# HG changeset patch
# User rhpvorderman
# Date 1531317817 14400
# Node ID 645c33d0786a0e89a81fcb4b6dfb92da625d8c5c
# Parent  cd78c64fe35b13d367a79dba2ae3b0a2a0598ad2
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit cb6d569e0496fac22e0e9c7fffa884338cef09c8

diff -r cd78c64fe35b -r 645c33d0786a README
--- a/README	Thu Jul 05 09:29:08 2018 -0400
+++ b/README	Wed Jul 11 10:03:37 2018 -0400
@@ -8,4 +8,4 @@
 The tool has drastically changed since then, with a complete refactoring
 of the python script and the addition of unit tests for all functionality
 within the python script. A lot of indexes are now supported in addition to
-just the all_fasta one.
\ No newline at end of file
+just the all_fasta one.
diff -r cd78c64fe35b -r 645c33d0786a data_manager/.pytest_cache/v/cache/nodeids
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/.pytest_cache/v/cache/nodeids	Wed Jul 11 10:03:37 2018 -0400
@@ -0,0 +1,27 @@
+[
+  "test_path_name_value_key_manager.py::test_validate_indexes_yaml",
+  "test_path_name_value_key_manager.py::test_schema",
+  "test_path_name_value_key_manager.py::test_schema_fail",
+  "test_path_name_value_key_manager.py::test_application",
+  "test_path_name_value_key_manager.py::test_application_overwrite_file",
+  "test_path_name_value_key_manager.py::test_application_star_index",
+  "test_path_name_value_key_manager.py::test_application_star_index_fail_wrong_yaml",
+  "test_path_name_value_key_manager.py::test_check_tab",
+  "test_path_name_value_key_manager.py::test_check_tab_fail",
+  "test_path_name_value_key_manager.py::test_data_table",
+  "test_path_name_value_key_manager.py::test_non_existing_table",
+  "test_path_name_value_key_manager.py::test_rnastar_index_fail_no_extra_column",
+  "test_path_name_value_key_manager.py::test_rnastar_index_fail_wrong_dir",
+  "test_path_name_value_key_manager.py::test_all_fasta_table_fail_extra_columns",
+  "test_path_name_value_key_manager.py::test_all_fasta_table",
+  "test_path_name_value_key_manager.py::test_index_path_not_exist",
+  "test_path_name_value_key_manager.py::test_index_path_is_a_dir",
+  "test_path_name_value_key_manager.py::test_bowtie2_index",
+  "test_path_name_value_key_manager.py::test_bowtie2_index_fail",
+  "test_path_name_value_key_manager.py::test_bwa_index",
+  "test_path_name_value_key_manager.py::test_bowtie_index",
+  "test_path_name_value_key_manager.py::test_bowtie_index_color",
+  "test_path_name_value_key_manager.py::test_hisat2_index",
+  "test_path_name_value_key_manager.py::test_picard_index",
+  "test_path_name_value_key_manager.py::test_sam_index"
+]
\ No newline at end of file
diff -r cd78c64fe35b -r 645c33d0786a data_manager/__pycache__/path_name_value_key_manager.cpython-35.pyc
Binary file data_manager/__pycache__/path_name_value_key_manager.cpython-35.pyc has changed
diff -r cd78c64fe35b -r 645c33d0786a data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc
Binary file data_manager/__pycache__/test_path_name_value_key_manager.cpython-35-PYTEST.pyc has changed
diff -r cd78c64fe35b -r 645c33d0786a data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Thu Jul 05 09:29:08 2018 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Wed Jul 11 10:03:37 2018 -0400
@@ -3,6 +3,7 @@
         <!-- Away with python 2! -->
         <requirement type="package" version="3.5">python</requirement>
         <requirement type="package" version="3.12">pyyaml</requirement>
+        <requirement type="package" version="0.6.6">schema</requirement>
     </requirements>
     <description>Link to indexes on the filesystem that have already been built</description>
     <command detect_errors="exit_code"><![CDATA[
diff -r cd78c64fe35b -r 645c33d0786a data_manager/indexes.yml
--- a/data_manager/indexes.yml	Thu Jul 05 09:29:08 2018 -0400
+++ b/data_manager/indexes.yml	Wed Jul 11 10:03:37 2018 -0400
@@ -1,5 +1,5 @@
 ---
-# This is a file containing information about all the indexes.
+# This file contains information about all the indexes.
 #
 # Top keys are table names as used in Galaxy.
 # These names can be viewed in the 'local data' part of the admin menu
diff -r cd78c64fe35b -r 645c33d0786a data_manager/path_name_value_key_manager.py
--- a/data_manager/path_name_value_key_manager.py	Thu Jul 05 09:29:08 2018 -0400
+++ b/data_manager/path_name_value_key_manager.py	Wed Jul 11 10:03:37 2018 -0400
@@ -6,6 +6,17 @@
 from pathlib import Path
 
 import yaml
+from schema import Schema, Optional
+
+
+def indexes_schema():
+    return Schema(
+        {'name': str,
+         Optional('prefix'): bool,
+         Optional('extensions'): [str],
+         Optional('prefix_strip_extension'): bool,
+         Optional('extra_columns'): [str],
+         Optional('folder'): [str]})
 
 
 def argument_parser():
@@ -31,8 +42,8 @@
 def check_tab(name: str, value: str):
     if '\t' in value:
         raise ValueError(
-            '\'{0}\' is not a valid \'{1}\'. It may not contain a tab because '
-            'these are used as seperators by galaxy .'.format(
+            "'{0}' is not a valid '{1}'. It may not contain a tab because "
+            "these are used as seperators by galaxy .".format(
                 value, name))
 
 
@@ -92,7 +103,7 @@
                         str(index_extra_columns).strip("{}")))
             if len(index_extra_columns) == 0:
                 raise ValueError(
-                    "The table \'{0}\' does not have extra columns".format(
+                    "The table '{0}' does not have extra columns".format(
                         self.data_table_name))
         for key, value in self.extra_columns.items():
             check_tab(key, value)
@@ -103,14 +114,16 @@
         index_properties = indexes.get(self.data_table_name)
         if index_properties is None:
             raise ValueError(
-                "\'{0}\' not a supported table name".format(
+                "'{0}' not a supported table name".format(
                     self.data_table_name))
-        return index_properties
+        return indexes_schema().validate(index_properties)
 
     def check_index_file_presence(self):
-        index_name = self.index_properties.get(
-            'name',
-            '[Index name not found. Please report to developers]')
+        index_name = self.index_properties.get('name')
+        if index_name is None:
+            raise NotImplementedError(
+                "Property 'name' not defined for '{0}',"
+                " please contact the developers to correct the mistake.")
         index_extensions = self.index_properties.get('extensions', [''])
 
         # Sometimes an index path is a prefix.
@@ -132,8 +145,8 @@
                 if not prefix_plus_extension_exists(self.index_path.parent,
                                                     prefix, extension):
                     raise FileNotFoundError(
-                        'Unable to find files with prefix \'{0}\' '
-                        'and extension \'{1}\' in {2}. Is this a valid {3}?'
+                        "Unable to find files with prefix '{0}' "
+                        "and extension '{1}' in {2}. Is this a valid {3}?"
                         .format(
                             prefix,
                             extension,
@@ -143,12 +156,21 @@
             for file in self.index_properties.get('folder'):
                 if not (self.index_path / Path(file)).exists():
                     raise FileNotFoundError(
-                        "A file named \'{0}\' was not found in \'{1}\'".format(
+                        "A file named '{0}' was not found in '{1}'".format(
                             file, str(self.index_path)))
+        elif not self.index_path.exists() and not self.index_path.is_dir():
+            raise FileNotFoundError(
+                'Unable to find path {0}.'.format(self.index_path))
+        elif self.index_path.is_dir() and self.index_properties.get(
+                'folder') is None:
+            raise IsADirectoryError(
+                '{0} is a directory not a file'.format(self.index_path))
+        elif self.index_path.exists():
+            pass
         else:
-            if not self.index_path.exists():
-                raise FileNotFoundError(
-                    'Unable to find path {0}.'.format(self.index_path))
+            raise NotImplementedError("This condition was not expected "
+                                      "and should not be reached. Please "
+                                      "contact the developers.")
 
     @property
     def data_manager_dict(self) -> dict: