diff query_tabular.py @ 0:926c62f7fa09 draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/query_tabular commit 9ae87502ea7c3da33ecc453872c4eb2f41ecea4a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/query_tabular.py	Thu Jan 21 08:23:45 2016 -0500
@@ -0,0 +1,247 @@
+#!/usr/bin/env python
+"""
+"""
+import sys
+import re
+import os.path
+import json
+import sqlite3 as sqlite
+import optparse
+from optparse import OptionParser
+
+"""
+TODO:
+- could read column names from comment lines, but issues with legal names
+- could add some transformations on tabular columns,
+  e.g. a regex to format date/time strings
+    c2 : re.sub('pat', 'sub', c2)
+    c3 :
+- column_defs dict of columns to create from tabular input
+    column_defs : { 'name1' : 'expr', 'name2' : 'expr'}
+- allow multiple queries and outputs
+- add a --json input for table definitions (or yaml)
+JSON config:
+{ tables : [
+    { file_path : '/home/galaxy/dataset_101.dat',
+            table_name : 't1',
+            column_names : ['c1', 'c2', 'c3'],
+            comment_lines : 1
+    },
+    { file_path : '/home/galaxy/dataset_102.dat',
+            table_name : 't2',
+            column_names : ['c1', 'c2', 'c3']
+    },
+    { file_path : '/home/galaxy/dataset_103.dat',
+            table_name : 'test',
+            column_names : ['c1', 'c2', 'c3']
+    }
+    ]
+}
+"""
+
+tables_query = \
+    "SELECT name, sql FROM sqlite_master WHERE type='table' ORDER BY name"
+
+
+def getValueType(val):
+    if val or 0. == val:
+        try:
+            int(val)
+            return 'INTEGER'
+        except:
+            try:
+                float(val)
+                return 'REAL'
+            except:
+                return 'TEXT'
+    return None
+
+
+def get_column_def(file_path, table_name, skip=0, comment_char='#',
+                   column_names=None, max_lines=100):
+    col_pref = ['TEXT', 'REAL', 'INTEGER', None]
+    col_types = []
+    data_lines = 0
+    try:
+        with open(file_path, "r") as fh:
+            for linenum, line in enumerate(fh):
+                if linenum < skip:
+                    continue
+                if line.startswith(comment_char):
+                    continue
+                data_lines += 1
+                try:
+                    fields = line.split('\t')
+                    while len(col_types) < len(fields):
+                        col_types.append(None)
+                    for i, val in enumerate(fields):
+                        colType = getValueType(val)
+                        if col_pref.index(colType) < col_pref.index(col_types[i]):
+                            col_types[i] = colType
+                except Exception, e:
+                    print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
+    except Exception, e:
+        print >> sys.stderr, 'Failed: %s' % (e)
+    for i, col_type in enumerate(col_types):
+        if not col_type:
+            col_types[i] = 'TEXT'
+    col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
+    if column_names:
+        for i, cname in enumerate([cn.strip() for cn in column_names.split(',')]):
+            if cname and i < len(col_names):
+                col_names[i] = cname
+    col_def = []
+    for i, col_name in enumerate(col_names):
+        col_def.append('%s %s' % (col_names[i], col_types[i]))
+    return col_names, col_types, col_def
+
+
+def create_table(conn, file_path, table_name, skip=0, comment_char='#', column_names=None):
+    col_names, col_types, col_def = get_column_def(file_path, table_name, skip=skip, comment_char=comment_char, column_names=column_names)
+    col_func = [float if t == 'REAL' else int if t == 'INTEGER' else str for t in col_types]
+    table_def = 'CREATE TABLE %s (\n    %s\n);' % (table_name, ', \n    '.join(col_def))
+    # print >> sys.stdout, table_def
+    insert_stmt = 'INSERT INTO %s(%s) VALUES(%s)' % (table_name, ','.join(col_names), ','.join(["?" for x in col_names]))
+    # print >> sys.stdout, insert_stmt
+    data_lines = 0
+    try:
+        c = conn.cursor()
+        c.execute(table_def)
+        with open(file_path, "r") as fh:
+            for linenum, line in enumerate(fh):
+                if linenum < skip or line.startswith(comment_char):
+                    continue
+                data_lines += 1
+                try:
+                    fields = line.rstrip('\r\n').split('\t')
+                    vals = [col_func[i](x) if x else None for i, x in enumerate(fields)]
+                    c.execute(insert_stmt, vals)
+                except Exception, e:
+                    print >> sys.stderr, 'Failed at line: %d err: %s' % (linenum, e)
+        conn.commit()
+        c.close()
+    except Exception, e:
+        print >> sys.stderr, 'Failed: %s' % (e)
+        exit(1)
+
+
+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 get_connection(sqlitedb_path, addfunctions=False):
+    conn = sqlite.connect(sqlitedb_path)
+    if addfunctions:
+        conn.create_function("re_match", 2, regex_match)
+        conn.create_function("re_search", 2, regex_search)
+        conn.create_function("re_sub", 3, regex_sub)
+    return conn
+
+
+def __main__():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option('-s', '--sqlitedb', dest='sqlitedb', default=None, help='The SQLite Database')
+    parser.add_option('-t', '--table', dest='tables', action="append", default=[], help='Tabular file: file_path[=table_name[:column_name, ...]')
+    parser.add_option('-j', '--jsonfile', dest='jsonfile', default=None, help='Tabular file: file_path[=table_name[:column_name, ...]')
+    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()
+
+    # open sqlite connection
+    conn = get_connection(options.sqlitedb)
+    # 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
+
+    # get table defs
+    if options.tables:
+        for ti, table in enumerate(options.tables):
+            table_name = 't%d' % (ti + 1)
+            column_names = None
+            fields = table.split('=')
+            path = fields[0]
+            if len(fields) > 1:
+                names = fields[1].split(':')
+                table_name = names[0] if names[0] else table_name
+                if len(names) > 1:
+                    column_names = names[1]
+            # print >> sys.stdout, '%s %s' % (table_name, path)
+            create_table(conn, path, table_name, column_names=column_names)
+    if options.jsonfile:
+        try:
+            fh = open(options.jsonfile)
+            tdef = json.load(fh)
+            if 'tables' in tdef:
+                for ti, table in enumerate(tdef['tables']):
+                    path = table['file_path']
+                    table_name = table['table_name'] if 'table_name' in table else 't%d' % (ti + 1)
+                    column_names = table['column_names'] if 'column_names' in table else None
+                    comment_lines = table['comment_lines'] if 'comment_lines' in table else 0
+                    create_table(conn, path, table_name, column_names=column_names, skip=comment_lines)
+        except Exception, exc:
+            print >> sys.stderr, "Error: %s" % exc
+    conn.close()
+
+    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 = get_connection(options.sqlitedb)
+            c = conn.cursor()
+            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)
+    # if not sqlite.is_read_only_query(query):
+    #    print >> sys.stderr, "Error: Must be a read only query"
+    #    exit(2)
+    try:
+        conn = get_connection(options.sqlitedb, addfunctions=True)
+        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]))
+            # yield [col[0] for col in cur.description]
+        for i, row in enumerate(results):
+            # yield [val for val in row]
+            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__()