FAQ

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General

What is mx being used for?

What software is needed to run mx?

  • Mx can run on a wide range of platforms. See Installation.

Can you run mx locally and then sync your data to the server?

  • answer

Can I run mx without a web-based server?

  • Yes, the application can be run locally, though it hasn't been designed with this in mind or optimized (speed) for this usage. Keep in mind you won't be able to share the application over the network or internet, i.e. it could only be accessed at one machine.

Data model

Can I see the schema?

  • The database is built through rails migrations. After installation you can dump a copy of the schema with the rake task 'rake db:schema:dump'. You can also see a little preview in this figure.

What do all the abbreviations in tables/fields mean?

Data entry/import

How do I load a Nexus file into mx?

  • See the "Phylo" tab and follow the directions here.

What mechanisms are available for entering data?

  • Data can be entered in a number of different ways
    • individually via forms
    • in batches via the web interface
    • in batches via the server side console (Rake tasks)
    • individually via the Rails console

Manually entering data one a time can be very annoying, what kind of data can I batch load into mx?

  • Nexus formatted matrices
  • Lucid's .xls formatted exports
  • .obo formatted files (in part)
  • Newick formatted trees
  • Specimens and lots
  • Individual Otu names
  • Verbatim collecting events (labels)
  • Single word epithets (children) of taxon names (e.g. species names for a genus or genera of a family)
  • Image files (via a Rake task/command line)
  • References to MorphBank images
  • Endnote
  • FASTA

Can projects be merged?

  • Yes, data can be moved from one project to another, though not all synonymous data are merged at present. You'll need to use the console interface to do this. See the Proj#merge_to_project.

Data export/access

What formats can matrices be exported to?

  • NeXML, Nexus, TNT, ASCII tables, and mx database tables

Production servers

What's the preferred production/development update path?

  • BACKUP DATA with 'rake mx:db:dump_data', a dump goes in /db/dumps. Update source (at present the latest source is on the relatively stable /edge/branch). Migrate the database with 'rake db:migrate RAILS_ENV=development' (you may want to test prior to or after this step with 'rake test'). Dump the data again (first step). Copy this copy to db/dumps in your development environment. Load it with 'rake mx:db:restore_last' (note his dumps the current development, so if the reload fails you'll have to delete this dump as it will be more recent than your production copy). Develop. Repeat.

Clicking on a figure on a public site is giving me a 404, how do I fix this?

  • Choose edit for project settings and make the figure controller public by checking it.

Matrix based species descriptions

Can mx generate matrix based descriptions?

Yes. Mx has a very flexible content handling system which includes the functionality of using coded characters (sensu morphological phylogenetics) into species descriptions. This is similar functionality to that done in Delta, Lucid, or vSysLab, but with some modifications. See Matrix based descriptions.

Taxonomic names

Why can't I see taxonomic names in my project?

  • Visibility of names is dynamically set. Go to the Taxon names tab, then more options->visibility select the parent node you want visible. The taxon names will now be visible and available for use. Removing names from visibility does not delete them, nor invalidate records that reference those names. Visibility is used to focus your workflow, limiting the options in the dropdown, and the data you are reviewing.

General errors

I can't upload files, particularly pdfs, why?

  • Firefox has a known bug in which the MimeType can be corrupted. See [this page]. Close FF. Delete your mimeTypes.rdf file in your FF profile, reopen.

Production/server gotchas.

mx suddenly can't load pdfs or images.

rake db:migrate RAILS_ENV=production fails when a model is not found

  • This can occur when updates occur out of sync on in large groups. To resolve edit config/environments/production.rb and change the following line from true to false config.cache_classes = false, run the migrations, then set back to true.

This wiki

There used to be some pages on this wiki, now I can't find them?

  • Mx has been used/in development for over 5 years now, as such there are various "legacy" pages here on the wiki that may or may not have as much relevance as they do now. Legacy pages for references to these.
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