def change_document(part, page):
fragment = ''
item = 'index.xaml'
loc = 'docs/'
if part > 0:
# page can be -1
if page > 0:
item = 'item%s.xaml' % page
fragment = 'part%s-page%s' % (part, page)
else:
fragment = 'part%s' % part
loc += 'part%s/' % part
path = loc + item
if path in _xaml_cache:
document = _xaml_cache[path]
else:
document = load_document(path, page, console_textbox)
_xaml_cache[path] = document
if page < 1:
add_stackpanel(document, get_list(loc + 'list.txt'))
HtmlPage.Window.CurrentBookmark = fragment
documentContainer.Content = document
document.Width = documentContainer.Width - 30
@always_invoke
def scroll_and_focus():
documentContainer.ScrollToVerticalOffset(0)
focus_text_box()
scroll_and_focus()
change_title()
def change_document(part, page):
fragment = ""
item = "index.xaml"
loc = "docs/"
if part > 0:
# page can be -1
if page > 0:
item = "item%s.xaml" % page
fragment = "part%s-page%s" % (part, page)
else:
fragment = "part%s" % part
loc += "part%s/" % part
path = loc + item
if path in _xaml_cache:
document = _xaml_cache[path]
else:
document = load_document(path, page, console_textbox)
_xaml_cache[path] = document
if page < 1:
add_stackpanel(document, get_list(loc + "list.txt"))
HtmlPage.Window.CurrentBookmark = fragment
documentContainer.Content = document
document.Width = documentContainer.Width - 30
@always_invoke
def scroll_and_focus():
documentContainer.ScrollToVerticalOffset(0)
focus_text_box()
scroll_and_focus()
change_title()
def download(model_list_path, output_dir, force):
model_list = load_document(model_list_path)
if model_list is None:
sys.exit(1)
validate_schema(model_list)
target_root = os.path.join(output_dir, "models")
create_directory(target_root, False)
for model in model_list:
download_and_convert_model(target_root, model, force)
def create_db(system_password):
"Create the database and load the designs and the 'system' account."
site = configuration.site
server = couchdb.Server(site.COUCHDB_SERVER)
db = server.create(site.COUCHDB_DATABASE)
utils.load_designs(db)
doc = utils.load_document(db,
'account',
identifier='system',
role='admin',
password=utils.get_hexdigest(system_password),
fullname='System',
initials='SYS')
utils.load_document(db,
'log',
docid=doc['_id'],
action='created',
account='system')
utils.load_document(db,
'system',
identifier='settings',
project_steps=[
"contract",
"QC incoming samples",
"queued",
"library prep",
"qPCR",
"SOLiD WFA",
"454 titration",
"amplification",
"sequencing",
"data transfer",
"data analysis",
"data delivery",
"invoice",
"payment"
],
project_references=[
"hg19",
"other",
"unknown"
],
project_platforms=[
"Illumina Hiseq",
"SOLiD",
"GS-FLX"
],
project_applications=[
"total RNA",
"small RNA",
"MP de novo",
"MP metagenomics",
"custom sequence capture",
"metagenomics",
"exome sequencing",
"de novo",
"WGS",
"ChipSeq",
"epigenomics",
"finished library"
],
project_lab_protocols=[
"DNA standard",
"total RNA",
"small RNA",
"mate pair",
"sequence capture"
],
project_sequencing_setups=[
"Illumina PE 2*100",
"Illumina PE 2*50",
"Illumina SR 1*100",
"Illumina SR 1*50",
"SOLiD 2*75",
"SOLiD 1*50",
"SOLiD 1*35",
"SOLiD 75+35",
"SOLiD 50+35",
"454 400",
"454 850"
],
sample_steps=[
"arrival",
"QC incoming",
"library prep",
"QC library prep",
"qPCR",
"sequencing",
"QC sequencing"
],
sample_types=[
"DNA",
"cDNA",
"total RNA",
"mRNA",
"small RNA",
"metagenomics",
"ChipSeq",
"epigenetics",
"library prep",
"captured library",
"other"
],
workset_steps=[
"designed",
"sequencing",
"clustering"
],
workset_types=[
"collection",
"plate",
"lane",
"flowcell"
]
)