def iiif_info_url(msid, filename):
kwargs = {
'padded-msid': utils.pad_msid(msid),
'fname': filename
}
raw_link = (conf.IIIF % kwargs)
return utils.pad_filename(msid, raw_link)
def test_expand_image(self):
msid = 1234
given = [
{
"type": "video",
"image": "https://foo.bar/baz.bup"
},
{
"type": "image",
"image": {
"uri": "https://foo.bar/baz.bup"
}
},
]
expected = [
{
"type": "video",
"image": utils.pad_filename(msid,
main.cdnlink(msid, "baz.bup"))
},
main.expand_iiif_uri(msid, {
"type": "image",
"image": {
"uri": "https://foo.bar/baz.bup"
}
}, "image"),
]
self.assertEqual(main.expand_image(msid, given), expected)
def fn(element):
if element.get("type") == "video":
element["image"] = cdnlink(msid, element["image"].split('/')[-1])
element["image"] = utils.pad_filename(msid, element["image"])
else:
if isinstance(element.get("image"), dict) and element.get("image").get("uri"):
element = expand_iiif_uri(msid, element, "image")
return element
def fn(element):
if element.get("type") == "video":
element["image"] = cdnlink(msid, element["image"].split('/')[-1])
element["image"] = utils.pad_filename(msid, element["image"])
else:
if isinstance(element.get("image"),
dict) and element.get("image").get("uri"):
element = expand_iiif_uri(msid, element, "image")
return element
def test_pad_filename(self):
cases = [
((1234, "https://foo.bar/baz.bup"), "https://foo.bar/baz.bup"),
((10001234,
"https://publishing-cdn.elifesciences.org/01234/elife-01234-v1.pdf"
),
"https://publishing-cdn.elifesciences.org/01234/elife-10001234-v1.pdf"
),
]
for (msid, filename), expected in cases:
self.assertEqual(utils.pad_filename(msid, filename), expected)
# Reading in the hdf5 data
data = h5py.File(file_hdf5, "r")
xyz = np.array(data.get("xyz"))
zs = np.array(data.get("zs"), dtype=np.int32)
traj_idx = np.array(data.get("traj_idx"), dtype=np.int32)
# Generating a new molpro directory
os.mkdir(molpro_dir_name)
# The Molpro input file header and footer
n_electrons = np.sum(zs[0])
header = "memory,500,m\ngeomtyp=xyz\nnosym\nnoorient\ngdirect\ngeometry={\n"
footer = "}\nbasis={ default,tzvp }\n{uks,b3lyp,direct;wf,%s,1,1}\nforce\n{ibba,bonds=1}" % str(
n_electrons)
# The loop to create each input file
n_files = xyz.shape[0]
for n in range(n_files):
filenumber = utils.pad_filename(n)
file_name = filenumber + "_" + str(traj_idx[n]) + "_ccsd.com"
utils.write_molpro_input(xyz[n], zs[n], file_name, molpro_dir_name, header,
footer)
if n == 5:
exit()
def iiiflink(msid, filename):
kwargs = {'padded-msid': utils.pad_msid(msid), 'fname': filename}
raw_link = (conf.CDN_IIIF % kwargs)
return utils.pad_filename(msid, raw_link)