def isotype_page(isotype_name, release=config['DATASET_RELEASE']):
"""
Isotype page
"""
isotype = query_strains(isotype_name=isotype_name)
if not isotype:
abort(404)
# Fetch isotype images
photos = list_release_files(f"photos/isolation/{isotype_name}")
photo_set = {}
for row in photos:
if 'thumb' not in row:
strains = basename(row).replace(".jpg", "").split("_")[1:]
photo_set[row.replace(".jpg", ".thumb.jpg")] = strains
# High impact variants
logger.info(release)
VARS = {
"title": f"Isotype {isotype_name}",
"isotype": isotype,
"isotype_name": isotype_name,
"isotype_ref_strain": [x for x in isotype if x.isotype_ref_strain][0],
"strain_json_output": dump_json(isotype),
"photo_set": photo_set
}
return render_template('strain/isotype.html', **VARS)
def map_page():
"""
Global strain map shows the locations of all wild isolates
within the SQLite database.
"""
VARS = {
'title': "Global Strain Map",
'strain_listing': dump_json(get_strains(known_origin=True))
}
return render_template('strain/global_strain_map.html', **VARS)
def store_item(kind, name, **kwargs):
ds = google_datastore()
try:
exclude = kwargs.pop('exclude_from_indexes')
except KeyError:
exclude = False
if exclude:
m = datastore.Entity(key=ds.key(kind, name), exclude_from_indexes=exclude)
else:
m = datastore.Entity(key=ds.key(kind, name))
for key, value in kwargs.items():
if isinstance(value, dict):
m[key] = 'JSON:' + dump_json(value)
else:
m[key] = value
ds.put(m)
def isotype_page(isotype_name):
"""
Isotype page
"""
isotype = query_strains(isotype_name=isotype_name)
if not isotype:
abort(404)
# Fetch isotype images
photos = list_release_files(f"photos/isolation/{isotype_name}")
photo_set = {}
for row in photos:
if 'thumb' not in row:
strains = basename(row).replace(".jpg", "").split("_")[1:]
photo_set[row.replace(".jpg", ".thumb.jpg")] = strains
# High impact variants
soft_variant = requests.get(
f"https://storage.googleapis.com/elegansvariation.org/releases/{DATASET_RELEASE}/variation/sample_summary/soft.isotype_summary.json"
).json()
hard_variant = requests.get(
f"https://storage.googleapis.com/elegansvariation.org/releases/{DATASET_RELEASE}/variation/sample_summary/hard.isotype_summary.json"
).json()
soft_variant = [x for x in soft_variant if x['isotype'] == isotype_name][0]
hard_variant = [x for x in hard_variant if x['isotype'] == isotype_name][0]
VARS = {
"title": isotype_name,
"isotype": isotype,
"isotype_name": isotype_name,
"reference_strain": [x for x in isotype if x.reference_strain][0],
"strain_json_output": dump_json(isotype),
"photo_set": photo_set,
"soft_variant": soft_variant,
"hard_variant": hard_variant
}
return render_template('strain/strain.html', **VARS)