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galaxy/lib/galaxy_test/selenium/test_uploads.py
T
Ahmed Awan fe353dc405 add selenium test for upload modal not losing content on close 
This selenium makes sure that when users reopen upload modal, the content from prior or inprogress uploads is still there
2024-01-24 17:23:39 +05:00

537 lines
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Python
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import os
import pytest
from .framework import (
selenium_test,
SeleniumTestCase,
UsesHistoryItemAssertions,
)
class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions):
@selenium_test
def test_upload_file(self):
self.perform_upload(self.get_filename("1.sam"))
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
self.history_panel_click_item_title(hid=1, wait=True)
self.assert_item_summary_includes(1, "28 lines")
@selenium_test
def test_upload_pasted_content(self):
pasted_content = "this is pasted"
self.perform_upload_of_pasted_content(pasted_content)
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
@selenium_test
def test_upload_pasted_url_content(self):
pasted_content = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/LICENSE.txt"
self.perform_upload_of_pasted_content(pasted_content)
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
@selenium_test
def test_upload_composite_dataset_pasted_data(self):
paste_content = ["a", "b", "c"]
self.perform_upload_of_composite_dataset_pasted_data("velvet", paste_content)
self.history_panel_wait_for_hid_ok(1)
history_count = len(self.history_contents())
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
self.history_panel_click_item_title(hid=1, wait=True)
self.history_panel_item_view_dataset_details(1)
param_values = self.driver.find_elements(self.by.CSS_SELECTOR, "#tool-parameters td.tool-parameter-value")
request_json = param_values[1].text
for data in paste_content:
assert f'"paste_content": "{data}"' in request_json
@selenium_test
def test_upload_simplest(self):
self.perform_upload(self.get_filename("1.sam"))
self.history_panel_wait_for_hid_ok(1)
history_contents = self.history_contents()
history_count = len(history_contents)
assert history_count == 1, "Incorrect number of items in history - expected 1, found %d" % history_count
hda = history_contents[0]
assert hda["name"] == "1.sam", hda
assert hda["extension"] == "sam", hda
self.history_panel_click_item_title(hid=1, wait=True)
self.assert_item_dbkey_displayed_as(1, "?")
@selenium_test
def test_upload_specify_ext(self):
self.perform_upload(self.get_filename("1.sam"), ext="txt")
self.history_panel_wait_for_hid_ok(1)
history_contents = self.history_contents()
hda = history_contents[0]
assert hda["name"] == "1.sam"
assert hda["extension"] == "txt", hda
@selenium_test
def test_upload_specify_genome(self):
self.perform_upload(self.get_filename("1.sam"), genome="hg18")
self.history_panel_wait_for_hid_ok(1)
self.history_panel_click_item_title(hid=1, wait=True)
self.assert_item_dbkey_displayed_as(1, "hg18")
@selenium_test
def test_upload_specify_ext_all(self):
self.perform_upload(self.get_filename("1.sam"), ext_all="txt")
self.history_panel_wait_for_hid_ok(1)
history_contents = self.history_contents()
hda = history_contents[0]
assert hda["name"] == "1.sam"
assert hda["extension"] == "txt", hda
@selenium_test
def test_upload_specify_genome_all(self):
self.perform_upload(self.get_filename("1.sam"), genome_all="hg18")
self.history_panel_wait_for_hid_ok(1)
self.history_panel_click_item_title(hid=1, wait=True)
self.assert_item_dbkey_displayed_as(1, "hg18")
@selenium_test
def test_upload_deferred(self):
self.perform_upload_of_pasted_content(
"https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed", deferred=True
)
hid = 1
self.history_panel_wait_for_hid_deferred(hid)
self.history_panel_click_item_title(hid=hid, wait=True)
self.screenshot("history_panel_dataset_deferred")
@selenium_test
def test_upload_list(self):
self.upload_list([self.get_filename("1.tabular")], name="Test List")
self.history_panel_wait_for_hid_ok(3)
# Make sure modals disappeared - both List creator (TODO: upload).
self.wait_for_selector_absent_or_hidden(".collection-creator")
self.assert_item_name(3, "Test List")
# Make sure source item is hidden when the collection is created.
self.history_panel_wait_for_hid_hidden(1)
@selenium_test
def test_upload_pair(self):
self.upload_list([self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Pair")
self.history_panel_wait_for_hid_ok(5)
# Make sure modals disappeared - both collection creator (TODO: upload).
self.wait_for_selector_absent_or_hidden(".collection-creator")
self.assert_item_name(5, "Test Pair")
# Make sure source items are hidden when the collection is created.
self.history_panel_wait_for_hid_hidden(1)
self.history_panel_wait_for_hid_hidden(2)
self.history_panel_wait_for_hid_hidden(3)
self.history_panel_wait_for_hid_hidden(4)
@selenium_test
def test_upload_pair_specify_extension(self):
self.upload_list(
[self.get_filename("1.tabular"), self.get_filename("2.tabular")],
name="Test Pair",
ext="txt",
hide_source_items=False,
)
self.history_panel_wait_for_hid_ok(5)
self.history_panel_wait_for_hid_ok(1)
history_contents = self.history_contents()
hda = history_contents[0]
assert hda["name"] == "1.tabular"
assert hda["extension"] == "txt", hda
@selenium_test
def test_upload_paired_list(self):
self.upload_paired_list(
[self.get_filename("1.tabular"), self.get_filename("2.tabular")], name="Test Paired List"
)
self.history_panel_wait_for_hid_ok(5)
# Make sure modals disappeared - both collection creator (TODO: upload).
self.wait_for_selector_absent_or_hidden(".collection-creator")
self.assert_item_name(5, "Test Paired List")
# Make sure source items are hidden when the collection is created.
self.history_panel_wait_for_hid_hidden(1)
self.history_panel_wait_for_hid_hidden(2)
self.history_panel_wait_for_hid_hidden(3)
self.history_panel_wait_for_hid_hidden(4)
@selenium_test
def test_upload_modal_retains_content(self):
self.home()
# initialize 2 uploads and close modal
self.upload_start_click()
self.upload_queue_local_file(self.get_filename("1.sam"))
self.upload_paste_data("some pasted data")
self.wait_for_and_click_selector("button#btn-close")
# reopen modal and check that the files are still there
self.upload_start_click()
self.wait_for_selector_visible("#upload-row-0.upload-init")
self.wait_for_selector_visible("#upload-row-1.upload-init")
# perform upload and close modal
self.upload_start()
self.wait_for_and_click_selector("button#btn-close")
# add another pasted file, but don't upload it
self.upload_start_click()
self.upload_paste_data("some more pasted data")
self.wait_for_and_click_selector("button#btn-close")
# reopen modal and see 2 uploaded, 1 yet to upload
self.upload_start_click()
self.wait_for_selector_visible("#upload-row-0.upload-success")
self.wait_for_selector_visible("#upload-row-1.upload-success")
self.wait_for_selector_visible("#upload-row-2.upload-init")
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_1_datasets(self):
# Test case generated for:
# https://www.ebi.ac.uk/ena/data/view/PRJDA60709
self.home()
self.upload_rule_start()
self.sleep_for(self.wait_types.UX_RENDER)
self.screenshot("rules_example_1_1_rules_landing")
self.components.upload.rule_source_content.wait_for_and_send_keys(
"""study_accession sample_accession experiment_accession fastq_ftp
PRJDA60709 SAMD00016379 DRX000475 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000770/DRR000770.fastq.gz
PRJDA60709 SAMD00016383 DRX000476 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000771/DRR000771.fastq.gz
PRJDA60709 SAMD00016380 DRX000477 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000772/DRR000772.fastq.gz
PRJDA60709 SAMD00016378 DRX000478 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000773/DRR000773.fastq.gz
PRJDA60709 SAMD00016381 DRX000479 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000774/DRR000774.fastq.gz
PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz"""
)
self._wait_for_upload_modal()
self.screenshot("rules_example_1_2_paste")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_example_1_3_initial_rules")
rule_builder.menu_button_filter.wait_for_and_click()
self.screenshot("rule_builder_filters")
rule_builder.menu_item_rule_type(rule_type="add-filter-count").wait_for_and_click()
filter_editor = rule_builder.rule_editor(rule_type="add-filter-count")
filter_editor_element = filter_editor.wait_for_visible()
filter_input = filter_editor_element.find_element(self.by.CSS_SELECTOR, "input[type='number']")
filter_input.clear()
filter_input.send_keys("1")
self.screenshot("rules_example_1_4_filter_header")
rule_builder.rule_editor_ok.wait_for_and_click()
self.rule_builder_set_mapping("url", "D")
self.rule_builder_set_mapping("name", "C", screenshot_name="rules_example_1_5_mapping_edit")
self.screenshot("rules_example_1_6_mapping_set")
self.rule_builder_set_extension("fastqsanger.gz")
self.screenshot("rules_example_1_7_extension_set")
# rule_builder.main_button_ok.wait_for_and_click()
# self.history_panel_wait_for_hid_ok(6)
# self.screenshot("rules_example_1_6_download_complete")
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_2_list(self):
self.perform_upload(self.get_filename("rules/PRJDA60709.tsv"))
self.history_panel_wait_for_hid_ok(1)
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.upload_rule_dataset_dialog()
self.upload_rule_set_dataset(1)
self.screenshot("rules_example_2_1_inputs")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_example_2_2_initial_rules")
# Filter header.
self.rule_builder_filter_count(1)
self.rule_builder_set_mapping("url", "D")
self.rule_builder_set_mapping("list-identifiers", "C")
self.rule_builder_set_extension("fastqsanger.gz")
self.screenshot("rules_example_2_3_rules")
self.rule_builder_set_collection_name("PRJDA60709")
self.screenshot("rules_example_2_4_name")
# rule_builder.main_buton_ok.wait_for_and_click()
# self.history_panel_wait_for_hid_ok(2)
# self.screenshot("rules_example_2_5_download_complete")
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_3_list_pairs(self):
self.perform_upload(self.get_filename("rules/PRJDB3920.tsv"))
self.history_panel_wait_for_hid_ok(1)
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.upload_rule_dataset_dialog()
self.upload_rule_set_dataset(1)
self._wait_for_upload_modal()
self.screenshot("rules_example_3_1_inputs")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_example_3_2_initial_rules")
# Filter header.
self.rule_builder_filter_count(1)
self.rule_builder_set_mapping("list-identifiers", "C")
self.rule_builder_set_extension("fastqsanger.gz")
self.screenshot("rules_example_3_3_old_rules")
self.rule_builder_add_regex_groups("D", 2, r"(.*);(.*)", screenshot_name="rules_example_3_4_regex")
self.screenshot("rules_example_3_6_with_regexes")
# Remove A also?
self.rule_builder_remove_columns(["D"], screenshot_name="rules_example_3_7_removed_column")
self.rule_builder_split_columns(["D"], ["E"], screenshot_name="rules_example_3_8_split_columns")
self.screenshot("rules_example_3_9_columns_are_split")
self.rule_builder_add_regex_groups(
"D", 1, r".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired"
)
self.screenshot("rules_example_3_11_has_paired_id")
self.rule_builder_swap_columns("D", "E", screenshot_name="rules_example_3_12_swap_columns")
self.screenshot("rules_example_3_13_swapped_columns")
self.rule_builder_set_mapping("paired-identifier", "D")
self.rule_builder_set_mapping("url", "E")
self.rule_builder_set_collection_name("PRJDB3920")
self.screenshot("rules_example_3_14_paired_identifier_set")
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_4_accessions(self):
# http://www.uniprot.org/uniprot/?query=proteome:UP000052092+AND+proteomecomponent:%22Genome%22
self._setup_uniprot_example()
self._wait_for_upload_modal()
self.screenshot("rules_example_4_1_inputs")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_example_4_2_initial_rules")
self.rule_builder_filter_count(1)
self.rule_builder_remove_columns(["B", "C", "E", "F", "G"])
self.rule_builder_set_mapping("info", "B")
self.screenshot("rules_example_4_3_basic_rules")
self.rule_builder_sort("A", screenshot_name="rules_example_4_4_sort")
self.rule_builder_add_regex_replacement(
"A", ".*", "http://www.uniprot.org/uniprot/\\0.fasta", screenshot_name="rules_example_4_5_url"
)
self.screenshot("rules_example_4_6_url_built")
self.rule_builder_set_mapping("list-identifiers", "A")
self.rule_builder_set_mapping("url", "C")
self.rule_builder_set_extension("fasta")
self.rule_builder_set_collection_name("UP000052092")
self.screenshot("rules_example_4_7_mapping_extension_and_name")
rule_builder.view_source.wait_for_and_click()
text_area_elem = rule_builder.source.wait_for_visible()
self.screenshot("rules_example_4_8_source")
self.write_screenshot_directory_file("rules_example_4_8_text", text_area_elem.get_attribute("value"))
rule_builder.main_button_ok.wait_for_and_click()
rule_builder.view_source.wait_for_visible()
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_5_matching_collections(self):
self._setup_uniprot_example()
self._wait_for_upload_modal()
self.screenshot("rules_example_5_1_inputs")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder.view_source.wait_for_and_click()
content = self._read_rules_test_data_file("uniprot.json")
self.rule_builder_enter_source_text(content)
self.screenshot("rules_example_5_2_source")
rule_builder.main_button_ok.wait_for_and_click()
rule_builder.view_source.wait_for_visible()
self.screenshot("rules_example_5_3_initial_rules")
self.rule_builder_add_value("fasta", screenshot_name="rules_example_5_4_fasta")
self.rule_builder_add_value("UP000052092 FASTA")
self.rule_builder_add_regex_replacement(
"A", ".*", "http://www.uniprot.org/uniprot/\\0.gff", screenshot_name="rules_example_5_5_url"
)
self.rule_builder_add_value("gff3")
self.rule_builder_add_value("UP000052092 GFF3")
self._scroll_to_end_of_table()
self.screenshot("rules_example_5_6_presplit")
self.rule_builder_split_columns(
["C", "D", "E"], ["F", "G", "H"], screenshot_name="rules_example_5_7_split_columns"
)
self.screenshot("rules_example_5_8_split")
self.rule_builder_set_mapping("file-type", "D")
self.rule_builder_set_mapping("collection-name", "E")
self.screenshot("rules_example_5_9_mapping")
@selenium_test
@pytest.mark.gtn_screenshot
@pytest.mark.local
def test_rules_example_6_nested_lists(self):
self.home()
self.perform_upload(self.get_filename("rules/PRJNA355367.tsv"))
self.history_panel_wait_for_hid_ok(1)
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.upload_rule_dataset_dialog()
self.upload_rule_set_dataset(1)
self._wait_for_upload_modal()
self.screenshot("rules_example_6_1_paste")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_example_6_2_rules_landing")
self.rule_builder_filter_count(1)
self.rule_builder_set_mapping("url", "J")
self.rule_builder_set_extension("sra")
self._scroll_to_end_of_table()
self.screenshot("rules_example_6_3_end_of_table")
self.rule_builder_add_regex_groups("L", 1, r"([^\d]+)\d+", screenshot_name="rules_example_6_4_regex")
self.rule_builder_set_mapping(
"list-identifiers", ["M", "A"], screenshot_name="rules_example_6_5_multiple_identifiers_edit"
)
self._scroll_to_end_of_table()
self.screenshot("rules_example_6_6_multiple_identifiers")
self.rule_builder_set_collection_name("PRJNA355367")
self.screenshot("rules_example_6_7_named")
@selenium_test
@pytest.mark.local
def test_rules_deferred_datasets(self):
# Test case generated for:
# https://www.ebi.ac.uk/ena/data/view/PRJDA60709
self.home()
self.upload_rule_start()
self.sleep_for(self.wait_types.UX_RENDER)
self.screenshot("rules_deferred_datasets_1_rules_landing")
self.components.upload.rule_source_content.wait_for_and_send_keys(
"""study_accession sample_accession experiment_accession fastq_ftp
PRJDA60709 SAMD00016379 DRX000475 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000770/DRR000770.fastq.gz
PRJDA60709 SAMD00016383 DRX000476 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000771/DRR000771.fastq.gz
PRJDA60709 SAMD00016380 DRX000477 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000772/DRR000772.fastq.gz
PRJDA60709 SAMD00016378 DRX000478 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000773/DRR000773.fastq.gz
PRJDA60709 SAMD00016381 DRX000479 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000774/DRR000774.fastq.gz
PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz"""
)
self._wait_for_upload_modal()
self.screenshot("rules_deferred_datasets_2_paste")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_deferred_datasets_3_initial_rules")
rule_builder.menu_button_filter.wait_for_and_click()
self.screenshot("rule_builder_filters")
rule_builder.menu_item_rule_type(rule_type="add-filter-count").wait_for_and_click()
filter_editor = rule_builder.rule_editor(rule_type="add-filter-count")
filter_editor_element = filter_editor.wait_for_visible()
filter_input = filter_editor_element.find_element(self.by.CSS_SELECTOR, "input[type='number']")
filter_input.clear()
filter_input.send_keys("1")
self.screenshot("rules_deferred_datasets_4_filter_header")
rule_builder.rule_editor_ok.wait_for_and_click()
self.rule_builder_set_mapping("url-deferred", "D")
self.rule_builder_set_mapping("name", "C", screenshot_name="rules_deferred_datasets_5_mapping_edit")
self.screenshot("rules_deferred_datasets_6_mapping_set")
self.rule_builder_set_extension("fastqsanger.gz")
self.screenshot("rules_deferred_datasets_7_extension_set")
rule_builder.main_button_ok.wait_for_and_click()
self.history_panel_wait_for_hid_deferred(6)
self.screenshot("rules_deferred_datasets_8_download_complete")
@selenium_test
@pytest.mark.local
def test_rules_deferred_list(self):
self.home()
self.perform_upload(self.get_filename("rules/PRJNA355367.tsv"))
self.history_panel_wait_for_hid_ok(1)
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.upload_rule_dataset_dialog()
self.upload_rule_set_dataset(1)
self._wait_for_upload_modal()
self.screenshot("rules_deferred_list_1_paste")
self.upload_rule_build()
rule_builder = self.components.rule_builder
rule_builder._.wait_for_and_click()
self.screenshot("rules_deferred_list_2_rules_landing")
self.rule_builder_filter_count(1)
self.rule_builder_set_mapping("url-deferred", "J")
self.rule_builder_set_extension("sra")
self._scroll_to_end_of_table()
self.screenshot("rules_deferred_list_3_end_of_table")
self.rule_builder_add_regex_groups("L", 1, r"([^\d]+)\d+", screenshot_name="rules_deferred_list_4_regex")
self.rule_builder_set_mapping(
"list-identifiers", ["M", "A"], screenshot_name="rules_deferred_list_5_multiple_identifiers_edit"
)
self._scroll_to_end_of_table()
self.screenshot("rules_deferred_list_6_multiple_identifiers")
self.rule_builder_set_collection_name("PRJNA355367")
self.screenshot("rules_deferred_list_7_named")
rule_builder.main_button_ok.wait_for_and_click()
hid = 2
self.history_panel_wait_for_hid_ok(hid)
self.screenshot("rules_deferred_list_7_download_complete")
def _read_rules_test_data_file(self, name):
with open(self.test_data_resolver.get_filename(os.path.join("rules", name))) as f:
return f.read()
def _wait_for_upload_modal(self):
self.components.upload.build_button.wait_for_visible()
self.components.upload.build_button.wait_for_clickable()
def _scroll_to_end_of_table(self):
rule_builder = self.components.rule_builder
table_elem = rule_builder.table.wait_for_visible()
first_cell = table_elem.find_elements(self.by.CSS_SELECTOR, "td")[0]
action_chains = self.action_chains()
action_chains.move_to_element(first_cell)
action_chains.click(first_cell)
for _ in range(15):
action_chains.send_keys(self.keys.ARROW_RIGHT)
action_chains.perform()
def _setup_uniprot_example(self):
self.perform_upload(self.get_filename("rules/uniprot.tsv"))
self.history_panel_wait_for_hid_ok(1)
self.upload_rule_start()
self.upload_rule_set_data_type("Collections")
self.upload_rule_dataset_dialog()
self.upload_rule_set_dataset(1)
# @selenium_test
# def test_rules_example_5_matching_collections(self):
# self.rule_builder_add_value("Protein FASTA")
# self.rule_builder_add_value("gff")
# self.rule_builder_add_value("Protein GFF")
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