Real world use of Morpho

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Real world use of Morpho

• KNB Data Management Tools Workshop
• Saurabh Garg
• National Center for Ecological Analysis and
  Synthesis
• University of California, Santa Barbara

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Real world use of Morpho

• Tips for Morpho users
• Morpho backdoors
• Modifying Morpho

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Real world use of Morpho

• Tips for Morpho users
• Morpho backdoors
• Modifying Morpho

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Real world use of Morpho

• Tips for Morpho users
• Save your data package
• Documentation and Data Menu
• stderr.log
• Morpho backdoors
• Modifying Morpho

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Save your data package

• Save your data package whenever you make any
  changes
• If Morpho crashes, you wont loose the changes
  which you have already made
• Avoid the frustration of making those changes
  again

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Save your data package

• On the last screen of Data Package Wizard, there
  is a link for importing data into the data
  package
• Recommended to finish and save your data package
  and then start Data table wizard.

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Before the document is saved
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After the document is saved

• Local Save

• Network
• Save

• Local Network Save

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Documentation and Data menu

• Data packages can be edited using the following
• Documentation Menu
• Data Menu
• Tree Editor

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Documentation menu
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Data menu
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Tree editor
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Documentation and Data menu vs. Tree Editor

• Tree editor is more complex as compared to using
  the menus. It is for advance users as its easy
  to mess up your data package using the tree
  editor.
• Use Documentation and Data menu whenever possible
• Use Tree editor only for tags which can not be
  modified using Documentation and Data menu

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Morpho can do cool things

• Current Morpho release version is 1.5.1
• Morpho can do many cool things like
• Data package wizard
• Geographic coverage screen
• Access screen
• Select creator or contacts from other data
  packages
• New data table wizard
• Parse the table and fills out some metadata for
  you

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But

• sometimes the butterfly keeps on flapping

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stderr.log the Morpho log

• stderr.log is the log file for Morpho which
  contains information about the events that
  occurred as you ran Morpho
• When Morpho hangs or crashes - stderr.log is
  helpful in debugging the problem
• Include stderr.log when you report a Morpho
  problem to Morpho developers.
• Email address for Morpho developers
• morpho-dev_at_ecoinformatics.org

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stderr.log Where is it located?

• stderr.log is located in the directory where
  Morpho was installed.
• On Windows, by default this would be C\Program
  Files\Morpho-1.5.1

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Real world use of Morpho

• Tips for Morpho users
• Morpho backdoors
• Modifying Morpho

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Real world use of Morpho

• Morpho crashing
• Morpho backdoors
• Where is the EML saved locally?
• Importing eml documents
• Using a template for creating data packages
• Modifying Morpho

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Why cant the user specify the location?

• When you save your data package locally, Morpho
  doesnt ask you where you want to save the data
  package
• Users expect to see a Save window in which they
  can browse and specify the save location
• Morpho doesnt have this functionality because it
  has to keep track of all the eml documents for
  the open and search functionalities to work.

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Where are the documents saved?

• Morpho saves EML documents in a location which is
  hidden from the user
• This is because Morpho depends on the way EML
  documents are named in that directory. Hence it
  is easy to mess up the file name format which can
  result in crashing of Morpho

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Eml documents are stored locally in

• . .morpho directory inside user home
  directory
• On Windows XP and Windows 2000, the user home is
  inside Documents and Settings folder
• On Linux, most of times it is going to be inside
  /home

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Versioning and Identifiers

• Metacat and Morpho follow a defined format for
  naming eml documents
• Inside the data directory, there are directories
  representing various scopes
• Inside the scope directories, eml documents are
  stored
• The name given to the eml document doesnt
  include the scope

sgarg.96.1
scope
identifier
revision
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Inside Morpho Open Dialog box
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Importing eml documents into Morpho

• The name of document should in the following
  format a.b.c where
• a is alphanumeric and represents the scope
• b is numeric and represents the identifier
• c is numeric and represents the revision number
• Steps to import an eml document (e.g. a.b.c) into
  Morpho
• Inside the data directory, create a directory
  with the name as the scope. In this case it would
  be a
• Remove the scope from the file name i.e rename
  the document from a.b.c to b.c
• Copy the document to the scope directory.

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Expected results when

• .. the imported document is not a valid eml
  document or is not an eml document at all
• That document wont be shown in the Morpho open
  dialog box
• .. the imported document is not named correctly
• No document would show in the Morpho open dialog
  box

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Using a template for creating data packages

• Sometimes you want to document datasets which
  have same metadata.
• For example, creator, contact, methods and access
  information is same for 5 datasets that you want
  to document. Only the title varies.
• This is a common scenario and users have
  requested the functionality to create templates.

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Create a template

• Create a document in Morpho which can be used as
  a template
• Define all the tags which would be common for the
  documents which you want to include
• This would include the required tags also even if
  they wont be common for all the documents. This
  is because these tags are required for the eml
  document to be valid

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Copy the template

• Once you have the template, you can copy that
  template inside the data/scope_name directory
• The name of the new files should be in the format
  b.c
• Open the file in a text editor and rename
  packageId to the new file name

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Copy the template continued

• Modify the xml file in the profiles directory

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Modify the new data packages

• The new data packages should show up in the
  Morpho Open data package dialog box
• Use Morpho to edit the new data package and save
  the data package after the changes.

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Real world use of Morpho

• Morpho crashing
• Morpho backdoors
• Modifying Morpho

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Modifying Morpho

• Morpho is a open source
• The source code can be downloaded from
  http//knb.ecoinformatics.org/morphoportal.jsp
• You can submit bug fixes and new code back to KNB
  and it will be included in the next release of
  Morpho
• For example Microsoft Access Plugin

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Microsoft Access Plugin

• Microsoft Access Plugin has been created by
  Michael Finch from Scientific Database
  Laboratory, Evergreen State College
• A plugin for Morpho that imports the data
  descriptions for all tables, attributes,
  descriptions, primary keys, and notNullable
  constraints from a given Microsoft Access
  database (description taken from
  http//scidb.evergreen.edu/Members/mike/morphoPlug
  in)
• This uses the plugin architecture inside Morpho

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Acknowledgements
This material is based upon work supported
by The National Science Foundation under Grant
Numbers 9980154, 9904777, 0131178, 9905838,
0129792, and 0225676. The National Center for
Ecological Analysis and Synthesis, a Center
funded by NSF (Grant Number 0072909), the
University of California, and the UC Santa
Barbara campus. The Andrew W. Mellon
Foundation. PBI Collaborators NCEAS, University
of New Mexico (Long Term Ecological Research
Network Office), San Diego Supercomputer Center,
University of Kansas (Center for Biodiversity
Research) Kepler contributors SEEK, Ptolemy II,
SDM/SciDAC, GEON
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Questions/Comments?