def test_add_field(self):
global dbconfig
# call without changes
self.db.update_fields()
# call with appending column
dbconfig.DB_MATERIALS_FIELDS.append('testadd')
dbconfig.DB_MATERIALS_CONVERTERS.append(
dbconfig.DB_MATERIALS_CONVERTERS[-1])
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.append(
dbconfig.DB_MATERIALS_FIELD_DEFAULTS[-1])
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db.update_fields()
# call with inserted column
dbconfig.DB_MATERIALS_FIELDS.insert(5, 'testadd2')
dbconfig.DB_MATERIALS_CONVERTERS.insert(
5, dbconfig.DB_MATERIALS_CONVERTERS[-1])
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.insert(
5, dbconfig.DB_MATERIALS_FIELD_DEFAULTS[-1])
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db.update_fields()
#reset database
dbconfig.DB_MATERIALS_FIELDS.pop(-1)
dbconfig.DB_MATERIALS_FIELDS.pop(5)
dbconfig.DB_MATERIALS_CONVERTERS.pop(-1)
dbconfig.DB_MATERIALS_CONVERTERS.pop(5)
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.pop(-1)
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.pop(5)
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db = SLDDB(':memory:')
self.db.create_database()
def enter_water():
db = SLDDB(DB_FILE)
for T, dens in WATER_DENSITY:
print(f'Water at {T}°C with density {dens}')
db.add_material(f'Water',
'H2O',
description=f"Water at {T}°C",
reference=WATER_DENSITY_REF,
ref_website=WATER_DENSITY_LINK,
density=dens,
temperature=T0 + T,
physical_state='liquid',
data_origin='textbook')
def select_api(args):
db = SLDDB(DB_FILE)
res = db.search_material(filter_invalid=False, ID=int(args['ID']))
try:
material = db.select_material(res[0])
except IndexError:
return '## ID not found in database'
except Exception as e:
return repr(
e) + '<br >' + "Raised when tried to parse material = %s" % res[0]
out = material.export(xray_units=args.get('xray_unit', 'edens'))
return json.dumps(out, indent=' ')
def enter_amino():
db = SLDDB(DB_FILE)
for name, formula, fu_volume in AMINO_DATA:
print(f'{name}: {formula} {fu_volume}')
db.add_material(name,
formula,
description=f"Amino acid in protein",
reference=f'{AMINO_DENS_REF}|{AMINO_HEX_REF}',
ref_website=AMINO_REF_LINK,
doi=AMINO_REF_DOI,
FU_volume=fu_volume,
tags=['biology', 'small organic'],
physical_state='solution',
data_origin='textbook')
def get_periodic_table(requested_element=None, plot_scale=None):
if requested_element:
db = SLDDB(DB_FILE)
try:
res = db.search_material(formula=requested_element, name=ELEMENT_FULLNAMES[requested_element])
except ValueError:
res=[]
if len(res)>0:
return redirect(url_for('calculate_sld', _anchor='results_header', ID=res[0]['ID']))
else:
flash(f'No SLD for {ELEMENT_FULLNAMES[requested_element]}')
scale_colors=PLOT_SCALES[plot_scale]
return render_template('periodic_table.html', elements=ELEMENTS, group_colors=GROUP_COLORS,
element_names=ELEMENT_NAMES, element_colors=ELEMENT_COLORS,
element_fullnames=FULLNAMES_OF_Z, element_weight=ELEMENT_WEIGHT,
element_b=ELEMENT_B, element_f=ELEMENT_F, element_fMo=ELEMENT_F_MO,
scale_colors=scale_colors)
def search_db(query, invalids=False, offset=0):
db=SLDDB(DB_FILE)
if current_user.is_authenticated:
user="******"%(current_user.name, current_user.email)
else:
user=None
res=db.search_material(filter_invalid=not invalids, offset=offset, **query)
if len(res)==0:
return show_search(unsuccessful_query=query)
hidden_columns=[True for field in DB_MATERIALS_FIELDS]
advanced_search=any([key in advanced_fields for key in query.keys()])
for row in res:
row['color_class']='entry_used'
if row['selected']==0:
row['color_class']='entry_unused'
if row['validated'] is not None:
row['color_class']='orso_validated'
if row['invalid'] is not None:
row['color_class']='orso_invalid'
if row['created_by'] is not None:
row['created_by']=encryptor.decrypt(row['created_by'])
for i, field in enumerate(DB_MATERIALS_FIELDS):
if row[field] is not None and field not in DB_MATERIALS_HIDDEN_DATA:
hidden_columns[i]=False
if offset>0 or len(res)==100:
count=db.count_material(filter_invalid=not invalids, **query)
multipage='result range:<br />'
if offset<99:
multipage+=f' | {offset+1}-{offset+100} of {count} | <input type="submit" name="next" value="next">'
elif offset>(count-100):
multipage+=f'<input type="submit" name="prev" value="prev"> | {offset+1}-{count} of {count} |'
else:
multipage+=f'<input type="submit" name="prev" value="prev"> | {offset+1}-{offset+100} of {count} | ' \
f'<input type="submit" name="next" value="next">'
else:
multipage=None
flt_fields=[item[1] for item in enumerate(DB_MATERIALS_FIELDS) if not hidden_columns[item[0]]]
flt_fields_names=[item[1].capitalize() for item in enumerate(DB_MATERIALS_FIELDS) if not hidden_columns[item[0]]]
hidden_fields_names=[item.capitalize() for item in DB_MATERIALS_HIDDEN_DATA]
return render_template('search.html', flt_fields=flt_fields, flt_fields_names=flt_fields_names,
hidden_fields=DB_MATERIALS_HIDDEN_DATA, hidden_fields_names=hidden_fields_names,
query_result=res, orso_user=user, main_fields=main_fields,
advanced_fields=advanced_fields, get_input=get_input,
advanced_search=advanced_search, multipage=multipage, offset=offset)
def custom_query(query):
db=SLDDB(DB_FILE)
c=db.db.cursor()
for qitem in query.splitlines():
c.execute(qitem)
res=c.fetchall()
columns=c.description
c.close()
db.db.commit()
return columns, res
def edit_selection(ID, user):
db = SLDDB(DB_FILE)
res = db.search_material(ID=ID, filter_invalid=False)[0]
def get_input_args(field):
conv = db_lookup[field][1]
if field in res:
value = res[field]
if value is None:
value = ""
elif field == 'created_by':
value = encryptor.decrypt(value)
else:
value = ""
return conv.html_input(field, value)
return render_template('input.html',
fields=input_fields,
get_input=get_input_args,
get_unit=get_unit,
editing_entry=ID)
def collect_blendIDs(formula):
db = SLDDB(DB_FILE)
elements=[]
loaded_ids={}
items=[]
while '(' in clean_str(formula):
pre, formula=formula.split(')',1)
number=float(pre.split('*',1)[0].strip('(').strip())
ID=int(pre.split('*',1)[1].strip())
items.append((number, ID))
for number, ID in items:
if not ID in loaded_ids:
entry=db.search_material(ID=ID)[0]
m=db.select_material(entry)
loaded_ids[ID]=m
elements.append(number*loaded_ids[ID])
result=elements[0]
for element in elements[1:]:
# combine molecule matierials
result+=element
return result
def collect_combination(ids, name_dict):
db = SLDDB(DB_FILE)
elements=[]
loaded_ids={}
for id in ids:
if not id in loaded_ids:
try:
entry=db.search_material(name=ExactString(name_dict[id]))[0]
except KeyError:
possible_ids=name_dict.keys()
raise SequenceParseError(f"Not a valid identifier {id}, options are {''.join(possible_ids)}")
except IndexError:
raise SequenceParseError(f"Molecule {name_dict[id]} not found in database")
m=db.select_material(entry)
loaded_ids[id]=m
elements.append(loaded_ids[id])
result=elements[0]
for element in elements[1:]:
# combine molecule matierials
result+=element
return result
def input_material(args):
db = SLDDB(DB_FILE)
def get_input_args(field):
return fill_input(field, args)
if args['name'] == '' or args['formula'] == '':
flash("You have to supply a name and Formula!")
return render_template('input.html',
fields=input_fields,
get_input=get_input_args,
get_unit=get_unit)
useargs = dict(args.items())
name = args['name']
formula = args['formula']
del (useargs['material'])
del (useargs['name'])
del (useargs['formula'])
for key, value in list(useargs.items()):
if key == 'created_by' and value != '':
# encrypt the users email information
value = encryptor.enrypt(value)
useargs[key] = value
if db_lookup[key][1].html_list:
useargs[key] = request.form.getlist(key)
if value == '':
del (useargs[key])
try:
db.add_material(name, formula, **useargs)
except Exception as e:
flash("Error when trying to insert data:\n" + repr(e))
return render_template('input.html',
fields=input_fields,
get_input=get_input_args,
get_unit=get_unit)
return search_db(useargs)
def calculate_selection(ID):
db=SLDDB(DB_FILE)
res=db.search_material(ID=ID, filter_invalid=False)
try:
material=db.select_material(res[0])
except Exception as e:
return render_template('base.html', error=repr(e)+'<br >'+"Raised when tried to parse material = %s"%res[0])
match_point=0.
E, rho_x=material.rho_vs_E()
_, delta=material.delta_vs_E()
_, beta=material.beta_vs_E()
script='' # get_graph(E, rho_x.real, rho_x.imag, res[0]['name'])
if 'H' in material.formula or 'Hx' in material.formula:
deuterated=material.deuterated
if 'Hx' in material.formula:
exchanged=material.exchanged
match_point = 100.*material.match_exchange()
else:
exchanged=None
else:
deuterated=None
exchanged=None
if 'H' in material.formula or 'Hx' in material.formula or 'D' in material.formula \
or any([tag in res[0].get('tags', []) for tag in
['polymer', 'biology', 'membrane', 'lipid', 'small organic', 'surfactant', 'protein']]):
contrast_matching = True
else:
contrast_matching = False
return render_template('sldcalc.html', material=material, material_name=res[0]['name'],
material_description=res[0]['description'], deuterated=deuterated,
exchanged=exchanged, match_point=match_point,
contrast_matching=contrast_matching, xray_E=E.tolist(),
xray_rho_real=nan_to_num(rho_x.real).tolist(),
xray_rho_imag=nan_to_num(rho_x.imag).tolist(),
xray_delta=nan_to_num(delta).tolist(), xray_beta=nan_to_num(beta).tolist(),
validated=res[0]['validated'], validated_by=res[0]['validated_by'],
invalid=res[0]['invalid'], invalid_by=res[0]['invalid_by'],
formula=res[0]['formula'], density=material.dens, mu=material.mu)
def search_api(args):
query = {}
for key, value in args.items():
if value.strip() == '':
continue
if key in DB_MATERIALS_FIELDS:
try:
query[key] = db_lookup[key][1].convert(value)
except Exception as e:
return repr(
e) + '<br >' + "Raised when tried to parse %s = %s" % (
key, value)
db = SLDDB(DB_FILE)
res = db.search_material(serializable=True, limit=10000, **query)
# remove hidden database fields besides ORSO validation
for ri in res:
for field in DB_MATERIALS_HIDDEN_DATA:
if field.startswith('validated'):
continue
del ri[field]
return json.dumps(res, indent=' ')
def update_material(args):
db = SLDDB(DB_FILE)
def get_input_args(field):
return fill_input(field, args)
if args['name'] == '' or args['formula'] == '':
flash("You have to supply a name and Formula!")
return render_template('input.html',
fields=input_fields,
get_input=get_input_args,
get_unit=get_unit,
editing_entry=args['ID'])
useargs = dict(args.items())
del (useargs['material'])
del (useargs['ID'])
for key, value in list(useargs.items()):
if db_lookup[key][1].html_list:
useargs[key] = request.form.getlist(key)
if value == '':
useargs[key] = None
try:
db.update_material(args['ID'], **useargs)
except Exception as e:
flash("Error when trying to insert data:\n" + repr(e))
return render_template('input.html',
fields=input_fields,
get_input=get_input_args,
get_unit=get_unit,
editing_entry=args['ID'])
for key, value in list(useargs.items()):
if value is None:
del (useargs[key])
return search_db(useargs)
def main():
db = SLDDB(DB_FILE)
for item in data:
print(item)
if len(item) > 3:
db.add_material(item[0],
item[0],
description=item[3],
reference="Christy Kinane",
density=item[1],
mu=item[2])
else:
db.add_material(item[0],
item[0],
reference="Christy Kinane",
density=item[1],
mu=item[2])
def enter_rnadna():
db = SLDDB(DB_FILE)
for name, formula, fu_volume in RNA_ABRV:
print(f'{name}: {formula} {fu_volume}')
db.add_material(name,
formula,
description=f"Nucleotides in RNA",
reference=AMINO_DENS_REF,
ref_website=AMINO_REF_LINK,
FU_volume=fu_volume,
tags=['biology', 'small organic'],
physical_state='solution',
data_origin='textbook')
for name, formula, fu_volume in DNA_ABRV:
print(f'{name}: {formula} {fu_volume}')
db.add_material(name,
formula,
description=f"Nucleotides in DNA",
reference=AMINO_DENS_REF,
ref_website=AMINO_REF_LINK,
FU_volume=fu_volume,
tags=['biology', 'small organic'],
physical_state='solution',
data_origin='textbook')
class SLDDBWindow(QtWidgets.QMainWindow):
selected_material=None
def __init__(self):
super(SLDDBWindow, self).__init__() # Call the inherited classes __init__ method
self.ui=uic.loadUi('qt_interface/slddb_window.ui', self) # Load the .ui file
self.setColumns()
self.show() # Show the GUI
self.db=SLDDB(DB_FILE)
def setColumns(self):
tbl=self.ui.resultTable
tbl.setColumnCount(len(DB_MATERIALS_FIELDS)-len(DB_MATERIALS_HIDDEN_DATA))
self.headers=[]
for field in DB_MATERIALS_FIELDS:
if field in DB_MATERIALS_HIDDEN_DATA:
continue
self.headers.append(field)
tbl.setHorizontalHeaderLabels(self.headers)
for i in range(len(self.headers)):
tbl.setColumnHidden(i, True)
tbl=self.ui.entryTable
tbl.setRowCount(len(self.headers))
tbl.setVerticalHeaderLabels(self.headers)
def searchDatabase(self):
name=self.ui.nameEdit.text()
description=self.ui.descriptionEdit.text()
formula=self.ui.formulaEdit.text()
search={'name': name, 'description': description, 'formula': formula}
for key, value in list(search.items()):
if value.strip()=='':
del(search[key])
results=self.db.search_material(**search)
hidden_columns=[True for field in self.headers]
for row in results:
for i, field in enumerate(self.headers):
if row[field] is not None:
hidden_columns[i]=False
tbl=self.ui.resultTable
tbl.sortByColumn(-1, QtCore.Qt.AscendingOrder)
tbl.setRowCount(len(results))
for i, hidden in enumerate(hidden_columns):
tbl.setColumnHidden(i, hidden)
for i,result in enumerate(results):
for j, field in enumerate(self.headers):
item=result[field]
if type(item) is datetime:
item=str(item)
titem=QtWidgets.QTableWidgetItem()
titem.setData(QtCore.Qt.DisplayRole, item)
tbl.setItem(i, j, titem)
tbl.resizeColumnsToContents()
self.results=results
if len(results)==1:
tbl.setRangeSelected(QtWidgets.QTableWidgetSelectionRange(0, -1, 1, -1), True)
self.selectItem(0, 0)
def selectItem(self, row, col):
tbl=self.ui.resultTable
ID=tbl.indexFromItem(tbl.item(row, 0)).data()
orig_row=[res['ID'] for res in self.results].index(ID)
result=self.results[orig_row]
try:
material=self.db.select_material(result)
except Exception as e:
return
self.selected_material=material
self.ui.resultName.setText(result['name'])
self.updateResult()
def updateResult(self):
material=self.selected_material
if material is None:
return
if self.ui.densityVolumeSelect.currentIndex()==0:
self.ui.densityVolume.setText('%.4f'%material.dens)
else:
self.ui.densityVolume.setText('%.4g'%(1000./material.fu_dens))
self.ui.neutronSLD.setText("%.6f"%(1e6*material.rho_n.real))
self.ui.neutronSLDimag.setText("%.6f"%(1e6*material.rho_n.imag))
try:
rhox=material.rho_of_E(float(self.ui.xrayEnergyEdit.currentText()))
except ValueError:
self.ui.xraySLD.setText("")
self.ui.xraySLDimag.setText("")
else:
self.ui.xraySLD.setText("%.6f"%(1e6*rhox.real))
self.ui.xraySLDimag.setText("%.6f"%(1e6*rhox.imag))
def invalidate_selection(ID, user):
db=SLDDB(DB_FILE)
db.invalidate_material(ID, user)
return calculate_selection(ID)
def setUpClass(cls):
cls.db = SLDDB(':memory:')
cls.db.create_database()
class TestCreateDB(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.db = SLDDB(':memory:')
cls.db.create_database()
@classmethod
def tearDownClass(cls):
del (cls.db)
def test_tables(self):
c = self.db.db.cursor()
c.execute("SELECT name FROM sqlite_master WHERE type='table'")
items = c.fetchall()
for i, tbl in enumerate([dbconfig.DB_MATERIALS_NAME]):
with self.subTest(msg=tbl, i=i):
self.assertTrue((tbl, ) in items)
def test_element_search(self):
with self.subTest('database search', i=0):
s1 = element_table.get_element('Si')
s2 = element_table.get_element(14)
with self.subTest('equality', i=0):
self.assertEqual(s1.Z, s2.Z)
self.assertEqual(s1.symbol, s2.symbol)
self.assertEqual(s1.mass, s2.mass)
self.assertEqual(s1.b, s2.b)
testing.assert_array_equal(s1._xdata, s2._xdata)
def test_add_field(self):
global dbconfig
# call without changes
self.db.update_fields()
# call with appending column
dbconfig.DB_MATERIALS_FIELDS.append('testadd')
dbconfig.DB_MATERIALS_CONVERTERS.append(
dbconfig.DB_MATERIALS_CONVERTERS[-1])
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.append(
dbconfig.DB_MATERIALS_FIELD_DEFAULTS[-1])
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db.update_fields()
# call with inserted column
dbconfig.DB_MATERIALS_FIELDS.insert(5, 'testadd2')
dbconfig.DB_MATERIALS_CONVERTERS.insert(
5, dbconfig.DB_MATERIALS_CONVERTERS[-1])
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.insert(
5, dbconfig.DB_MATERIALS_FIELD_DEFAULTS[-1])
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db.update_fields()
#reset database
dbconfig.DB_MATERIALS_FIELDS.pop(-1)
dbconfig.DB_MATERIALS_FIELDS.pop(5)
dbconfig.DB_MATERIALS_CONVERTERS.pop(-1)
dbconfig.DB_MATERIALS_CONVERTERS.pop(5)
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.pop(-1)
dbconfig.DB_MATERIALS_FIELD_DEFAULTS.pop(5)
dbconfig.db_lookup = dict([
(field, (i, converter, default))
for i, (field, converter, default) in enumerate(
zip(dbconfig.DB_MATERIALS_FIELDS,
dbconfig.DB_MATERIALS_CONVERTERS,
dbconfig.DB_MATERIALS_FIELD_DEFAULTS))
])
self.db = SLDDB(':memory:')
self.db.create_database()
def test_backup(self):
self.db.backup(':memory:')
import slddb
from slddb import __version__, dbconfig
# for flask use database file in startup folder
DB_FILE = 'slddb.db'
dbconfig.DB_FILE = DB_FILE
slddb.DB_FILE = DB_FILE
from slddb import SLDDB
from slddb.dbconfig import DB_FILE
import sqlite3
if __name__ == '__main__':
db = SLDDB(DB_FILE)
try:
db.create_database()
db.add_elements()
except sqlite3.OperationalError:
db.update_fields()
def __init__(self):
super(SLDDBWindow, self).__init__() # Call the inherited classes __init__ method
self.ui=uic.loadUi('qt_interface/slddb_window.ui', self) # Load the .ui file
self.setColumns()
self.show() # Show the GUI
self.db=SLDDB(DB_FILE)