def object_description_sentence( objid, type, director):
"""given an object's id, return a sentence describing
the object.
In case the id is empty, return a sentence saying
the object is not yet created, please create it.
In case the id is valid, return a sentence describing
the object, and a link to configure the object.
"""
if objid == '':
link = action_link(
actionRequireAuthentication(
type.lower(), director.sentry,
label = 'create', routine = 'new',
), director.cgihome)
obj_ctrl = "%s has not been defined. Please %s a %s" % (
type, link, type.lower())
else:
link = action_link(
actionRequireAuthentication(
type.lower(), director.sentry,
label = 'configure', routine = 'new',
), director.cgihome)
method = 'get%s' % type
method = getattr( director.clerk, method )
obj_record = method( objid )
obj_ctrl = "%s (%s)" % (
obj_record.short_description, link)
pass
return obj_ctrl
class NeutronExperiment(base):
class Inventory(base.Inventory):
import pyre.inventory
id = pyre.inventory.str("id", default=None)
id.meta['tip'] = "the unique identifier of the experiment"
ncount = pyre.inventory.float( 'ncount', default = 1e6 )
ncount.meta['tip'] = 'number of neutrons'
pass # end of Inventory
def default(self, director):
try:
page = director.retrieveSecurePage( 'neutronexperiment' )
except AuthenticationError, err:
return err.page
main = page._body._content._main
# populate the main column
document = main.document(title='Neutron Experiment')
document.description = ''
document.byline = 'byline?'
p = document.paragraph()
action = actionRequireAuthentication(
actor = 'neutronexperimentwizard', sentry = director.sentry,
label = 'this wizard', routine = 'start',
)
wizard_link = action_link( action, director.cgihome )
action = actionRequireAuthentication(
actor = 'neutronexperiment', sentry = director.sentry,
label = 'experiments', routine = 'listall',
)
list_link = action_link( action, director.cgihome )
p.text = [
'In this virtual neutron facility, you can set up',
'a new experiment by using %s.' % wizard_link,
'Or you can select from one of the %s you have run' % list_link,
'and rerun it with new settings.',
]
return page
def listall(self, director):
page = director.retrievePage('scatteringKernel')
main = page._body._content._main
# populate the main column
document = main.document(title='List of scattering kernels')
document.description = ''
document.byline = 'byline?'
# retrieve id:record dictionary from db
clerk = director.clerk
scatteringKernels = clerk.indexScatteringKernels().values()
scatteringKernels = [ clerk.getHierarchy(scatteringKernel) for scatteringKernel in scatteringKernels]
p = document.paragraph()
numScatteringKernels = len(scatteringKernels)
columns = ['id', 'reference', 'short_description', 'type', 'creator', 'date' ]
columnTitles = ['Short description', 'Type of scattering kernel', 'Creator', 'Date of creation']
from PyHtmlTable import PyHtmlTable
t = PyHtmlTable(numScatteringKernels, len(columnTitles), {'width':'400','border':2})#,'bgcolor':'white'})
for colNum, col in enumerate(columnTitles):
t.setc(0,colNum,col)
for row, sk in enumerate(scatteringKernels):
for colNum, colName in enumerate( columns[2:] ):
value = sk.getColumnValue(colName)
if colName == 'short_description':
link = action_link(
actionRequireAuthentication(
'scatteringKernel',
director.sentry,
label = value,
routine = 'show',
id = sk.id,
), director.cgihome
)
value = link
t.setc(row+1,colNum,value)
p.text = [t.return_html()]
p = document.paragraph()
p.text = [action_link(
actionRequireAuthentication(
'scatteringKernelInput', director.sentry,
label = 'Add a new scattering kernel'), director.cgihome
),
'<br>']
return page
def list( container, document, actor, director,
routines = ['edit'] ):
p = document.paragraph()
formatstr = '%(index)s: %(name)s '
formatstr += ' '.join(
[ '(%'+'(%slink)s)' % routine for routine in routines ]
)
for i, element in enumerate( container ):
p = document.paragraph()
subs = {'name': element.short_description,
'index': i+1}
#links
for routine in routines:
link = action_link(
actionRequireAuthentication(
actor, director.sentry,
routine = routine,
label = routine,
id = element.id,
), director.cgihome
)
subs[ '%slink' % routine ] = link
continue
p.text += [
formatstr % subs,
]
continue
return
def listall(self, director):
page = director.retrievePage( 'job' )
main = page._body._content._main
# populate the main column
document = main.document(title='List of computational jobs')
document.description = ''
document.byline = 'byline?'
# retrieve id:record dictionary from db
clerk = director.clerk
jobs = clerk.getJobs( where = 'owner=%r' % director.sentry.username )
p = document.paragraph()
numJobs = len(jobs)
columns = [
'jobName', 'id', 'owner', 'server',
'numprocessors', 'status', 'timeStart', 'timeCompletion',
]
numColumns=len(columns)
from PyHtmlTable import PyHtmlTable
t=PyHtmlTable(numJobs,numColumns, {'width':'400','border':2,'bgcolor':'white'})
for colNum, col in enumerate(columns):
t.setc(0,colNum,col)
continue
for row, job in enumerate( jobs ):
for colNum, colName in enumerate( columns ):
value = job.getColumnValue(colName)
if colName == 'jobName':
link = action_link(
actionRequireAuthentication(
'job',
director.sentry,
label = value,
routine = 'show',
id = job.id,
), director.cgihome
)
value = link
pass # endif
t.setc(row+1,colNum,value)
#colNum+=1
p.text = [t.return_html()]
return page
def _add_delete_sentence(self, document, director):
p = document.paragraph()
action = actionRequireAuthentication(
label = 'here',
actor = 'neutronexperiment',
routine = 'delete',
sentry = director.sentry,
id = self.inventory.id)
link = action_link( action, director.cgihome )
p.text = [
'To delete this experiment, please click %s.' % link,
]
return
def _add_run_sentence(self, document, director):
p = document.paragraph()
action = actionRequireAuthentication(
label = 'here',
actor = 'neutronexperiment',
routine = 'run',
sentry = director.sentry,
id = self.inventory.id)
link = action_link( action, director.cgihome )
p.text = [
'If you are done with experiment configuration,',
'please click %s to start this experiment.' % link,
]
return
def _add_revision_sentence(self, document, director):
p = document.paragraph()
action = actionRequireAuthentication(
label = 'here',
actor = 'neutronexperimentwizard',
routine = 'start',
sentry = director.sentry,
id = self.inventory.id)
link = action_link( action, director.cgihome )
p.text = [
'If you need to make changes to this experiment,',
'please click %s.' % link,
]
return
def _footer(self, document, director):
#
document.paragraph()
p = document.paragraph(align='right')
action = actionRequireAuthentication(label='Cancel',
actor='neutronexperimentwizard',
routine='cancel',
id=self.inventory.id,
sentry=director.sentry)
link = action_link(action, director.cgihome)
p.text = [
'%s this experiment planning.' % link,
]
return
def _footer(self, document, director):
#
document.paragraph()
p = document.paragraph(align = 'right')
action = actionRequireAuthentication(
label = 'Cancel',
actor = 'neutronexperimentwizard',
routine = 'cancel',
id = self.inventory.id,
sentry = director.sentry)
link = action_link( action, director.cgihome )
p.text = [
'%s this experiment planning.' % link,
]
return
def noscatterer(document, director):
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'scatterer',
director.sentry,
label='add',
routine='new',
), director.cgihome)
p.text = [
"There is no scatterer in this sample assembly. ",
'Please %s a scatter.' % (director.cgihome, link)
]
return
def noscatterer( document, director ):
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'scatterer', director.sentry,
label = 'add', routine = 'new',
), director.cgihome
)
p.text = [
"There is no scatterer. ",
'Please %s a scatter.' % (
director.cgihome, link)
]
return
main = page._body._content._main
# populate the main column
document = main.document(title='Experiments')
document.description = ''
document.byline = 'byline?'
#
p = document.paragraph()
action = actionRequireAuthentication(
label = 'this wizard',
actor = 'neutronexperimentwizard',
routine = 'start',
sentry = director.sentry,
)
link = action_link( action, director.cgihome )
p.text = [
'You can perform various kinds of neutron experiments in',
'this virtual neutron facility.',
'To start, you can plan a new experiment by following %s.' % link,
]
# retrieve id:record dictionary from db
clerk = director.clerk
experiments = clerk.indexNeutronExperiments()
# make a list of all experiments
listexperiments( experiments.values(), document, director )
return page
def view(self, director):
def listexperiments( experiments, document, director ):
p = document.paragraph()
n = len(experiments)
p.text = [ 'Here is a list of experiments you have planned or run:' ]
formatstr = '%(index)s: %(viewlink)s (%(status)s) is a measurement of %(sample)r in %(instrument)r (%(deletelink)s)'
actor = 'neutronexperiment'
container = experiments
for i, element in enumerate( container ):
p = document.paragraph()
name = element.short_description
if name in ['', None, 'None'] : name = 'undefined'
action = actionRequireAuthentication(
actor, director.sentry,
routine = 'view',
label = name,
id = element.id,
)
viewlink = action_link( action, director.cgihome )
action = actionRequireAuthentication(
actor, director.sentry,
routine = 'delete',
label = 'delete',
id = element.id,
)
deletelink = action_link( action, director.cgihome )
element = director.clerk.getHierarchy( element )
if element.instrument is None \
or element.instrument.instrument is None:
action = actionRequireAuthentication(
'neutronexperimentwizard', sentry = director.sentry,
label = 'select instrument',
routine = 'select_instrument',
id = element.id,
)
link = action_link( action, director.cgihome )
instrument = link
else:
instrument = element.instrument.instrument
instrument = instrument.short_description
pass # end if
subs = {'index': i+1,
'viewlink': viewlink,
'deletelink': deletelink,
'status': element.status,
'instrument': instrument,
'sample': 'sample',
}
p.text += [
formatstr % subs,
]
continue
return
label='',
id=self.inventory.id,
arguments={'form-received': formcomponent.name},
)
from vnf.weaver import action_formfields
action_formfields(action, form)
# expand the form with fields of the data object that is being edited
formcomponent.expand(form)
p = form.paragraph()
p.text = [
action_link(
actionRequireAuthentication(
'neutronexperimentwizard',
director.sentry,
label='Add a new sample',
#routine = 'create_new_sample',
routine='input_material',
id=self.inventory.id),
director.cgihome),
'<br>'
]
submit = form.control(name='submit', type="submit", value="next")
#self.processFormInputs(director)
# self._footer( form, director )
return page
def input_material(self, director):
try:
page = director.retrieveSecurePage('neutronexperimentwizard')
try:
page = director.retrieveSecurePage( 'sampleassembly' )
except AuthenticationError, err:
return err.page
id = self.inventory.id
record = director.clerk.getSampleAssembly( id )
record = director.getHierarchy( record )
scatterers = record.scatterers
for scatterer in scatterers:
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'scatterer',
director.sentry,
routine = 'addscatterer',
label = 'add',
), director.cgihome
)
continue
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'sampleassemblywizard',
director.sentry,
routine = 'addscatterer',
label = 'add',
), director.cgihome
)
p.text = [
def listall(self, director):
page = director.retrievePage('sample')
main = page._body._content._main
# populate the main column
document = main.document(title='List of samples')
document.description = ''
document.byline = 'byline'
# retrieve id:record dictionary from db
clerk = director.clerk
scatterers = clerk.indexScatterers(where='template=True').values()
scatterers = [
clerk.getHierarchy(scatterer) for scatterer in scatterers
]
samples = scatterers
p = document.paragraph()
import operator
generators = [
operator.attrgetter('short_description'),
lambda s: s.matter.realmatter.chemical_formula,
lambda s: format_lattice_parameters(s.matter.realmatter),
lambda s: format_atoms(s.matter.realmatter),
lambda s: format_shape(s.shape.realshape),
]
columnTitles = [
'Sample description', 'Chemical formula', 'Cartesian lattice',
'Atom positions', 'Shape'
]
t = PyHtmlTable(len(samples), len(columnTitles), {
'width': '90%',
'border': 2,
'bgcolor': 'white'
})
# first row for labels
for colNum, col in enumerate(columnTitles):
t.setc(0, colNum, col)
# other rows for values
for row, sample in enumerate(samples):
#first put in the radio button
#selection = "<input type='radio' name='actor.form-received.kernel_id' value="+sample.id+" id='radio'/>"
#t.setc(row+1, 0, selection)
for colNum, generator in enumerate(generators):
value = generator(sample)
t.setc(row + 1, colNum, value)
p.text = [t.return_html()]
p = document.paragraph()
p.text = [
action_link(
actionRequireAuthentication('sampleInput',
director.sentry,
label='Add a new sample',
routine='default'),
director.cgihome), '<br>'
]
return page
routine = 'configure_scatteringkernels',
label = '',
id=self.inventory.id,
arguments = {'form-received': formcomponent.name },
)
from vnf.weaver import action_formfields
action_formfields( action, form )
# expand the form with fields of the data object that is being edited
formcomponent.expand( form )
p = form.paragraph()
p.text = [action_link(
actionRequireAuthentication(
'neutronexperimentwizard', director.sentry,
label = 'Add a new sample',
#routine = 'create_new_sample',
routine = 'input_material',
id=self.inventory.id
), director.cgihome),'<br>']
submit = form.control(name='submit',type="submit", value="next")
#self.processFormInputs(director)
# self._footer( form, director )
return page
def input_material(self, director):
try:
page = director.retrieveSecurePage( 'neutronexperimentwizard' )
except AuthenticationError, err:
return err.page
id = self.inventory.id
record = director.clerk.getJob( id )
assert record.owner == director.sentry.username
main = page._body._content._main
document = main.document( title = 'Job # %s: %s' % (
record.id, record.status ) )
if record.status == 'created':
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'job',
director.sentry,
label = 'submit',
routine = 'edit',
id = record.id,
), director.cgihome
)
p.text = [
'This job is created but not submitted.',
'Please %s it first' % link,
]
return page
if record.status not in ['created', 'finished']:
status = check( record, director )
props = record.getColumnNames()
try:
page = director.retrieveSecurePage('sampleassembly')
except AuthenticationError, err:
return err.page
id = self.inventory.id
record = director.clerk.getSampleAssembly(id)
record = director.getHierarchy(record)
scatterers = record.scatterers
for scatterer in scatterers:
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'scatterer',
director.sentry,
routine='addscatterer',
label='add',
), director.cgihome)
continue
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'sampleassemblywizard',
director.sentry,
routine='addscatterer',
label='add',
), director.cgihome)
p.text = [
'There is no scatterer in sample assembly at this moment. ',
def listall(self, director):
page = director.retrievePage('job')
main = page._body._content._main
# populate the main column
document = main.document(title='List of computational jobs')
document.description = ''
document.byline = 'byline?'
# retrieve id:record dictionary from db
clerk = director.clerk
jobs = clerk.getJobs(where='owner=%r' % director.sentry.username)
p = document.paragraph()
numJobs = len(jobs)
columns = [
'jobName',
'id',
'owner',
'server',
'numprocessors',
'status',
'timeStart',
'timeCompletion',
]
numColumns = len(columns)
from PyHtmlTable import PyHtmlTable
t = PyHtmlTable(numJobs, numColumns, {
'width': '400',
'border': 2,
'bgcolor': 'white'
})
for colNum, col in enumerate(columns):
t.setc(0, colNum, col)
continue
for row, job in enumerate(jobs):
for colNum, colName in enumerate(columns):
value = job.getColumnValue(colName)
if colName == 'jobName':
link = action_link(
actionRequireAuthentication(
'job',
director.sentry,
label=value,
routine='show',
id=job.id,
), director.cgihome)
value = link
pass # endif
t.setc(row + 1, colNum, value)
#colNum+=1
p.text = [t.return_html()]
return page
return err.page
id = self.inventory.id
record = director.clerk.getJob(id)
assert record.owner == director.sentry.username
main = page._body._content._main
document = main.document(title='Job # %s: %s' %
(record.id, record.status))
if record.status == 'created':
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'job',
director.sentry,
label='submit',
routine='edit',
id=record.id,
), director.cgihome)
p.text = [
'This job is created but not submitted.',
'Please %s it first' % link,
]
return page
if record.status not in ['created', 'finished']:
status = check(record, director)
props = record.getColumnNames()
lines = ['%s=%s' % (prop, getattr(record, prop)) for prop in props]
page = director.retrieveSecurePage( 'sampleassembly' )
except AuthenticationError, err:
return err.page
main = page._body._content._main
# populate the main column
document = main.document(title='List of sample assemblies')
document.description = ''
document.byline = 'byline?'
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'sampleassembly',
director.sentry,
label = 'link',
routine = 'new',
), director.cgihome
)
p.text = [
'To create a new sample assembly, please use this %s' % link
]
p = document.paragraph()
p = document.paragraph()
# retrieve id:record dictionary from db
clerk = director.clerk
sampleassemblies = clerk.indexSampleAssemblies()
listsampleassemblies( sampleassemblies.values(), document, director )
def listall(self, director):
page = director.retrievePage('scatteringKernel')
main = page._body._content._main
# populate the main column
document = main.document(title='List of scattering kernels')
document.description = ''
document.byline = 'byline?'
# retrieve id:record dictionary from db
clerk = director.clerk
scatteringKernels = clerk.indexScatteringKernels().values()
scatteringKernels = [
clerk.getHierarchy(scatteringKernel)
for scatteringKernel in scatteringKernels
]
p = document.paragraph()
numScatteringKernels = len(scatteringKernels)
columns = [
'id', 'reference', 'short_description', 'type', 'creator', 'date'
]
columnTitles = [
'Short description', 'Type of scattering kernel', 'Creator',
'Date of creation'
]
from PyHtmlTable import PyHtmlTable
t = PyHtmlTable(numScatteringKernels, len(columnTitles), {
'width': '400',
'border': 2
}) #,'bgcolor':'white'})
for colNum, col in enumerate(columnTitles):
t.setc(0, colNum, col)
for row, sk in enumerate(scatteringKernels):
for colNum, colName in enumerate(columns[2:]):
value = sk.getColumnValue(colName)
if colName == 'short_description':
link = action_link(
actionRequireAuthentication(
'scatteringKernel',
director.sentry,
label=value,
routine='show',
id=sk.id,
), director.cgihome)
value = link
t.setc(row + 1, colNum, value)
p.text = [t.return_html()]
p = document.paragraph()
p.text = [
action_link(
actionRequireAuthentication(
'scatteringKernelInput',
director.sentry,
label='Add a new scattering kernel'), director.cgihome),
'<br>'
]
return page
page = director.retrieveSecurePage('sampleassembly')
except AuthenticationError, err:
return err.page
main = page._body._content._main
# populate the main column
document = main.document(title='List of sample assemblies')
document.description = ''
document.byline = 'byline?'
p = document.paragraph()
link = action_link(
actionRequireAuthentication(
'sampleassembly',
director.sentry,
label='link',
routine='new',
), director.cgihome)
p.text = ['To create a new sample assembly, please use this %s' % link]
p = document.paragraph()
p = document.paragraph()
# retrieve id:record dictionary from db
clerk = director.clerk
sampleassemblies = clerk.indexSampleAssemblies()
listsampleassemblies(sampleassemblies.values(), document, director)
return page
class Greeter(Actor):
class Inventory(Actor.Inventory):
import pyre.inventory
def default(self, director):
try:
page = director.retrieveSecurePage('greet')
except AuthenticationError, error:
return error.page
main = page._body._content._main
# populate the main column
username = director.sentry.username
userrecord = director.clerk.getUser(username)
fullname = userrecord.fullname
title = 'Welcome to the Virtual Neutron Facility, %s!' % (fullname, ),
document = main.document(title=title)
p = document.paragraph()
action = actionRequireAuthentication(
actor='neutronexperiment',
sentry=director.sentry,
label='run virtual neutron experiments',
routine='default',
)
link = action_link(action, director.cgihome)
p.text = [
'In this web service facility, you can %s. ' % link,
'In a virtual neutron experiment, ',
'virtual neutrons are generated from a virtual neutron moderator,',
'guided by virtual neutron guides,',
'scattered by a virtual sample and sample environment,',
'and intercepted by detectors.',
]
p = document.paragraph()
action = actionRequireAuthentication(
actor='instrument',
sentry=director.sentry,
label='neutron instruments',
routine='listall',
)
link = action_link(action, director.cgihome)
p.text = [
'You can do your experiments on a variety of %s,' % link,
'both actual physical instruments and conceptual, nonphysical instruments'
]
p = document.paragraph()
action = actionRequireAuthentication(
actor='scatteringKernel',
sentry=director.sentry,
label='scattering kernels',
routine='default',
)
link = action_link(action, director.cgihome)
p.text = [
'You can also create your sample and predict its neutron',
'scattering properties by calculating its structure or dynamics.',
'For example, the material behaviors calculated by ab initio',
'or molecular dynamics methods become',
'%s that can be used in the sample simulation' % link,
'part of your virtual experiment.',
]
p = document.paragraph()
p.text = [
'On the left, several menu items link to a variety of',
'functions.',
'You can review past experiments by clicking "Experiments",',
'or browse your personal library of sample assemblies by',
'clicking "Sample Assemblies".',
'Neutron instruments in which you can run your experiments',
'are accessible through "Instruments".',
'When you start a virtual experiment, or a material',
'simulation, they became jobs submitted to computing',
'resources. You can monitor their progress by clicking',
'"Jobs".',
]
p = document.paragraph()
email = '<a href="mailto:[email protected]">us</a>'
p.text = [
'We welcome your comments on this web service, ',
'suggestions for new features, and reports of',
'discrepancies or bugs.'
]
return page