  doi.titlePrefix = Phylolink visualisation -
  #doi.citationUrlPrefix = https://doi.org/
  doi.licences.1 = Creative Commons Attribution (Australia) (CC-BY 3.0 (Au))
  doi.licences.2 = Creative Commons Attribution (International) (CC-BY 4.0 (Int))