This describes the BioQ database documentation tools, sometimes referred to as dbDoc, including the tracing diagrams and the use of the Biologic-Experiment-Result (BERT) relational model. The code can be found on our
dbdoc |
Create the back trace diagram, based on the Biologic-Experiment-Results (BERT) model, using dbdoc_util.pl.
Details on a specific column.
These options should be specified in the main options file. |
Details on a specific database.
Options for running dbdoc_util.pl.
Details on a specific flow group from the BERT model.
This supplied the data to jqGrid options created in JavaScript. For example, to show a list of tables in db.php, in js/db.js we have the code
// List of tables $('#dbDocTableTable-jqgrid').jqGrid({ url:'jqgrid_query_table.php', postData: {db_name: dbDocDbName, filter: dbDocFilter}, datatype: 'xml', mtype: 'GET', pager: '#dbDocTableTable-jqgridPager', altRows: true, altclass: 'dbDocjqGridZebra', height: 'auto', //rowNum: 1000000, rowNum: 30, rowList: [10,20,30,50,100], //caption: 'Tables', hidegrid: false, sortname: 'table_name', sortorder: 'asc', viewrecords: true, pagerpos: 'left', recordpos: 'center', colNames: ['Name','Description','Rows','Size (Mb)'], colModel: [ {name: 'Name', index: 'table_name', width: '225', align: 'left'}, {name: 'Description', index: 'short_descrip', width: '500', align: 'left'}, {name: 'Rows', index: 'rows', width: '90', align: 'right', formatter: 'integer', formatoptions: {thousandsSeparator: ',', defaultValue: '-' }}, {name: 'Table Size (Mb)', index: 'table_size', width: '80', align: 'right', formatter: 'integer', formatoptions: {thousandsSeparator: ',', decimalPlaces: 2, defaultValue: '-' }} ] }); |
This uses jqgrid_query_table.php to get the data from MySQL. The data is sent via Ajax in XML format.
Need to move this code to bioq/common.php. |
Details on a specific process from the BERT model.
This may be obsolete, it was originally used to show a large process trace diagram after clicking a thumbnail. |
This page shows the results of a search.
This is used for the jQuery UI autocomplete widget. It sends the data for the autocomplete entries via Ajax.
This script is obsolete and needs to be replaced by something more sophisticated that populates the table `search_terms` from existing dbDoc databases. See http://deku.psych.wucon.wustl.edu:8081/browse/BIOQ-18. |
This sets up PHP sessions for those pages that need it.
Details on a specific table.
This may be obsolete, it was originally used to show a large table trace diagram after clicking a thumbnail. |
Details on a specific tag.
The legend shown in the back trace section of BioQ::Documentation.
This needs to be updated whenever the code for displaying diagrams is updated. See http://deku.psych.wucon.wustl.edu:8081/browse/BIOQ-9. |
In order to show a test database in the main table of databases, in bioq/dbdoc/jqgrid_query_db.php, search for 'bioq_test_db' and follow the commented instructions to show some test documentation. This is useful for testing out macros and things, such as _tbl_link().
When done correctly, you should see something like this:
which shows this entry from the dbdoc `db` database:
Test DB: _db_link(bioq_dbsnp_human_132), _db_tbl_link(bioq_dbsnp_human_132._loc_snp_summary), _db_tbl_col_link(bioq_dbsnp_human_132._loc_snp_summary.snp_id)