Morpho User Guide

 

Help Index

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Frequently Asked Questions
1. How do I get Help?
2. How can I get more information on problems?
3. What are the system requirements for running Morpho?
4. Can I customize Morpho in any way?
5. Where are my local data packages stored? What happens to my local data packages when I upgrade to a newer version of Morpho?
6. How can I automatically extract data documentation from a data file for entry into Morpho?
7. How do I import an Excel file into Morpho?
8. How can I add data to a data table?
9. How do I provide information on taxonomic coverage in the form of a data table?
10. How can I add an image to my data package?
11. How do I view and edit documentation on my attributes?
12. What is the difference between synchronizing a data package and saving a data package to the network?
13. What happens with network data packages created with older versions of Morpho?
14. How do I delete a saved search?
15. How do I delete a profile?
16. How can I "Export" a data package? The Export menu item doesn't seem to work.
17. What are the keyboard shortcuts available in Morpho?

1. How do I get help?

If Morpho is running, you should be able to use the "Help" menu located at the top of each window. You can also open the "docs/user" directory in the directory where Morpho was installed and then open the file "index.html" in your browser (usually by double clicking on the file name). This will display the same help files as you would see when using Morpho's Help menu. The Morpho User Guide, found under the "Help" menu, contains information on a variety of topics and uses of Morpho. Examine the index of the Morpho User Guide to determine where to find information you need. Also, check the Frequently Asked Questions section for answers to some of the more common questions. If you cannot find the help you need using these resources, then email morpho-dev@ecoinformatics.org.

 

2. How can I get more information on problems?

Morpho sends a number of messages about operations that are normally not visible when you start Morpho using the icons created by the installer. On a Windows machine, the program that normally launches Morpho is called "Morpho.exe". An alternate method for launching Morpho (Windows only) is to execute the batch file "morpho.bat" which is located in the directory where Morpho was installed. When launched using the batch file, a background command window will appear and a number of messages will appear in this window while Morpho is running. These can give you hints about problems. You can also see all these messages in a log file that is created when the "<log_file>" parameter is set to "true" in the configuration file (see question #4 for instructions on accessing the config.xml file).

 

3. What are the system requirements for running Morpho?

For reasonable performance, a fairly new computer system is recommended (i.e. a clock speed or 700MHz or greater and 256 MB of RAM or greater). Morpho will run on slower systems with less RAM, but some operations may be very slow.  More RAM is especially useful if there are a large number of local data packages, since the local data is cached in RAM at startup. Some operations will require several minutes to complete even on newer computers. One example is the initial display of very large (10s of MB) data files.

 

4. Can I customize Morpho in any way?

In Morph 1.4.0 and later versions, there is a "Set preferences..." menu item in the "File" menu. That menu allows the user to change the look and feel of the Morpho windows, as well as change other options. However, in versions 1.3 and earlier, there is no command within the Morpho program to set any preferences, therefore you would need to set them manually, as described below:

 

There are some preferences (and additional data) that are read from the "config.xml" file that is stored in the ".morpho" directory in the user's home directory. Only a few of these should be set by the user. These include:

<lookAndFeel></lookAndFeel>  ---  As shown on the left, there is nothing between the pair of "lookAndFeel" tags in the default config.xml file. This causes the look of the Morpho display to mimic that of the current operating system - e.g. Windows, Mac, etc. You can see a different look by changing the tag set to be "<lookAndFeel>kunststoff</lookAndFeel>". This will cause a variety of minor changes in the look of buttons, scroll bars, etc. The "kunststoff" is a customized look-and-feel created for Java applications.

<log_file>false</log_file> --- Changing the value within these tags from "false" to "true" will send all error messages to a log file. This may be useful if you are having problems.  Note that in version 1.5 and later, the default setting for this parameter has been set to "true". Messages are thus automatically written to the log file (which is written to the Morpho startup directory and called "stderr.log"). If problems occur, this log file can be examined (or sent to the Morpho developers) to help determine the cause of the problem. Note that the log file is rewritten every time Morpho starts up, so you will need to rename it  if you want to save the results.

 

<metacat_url>http://metacat.nceas.ucsb.edu/knb/servlet/metacat</metacat_url> --- The url of the network server where data is stored is set here. You may need to change this if you are using a custom server.

 

5. Where are my local data packages stored?  What happens to my local data packages when I upgrade to a newer version of Morpho?

If you have used a previous version of Morpho, then you may have local data packages stored in a "profiles" directory inside the main Morpho data directory. The location where the "profiles" directory is created and accessed is in a subdirectory within the user's "home" directory. On Windows 2000 or XP machines, the home directory is named after the user name (e.g. "smith") and is located inside the "Documents and Settings" folder, usually under C:\. A directory named ".morpho" is created inside the user's home directory and the new "profiles" subdirectory is created there when Morpho is first executed. There is a subdirectory under "profiles" with the profile name and another subdirectory under that with the name "data" where local data for that profile are actually stored. Note that this is (usually) not the same directory as the one where the Morpho executable is installed. You should thus be able to uninstall Morpho and update it to newer versions without fear of losing any locally stored data packages.

 

6. How can I automatically extract data documentation from a data file for entry into Morpho?

 

Begin by opening the data package you would like to add data to, or by creating a new data package using the New Data Package Wizard. Next, open the New Data table Wizard, which can be found under the "Data" menu by clicking "Create/Import New Data table", or can be accessed on the last screen of the New Data Package Wizard. Choose either "IMPORT" or "DESCRIBE" under "What do you want to do?". You can then choose "AUTOMATIC" to have Morpho automatically extract documentation from the data file.

 

Note that at this time, Morpho can only extract documentation from a data file that is in text format. For data files saved in other formats, you can often change that format into text format. For example, if you have data tables created in Microsoft Access, you can click on each data table in that database and export it as a text file (under File -> Export...). These text files can then be added one at a time to Morpho, and the documentation extracted automatically. If you have data in an Excel workbook, you can simply save each worksheet as a text file using "Save As" and choosing the "Text (Tab-delimited)" format from the "Save as type" menu. Chart objects in Excel cannot be saved as text files. Also, documentation cannot be automatically extracted from image files. For these and other types of data files, you should manually enter their documentation in the New Data table Wizard.

 

7. How do I import an Excel file into Morpho?

 

Begin by opening the data package you would like to add data to, or by creating a new data package using the New Data Package Wizard. Next, open the New Data table Wizard, which can be found under the "Data" menu by clicking "Create/Import New Data table", or can be accessed on the last screen of the New Data Package Wizard. Choose "IMPORT" and "MANUAL", and locate your Excel file on your computer. Click "Next" to move to the "Data File Information" window and choose "Non-text or proprietary formatted file that is externally defined" for the file format. Complete the New Data table Wizard by providing information about the data table contained in your Excel file.

 

Morpho cannot currently display the content of an Excel file (only the data documentation you provided in the New Data table Wizard will be displayed). However, when you save the data package to which you added the Excel file, the Excel file itself will be saved. If you export the data package (see question #16 for exporting data packages), the Excel file will be exported and you will be able to open it from the directory where it was saved.

8. How can I add data to a data table?

One can simply paste data from the clipboard into a data table displayed in Morpho. However, currently Morpho does not automatically add rows to the data table when information is pasted. Thus, if you want to add data, you will need to create additional rows before pasting the new data. Select the last row and then use the "Data" menu, the pop-up menu you get when you right-click on the data table, or press CTRL-I to insert a new empty row. When enough rows have been created, you can select the top empty row and paste new data. Note that the default when copying/pasting from Excel is tab-delimited data. All the data will end up in the first cell if the data being pasted uses a different delimiter that the existing data (e.g. pasting from Excel when the existing data is comma-delimited). Alternatively, you may add data using the New Data Table Wizard, explained in the Adding Data to a Data Package section.

 

9. How do I provide information on taxonomic coverage in the form of a data table?

 

If your information about the taxonomic coverage is extensive, you can import this information in the form of a table instead of typing it into the Taxonomic Coverage section of the New Data Package Wizard. For example, if your taxonomic information constitutes a list of species, save this list as a text file. Once you have completed the New Data Package Wizard to create your data package, go to the "Data" menu and click on "Create/Import New Data table". Click on "IMPORT" and "AUTOMATIC", and locate your text file on your computer. Complete the rest of the New Data Table Wizard (you might need to uncheck the space delimiter box in step #2 of the wizard to fit your species names in a single column). If needed, see the Adding Data to a Data Package section for more information on the New Data Table Wizard. Go to the "Documentation" menu, click on "Taxonomic Coverage", and click on the "Import Taxon Information from Data table" link. Select the column(s) corresponding to your taxonomic information, choose the taxon category, and click on "OK". Your taxonomic information will appear in the Taxonomic Coverage window. Click on "OK".

 

10. How can I add an image to my data package?

Complex, geospatially indexed images can be included and described in eml 2.0 and newer versions using the "spatialRaster" or "spatialVector" entity modules.  However, Morpho currently has no features directly supporting these modules. Later versions of Morpho will have this feature. Nevertheless, images that are stored in .gif or .jpeg formats (standards for web pages) can be added to data packages as "dataTable" elements (even though they are not really "dataTables"). To add such an image to an existing package using the "Create/Import New Data table..." command under the "Data" menu. Choose the "Import" and then "Manual" radio buttons. Then select the image file that you wish to include. Then click the "Next" button.  Select the "Non-text or proprietary formatted file" radio button and then select "other".  You should then type "image", ".gif", ".jpeg", or ".jpg" in the text box below the "other" button. This tells Morpho to display the data as an image when the package is viewed later. Then continue through the Wizard as with any other data file. You will need to fill out at least the minimal information indicated on several of the next screens.

 

11. How do I view and edit documentation on attributes?

 

Documentation on attributes can be viewed from the table documentation panel (see the Introduction to Data Packages section for a description of Morpho's three panels) or by using the "View Documentation" option under the "Documentation" menu. When in a data table, click on the column header representing the attribute of interest: documentation on this attribute will be displayed in the table documentation panel (located to the right of the data table panel). Alternatively, click on "View Documentation" under the "Documentation" menu. This will open a window displaying all of the documentation contained in the data package. Scroll down to the "Data Tables, Images, and Other Entities" section: you will find documentation on all attributes of a given entity under "Attribute(s) Info".

 

To edit documentation on an attribute, bring up the documentation for that attribute in the table documentation panel (as described above) and click on the edit button located beneath the "hide" button in the upper-right corner of the panel. This will open Morpho Editor and show the current documentation for the attribute. Make your changes and click on "OK".

 

Alternatively, click on "Add/Edit Documentation" under the "Documentation" menu. This will also open Morpho Editor, but you will have to locate the node corresponding to your attribute of interest. From the drop-down list located next to "Find" (top-left corner of the editor), select "dataTable". This will expand the node where documentation on the data tables contained in the data package is located. If there are several data tables in the data package, find your data table of interest by going down the list and clicking on "dataTable" to bring up the documentation for each data table (the documentation will appear on the panel to the right). Once you have selected your table of interest, go back to the "Find" drop-down menu and select "attributeList". Click on the "+" sign next to the "attributeList" node. A list of the attributes contained in the data table will appear. Select the attribute of interest and make your changes in the panel to the right.

12. What is the difference between synchronizing a data package and saving a data package to the network?

 

When synchronizing a data package, you can either save a local copy of a data package to the network, or save a copy of a data package from the network to your local machine. Synchronizing will make the network and your local machine have the same copy (of the data package(s) you choose to synchronize). When saving a data package, you can essentially achieve the same result as synchronizing. You can save a local data package to the network (as well as locally after making edits), or you can save a network data package locally (or back to the network after making edits). One difference between the two choices is that the synchronize command is made available when you right-click on a data package in a search results box, whereas the save command is only available after you have opened a data package.

 

13. What happens with network data packages created with older versions of Morpho?

Previous versions of Morpho worked with a now obsolete version of EML called "Beta 6".  Morpho versions 1.5 and later will still read these older packages, but it will automatically convert them to the newer EML 2.0 (or later versions of EML) format for display. These older data packages will not be converted to EML 2.0 (or later) until the owner saves them, at which time a new ID will also be assigned.

 

14. How do I delete a saved search?

There is no direct way in Morpho to delete a saved search. One can, however, look in the .morpho/profiles/<profilename> directory and delete the "queries" subdirectory (or one of the files in it) to remove all queries (or one of them).

 

15. How do I delete a profile?

There is no method for deleting an old profile that you no longer need in Morpho itself. Instead, you delete the file (saved on your computer) that corresponds with the profile you would like to delete. These profile files are located in the profiles folder, which can be found in the ".morpho" folder. Delete the entire profile folder for the profile you wish to delete - be warned however that by deleting the profile folder you are also deleting all the local copies of data packages that were created or saved using that profile. Therefore data loss may happen unless you have previously extracted the data package and saved it elsewhere on your computer, or unless you have saved the data package to a network server, like metacat.

 

16. How can I "Export" a data package? The Export menu item doesn't seem to work.

There may be some confusion because the Export command asks you to select a "directory", not a file. Select a directory where you want the package exported to. On the Mac, you may need to actually type in the name of directory after selecting its parent directory. The exported metadata and data (if your data package includes data) will be exported to the directory you selected.

 

17. What are the keyboard shortcuts available in Morpho?

 

In Morpho, you can use the following keyboard shortcuts:

  • Ctrl-X to cut text.
  • Ctrl-C to copy text.
  • Ctrl-V to paste text.
  • Ctrl-I to insert table rows one at a time into a data table (see question #8 for more detail).

In the New Data Package Wizard, you can also use the following keys to quickly navigate through the wizard:

  • Left and right arrows take you forward and back through the steps in the wizard. "Esc" exits the wizard. "Tab" allows you to move from one field to the next.
  • "Enter" brings you to the next required field, and can also be used to open new windows (such as the owners window in step 5 of the New Data Package Wizard).

Additional keyboard shortcuts may be implemented in later versions of Morpho.

 

Help Index

PreviousUploading and Downloading Data Packages