DNA Configuration Parameters
The configuration parameters are stored in three different ways: as
environmental variables, in the java property
file and as an XML confguration file.
1. Environment variables.
The parameters stored as environment variables are mostly used for the local DNA
installation. The DNAHOME and DNANAME variables are compulsory,
all the other variables are optional :
- DNAHOME: The toplevel directory corresponding to the CVS repository
toplevel, e.g. where all the CVS files have been checked out.
- DNANAME: A name used for finding the appropriate configuration files
in $DNAHOME/config, i.e. the directory $DNAHOME/config/$DNANAME should contain
the java properties file and the DNA configuration XML file.
- DNACONFIG: Path to the dna_config file if it's in a different position
than $DNAHOME/config/$DNANAME.
- DNAJDK: If not present the default java version is used, if present
$DNAJDK/bin/java is used.
- CCP4_SETUP: Command line for setting up the CCP4 variables, e.g.
"source /opt/pxsoft/ccp4/include/ccp4.setup".
- DNALOG: If present all the DNA logfiles are written to this directory,
otherwise they are written to the current working directory.
- DNATMP: If present all temporary files (e.g. MOSFLM spot files) are
written to this directory, otherwise they are written to the current working
directory.
2. Java properties.
The parameters stored in the java properties file is only used by the DNA GUI.
The java properties file is always called "java.properties" and should
be located in $DNAHOME/config/$DNANAME (see above). The following properties
should be defined in this file:
- dna.home: This property should correspond to the envrironment variable
$DNAHOME.
- dna.referenceImagesTimeout: The length in milliseconds for the GUI
to timeout after havling sent a collect request command.
- dna.autoIndexTimeout: The length in milliseconds for the GUI to timeout
after havling sent an index reuqest command.
- dna.strategyTimeout: The length in milliseconds for the GUI to timeout
after havling sent a strategy request command.
- dna.fraction: A decimal value that determines the shape of the GUI,
e.g. if it's 0.5 the height of the GUI will be 0.5 times the width.
- dna.width: The width of the GUI in pixels. Has no effect in dna.fraction
is present.
- dna.height: The height of the GUI in pixels. Has no effect in dna.fraction
is present.
- dna.indexFilesEditable: Boolean value for determining if the index
files should be editable by default or not.
- dna.passes: If set to "on" the number of passes is shown
on the strategy panel and is editable, if "off" it isn't showed
and the number of passes is set to 1.
- dna.runNumber: If set to "on" an input field for the run-number
in the reference image panel is displayed, if set to "off" it's
up to the ES or BCM to determine the run number..
3. XML configuration file.
The XML configuration file contains configuration parameters in XML format
as defined by dna_config.xsd, below
I give a brief overview of the different parameters:
- <server_data>: This group of parameters are for the different
HTTP servers.
- <expert_system_host_name>
- <expert_system_port_number>
- <dpm_host_name>
- <dpm_port_number>
- <dpm_log_file>: Path to the file to which the output of
the DPM is written.
- <mosflm_executable>: Path to the MOSFLM executable.
- <bcm_host_name>
- <bcm_port_number>
- <gui_host_name>
- <gui_port_number>
- <timeout_length>: Timeout in seconds for all HTTP calls.
- <local_info>:
- <dna_contact_email>: Email address to the DNA contact person.
Emails are sent to this address in case of anomalies.
- <default_values>
- <fileinfo>
- <oscillation_sequence>
- <detector>
- <beam>
- <resolution>
- <index_parameters>: These parameters are used for the indexing
and the evaluation of the indexing results.
- <max_index_spot_rms_error>
- <min_index_spot_frac_indexed>
- <max_index_spot_frac_rejected>
- <min_threshold_I_sigma>