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Source code for galaxy_test.base.rules_test_data
[docs]def check_example_1(hdca, dataset_populator):
assert hdca["collection_type"] == "list"
assert hdca["element_count"] == 2
first_dce = hdca["elements"][0]
first_hda = first_dce["object"]
assert first_hda["hid"] > 3
[docs]def check_example_2(hdca, dataset_populator):
assert hdca["collection_type"] == "list:list"
assert hdca["element_count"] == 2
first_collection_level = hdca["elements"][0]
assert first_collection_level["element_type"] == "dataset_collection"
second_collection_level = first_collection_level["object"]
assert second_collection_level["collection_type"] == "list"
assert second_collection_level["elements"][0]["element_type"] == "hda"
[docs]def check_example_3(hdca, dataset_populator):
assert hdca["collection_type"] == "list"
assert hdca["element_count"] == 2
first_element = hdca["elements"][0]
assert first_element["element_identifier"] == "test0forward"
[docs]def check_example_4(hdca, dataset_populator):
assert hdca["collection_type"] == "list:list"
assert hdca["element_count"] == 2
first_collection_level = hdca["elements"][0]
assert first_collection_level["element_identifier"] == "single", hdca
assert first_collection_level["element_type"] == "dataset_collection"
second_collection_level = first_collection_level["object"]
assert "elements" in second_collection_level, hdca
assert len(second_collection_level["elements"]) == 1, hdca
i1_element = second_collection_level["elements"][0]
assert "object" in i1_element, hdca
assert "element_identifier" in i1_element
assert i1_element["element_identifier"] == "i1", hdca
assert len(i1_element["object"]["tags"]) == 0
[docs]def check_example_5(hdca, dataset_populator):
assert hdca["collection_type"] == "list:list"
assert hdca["element_count"] == 2
first_collection_level = hdca["elements"][0]
assert first_collection_level["element_identifier"] == "single", hdca
assert first_collection_level["element_type"] == "dataset_collection"
second_collection_level = first_collection_level["object"]
assert "elements" in second_collection_level, hdca
assert len(second_collection_level["elements"]) == 1, hdca
i1_element = second_collection_level["elements"][0]
assert "object" in i1_element, hdca
assert "element_identifier" in i1_element
assert i1_element["element_identifier"] == "i1", hdca
tags = i1_element["object"]["tags"]
assert len(tags) > 0
assert "group:single" in tags, tags
assert "i1" in tags, tags
[docs]def check_example_6(hdca, dataset_populator):
assert hdca["collection_type"] == "list"
assert hdca["element_count"] == 3
i1_element = hdca["elements"][0]
assert "object" in i1_element, hdca
assert "element_identifier" in i1_element
assert i1_element["element_identifier"] == "i1", hdca
tags = i1_element["object"]["tags"]
assert len(tags) == 2
assert "random" in tags
assert "group:type:single" in tags
EXAMPLE_1 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
}
],
"mapping": [
{
"type": "list_identifiers",
"columns": [0],
}
],
},
"test_data": {
"type": "list",
"elements": [
{
"identifier": "i1",
"contents": "0",
"class": "File",
},
{
"identifier": "i2",
"contents": "1",
"class": "File",
},
],
},
"check": check_example_1,
"output_hid": 6,
}
EXAMPLE_2 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_column_metadata",
"value": "identifier0",
},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [0, 1],
}
],
},
"test_data": {
"type": "list",
"elements": [
{
"identifier": "i1",
"contents": "0",
"class": "File",
},
{
"identifier": "i2",
"contents": "1",
"class": "File",
},
],
},
"check": check_example_2,
"output_hid": 6,
}
# Flatten
EXAMPLE_3 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_column_metadata",
"value": "identifier1",
},
{
"type": "add_column_concatenate",
"target_column_0": 0,
"target_column_1": 1,
},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [2],
}
],
},
"test_data": {
"type": "list:paired",
"elements": [
{
"identifier": "test0",
"elements": [
{"identifier": "forward", "class": "File", "contents": "TestData123"},
{"identifier": "reverse", "class": "File", "contents": "TestData123"},
],
}
],
},
"check": check_example_3,
"output_hid": 6,
}
# Nesting with group tags.
EXAMPLE_4 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{"type": "add_column_group_tag_value", "value": "type", "default_value": "unused"},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [1, 0],
}
],
},
"test_data": {
"type": "list",
"elements": [
{"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
{"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
{"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
],
},
"check": check_example_4,
"output_hid": 8,
}
EXAMPLE_5 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{"type": "add_column_group_tag_value", "value": "type", "default_value": "unused"},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [1, 0],
},
{
"type": "group_tags",
"columns": [1],
},
{
"type": "tags",
"columns": [0],
},
],
},
"test_data": {
"type": "list",
"elements": [
{"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
{"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
{"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
],
},
"check": check_example_5,
"output_hid": 8,
}
EXAMPLE_6 = {
"rules": {
"rules": [
{
"type": "add_column_metadata",
"value": "identifier0",
},
{
"type": "add_column_metadata",
"value": "tags",
},
],
"mapping": [
{
"type": "list_identifiers",
"columns": [0],
},
{
"type": "tags",
"columns": [1],
},
],
},
"test_data": {
"type": "list",
"elements": [
{"identifier": "i1", "contents": "0", "class": "File", "tags": ["random", "group:type:single"]},
{"identifier": "i2", "contents": "1", "class": "File", "tags": ["random", "group:type:paired"]},
{"identifier": "i3", "contents": "2", "class": "File", "tags": ["random", "group:type:paired"]},
],
},
"check": check_example_6,
"output_hid": 8,
}