# HG changeset patch
# User jjohnson
# Date 1453386935 18000
# Node ID cf32fc695e726cdcbf49bb83073369675d07ca49

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/sqlite_to_tabular commit 64a950cafd655311c99a54f96a27b49f0bdf2731-dirty

diff -r 000000000000 -r cf32fc695e72 sqlite_to_tabular.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sqlite_to_tabular.py	Thu Jan 21 09:35:35 2016 -0500
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import sys
+import re
+import os.path
+import optparse
+import sqlite3 as sqlite
+
+
+def regex_match(expr, item):
+    return re.match(expr, item) is not None
+
+
+def regex_search(expr, item):
+    return re.search(expr, item) is not None
+
+
+def regex_sub(expr, replace, item):
+    return re.sub(expr, replace, item)
+
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
+    parser.add_option('-q', '--query', dest='query', default=None, help='SQL query')
+    parser.add_option('-Q', '--query_file', dest='query_file', default=None, help='SQL query file')
+    parser.add_option('-n', '--no_header', dest='no_header', action='store_true', default=False, help='Include a column headers line')
+    parser.add_option('-o', '--output', dest='output', default=None, help='Output file for query results')
+    (options, args) = parser.parse_args()
+
+    # determine output destination
+    if options.output is not None:
+        try:
+            outputPath = os.path.abspath(options.output)
+            outputFile = open(outputPath, 'w')
+        except Exception, e:
+            print >> sys.stderr, "failed: %s" % e
+            exit(3)
+    else:
+        outputFile = sys.stdout
+
+    query = None
+    if (options.query_file is not None):
+        with open(options.query_file, 'r') as fh:
+            query = ''
+            for line in fh:
+                query += line
+    elif (options.query is not None):
+        query = options.query
+
+    if (query is None):
+        try:
+            conn = sqlite.connect(options.sqlitedb)
+            c = conn.cursor()
+            tables_query = "SELECT name,sql FROM sqlite_master WHERE type='table' ORDER BY name"
+            rslt = c.execute(tables_query).fetchall()
+            for table, sql in rslt:
+                print >> sys.stderr, "Table %s:" % table
+                try:
+                    col_query = 'SELECT * FROM %s LIMIT 0' % table
+                    cur = conn.cursor().execute(col_query)
+                    cols = [col[0] for col in cur.description]
+                    print >> sys.stderr, " Columns: %s" % cols
+                except Exception, exc:
+                    print >> sys.stderr, "Error: %s" % exc
+        except Exception, exc:
+            print >> sys.stderr, "Error: %s" % exc
+        exit(0)
+    try:
+        conn = sqlite.connect(options.sqlitedb)
+        conn.create_function("re_match", 2, regex_match)
+        conn.create_function("re_search", 2, regex_search)
+        conn.create_function("re_sub", 3, regex_sub)
+        cur = conn.cursor()
+        results = cur.execute(query)
+        if not options.no_header:
+            outputFile.write("#%s\n" % '\t'.join([str(col[0]) for col in cur.description]))
+        for i, row in enumerate(results):
+            outputFile.write("%s\n" % '\t'.join([str(val) for val in row]))
+    except Exception, exc:
+        print >> sys.stderr, "Error: %s" % exc
+        exit(1)
+
+if __name__ == "__main__":
+    __main__()
diff -r 000000000000 -r cf32fc695e72 sqlite_to_tabular.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sqlite_to_tabular.xml	Thu Jan 21 09:35:35 2016 -0500
@@ -0,0 +1,102 @@
+<?xml version="1.0"?>
+<tool id="sqlite_to_tabular" name="SQLite to tabular" version="0.0.1">
+    <description>for SQL query</description>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python"><![CDATA[
+    sqlite_to_tabular.py 
+    --sqlitedb="$sqlitedb" 
+    --query_file="$query_file"
+    $no_header 
+    --output="$query_results"
+    ]]></command>
+    <configfiles>
+        <configfile name="query_file">
+$sqlquery
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="sqlitedb" type="data" format="sqlite" label="SQLite Database"/>
+        <param name="sqlquery" type="text" area="True" size="120x20" label="SQL query">
+            <validator type="regex">^(?im)\s*SELECT\s.*\sFROM\s.*$</validator>
+            <sanitizer sanitize="False"/>
+        </param>
+        <param name="no_header" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Omit column headers"/>
+    </inputs>
+    <outputs>
+        <data name="query_results" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="sqlitedb" ftype="sqlite" value="testdb.sqlite" />
+            <param name="sqlquery" value="SELECT first_name, last_name, age FROM contacts WHERE first_name = 'Sam'" />
+            <output name="query_results">
+                <assert_contents>
+                    <has_text text="Smith" />
+                    <not_has_text text="Doe" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Outputs the results of a query on a SQLite_ Database as a tabular file. 
+
+In addition to the standard SQLite_functions_ regular_expression_ functions are included.
+
+For example, with SQLite table "customers":
+
+    =========== ========== ========== ===================== ========== ============
+    #CustomerID FirstName  LastName   Email                 BirthDate  Phone
+    =========== ========== ========== ===================== ========== ============
+    1           John       Smith      John.Smith@yahoo.com  1968-02-04 626 222-2222
+    2           Steven     Goldfish   goldfish@fishhere.net 1974-04-04 323 455-4545
+    3           Paula      Brown      pb@herowndomain.org   1978-05-24 416 323-3232
+    4           James      Smith      jim@supergig.co.uk    1980-10-20 416 323-8888
+    =========== ========== ========== ===================== ========== ============
+
+  ::
+
+    matching:      re_match('pattern',column) 
+
+    SELECT FirstName, LastName
+    FROM customers
+    WHERE re_match('^.*\.(net|org)$',Email)
+
+  Results:
+
+    =========== ==========
+    #FirstName  LastName
+    =========== ==========
+    Steven      Goldfish
+    Paula       Brown
+    =========== ==========
+
+
+  ::
+
+    searching:     re_search('pattern',column)
+    substituting:  re_sub('pattern','replacement,column)
+
+    SELECT FirstName, LastName, re_sub('^\d{2}(\d{2})-(\d\d)-(\d\d)','\3/\2/\1',BirthDate) as "DOB"
+    FROM customers
+    WHERE re_search('[hp]er',Email)
+
+  Results:
+
+    =========== ========== ==========
+    #FirstName  LastName   DOB
+    =========== ========== ==========
+    Steven      Goldfish   04/04/74
+    Paula       Brown      24/05/78
+    James       Smith      20/10/80
+    =========== ========== ==========
+
+
+
+.. _Regular_expression: https://docs.python.org/release/2.7/library/re.html
+.. _SQLite: http://www.sqlite.org/index.html
+.. _SQLite_functions: http://www.sqlite.org/docs.html
+
+    ]]></help>
+</tool>
diff -r 000000000000 -r cf32fc695e72 test-data/testdb.sqlite
Binary file test-data/testdb.sqlite has changed