Merge branch 'master' of github.com:open-research/sumatra

sumatra/commands.py

@@ -54,6 +54,17 @@ def _warning(
     print(message)
 warnings.showwarning = _warning
 
+def _convertStr(s):
+ 	"""Convert string to either int or float or not both."""
+ 	try:
+ 		ret = int(s)
+ 	except ValueError:
+         try:
+             ret = float(s)
+         except ValueError:
+             ret = s
+ 	return ret
+
 def parse_executable_str(exec_str):
     """
     Split the string describing the executable into a path part and an
@@ -433,6 +444,7 @@ def list(argv):  # add 'report' and 'log' as aliases
     parser.add_argument('-m', '--main_file', help="filter list of records by main file")
     parser.add_argument('-P', '--parameter_table', action="store_const", const="parameter_table",
                         dest="mode", help="list records with parameter values")
+    parser.add_argument('-p', '--parameters', metavar='parameters', default=None, help="filter records by parameter values, separated by comma")
     args = parser.parse_args(argv)
 
     project = load_project()
@@ -442,6 +454,14 @@ def list(argv):  # add 'report' and 'log' as aliases
 
     kwargs = {'tags':args.tags, 'mode':args.mode, 'format':args.format, 'reverse':args.reverse}
     if args.main_file is not None: kwargs['main_file__startswith'] = args.main_file
+    if args.parameters:
+        parameters = {}
+        for pp in args.parameters.split(','):
+            for operator in ['=',':']:
+                if operator in pp:
+                    pkey,pval = pp.split(operator)
+                    parameters.update({pkey:_convertStr(pval)})
+        kwargs.update({'parameters':parameters})
     print(project.format_records(**kwargs))
 
 

sumatra/projects.py

@@ -296,16 +296,18 @@ def get_labels(self, tags=None, reverse=False):
             labels.reverse()
         return labels
 
-    def find_records(self, tags=None, reverse=False, *args, **kwargs):
+    def find_records(self, tags=None, reverse=False, parameters=None, *args, **kwargs):
         records = self.record_store.list(self.name, tags, *args, **kwargs)
         if reverse:
             records.reverse()
+        if parameters is not None:
+            records = [rec for rec in records if len(rec.parameters.diff(parameters)[-1]) == 0]
         return records
 
     # def find_data() here?
 
     def format_records(self, format='text', mode='short', tags=None, reverse=False, *args, **kwargs):
-        if format=='text' and mode=='short':
+        if format=='text' and mode=='short' and ('parameters' not in kwargs.keys()):
             return '\n'.join(self.get_labels(tags=tags, reverse=reverse))
         else:
             records = self.find_records(tags=tags, reverse=reverse, *args, **kwargs)

test/system/test_webui.py

@@ -0,0 +1,225 @@
+"""
+Tests of the web browser interface (smtweb) using Selenium
+
+
+"""
+
+from __future__ import print_function
+from __future__ import unicode_literals
+import os
+from time import sleep
+from builtins import input
+try:
+    from unittest2 import SkipTest
+except ImportError:
+    from unittest import SkipTest
+try:
+    from selenium import webdriver
+    have_selenium = True
+except ImportError:
+    have_selenium = False
+
+from subprocess import PIPE
+import sarge
+
+from nose.tools import assert_equal, assert_dict_contains_subset, assert_in
+
+import utils
+from utils import (setup as default_setup, teardown as default_teardown,
+                   run, run_test, build_command, assert_file_exists, assert_in_output,
+                   assert_config, assert_label_equal, assert_records, assert_return_code,
+                   edit_parameters, expected_short_list, substitute_labels)
+
+
+repository = "https://bitbucket.org/apdavison/ircr2013"
+#repository = "/Users/andrew/dev/ircr2013"
+
+
+def modify_script(filename):
+    def wrapped():
+        with open(os.path.join(utils.working_dir, filename), 'r') as fp:
+            script = fp.readlines()
+        with open(os.path.join(utils.working_dir, filename), 'w') as fp:
+            for line in script:
+                if "print(mean_bubble_size, median_bubble_size)" in line:
+                    fp.write('print("Mean:", mean_bubble_size)\n')
+                    fp.write('print("Median:", median_bubble_size)\n')
+                else:
+                    fp.write(line)
+    return wrapped
+
+
+setup_steps = [
+    ("Get the example code",
+     "hg clone %s ." % repository,
+     assert_in_output, "updating to branch default"),
+    ("Set up a Sumatra project",
+     "smt init -d Data -i . -e python -m glass_sem_analysis.py --on-changed=store-diff ProjectGlass",
+     assert_in_output, "Sumatra project successfully set up"),
+    ("Run the ``glass_sem_analysis.py`` script with Sumatra",
+     "smt run -r 'initial run' default_parameters MV_HFV_012.jpg",
+     assert_in_output, ("2416.86315789 60.0", "histogram.png")),
+    ("Comment on the outcome",
+     "smt comment 'works fine'"),
+    edit_parameters("default_parameters", "no_filter", "filter_size", 1),
+    ("Run with changed parameters and user-defined label",
+     "smt run -l example_label -r 'No filtering' no_filter MV_HFV_012.jpg",
+     assert_in_output, "phases.png",
+     assert_label_equal, "example_label"),
+    ("Change parameters from the command line",
+     "smt run -r 'Trying a different colourmap' default_parameters MV_HFV_012.jpg phases_colourmap=hot"),
+    ("Add another comment",
+     "smt comment 'The default colourmap is nicer'"),  # TODO  add a comment to an older record (e.g. this colourmap is nicer than 'hot')")
+    ("Add tags on the command line",
+     build_command("smt tag mytag {0} {1}", "labels")),
+    modify_script("glass_sem_analysis.py"),
+    ("Run the modified code",
+     "smt run -r 'Added labels to output' default_parameters MV_HFV_012.jpg"),
+]
+
+
+def setup():
+    global server, driver
+    if not have_selenium:
+        raise SkipTest("Tests require Selenium")
+    default_setup()
+    for step in setup_steps:
+        if callable(step):
+            step()
+        else:
+            print(step[0])  # description
+            run_test(*step[1:])
+
+    server = sarge.Command("smtweb -p 8765 --no-browser", cwd=utils.working_dir,
+                           stdout=sarge.Capture(), stderr=sarge.Capture())
+    server.run(async=True)
+    driver = webdriver.Firefox()
+
+
+def teardown():
+    driver.close()
+    server.terminate()
+    default_teardown()
+
+
+def test_start_page():
+    driver.get("http://127.0.0.1:8765")
+    # on homepage
+    assert_equal(driver.title, "List of projects")
+    # assert there is one project, named "ProjectGlass"
+    projects = driver.find_elements_by_tag_name("h3")
+    assert_equal(len(projects), 1)
+    assert_equal(projects[0].text, "ProjectGlass")
+    # click on ProjectGlass --> record list
+    projects[0].click()
+    assert_equal(driver.title, "ProjectGlass: List of records")
+    assert_equal(driver.current_url, "http://127.0.0.1:8765/ProjectGlass/")
+
+
+def test_record_list():
+    driver.get("http://127.0.0.1:8765/ProjectGlass/")
+    # assert there are four records
+    rows = driver.find_elements_by_tag_name('tr')
+    assert_equal(len(rows), 4 + 1)  # first row is the header
+    column_headers = [elem.text for elem in rows[0].find_elements_by_tag_name('th')]
+    # assert the labels are correct and that the reason and outcome fields are correct
+    expected_content = substitute_labels([
+         {'label': 0, 'outcome': 'works fine', 'reason': 'initial run',
+          'version': '6038f9c...', 'main': 'glass_sem_analysis.py'},
+         {'label': 1, 'outcome': '', 'reason': 'No filtering'},
+         {'label': 2, 'outcome': 'The default colourmap is nicer', 'reason': 'Trying a different colourmap'},
+         {'label': 3, 'outcome': '', 'reason': 'Added labels to output', 'version': '6038f9c...*'}])(utils.env)
+    for row, expected in zip(rows[1:], reversed(expected_content)):
+        cells = row.find_elements_by_tag_name('td')
+        label = cells[0].text
+        assert_equal(row.get_attribute('id'), label)
+        actual = dict((key.lower(), cell.text) for key, cell in zip(column_headers, cells))
+        assert_dict_contains_subset(expected, actual)
+
+
+def test_column_settings_dialog():
+    driver.get("http://127.0.0.1:8765/ProjectGlass/")
+    # test the column settings dialog
+    row0 = driver.find_element_by_tag_name('tr')
+    column_headers = [elem.text for elem in row0.find_elements_by_tag_name('th')]
+    cog = driver.find_element_by_class_name("glyphicon-cog")
+    cog.click()
+    sleep(0.5)
+    options = driver.find_elements_by_class_name("checkbox")
+    displayed_columns = [option.text for option in options if option.find_element_by_tag_name("input").is_selected()]
+    assert_equal(displayed_columns, column_headers[1:])  # can't turn off "Label" column
+    # turn on all columns
+    for option in options:
+        checkbox = option.find_element_by_tag_name("input")
+        if not checkbox.is_selected():
+            checkbox.click()
+    apply_button, = [elem for elem in driver.find_elements_by_tag_name("button") if elem.text == "Apply"]
+    apply_button.click()
+    sleep(0.5)
+    column_headers = [elem.text for elem in row0.find_elements_by_tag_name('th')]
+    assert_equal(column_headers,
+                 ["Label", "Date/Time", "Reason", "Outcome", "Input data", "Output data",
+                  "Duration", "Processes", "Executable", "Main", "Version", "Arguments", "Tags"])
+
+
+def test_comparison_view():
+    driver.get("http://127.0.0.1:8765/ProjectGlass/")
+    # test that "Compare selected" gives an error message with no records selected
+    alert = driver.find_element_by_id("alert")
+    assert not alert.is_displayed()
+    compare_button, = [elem for elem in driver.find_elements_by_tag_name("button") if "Compare" in elem.text]
+    compare_button.click()
+    sleep(0.5)
+    assert alert.is_displayed()
+    assert "Need at least two records to compare" in alert.text
+    alert.click()
+    sleep(0.5)
+    assert not alert.is_displayed()
+
+    # select two records and click on compare selected
+    rows = driver.find_elements_by_tag_name('tr')
+    target_records = utils.env["labels"][::2]
+    for row in rows[1:]:
+        if row.get_attribute("id") in target_records:
+            row.click()
+
+    # scroll back to the top of the screen
+    driver.execute_script("window.scrollTo(0, 0)")
+    compare_button.click()
+    # assert go to comparison page
+    assert_in("compare", driver.current_url)
+
+
+def test_data_detail_view():
+    driver.get("http://127.0.0.1:8765/ProjectGlass/")
+    rows = driver.find_elements_by_tag_name('tr')
+    rows[1].find_element_by_tag_name('td').find_element_by_tag_name('a').click()
+    assert_equal(driver.current_url, "http://127.0.0.1:8765/ProjectGlass/{}/".format(utils.env["labels"][-1]))
+
+    dl = driver.find_element_by_tag_name('dl')
+    general_attributes = dict(zip((item.text for item in dl.find_elements_by_tag_name("dt")),
+                                  (item.text for item in dl.find_elements_by_tag_name("dd"))))
+    assert_equal(general_attributes["Code version:"], '6038f9c500d1* (diff)')
+    assert_in("Added labels to output", general_attributes["Reason:"])
+
+
+if __name__ == '__main__':
+    # Run the tests without using Nose.
+    setup()
+    try:
+        test_start_page()
+        test_record_list()
+        test_column_settings_dialog()
+        test_comparison_view()
+        test_data_detail_view()
+        # test filter by tags
+        # test editing reason
+        # test "Add outcome" button
+        # test deleting records
+    except Exception as err:
+        print(err)
+    response = input("Do you want to delete the temporary directory (default: yes)? ")
+    if response not in ["n", "N", "no", "No"]:
+        teardown()
+    else:
+        print("Temporary directory %s not removed" % utils.temporary_dir)