def _test_HTMLfile(self):
"""
Create two html files (project and molecule) that have relative links to each other.
Exercising the machinery in HTMLfile class.
"""
entryId = "test_HTMLfile"
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
project.appendMolecule(molecule)
# initialize project html page
# per item always set 2 top level attributes:
project.htmlLocation = (project.path('index.html'), None)
project.html = HTMLfile(project.htmlLocation[0],
project,
title='Project')
nTdebug("project.htmlLocation[0]: %s" % project.htmlLocation[0])
#create new folders for Molecule/HTML
htmlPath = project.htmlPath()
if os.path.exists(htmlPath):
removedir(htmlPath)
os.makedirs(htmlPath)
nTdebug("htmlPath: %s" % htmlPath)
# initialize molecule html page
for subdir in htmlDirectories.values():
project.mkdir(project.molecule.name, moleculeDirectories.html,
subdir)
# NB project.htmlPath is different from project.path
molecule.htmlLocation = (project.htmlPath('indexMolecule.html'), None)
nTdebug("molecule.htmlLocation[0]: %s" % molecule.htmlLocation[0])
molecule.html = HTMLfile(molecule.htmlLocation[0],
project,
title='Molecule ' + molecule.name)
# nb: destination is a destination obj (eg molecule object) that is to
# have a html attribute that points to an HTMLfile instance.
# In the validate.py code, the source argument is the 'main' section in
# project.html. JFD doesn't understand why.
project.html.insertHtmlLinkInTag('li',
section=project.html.main,
source=project,
destination=molecule,
text='mol ref',
id=None)
# rerun for testing.
_link = project.html.findHtmlLocation(project, molecule, id=None)
# self.assertEquals('moleculeName/HTML/indexMolecule.html#_top', link)
project.html.main('ul', openTag=False)
for htmlObj in [project.html, molecule.html]:
self.assertFalse(htmlObj.render())
def testROGscore(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
# Add some crud to prevent warnings/errors later.
molecule.addChain('top')
top = molecule.allChains()[0]
# Disable warnings temporarily
v = cing.verbosity
cing.verbosity = verbosityNothing
for i in range(1 * 10):
res = top.addResidue(repr(random()), i)
for j in range(5):
_atom = res.addAtom(repr(random()), j)
cing.verbosity = v
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
a = Atom(resName='ALA', atomName='HN')
a.criticize()
self.assertTrue(a)
self.assertEquals(a.rogScore.colorLabel, COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][0], COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][1],
ROGscore.ROG_COMMENT_NO_COOR)
lotr_remark = 'One ring to rule them all'
preserved_remark = 'Preserved'
nowHasEffect_remark = 'Now has effect'
nowHasEffectToo_remark = 'Now has effect too'
# Next line will have to wipe out the orange comments.
a.rogScore.setMaxColor(COLOR_RED, lotr_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffect_remark)
a.rogScore.setMaxColor(COLOR_RED, preserved_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffectToo_remark)
self.assertEquals(len(a.rogScore.colorCommentList), 5)
self.assertEquals(a.rogScore.colorCommentList[0][1],
ROGscore.ROG_COMMENT_NO_COOR)
self.assertEquals(a.rogScore.colorCommentList[1][1],
nowHasEffect_remark)
myhtml = HTMLfile('testROGscore.html', project, 'A Test')
myhtml.main("a main")
a.rogScore.createHtmlForComments(myhtml.main)
kw = {}
a.rogScore.addHTMLkeywords(kw)
myhtml.main("a", 'or by popup', **kw)
myhtml.render()
def testMakeHtmlTableWithJS(self):
# CSS and Javascript is going to determine much of the formatting.
project = self.setupSimplestProject()
h = HTMLfile(project.htmlPath('test.html'), project)
columnFormats = [('col1', {}), ('col2', {}), ('col3', {})]
t = MakeHtmlTable(h.main,
showHeader=False,
classId="testJsTable",
id="testJsTableId",
columnFormats=columnFormats,
bla="0")
for row in t.rows(range(2)):
rStr = str(row)
t.nextColumn()
t(None, rStr)
t.nextColumn()
t('a', rStr + "." + str(2), href='someRefHere')
t.nextColumn() # empty one
t.nextColumn()
t(None, rStr + "." + str(4))
#end for
h.main('h3', 'Text to start below the table.')
h.render()
def testROGscore(self):
entryId = 'test'
project = Project(entryId)
self.failIf(project.removeFromDisk())
project = Project.open(entryId, status='new')
molecule = Molecule(name='moleculeName')
molecule.ensemble = Ensemble(molecule) # Needed for html.
project.appendMolecule(molecule) # Needed for html.
# Add some crud to prevent warnings/errors later.
molecule.addChain('top')
top = molecule.allChains()[0]
# Disable warnings temporarily
v = cing.verbosity
cing.verbosity = verbosityNothing
for i in range( 1*10):
res = top.addResidue( repr(random()),i )
for j in range( 5):
_atom = res.addAtom( repr(random()),j )
cing.verbosity = v
molecule.updateAll()
project.setupHtml() # Needed for creating the sub dirs.
a = Atom(resName='ALA', atomName='HN')
a.criticize()
self.assertTrue(a)
self.assertEquals(a.rogScore.colorLabel, COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][0], COLOR_ORANGE)
self.assertEquals(a.rogScore.colorCommentList[0][1], ROGscore.ROG_COMMENT_NO_COOR)
lotr_remark = 'One ring to rule them all'
preserved_remark = 'Preserved'
nowHasEffect_remark = 'Now has effect'
nowHasEffectToo_remark = 'Now has effect too'
# Next line will have to wipe out the orange comments.
a.rogScore.setMaxColor(COLOR_RED, lotr_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffect_remark )
a.rogScore.setMaxColor(COLOR_RED, preserved_remark)
a.rogScore.setMaxColor(COLOR_ORANGE, nowHasEffectToo_remark)
self.assertEquals(len(a.rogScore.colorCommentList), 5)
self.assertEquals(a.rogScore.colorCommentList[0][1], ROGscore.ROG_COMMENT_NO_COOR)
self.assertEquals(a.rogScore.colorCommentList[1][1], nowHasEffect_remark)
myhtml = HTMLfile('testROGscore.html', project, 'A Test')
myhtml.main("a main")
a.rogScore.createHtmlForComments(myhtml.main)
kw = {}
a.rogScore.addHTMLkeywords(kw)
myhtml.main("a", 'or by popup', **kw)
myhtml.render()
def testMakeHtmlTableWithJS(self):
# CSS and Javascript is going to determine much of the formatting.
project = self.setupSimplestProject()
h = HTMLfile(project.htmlPath('test.html'), project)
columnFormats = [ ('col1', {}),
('col2', {}),
('col3', {})
]
t = MakeHtmlTable(h.main, showHeader=False, classId="testJsTable", id="testJsTableId", columnFormats=columnFormats,
bla="0")
for row in t.rows(range(2)):
rStr = str(row)
t.nextColumn()
t(None, rStr)
t.nextColumn()
t('a', rStr + "." + str(2), href='someRefHere')
t.nextColumn() # empty one
t.nextColumn()
t(None, rStr + "." + str(4))
#end for
h.main('h3', 'Text to start below the table.')
h.render()
def test_HTMLfile_simple(self):
project = self.setupSimplestProject()
myhtml = HTMLfile('myTest.html', project, 'A Test')
myhtml.header("a header")
myhtml('h1', 'It is a test')
myhtml.main("a main")
myhtml.openTag('a', href="http://www.apple.com")
myhtml('img', src='apple1.jpg')
myhtml.closeTag('a')
myhtml('a', 'testing link', href="http://www.bioc.cam.ac.uk/")
myhtml.render()
###############
myhtml = HTMLfile('myTest2.html', project, 'A Test 2')
myhtml.header('h1', 'It is a test 2')
myhtml.header('h2', 'another line')
myhtml.main('a', href="http://www.apple.com", closeTag=False)
myhtml.main('img', src='apple1.jpg')
myhtml.main('a', openTag=False)
myhtml.main('a', 'testing link', href="http://www.bioc.cam.ac.uk/")
myhtml('br', 'used call')
myhtml.render()
def test_HTMLfile_simple(self):
project = self.setupSimplestProject()
myhtml = HTMLfile('myTest.html', project, 'A Test')
myhtml.header("a header")
myhtml('h1', 'It is a test')
myhtml.main("a main")
myhtml.openTag('a', href="http://www.apple.com")
myhtml('img', src = 'apple1.jpg')
myhtml.closeTag('a')
myhtml('a', 'testing link', href="http://www.bioc.cam.ac.uk/")
myhtml.render()
###############
myhtml = HTMLfile('myTest2.html', project, 'A Test 2')
myhtml.header('h1', 'It is a test 2')
myhtml.header('h2', 'another line')
myhtml.main('a', href="http://www.apple.com", closeTag=False)
myhtml.main('img', src = 'apple1.jpg')
myhtml.main('a', openTag=False)
myhtml.main('a', 'testing link', href="http://www.bioc.cam.ac.uk/")
myhtml('br', 'used call')
myhtml.render()
