mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
davelopez
441 lines
21 KiB
Python
441 lines
21 KiB
Python
import os
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import pytest
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from selenium.webdriver.common.by import By
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from selenium.webdriver.common.keys import Keys
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from .framework import (
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selenium_only,
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selenium_test,
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SeleniumTestCase,
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UsesHistoryItemAssertions,
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)
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from .upload_activity_helpers import UsesUploadActivity
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class TestUploads(SeleniumTestCase, UsesHistoryItemAssertions, UsesUploadActivity):
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_file(self):
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self.upload_context("local-file").stage_local_file(self.get_filename("1.sam")).start()
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self.history_panel_wait_for_hid_ok(1)
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history_count = len(self.history_contents())
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assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
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self.history_panel_click_item_title(hid=1, wait=True)
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self.assert_item_summary_includes(1, "28 lines")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_pasted_url_content(self):
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pasted_content = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/LICENSE.txt"
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self.upload_context("paste-content").stage_paste_content(pasted_content).start()
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self.history_panel_wait_for_hid_ok(1)
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history_count = len(self.history_contents())
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assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
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@selenium_test
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def test_upload_composite_dataset_pasted_data(self):
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paste_content = ["a", "b", "c"]
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(
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self.upload_context("composite-file")
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.select_composite("velvet")
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.stage_composite_paste_slot(slot=1, content=paste_content[0])
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.stage_composite_paste_slot(slot=2, content=paste_content[1])
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.stage_composite_paste_slot(slot=3, content=paste_content[2])
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.start()
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)
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self.history_panel_wait_for_hid_ok(1)
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history_count = len(self.history_contents())
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assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
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self.history_panel_click_item_title(hid=1, wait=True)
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self.history_panel_item_view_dataset_details(1)
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param_values = self.find_element_by_selector("#tool-parameters td.tool-parameter-value .vjs-tree")
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request_json = param_values.get_attribute("data-request-json")
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assert request_json
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for data in paste_content:
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assert f'"paste_content":"{data}"' in request_json
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_simplest(self):
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self.upload_context("local-file").stage_local_file(self.get_filename("1.sam")).start()
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self.history_panel_wait_for_hid_ok(1)
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history_contents = self.history_contents()
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history_count = len(history_contents)
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assert history_count == 1, f"Incorrect number of items in history - expected 1, found {history_count}"
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hda = history_contents[0]
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assert hda["name"] == "1.sam", hda
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assert hda["extension"] == "sam", hda
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self.history_panel_click_item_title(hid=1, wait=True)
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self.assert_item_dbkey_displayed_as(1, "?")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_deferred(self):
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uploader = self.upload_context("paste-links")
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url = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed"
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item = uploader.stage_paste_link(url)
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item.set_deferred(True)
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uploader.start()
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hid = 1
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self.history_panel_wait_for_hid_deferred(hid)
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self.history_panel_click_item_title(hid=hid, wait=True)
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self.screenshot("history_panel_dataset_deferred")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_list(self):
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self.upload_context("local-file").stage_local_file(self.get_filename("1.tabular")).to_list("Test List").start()
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self.history_panel_wait_for_hid_ok(1)
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self.assert_item_name(1, "Test List")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_pair(self):
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uploader = self.upload_context("local-file")
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uploader.stage_local_file(self.get_filename("1.tabular"))
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uploader.stage_local_file(self.get_filename("2.tabular"))
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uploader.to_paired_list("Test Pair").start()
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self.history_panel_wait_for_hid_ok(1)
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self.assert_item_name(1, "Test Pair")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_pair_specify_extension(self):
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uploader = self.upload_context("local-file")
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uploader.stage_local_file(self.get_filename("1.tabular"), {"extension": "txt"})
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uploader.stage_local_file(self.get_filename("2.tabular"), {"extension": "txt"})
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uploader.to_paired_list("Test Pair").start()
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self.history_panel_wait_for_hid_ok(1)
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self.assert_item_name(1, "Test Pair")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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def test_upload_paired_list(self):
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uploader = self.upload_context("local-file")
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uploader.stage_local_file(self.get_filename("1.tabular"))
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uploader.stage_local_file(self.get_filename("2.tabular"))
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uploader.to_paired_list("Test Paired List").start()
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self.history_panel_wait_for_hid_ok(1)
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self.assert_item_name(1, "Test Paired List")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_1_datasets(self):
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# Test case generated for:
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# https://www.ebi.ac.uk/ena/data/view/PRJDA60709
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self.home()
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rule_import = self.upload_context("rule")
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self.sleep_for(self.wait_types.UX_RENDER)
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self.screenshot("rules_example_1_1_rules_landing")
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rule_import.creating("datasets").from_source("pasted_table").paste_content(
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"""study_accession sample_accession experiment_accession fastq_ftp
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PRJDA60709 SAMD00016379 DRX000475 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000770/DRR000770.fastq.gz
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PRJDA60709 SAMD00016383 DRX000476 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000771/DRR000771.fastq.gz
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PRJDA60709 SAMD00016380 DRX000477 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000772/DRR000772.fastq.gz
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PRJDA60709 SAMD00016378 DRX000478 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000773/DRR000773.fastq.gz
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PRJDA60709 SAMD00016381 DRX000479 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000774/DRR000774.fastq.gz
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PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz"""
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)
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self.screenshot("rules_example_1_2_paste")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_example_1_3_initial_rules")
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rule_builder.menu_button_filter.wait_for_and_click()
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self.screenshot("rule_builder_filters")
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rule_builder.menu_item_rule_type(rule_type="add-filter-count").wait_for_and_click()
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filter_editor = rule_builder.rule_editor(rule_type="add-filter-count")
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filter_editor_element = filter_editor.wait_for_visible()
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filter_input = filter_editor_element.find_element(By.CSS_SELECTOR, "input[type='number']")
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filter_input.clear()
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filter_input.send_keys("1")
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self.screenshot("rules_example_1_4_filter_header")
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rule_builder.rule_editor_ok.wait_for_and_click()
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self.rule_builder_set_mapping("url", "D")
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self.rule_builder_set_mapping("name", "C", screenshot_name="rules_example_1_5_mapping_edit")
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self.screenshot("rules_example_1_6_mapping_set")
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self.rule_builder_set_extension("fastqsanger.gz")
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self.screenshot("rules_example_1_7_extension_set")
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# rule_builder.main_button_ok.wait_for_and_click()
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# self.history_panel_wait_for_hid_ok(6)
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# self.screenshot("rules_example_1_6_download_complete")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_2_list(self):
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self.upload_context("local-file").stage_local_file(self.get_filename("rules/PRJDA60709.tsv")).start()
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self.history_panel_wait_for_hid_ok(1)
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self.upload_context("rule").creating("collections").from_source("dataset_as_table").select_dataset(1)
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self.screenshot("rules_example_2_1_inputs")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_example_2_2_initial_rules")
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# Filter header.
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self.rule_builder_filter_count(1)
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self.rule_builder_set_mapping("url", "D")
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self.rule_builder_set_mapping("list-identifiers", "C")
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self.rule_builder_set_extension("fastqsanger.gz")
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self.screenshot("rules_example_2_3_rules")
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self.rule_builder_set_collection_name("PRJDA60709")
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self.screenshot("rules_example_2_4_name")
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# rule_builder.main_buton_ok.wait_for_and_click()
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# self.history_panel_wait_for_hid_ok(2)
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# self.screenshot("rules_example_2_5_download_complete")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_3_list_pairs(self):
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self.upload_context("local-file").stage_local_file(self.get_filename("rules/PRJDB3920.tsv")).start()
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self.history_panel_wait_for_hid_ok(1)
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self.upload_context("rule").creating("collections").from_source("dataset_as_table").select_dataset(1)
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self.screenshot("rules_example_3_1_inputs")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_example_3_2_initial_rules")
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# Filter header.
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self.rule_builder_filter_count(1)
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self.rule_builder_set_mapping("list-identifiers", "C")
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self.rule_builder_set_extension("fastqsanger.gz")
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self.screenshot("rules_example_3_3_old_rules")
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self.rule_builder_add_regex_groups("D", 2, r"(.*);(.*)", screenshot_name="rules_example_3_4_regex")
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self.screenshot("rules_example_3_6_with_regexes")
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# Remove A also?
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self.rule_builder_remove_columns(["D"], screenshot_name="rules_example_3_7_removed_column")
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self.rule_builder_split_columns(["D"], ["E"], screenshot_name="rules_example_3_8_split_columns")
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self.screenshot("rules_example_3_9_columns_are_split")
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self.rule_builder_add_regex_groups(
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"D", 1, r".*_(\d).fastq.gz", screenshot_name="rules_example_3_10_regex_paired"
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)
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self.screenshot("rules_example_3_11_has_paired_id")
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self.rule_builder_swap_columns("D", "E", screenshot_name="rules_example_3_12_swap_columns")
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self.screenshot("rules_example_3_13_swapped_columns")
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self.rule_builder_set_mapping("paired-identifier", "D")
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self.rule_builder_set_mapping("url", "E")
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self.rule_builder_set_collection_name("PRJDB3920")
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self.screenshot("rules_example_3_14_paired_identifier_set")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_4_accessions(self):
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# http://www.uniprot.org/uniprot/?query=proteome:UP000052092+AND+proteomecomponent:%22Genome%22
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self._setup_uniprot_example()
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self.screenshot("rules_example_4_1_inputs")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_example_4_2_initial_rules")
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self.rule_builder_filter_count(1)
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self.rule_builder_remove_columns(["B", "C", "E", "F", "G"])
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self.rule_builder_set_mapping("info", "B")
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self.screenshot("rules_example_4_3_basic_rules")
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self.rule_builder_sort("A", screenshot_name="rules_example_4_4_sort")
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self.rule_builder_add_regex_replacement(
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"A", ".*", "http://www.uniprot.org/uniprot/\\0.fasta", screenshot_name="rules_example_4_5_url"
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)
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self.screenshot("rules_example_4_6_url_built")
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self.rule_builder_set_mapping("list-identifiers", "A")
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self.rule_builder_set_mapping("url", "C")
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self.rule_builder_set_extension("fasta")
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self.rule_builder_set_collection_name("UP000052092")
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self.screenshot("rules_example_4_7_mapping_extension_and_name")
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rule_builder.view_source.wait_for_and_click()
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text_area_elem = rule_builder.source.wait_for_visible()
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self.screenshot("rules_example_4_8_source")
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self.write_screenshot_directory_file("rules_example_4_8_text", text_area_elem.get_attribute("value"))
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rule_builder.main_button_ok.wait_for_and_click()
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rule_builder.view_source.wait_for_visible()
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_5_matching_collections(self):
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self._setup_uniprot_example()
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self.screenshot("rules_example_5_1_inputs")
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rule_builder = self.components.rule_builder
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rule_builder.view_source.wait_for_and_click()
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content = self._read_rules_test_data_file("uniprot.json")
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self.rule_builder_enter_source_text(content)
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self.screenshot("rules_example_5_2_source")
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rule_builder.main_button_ok.wait_for_and_click()
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rule_builder.view_source.wait_for_visible()
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self.screenshot("rules_example_5_3_initial_rules")
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self.rule_builder_add_value("fasta", screenshot_name="rules_example_5_4_fasta")
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self.rule_builder_add_value("UP000052092 FASTA")
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self.rule_builder_add_regex_replacement(
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"A", ".*", "http://www.uniprot.org/uniprot/\\0.gff", screenshot_name="rules_example_5_5_url"
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)
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self.rule_builder_add_value("gff3")
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self.rule_builder_add_value("UP000052092 GFF3")
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self._scroll_to_end_of_table()
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self.screenshot("rules_example_5_6_presplit")
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self.rule_builder_split_columns(
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["C", "D", "E"], ["F", "G", "H"], screenshot_name="rules_example_5_7_split_columns"
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)
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self.screenshot("rules_example_5_8_split")
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self.rule_builder_set_mapping("file-type", "D")
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self.rule_builder_set_mapping("collection-name", "E")
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self.screenshot("rules_example_5_9_mapping")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.gtn_screenshot
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@pytest.mark.local
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def test_rules_example_6_nested_lists(self):
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self.home()
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self.upload_context("local-file").stage_local_file(self.get_filename("rules/PRJNA355367.tsv")).start()
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self.history_panel_wait_for_hid_ok(1)
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self.upload_context("rule").creating("collections").from_source("dataset_as_table").select_dataset(1)
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self.screenshot("rules_example_6_1_paste")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_example_6_2_rules_landing")
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self.rule_builder_filter_count(1)
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self.rule_builder_set_mapping("url", "J")
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self.rule_builder_set_extension("sra")
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self._scroll_to_end_of_table()
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self.screenshot("rules_example_6_3_end_of_table")
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self.rule_builder_add_regex_groups("L", 1, r"([^\d]+)\d+", screenshot_name="rules_example_6_4_regex")
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self.rule_builder_set_mapping(
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"list-identifiers", ["M", "A"], screenshot_name="rules_example_6_5_multiple_identifiers_edit"
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)
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self._scroll_to_end_of_table()
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self.screenshot("rules_example_6_6_multiple_identifiers")
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self.rule_builder_set_collection_name("PRJNA355367")
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self.screenshot("rules_example_6_7_named")
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@selenium_only("Not yet migrated to support Playwright backend")
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@selenium_test
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@pytest.mark.local
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def test_rules_deferred_datasets(self):
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# Test case generated for:
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# https://www.ebi.ac.uk/ena/data/view/PRJDA60709
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self.home()
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rule_import = self.upload_context("rule")
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self.sleep_for(self.wait_types.UX_RENDER)
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self.screenshot("rules_deferred_datasets_1_rules_landing")
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rule_import.creating("datasets").from_source("pasted_table").paste_content(
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"""study_accession sample_accession experiment_accession fastq_ftp
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PRJDA60709 SAMD00016379 DRX000475 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000770/DRR000770.fastq.gz
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PRJDA60709 SAMD00016383 DRX000476 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000771/DRR000771.fastq.gz
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PRJDA60709 SAMD00016380 DRX000477 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000772/DRR000772.fastq.gz
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PRJDA60709 SAMD00016378 DRX000478 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000773/DRR000773.fastq.gz
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PRJDA60709 SAMD00016381 DRX000479 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000774/DRR000774.fastq.gz
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PRJDA60709 SAMD00016382 DRX000480 ftp.sra.ebi.ac.uk/vol1/fastq/DRR000/DRR000775/DRR000775.fastq.gz"""
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)
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self.screenshot("rules_deferred_datasets_2_paste")
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rule_builder = self.components.rule_builder
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rule_builder._.wait_for_visible()
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self.screenshot("rules_deferred_datasets_3_initial_rules")
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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(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_only("Not yet migrated to support Playwright backend")
|
|
@selenium_test
|
|
@pytest.mark.local
|
|
def test_rules_deferred_list(self):
|
|
self.home()
|
|
self.upload_context("local-file").stage_local_file(self.get_filename("rules/PRJNA355367.tsv")).start()
|
|
self.history_panel_wait_for_hid_ok(1)
|
|
self.upload_context("rule").creating("collections").from_source("dataset_as_table").select_dataset(1)
|
|
|
|
self.screenshot("rules_deferred_list_1_paste")
|
|
|
|
rule_builder = self.components.rule_builder
|
|
rule_builder._.wait_for_visible()
|
|
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_state(hid, state="deferred", allowed_force_refreshes=1)
|
|
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 _scroll_to_end_of_table(self):
|
|
rule_builder = self.components.rule_builder
|
|
table_elem = rule_builder.table.wait_for_visible()
|
|
# handsontable
|
|
# first_cell = table_elem.find_elements(By.CSS_SELECTOR, "td")[0]
|
|
# aggrid
|
|
first_cell = table_elem.find_elements(By.CSS_SELECTOR, ".ag-cell")[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(Keys.ARROW_RIGHT)
|
|
action_chains.perform()
|
|
|
|
def _setup_uniprot_example(self):
|
|
self.upload_context("local-file").stage_local_file(self.get_filename("rules/uniprot.tsv")).start()
|
|
self.history_panel_wait_for_hid_ok(1)
|
|
self.upload_context("rule").creating("collections").from_source("dataset_as_table").select_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")
|