BioQ uses a MySQL relational database to store documentation on its genomic relational database. The Perl program
perl/dbdoc/dbdoc_util.pl |
dbdoc_util.pl command [options]
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 |
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 |
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 |
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 |
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 |
Determine if a table can be traced back to subjects and biologics.
Create a legend for the diagrams that trace experimental process flow using the BERT relational model.
Create a diagram that traces experimental process flow back from a table using the BERT relational model.
Create a diagram that traces experimental process flow back from a flow group using the BERT relational model.
Create a diagram that traces experimental process flow back from a process using the BERT relational model.
Dump MySQL databases. This is not yet implemented.
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 |