The dbdoc_util.pl utility
BioQ uses a MySQL relational database to store documentation on its genomic relational database. The Perl program creates, configures and maintains this database. It will initialize the database, copy documentation from one database to another, update documentation from an XML file, dump the database, and will also generate process flow diagrams using GraphViz.
Contents
Usage
dbdoc_util.pl command [options]
Commands
inituser
Create the MySQL user and set permissions. See the configuration page.
dbdoc_util.pl inituser --options-file=init_user.opt init_user.opt: db-user= bioq db-host= localhost db-root-user= root db-password-file= ./passwd
initdb
Create the database and initialize the schema using the dbdoc-init-script option.
Example
dbdoc_util.pl initdb --options-file=init_db.opt init_db.opt: dbdoc-db= bioq_dbdoc_1 dbdoc-init-script= db_doc_model.sql
copydb
Copy documentation from an existing database.
Example
dbdoc_util.pl copydb --options-file=copy_db.opt copy_db.opt: dbdoc-db= bioq_dbdoc_new dbdoc-init-script= db_doc_model.sql dbdoc-previous-db= bioq_dbdoc_old
initdoc
Create default documentation entries using the names of database, tables and columns found in the genomic relational databases themselves. In MySQL, this information is taken from the information_schema database. This must be done before additional documentation can be entered using the updatedoc command.
Example
dbdoc_util.pl initdoc --options-file=init_doc.opt init_doc.opt: dbdoc-db= bioq_dbdoc_1 dbdoc-target-db= bioq_hapmap_pr28_dbsnp132
updatedoc
Read documentation from XML and update the documentation database.dbdoc_util.pl initdoc --options-file=init_doc.opt
dbdoc_util.pl updatedoc --options-file=update_doc.opt update_doc.opt: dbdoc-db= bioq_dbdoc_1 dbdoc-target-db= bioq_hapmap_pr28_dbsnp132 dbdoc-xml-file= bioq_hapmap_pr28_dbsnp132_core.xml
traceresults
Determine if a table can be traced back to subjects and biologics.
makelegend
Create a legend for the diagrams that trace experimental process flow using the BERT relational model.
tracebacktable
Create a diagram that traces experimental process flow back from a table using the BERT relational model.
tracebackgroup
Create a diagram that traces experimental process flow back from a flow group using the BERT relational model.
tracebackprocess
Create a diagram that traces experimental process flow back from a process using the BERT relational model.
dump
Dump MySQL databases. This is not yet implemented.
Options
Option |
Value |
Default |
Description |
|---|---|---|---|
add-svn-rev-on-init |
0/1 |
0 |
Add the Subversion revision number to the 'reference' table when initializing the documentation database. |
db-delete-temp-tables |
0/1 |
1 |
Delete temporary tables |
db-dump-dir |
text |
|
Local directory used to store database dumps. Note that a subdirectory will be created for each database. |
db-engine |
text |
MyISAM |
Database engine to use when creating new tables. Example: MyISAM. |
db-host |
text |
|
Address of database host |
db-max-rows |
integer |
|
Maximum number of rows to load into database. See also max-snps. |
db-no-mysql-password |
0/1 |
0 |
Do not supply a password to MySQL. Assume this exists in ~/.my.cnf |
db-password |
text |
|
Database password |
db-password-file |
text |
|
File containing database password |
db-root-user |
text |
root |
Database root user or some user that has the GRANT OPTION privilege |
db-user |
text |
|
Database username |
dbdoc-db |
text |
|
Local documentation database |
dbdoc-db-old |
text |
|
Previous dbDoc database - for copying into dbdoc-db |
dbdoc-init-script |
text |
|
Path to the SQL script that defines the dbDoc schema |
dbdoc-previous-db |
text |
|
The database from which to copy documentation into the current database (dbdoc-db) |
dbdoc-target-db |
text |
|
Database to document |
dbdoc-trace-db |
text |
|
The database in which to trace a table or process |
dbdoc-trace-group |
text |
|
The group to trace |
dbdoc-trace-image-name |
text |
trace |
How to name the file. If option is 'trace_table' then it created trace_table.gif for GIF files. |
dbdoc-trace-make-thumb |
0/1 |
0 |
Whether to make a smaller thumbnail version |
dbdoc-trace-process |
text |
|
The process to trace |
dbdoc-trace-show-ref |
0/1 |
0 |
Whether to show reference elements in the diagram |
dbdoc-trace-table |
text |
|
The table to trace |
dbdoc-trace-thumb-width |
integer |
600 |
Width of thumbnail image in pixels for diagram |
dbdoc-xml-file |
text |
./doc.xml |
The XML file with the documentation to be used |
dbsnp-db |
text |
|
Local dbSNP database to use for mapping data if --plink-use-dbsnp-map is selected |
delete-temp-files |
0/1 |
1 |
Delete temporary files |
dot-dpi |
integer |
96 |
Resolution for DOT image file |
dot-flow-dir |
text |
LR |
Flow direction in DOT diagram |
dot-group-color |
text |
lightgrey |
Group color in BERT DOT diagrams |
dot-height |
text |
|
Height of DOT image file in inches |
dot-image-type |
text |
gif |
The type of image file created by the dot command for process flow diagrams. |
dot-node-font-size |
text |
12 |
Size of font in points used for text in nodes |
dot-node-height |
decimal |
0.3 |
Height of nodes in inches |
dot-process-color |
text |
|
Process color in BERT DOT diagrams |
dot-stylesheet-path |
text |
./svg_styles.css |
Path to .css file with dot stylesheet. This is for use with SVG output. |
dot-table-color |
text |
lightcyan |
Table color in BERT DOT diagrams |
dot-width |
decimal |
10.5 |
Width of DOT image file in inches |
help |
|
|
Display message and quit |
max-snps |
integer |
|
Maximum number of SNPs to process |
options-file |
text |
|
File containing option values |
print-options |
0/1 |
0 |
Whether to print the list of options and their values |
process-dir |
text |
|
Local directory where files are processed. |
verbose |
0/1 |
0 |
Verbose output |