stag-selectall_xmlp - Online in the Cloud

PROGRAM:

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

xml [default]
sxpr
lisp S-Expressions

itext
indented text

-color
shows results in color (sxpr and itext only)

-show
will show the parse of the SQL statement

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