dxpy 0.402.0__tar.gz → 0.403.0__tar.gz

{dxpy-0.402.0 → dxpy-0.403.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.402.0
+Version: 0.403.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.402.0 → dxpy-0.403.0}/dxpy/app_builder.py

@@ -64,12 +64,65 @@ class AppBuilderException(Exception):
     """
     pass
 
+def _validate_system_requirements(system_requirements):
+    """
+    Validates systemRequirements section of dxapp.json for instanceTypeSelector constraints.
+
+    :param system_requirements: The systemRequirements section from runSpec
+    :type system_requirements: dict
+    :raises AppBuilderException: If validation fails
+    """
+    if not isinstance(system_requirements, dict):
+        return
+
+    for entry_point, requirements in system_requirements.items():
+        if not isinstance(requirements, dict):
+            continue
+
+        has_instance_type = 'instanceType' in requirements
+        has_instance_type_selector = 'instanceTypeSelector' in requirements
+        has_cluster_spec = 'clusterSpec' in requirements
+
+        # Check mutual exclusivity: instanceType and instanceTypeSelector
+        if has_instance_type and has_instance_type_selector:
+            raise AppBuilderException(
+                "instanceType and instanceTypeSelector keywords are mutually exclusive "
+                "in systemRequirements for entry point '{}'".format(entry_point)
+            )
+
+        # Check mutual exclusivity: instanceTypeSelector and clusterSpec
+        if has_instance_type_selector and has_cluster_spec:
+            raise AppBuilderException(
+                "instanceTypeSelector and clusterSpec keywords are mutually exclusive "
+                "in systemRequirements for entry point '{}'".format(entry_point)
+            )
+
 def _validate_applet_spec(applet_spec):
     if 'runSpec' not in applet_spec:
         raise AppBuilderException("Required field 'runSpec' not found in dxapp.json")
 
+    # Validate systemRequirements for instanceTypeSelector constraints in runSpec
+    if 'systemRequirements' in applet_spec.get('runSpec', {}):
+        _validate_system_requirements(applet_spec['runSpec']['systemRequirements'])
+
+    # Validate systemRequirements in regionalOptions for each region
+    regional_options = applet_spec.get('regionalOptions', {})
+    if isinstance(regional_options, dict):
+        for region, options in regional_options.items():
+            if isinstance(options, dict) and 'systemRequirements' in options:
+                _validate_system_requirements(options['systemRequirements'])
+
 def _validate_app_spec(app_spec):
-    pass
+    # Validate systemRequirements for instanceTypeSelector constraints in runSpec
+    if 'runSpec' in app_spec and 'systemRequirements' in app_spec['runSpec']:
+        _validate_system_requirements(app_spec['runSpec']['systemRequirements'])
+
+    # Validate systemRequirements in regionalOptions for each region
+    regional_options = app_spec.get('regionalOptions', {})
+    if isinstance(regional_options, dict):
+        for region, options in regional_options.items():
+            if isinstance(options, dict) and 'systemRequirements' in options:
+                _validate_system_requirements(options['systemRequirements'])
 
 def _get_applet_spec(src_dir):
     applet_spec_file = os.path.join(src_dir, "dxapp.json")

dxpy-0.403.0/dxpy/toolkit_version.py

@@ -0,0 +1 @@
+version = '0.403.0'

{dxpy-0.402.0 → dxpy-0.403.0}/dxpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dxpy
-Version: 0.402.0
+Version: 0.403.0
 Summary: DNAnexus Platform API bindings for Python
 Home-page: https://github.com/dnanexus/dx-toolkit
 Author: Aleksandra Zalcman, Andrey Kislyuk, Anurag Biyani, Geet Duggal, Katherine Lai, Kurt Jensen, Marek Hrvol, Ohad Rodeh, Phil Sung

{dxpy-0.402.0 → dxpy-0.403.0}/test/test_dxpy.py

@@ -3191,6 +3191,335 @@ class TestAppBuilderUtils(unittest.TestCase):
         with self.assertRaises(app_builder.AppBuilderException):
             assert_consistent_regions({"aws:us-east-1": None}, ["azure:westus"], app_builder.AppBuilderException)
 
+    def test_validate_system_requirements_instance_type_selector(self):
+        """Test that instanceTypeSelector validation works correctly"""
+        validate = app_builder._validate_system_requirements
+
+        # Valid cases - should not raise exceptions
+
+        # instanceTypeSelector alone is valid
+        validate({
+            "main": {
+                "instanceTypeSelector": {
+                    "allowedInstanceTypes": ["mem1_ssd1_x4", "mem1_ssd1_x8"]
+                }
+            }
+        })
+
+        # instanceType alone is valid
+        validate({
+            "main": {
+                "instanceType": "mem1_ssd1_x4"
+            }
+        })
+
+        # clusterSpec alone is valid
+        validate({
+            "main": {
+                "clusterSpec": {
+                    "type": "generic",
+                    "numInstances": 3
+                }
+            }
+        })
+
+        # instanceType and clusterSpec together is valid
+        validate({
+            "main": {
+                "instanceType": "mem1_ssd1_x4",
+                "clusterSpec": {
+                    "type": "generic",
+                    "numInstances": 3
+                }
+            }
+        })
+
+        # Empty requirements is valid
+        validate({})
+
+        # None requirements is valid
+        validate(None)
+
+        # Invalid cases - should raise AppBuilderException
+
+        # instanceType and instanceTypeSelector are mutually exclusive
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate({
+                "main": {
+                    "instanceType": "mem1_ssd1_x4",
+                    "instanceTypeSelector": {
+                        "allowedInstanceTypes": ["mem1_ssd1_x4", "mem1_ssd1_x8"]
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("instanceType", str(cm.exception))
+        self.assertIn("instanceTypeSelector", str(cm.exception))
+
+        # instanceTypeSelector and clusterSpec are mutually exclusive
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate({
+                "main": {
+                    "instanceTypeSelector": {
+                        "allowedInstanceTypes": ["mem1_ssd1_x4", "mem1_ssd1_x8"]
+                    },
+                    "clusterSpec": {
+                        "type": "generic",
+                        "numInstances": 3
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("instanceTypeSelector", str(cm.exception))
+        self.assertIn("clusterSpec", str(cm.exception))
+
+        # Test with wildcard entry point
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate({
+                "*": {
+                    "instanceType": "mem1_ssd1_x4",
+                    "instanceTypeSelector": {
+                        "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+
+        # Test with multiple entry points - one invalid
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate({
+                "main": {
+                    "instanceTypeSelector": {
+                        "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                    }
+                },
+                "process": {
+                    "instanceType": "mem1_ssd1_x4",
+                    "instanceTypeSelector": {
+                        "allowedInstanceTypes": ["mem1_ssd1_x8"]
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("process", str(cm.exception))
+
+    def test_validate_system_requirements_in_regional_options(self):
+        """Test that instanceTypeSelector validation works for regionalOptions"""
+        validate_applet = app_builder._validate_applet_spec
+        validate_app = app_builder._validate_app_spec
+
+        # Valid cases - should not raise exceptions
+
+        # Valid: instanceTypeSelector in regionalOptions
+        validate_applet({
+            "name": "test_applet",
+            "runSpec": {
+                "interpreter": "python3",
+                "file": "code.py"
+            },
+            "regionalOptions": {
+                "aws:us-east-1": {
+                    "systemRequirements": {
+                        "main": {
+                            "instanceTypeSelector": {
+                                "allowedInstanceTypes": ["mem1_ssd1_x4", "mem1_ssd1_x8"]
+                            }
+                        }
+                    }
+                }
+            }
+        })
+
+        # Valid: Different system requirements per region
+        validate_applet({
+            "name": "test_applet",
+            "runSpec": {
+                "interpreter": "python3",
+                "file": "code.py"
+            },
+            "regionalOptions": {
+                "aws:us-east-1": {
+                    "systemRequirements": {
+                        "main": {
+                            "instanceType": "mem1_ssd1_x4"
+                        }
+                    }
+                },
+                "azure:westus": {
+                    "systemRequirements": {
+                        "main": {
+                            "instanceTypeSelector": {
+                                "allowedInstanceTypes": ["mem1_ssd1_x8"]
+                            }
+                        }
+                    }
+                }
+            }
+        })
+
+        # Valid: systemRequirements in both runSpec and regionalOptions (different entry points)
+        validate_applet({
+            "name": "test_applet",
+            "runSpec": {
+                "interpreter": "python3",
+                "file": "code.py",
+                "systemRequirements": {
+                    "main": {
+                        "instanceType": "mem1_ssd1_x2"
+                    }
+                }
+            },
+            "regionalOptions": {
+                "aws:us-east-1": {
+                    "systemRequirements": {
+                        "process": {
+                            "instanceTypeSelector": {
+                                "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                            }
+                        }
+                    }
+                }
+            }
+        })
+
+        # Invalid cases - should raise AppBuilderException
+
+        # Invalid: instanceType + instanceTypeSelector in regionalOptions
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate_applet({
+                "name": "test_applet",
+                "runSpec": {
+                    "interpreter": "python3",
+                    "file": "code.py"
+                },
+                "regionalOptions": {
+                    "aws:us-east-1": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceType": "mem1_ssd1_x4",
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x4", "mem1_ssd1_x8"]
+                                }
+                            }
+                        }
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("instanceType", str(cm.exception))
+        self.assertIn("instanceTypeSelector", str(cm.exception))
+
+        # Invalid: instanceTypeSelector + clusterSpec in regionalOptions
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate_applet({
+                "name": "test_applet",
+                "runSpec": {
+                    "interpreter": "python3",
+                    "file": "code.py"
+                },
+                "regionalOptions": {
+                    "azure:westus": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                                },
+                                "clusterSpec": {
+                                    "type": "generic",
+                                    "numInstances": 3
+                                }
+                            }
+                        }
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("instanceTypeSelector", str(cm.exception))
+        self.assertIn("clusterSpec", str(cm.exception))
+
+        # Invalid: Error in one region out of multiple
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate_applet({
+                "name": "test_applet",
+                "runSpec": {
+                    "interpreter": "python3",
+                    "file": "code.py"
+                },
+                "regionalOptions": {
+                    "aws:us-east-1": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceType": "mem1_ssd1_x4"
+                            }
+                        }
+                    },
+                    "azure:westus": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceType": "mem1_ssd1_x4",
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x8"]
+                                }
+                            }
+                        }
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+
+        # Test with app spec as well
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate_app({
+                "name": "test_app",
+                "version": "1.0.0",
+                "runSpec": {
+                    "interpreter": "python3",
+                    "file": "code.py"
+                },
+                "regionalOptions": {
+                    "aws:us-east-1": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceType": "mem1_ssd1_x4",
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                                }
+                            }
+                        }
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+
+        # Invalid: Multiple entry points with error in regionalOptions
+        with self.assertRaises(app_builder.AppBuilderException) as cm:
+            validate_applet({
+                "name": "test_applet",
+                "runSpec": {
+                    "interpreter": "python3",
+                    "file": "code.py"
+                },
+                "regionalOptions": {
+                    "aws:us-east-1": {
+                        "systemRequirements": {
+                            "main": {
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x4"]
+                                }
+                            },
+                            "process": {
+                                "instanceType": "mem1_ssd1_x4",
+                                "instanceTypeSelector": {
+                                    "allowedInstanceTypes": ["mem1_ssd1_x8"]
+                                }
+                            }
+                        }
+                    }
+                }
+            })
+        self.assertIn("mutually exclusive", str(cm.exception))
+        self.assertIn("process", str(cm.exception))
+
 class TestWorkflowBuilderUtils(testutil.DXTestCaseBuildWorkflows):
     def setUp(self):
         super(TestWorkflowBuilderUtils, self).setUp()

{dxpy-0.402.0 → dxpy-0.403.0}/test/test_extract_expression.py

@@ -22,57 +22,53 @@
 
 from __future__ import absolute_import
 
-import unittest
-import subprocess
-import sys
-import os
-import dxpy
 import copy
+import csv
 import json
+import os
+import shutil
+import subprocess
+import sys
 import tempfile
-import csv
+import unittest
 from collections import OrderedDict
-import pandas as pd
 
-import shutil
-from dxpy_testutil import cd, chdir
+import dxpy
+import pandas as pd
+from dxpy.bindings.apollo.cmd_line_options_validator import ArgsValidator
+from dxpy.bindings.apollo.data_transformations import transform_to_expression_matrix
+from dxpy.bindings.apollo.dataset import Dataset
 from dxpy.bindings.apollo.json_validation_by_schema import JSONValidator
-from dxpy.utils.resolver import resolve_existing_path
-
+from dxpy.bindings.apollo.schemas.assay_filtering_conditions import (
+    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_0,
+    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_1,
+    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_1_non_optimized,
+)
 from dxpy.bindings.apollo.schemas.assay_filtering_json_schemas import (
     EXTRACT_ASSAY_EXPRESSION_JSON_SCHEMA,
 )
-from dxpy.bindings.apollo.cmd_line_options_validator import ArgsValidator
 from dxpy.bindings.apollo.schemas.input_arguments_validation_schemas import (
     EXTRACT_ASSAY_EXPRESSION_INPUT_ARGS_SCHEMA,
 )
 from dxpy.bindings.apollo.vizclient import VizClient
-
-from dxpy.bindings.apollo.data_transformations import transform_to_expression_matrix
-from dxpy.cli.output_handling import write_expression_output
-from dxpy.cli.help_messages import EXTRACT_ASSAY_EXPRESSION_JSON_TEMPLATE
-from dxpy.bindings.dxrecord import DXRecord
-from dxpy.bindings.apollo.dataset import Dataset
-
 from dxpy.bindings.apollo.vizserver_filters_from_json_parser import JSONFiltersValidator
-from dxpy.bindings.apollo.schemas.assay_filtering_conditions import (
-    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_0,
-    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_1,
-    EXTRACT_ASSAY_EXPRESSION_FILTERING_CONDITIONS_1_1_non_optimized,
-)
 from dxpy.bindings.apollo.vizserver_payload_builder import VizPayloadBuilder
+from dxpy.bindings.dxrecord import DXRecord
+from dxpy.cli.help_messages import EXTRACT_ASSAY_EXPRESSION_JSON_TEMPLATE
+from dxpy.cli.output_handling import write_expression_output
 from dxpy.exceptions import err_exit
-
+from dxpy.utils.resolver import resolve_existing_path
+from dxpy_testutil import cd, chdir
 
 dirname = os.path.dirname(__file__)
 
+from expression_test_assets.expression_test_expected_output_dict import (
+    VIZPAYLOADERBUILDER_EXPECTED_OUTPUT,
+)
 from expression_test_assets.expression_test_input_dict import (
     CLIEXPRESS_TEST_INPUT,
-    VIZPAYLOADERBUILDER_TEST_INPUT,
     EXPRESSION_CLI_JSON_FILTERS,
-)
-from expression_test_assets.expression_test_expected_output_dict import (
-    VIZPAYLOADERBUILDER_EXPECTED_OUTPUT,
+    VIZPAYLOADERBUILDER_TEST_INPUT,
 )
 
 
@@ -1187,9 +1183,9 @@ class TestDXExtractExpression(unittest.TestCase):
 
     def test_dx_extract_cmd_location_expression_sample_sql(self):
         expected_sql_query = [
-            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` <= 8693350 AND `expr_annotation_1`.`end` >= 67440200) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` <= 148500700 AND `expr_annotation_1`.`end` >= 148994424) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` <= 75228160 AND `expr_annotation_1`.`end` >= 75235759)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
-            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
-            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE (`expr_annotation_1`.`chr` = '11' AND (`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350) OR `expr_annotation_1`.`chr` = 'X' AND (`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700) OR `expr_annotation_1`.`chr` = '17' AND (`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)) AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') AND `expression_1`.`value` >= 25.63 ORDER BY `feature_id` ASC, `sample_id` ASC",
+            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE ((`expr_annotation_1`.`chr` = '11' AND ((`expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200) OR (`expr_annotation_1`.`start` <= 8693350 AND `expr_annotation_1`.`end` >= 67440200))) OR (`expr_annotation_1`.`chr` = 'X' AND ((`expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424) OR (`expr_annotation_1`.`start` <= 148500700 AND `expr_annotation_1`.`end` >= 148994424))) OR (`expr_annotation_1`.`chr` = '17' AND ((`expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759) OR (`expr_annotation_1`.`start` <= 75228160 AND `expr_annotation_1`.`end` >= 75235759)))) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
+            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE ((`expr_annotation_1`.`chr` = '11' AND ((`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200) OR (`expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350))) OR (`expr_annotation_1`.`chr` = 'X' AND ((`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424) OR (`expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700))) OR (`expr_annotation_1`.`chr` = '17' AND ((`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759) OR (`expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)))) AND `expression_1`.`value` >= 25.63 AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') ORDER BY `feature_id` ASC, `sample_id` ASC",
+            "SELECT `expression_1`.`feature_id` AS `feature_id`, `expression_1`.`sample_id` AS `sample_id`, `expression_1`.`value` AS `expression`, `expr_annotation_1`.`gene_name` AS `feature_name`, `expr_annotation_1`.`chr` AS `chrom`, `expr_annotation_1`.`start` AS `start` FROM `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expression` AS `expression_1` LEFT OUTER JOIN `database_gzky7400vgpyzy621q43gkkf__molecular_expression1_db`.`expr_annotation` AS `expr_annotation_1` ON `expression_1`.`feature_id` = `expr_annotation_1`.`feature_id` WHERE ((`expr_annotation_1`.`chr` = '11' AND ((`expr_annotation_1`.`end` BETWEEN 8693350 AND 67440200 OR `expr_annotation_1`.`start` BETWEEN 8693350 AND 67440200) OR (`expr_annotation_1`.`end` >= 67440200 AND `expr_annotation_1`.`start` <= 8693350))) OR (`expr_annotation_1`.`chr` = 'X' AND ((`expr_annotation_1`.`end` BETWEEN 148500700 AND 148994424 OR `expr_annotation_1`.`start` BETWEEN 148500700 AND 148994424) OR (`expr_annotation_1`.`end` >= 148994424 AND `expr_annotation_1`.`start` <= 148500700))) OR (`expr_annotation_1`.`chr` = '17' AND ((`expr_annotation_1`.`end` BETWEEN 75228160 AND 75235759 OR `expr_annotation_1`.`start` BETWEEN 75228160 AND 75235759) OR (`expr_annotation_1`.`end` >= 75235759 AND `expr_annotation_1`.`start` <= 75228160)))) AND `expression_1`.`sample_id` IN ('sample_1', 'sample_2') AND `expression_1`.`value` >= 25.63 ORDER BY `feature_id` ASC, `sample_id` ASC",
         ]
         response = self.run_dx_extract_assay_expression_cmd(
             self.expression_dataset,

dxpy-0.402.0/dxpy/toolkit_version.py

@@ -1 +0,0 @@
-version = '0.402.0'