Merge github.com:genenetwork/genenetwork2 into acenteno

8 files changed, 0 insertions, 322 deletions

diff --git a/webtests/browser_run.py b/webtests/browser_run.py
deleted file mode 100644
index 2ec299c5..00000000
--- a/webtests/browser_run.py
+++ /dev/null
@@ -1,74 +0,0 @@
-from __future__ import absolute_import, division, print_function
-
-__all__ = ('sleep', 'testmod', 'test')
-
-from doctest import testmod
-
-from time import sleep
-
-import selenium
-from selenium import webdriver
-from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException
-from selenium.webdriver.common.keys import Keys
-
-class Test(object):
-    def __init__(self):
-        #self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver')
-        self.browser = webdriver.Firefox()
-
-    def get(self, url):
-        self.browser.get(url)
-        sleep(5)
-        self.title()
-
-    def click(self, xpath_selector):
-        el = self.browser.find_element_by_xpath(xpath_selector)
-        if el.text:
-            text = el.text.strip()
-        elif el.get_attribute("value"):
-            text = el.get_attribute("value").strip()
-        else:
-            text = "Notext"
-        el.click()
-        print("clicked:", text)
-        sleep(2)
-
-    def click_option(self, xpath_selector, option_text):
-        el = self.browser.find_element_by_xpath(xpath_selector)
-        for option in el.find_elements_by_tag_name('option'):
-            if option.text == option_text:
-                option.click() # select() in earlier versions of webdriver
-                break
-        sleep(2)
-
-    def enter_text(self, xpath_selector, text):
-        el = self.browser.find_element_by_xpath(xpath_selector)
-        sleep(10)
-        el.send_keys(text)
-        sleep(5)
-        # Just in case things get mangled by JavaScript, etc. we print the text for testing
-        self.get_text(xpath_selector)
-
-    def get_text(self, xpath_selector):
-        el = self.browser.find_element_by_xpath(xpath_selector)
-        text = el.text.strip() or el.get_attribute("value").strip()
-        print("text:", text)
-        
-    def get_element_style(self, xpath_selector):
-        el = self.browser.find_element_by_xpath(xpath_selector)
-        style = el.get_attribute("style").strip()
-        print("style:", style)
-
-    def switch_window(self):
-        self.browser.switch_to_window(self.browser.window_handles[-1])
-        sleep(2)
-        self.title()
-        sleep(2)
-
-
-    def title(self):
-        print("title:", self.browser.title)
-
-
-
-test = Test()
\ No newline at end of file
diff --git a/webtests/chromedriver b/webtests/chromedriver
deleted file mode 100644
index 754eb668..00000000
--- a/webtests/chromedriver
+++ /dev/null
diff --git a/webtests/correlation_matrix_test.py b/webtests/correlation_matrix_test.py
deleted file mode 100644
index 8529c265..00000000
--- a/webtests/correlation_matrix_test.py
+++ /dev/null
@@ -1,72 +0,0 @@
-"""
-
-Test Correlation matrix
-
->>> test.get("http://genenetwork.org/")
-title: GeneNetwork
-
-Choose the type
->>> test.click_option('''//*[@id="tissue"]''', 'Hippocampus mRNA')
-
-Enter the Get Any
->>> test.enter_text('''//*[@id="tfor"]''', 'grin2b')
-text: grin2b
-
-Search
->>> test.click('//*[@id="btsearch"]')
-clicked: Search
-
-Add 1430675_at
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[2]/td/input''')
-clicked: HC_M2_0606_P::1430675_at
-
-Add 1442370_at
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[3]/td/input''')
-clicked: HC_M2_0606_P::1442370_at
-
-Add 1457003_at
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[4]/td/input''')
-clicked: HC_M2_0606_P::1457003_at
-
-Add 1422223_at
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[5]/td/input''')
-clicked: HC_M2_0606_P::1422223_at
-
->>> sleep(5)
-
-Add to collection page
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[1]/td/table/tbody/tr[1]/td[4]/a''')
-clicked: Notext
-
->>> sleep(5)
-
-A new window is created, so we switch to it
->>> test.switch_window()
-title: BXD Trait Collection
-
-Select all records
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr/td/table/tbody/tr/td/table/tbody/tr/td/a/img''')
-clicked: Notext
-
-Click Matrix
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr/td/table/tbody/tr[2]/td/table/tbody/tr/td[2]/a/img''')
-clicked: Notext
-
-Another new window
->>> test.switch_window()
-title: Correlation Matrix
-
-Sleep a bunch because this can take a while
->>> sleep(10)
-
-Ensure that the correlation between Trait3 (HC_M2_0606_P::1457003_at) and Trait4 (HC_M2_0606_P::1422223_at) is 0.608
->>> test.get_text('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/blockquote/table/tbody/tr[5]/td[5]/a/font''')
-text: 0.608\n71
-
-"""
-
-from __future__ import absolute_import, division, print_function
-
-from browser_run import *
-
-testmod()
diff --git a/webtests/correlation_test.py b/webtests/correlation_test.py
deleted file mode 100644
index aad3a69f..00000000
--- a/webtests/correlation_test.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""
-Test calculate correlations
-
->>> test.get("http://genenetwork.org")
-title: GeneNetwork
-
-Choose the type
->>> test.click_option('''//*[@id="tissue"]''', 'Hippocampus mRNA')
-
-Enter the Get Any
->>> test.enter_text('''//*[@id="tfor"]''', 'ssh')
-text: ssh
-
-Search
->>> test.click('//*[@id="btsearch"]')
-clicked: Search
-
-Choose the first result
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[2]/td[2]/a''')
-clicked: 1455854_a_at
-
-A new window is created, so we switch to it
->>> test.switch_window()
-title: Hippocampus M430v2 BXD 06/06 PDNN : 1455854_a_at: Display Trait
-
-Click on Calculate Correlations
->>> test.click('''//*[@id="title3"]''')
-clicked: Calculate Correlations
-
-Click on Compute
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p[6]/table/tbody/tr/td/div/div/span/table/tbody/tr/td/input[3]''')
-clicked: Compute
-
-Another new window
->>> test.switch_window()
-title: Correlation
-
-Sleep a bunch because this can take a while
->>> sleep(25)
-
-Ensure the Sample rho is the exepcted 1.000 because it should be the same record
->>> test.get_text('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/table/tbody/tr[2]/td/div/table/tbody/tr[2]/td[9]/a''')
-text: 1.000
-
-"""
-
-from __future__ import absolute_import, division, print_function
-
-from browser_run import *
-
-testmod()
diff --git a/webtests/libpeerconnection.log b/webtests/libpeerconnection.log
deleted file mode 100644
index e69de29b..00000000
--- a/webtests/libpeerconnection.log
+++ /dev/null
diff --git a/webtests/marker_regression_test.py b/webtests/marker_regression_test.py
deleted file mode 100644
index c4f76f53..00000000
--- a/webtests/marker_regression_test.py
+++ /dev/null
@@ -1,55 +0,0 @@
-"""
-Test calculate correlations
-
->>> test.get("http://genenetwork.org")
-title: GeneNetwork
-
-Choose the type
->>> test.click_option('''//*[@id="tissue"]''', 'Liver mRNA')
-
-Enter the Get Any
->>> test.enter_text('''//*[@id="tfor"]''', 'grin2b')
-text: grin2b
-
-Search
->>> test.click('//*[@id="btsearch"]')
-clicked: Search
-
-Choose the second result
->>> test.click('''/html/body/table/tbody/tr[3]/td/table/tbody/tr/td/form/p/table/tbody/tr[3]/td/div/table/tbody/tr[3]/td[2]/a''')
-clicked: 1431700_at_A
-
-A new window is created, so we switch to it
->>> test.switch_window()
-title: GSE16780 UCLA Hybrid MDP Liver Affy HT M430A (Sep11) RMA : 1431700_at_A: Display Trait
-
-Click on Mapping Tools
->>> test.click('''//*[@id="title4"]''')
-clicked: Mapping Tools
-
-Click on Marker Regression tab
->>> test.click('''//*[@id="mapping_tabs"]/ul/li[2]/a''')
-clicked: Marker Regression
-
-Click on Compute
->>> test.click('''//*[@id="mappingtabs-2"]/span/table/tbody/tr[1]/td/input''')
-clicked: Compute
-
-Another new window
->>> test.switch_window()
-title: Genome Association Result
-
-Sleep a bunch because this can take a while
->>> sleep(60)
-
-Ensure that the LRS of the top record is the exepcted value
->>> test.get_text('''//*[@id="1"]/td[2]''')
-text: 11.511
-
-"""
-
-from __future__ import absolute_import, division, print_function
-
-from browser_run import *
-
-testmod()
diff --git a/webtests/show_trait_js_test.py b/webtests/show_trait_js_test.py
deleted file mode 100644
index 0fd2c16c..00000000
--- a/webtests/show_trait_js_test.py
+++ /dev/null
@@ -1,42 +0,0 @@
-"""
-Test if JS is working on the show trait page
-
->>> test.get("alexandria.uthsc.edu:89")
-title: GeneNetwork
-
-Choose the species
->>> test.click_option('''//*[@id="species"]''', 'Human')
-
-Choose the group
->>> test.click_option('''//*[@id="cross"]''', 'Human Brain Transcriptome (Yale/Kavli)')
-
-Choose the type
->>> test.click_option('''//*[@id="tissue"]''', 'Orbital Prefrontal Cortex mRNA')
-
-Enter the Get Any
->>> test.enter_text('''//*[@id="tfor"]''', 'shh')
-text: shh
-
-Search
->>> test.click('//*[@id="btsearch"]')
-clicked: Search
-
-Choose the first result
->>> test.click('''//*[@id="KIN_YSM_OFC_0711::3081205"]/td[2]/a''')
-clicked: 3081205
-
-A new window is created, so we switch to it
->>> test.switch_window()
-title: KIN/YSM Human OFC Affy Hu-Exon 1.0 ST (Jul11) Quantile : 3081205: Display Trait
-
-Check that the Calculate Correlations tab is closed (if javascript isn't working, it will be open)
->>> test.get_element_style('''//*[@id="sectionbody3"]''')
-style: display: none;
-
-"""
-
-from __future__ import absolute_import, division, print_function
-
-from browser_run import *
-
-testmod()
diff --git a/webtests/test_runner.py b/webtests/test_runner.py
deleted file mode 100644
index ef6d0d69..00000000
--- a/webtests/test_runner.py
+++ /dev/null
@@ -1,28 +0,0 @@
-from __future__ import absolute_import, division, print_function
-
-import unittest
-import doctest
-import glob
-
-tests = ("correlation_test",
-         "correlation_matrix_test",
-         "marker_regression_test",
-         "show_trait_js_test")
-
-
-def main():
-    tests = glob.glob("*_test.py")
-    
-    suite = unittest.TestSuite()
-    
-    for testname in tests:
-        test = testname.rsplit(".", 1)[0]
-        print("Test is:", test)
-        mod = __import__(test)
-        suite.addTest(doctest.DocTestSuite(mod))
-        
-    runner = unittest.TextTestRunner()
-    runner.run(suite)
-    
-if __name__ == '__main__':
-    main()
\ No newline at end of file