diff load_db.py @ 0:6fbd9d25ceef draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/load_db.py	Tue Jul 18 09:06:47 2017 -0400
@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import sys
+
+from filters import TabularReader
+
+
+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, load_named_columns=False,
+                   filters=None):
+    col_pref = ['TEXT', 'REAL', 'INTEGER', None]
+    col_types = []
+    col_idx = None
+    try:
+        tr = TabularReader(file_path, skip=skip, comment_char=comment_char,
+                           col_idx=None, filters=filters)
+        for linenum, fields in enumerate(tr):
+            if linenum > max_lines:
+                break
+            try:
+                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 as e:
+                print('Failed at line: %d err: %s' % (linenum, e),
+                      file=sys.stderr)
+    except Exception as e:
+        print('Failed: %s' % (e), file=sys.stderr)
+    for i, col_type in enumerate(col_types):
+        if not col_type:
+            col_types[i] = 'TEXT'
+    if column_names:
+        col_names = []
+        if load_named_columns:
+            col_idx = []
+            for i, cname in enumerate(
+                    [cn.strip() for cn in column_names.split(',')]):
+                if cname != '':
+                    col_idx.append(i)
+                    col_names.append(cname)
+            col_types = [col_types[i] for i in col_idx]
+        else:
+            col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
+            for i, cname in enumerate(
+                    [cn.strip() for cn in column_names.split(',')]):
+                if cname and i < len(col_names):
+                    col_names[i] = cname
+    else:
+        col_names = ['c%d' % i for i in range(1, len(col_types) + 1)]
+    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, col_idx
+
+
+def create_table(conn, file_path, table_name, skip=0, comment_char='#',
+                 pkey_autoincr=None, column_names=None,
+                 load_named_columns=False, filters=None,
+                 unique_indexes=[], indexes=[]):
+    col_names, col_types, col_def, col_idx = \
+        get_column_def(file_path, table_name, skip=skip,
+                       comment_char=comment_char, column_names=column_names,
+                       load_named_columns=load_named_columns, filters=filters)
+    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%s\n);' % (
+                table_name,
+                '%s INTEGER PRIMARY KEY AUTOINCREMENT,' %
+                pkey_autoincr if pkey_autoincr else '',
+                ', \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)
+        conn.commit()
+        c.close()
+        for i, index in enumerate(unique_indexes):
+            index_name = 'idx_uniq_%s_%d' % (table_name, i)
+            index_columns = index.split(',')
+            create_index(conn, table_name, index_name, index_columns,
+                         unique=True)
+        for i, index in enumerate(indexes):
+            index_name = 'idx_%s_%d' % (table_name, i)
+            index_columns = index.split(',')
+            create_index(conn, table_name, index_name, index_columns)
+        c = conn.cursor()
+        tr = TabularReader(file_path, skip=skip, comment_char=comment_char,
+                           col_idx=col_idx, filters=filters)
+        for linenum, fields in enumerate(tr):
+            data_lines += 1
+            try:
+                vals = [col_func[i](x)
+                        if x else None for i, x in enumerate(fields)]
+                c.execute(insert_stmt, vals)
+            except Exception as e:
+                print('Failed at line: %d err: %s' % (linenum, e),
+                      file=sys.stderr)
+        conn.commit()
+        c.close()
+    except Exception as e:
+        exit('Error: %s' % (e))
+
+
+def create_index(conn, table_name, index_name, index_columns, unique=False):
+    index_def = "CREATE %s INDEX %s on %s(%s)" % (
+                'UNIQUE' if unique else '', index_name,
+                table_name, ','.join(index_columns))
+    c = conn.cursor()
+    c.execute(index_def)
+    conn.commit()
+    c.close()