NAME¶

stag-selectall_xml - Query all elements from database with an XML output

SYNOPSIS¶

  stag-selectall_xml [-d <dbi>] [-f file of sql] [-nesting|n <nesting>] SQL

DESCRIPTION¶

This script will query a database using either SQL provided by the script user, or using an SQL templates; the query results will be turned into XML using the DBIx::DBStag module. The nesting of the XML can be controlled by the DBStag SQL extension "USE NESTING..."

EXAMPLES¶

  stag-selectall_xml -d "dbi:Pg:dbname=mydb;host=localhost"\
        "SELECT * FROM a NATURAL JOIN b"

TEMPLATES¶

A parameterized SQL template (canned query) can be used instead of specifying the full SQL For example:

  stag-selectall_xml -d genedb /genedb-gene gene_symbol=Adh

Or:

  stag-selectall_xml -d genedb /genedb-gene Adh

Or:

  stag-selectall_xml -d genedb /genedb-gene gene_symbol@=Adh,dpp,bam,indy

A template is indicated by the syntactic shorthand of using a slash to precede the template name; in this case the template is called genedb-gene. the -t option can also be used. All the remaining arguments are passed in as SQL template parameters. They can be passed in as either name=value pairs, or as a simple list of arguments which get passed into the template in order To use templates, you should have the environment variable DBSTAG_TEMPLATE_DIRS set. See DBIx::DBStag for details.

LISTING AVAILABLE TEMPLATES FOR A DB¶

   stag-selectall_xml -d mydb -h

LISTING VARIABLES FOR A TEMPLATE¶

   stag-selectall_xml /genedb-gene -h

ENVIRONMENT VARIABLES¶

DBSTAG_DBIMAP_FILE

A file containing configuration details for local databases

DBSTAG_TEMPLATE_DIRS

list of directories (separated by :s) to be searched when templates are requested

COMMAND LINE ARGUMENTS¶

-h|help

shows this page if no other arguments are given

 

if a template is specified, gives template details

 

if a db is specified, lists templates for that db

 

use in conjunction with -v for full descriptions

-d|dbname DBNAME

this is either a full DBI locator string (eg dbi:Pg:dbname=mydb;host=localhost) or it can also be a shortened "nickname", which is then looked up in the file pointed at by the environment variable DBSTAG_DBIMAP_FILE

-u|user USER

database user identity

-p|password PASS

database password

-f|file SQLFILE

this is a path to a file containing SQL that will be executed, as an alternative to writing the SQL on the command line

-n|nesting NESTING-EXPRESSIONS

a bracketed expression indicating how to the resulting objects/XML should be nested. See DBIx::DBStag for details.

-t|template TEMPLATE-NAME

the name of a template; see above

-wh|where WHERE-CLAUSE

used to override the WHERE clause of the query; useful for combining with templates

 

You can append to an existing where clause by using the prefix +

-s|select SELECT-COLS

used to override the SELECT clause of the query; useful for combining with templates

-rows

sometimes it is preferable to return the results as a table rather than xml or a similar nested structure. specifying -rows will fetch a table, one line per row, and columns separated by tabs

-pre SQL

a piece of SQL is that is executed immediately before the main query; e.g.:

 

  -pre "SET search_path=myschema,public"
    

-o|out FILE

a file to output the results to

-w|writer WRITER

writer class; can be any perl class, or one of these

-color

shows results in color (sxpr and itext only)

-show

will show the parse of the SQL statement