def findAllMembersInCategory(self, category, active, oper = '=', labID = 0):
db = self.db
cursor = self.cursor
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
ucMapper = UserCategoryMapper(db, cursor) # for category name/id mapping
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
members = [] # list of User **objects**
# When we include 'status=ACTIVE' restriction in the query, a DEP owner of an active project is not shown in project view. However, we should not add DEP members to a project.
# Therefore, the calling function should specify whether it wants to restrict query by status.
# If 'active' parameter is True, add 'status=ACTIVE' clause
# In any case, **remember to fill in 'category' column for DEP users before the launch**
if labID == 0:
if active:
cursor.execute("SELECT userID, firstname, lastname, description FROM Users_tbl u, UserCategories_tbl c WHERE c.categoryID " + oper + " " + `category_Name_ID_Map[category]` + " AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>'' AND u.status='ACTIVE'")
else:
cursor.execute("SELECT userID, firstname, lastname, description FROM Users_tbl u, UserCategories_tbl c WHERE c.categoryID " + oper + " " + `category_Name_ID_Map[category]` + " AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>''")
else:
if active:
cursor.execute("SELECT u.userID, u.firstname, u.lastname, u.description, l.lab_name FROM Users_tbl u, UserCategories_tbl c, LabInfo_tbl l WHERE c.categoryID " + oper + " " + `category_Name_ID_Map[category]` + " AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.labID=" + `labID` + " AND l.labID=u.labID AND u.status='ACTIVE'")
else:
cursor.execute("SELECT u.userID, u.firstname, u.lastname, u.description, l.lab_name FROM Users_tbl u, UserCategories_tbl c, LabInfo_tbl l WHERE c.categoryID " + oper + " " + `category_Name_ID_Map[category]` + " AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>'' AND u.labID=" + `labID` + " AND l.labID=u.labID")
results = cursor.fetchall()
for result in results:
userID = int(result[0])
firstName = result[1]
lastName = result[2]
description = result[3]
tmpLab = Laboratory(labID)
if len(result) == 5:
labName = result[4]
tmpLab.setName(labName)
# create a User object
tmpUser = User(userID, "", firstName, lastName, description, tmpLab, category, "", "")
members.append(tmpUser)
return members
def findLabByID(self, labID):
db = self.db
cursor = self.cursor
ucMapper = UserCategoryMapper(db, cursor)
category_ID_Name_Map = ucMapper.mapCategoryIDToName()
cursor.execute(
"SELECT lab_name, description, default_access_level, location, lab_head, labCode FROM LabInfo_tbl WHERE labID="
+ ` labID ` + " AND status='ACTIVE'")
result = cursor.fetchone()
if result:
labName = result[0]
labDescr = result[1]
accessLevel = int(result[2])
address = result[3]
labHead = result[4]
labCode = result[5].upper()
newLab = Laboratory(labID, labName, labDescr,
category_ID_Name_Map[accessLevel], address,
labHead, labCode)
return newLab
def checkPermissions(self, uname, pwd):
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
db = self.__db
cursor = self.__cursor
cursor.execute(
"SELECT u.userID, u.firstname, u.lastname, u.description, c.category, u.labID, l.lab_name, u.email FROM Users_tbl u, LabInfo_tbl l, UserCategories_tbl c WHERE u.username="******" AND u.password=MD5(" + ` pwd ` +
") AND u.labID=l.labID AND c.categoryID=u.category AND u.status='ACTIVE' AND l.status='ACTIVE'"
)
result = cursor.fetchone()
if result:
uid = int(result[0])
firstname = result[1]
lastname = result[2]
description = result[3]
category = result[4]
labID = int(result[5])
labname = result[6]
email = result[7]
newLab = Laboratory(labID, labname)
newUser = User(uid, uname, firstname, lastname, description,
newLab, category, email, pwd)
self.__user = newUser
return True
else:
return False
def getUserByDescription(self, descr):
db = self.db
cursor = self.cursor
cursor.execute(
"SELECT u.userID, u.username, u.firstname, u.lastname, c.category, u.labID, l.lab_name, u.email, u.password FROM Users_tbl u, LabInfo_tbl l, UserCategories_tbl c WHERE u.description="
+ ` descr ` +
" AND u.labID=l.labID AND c.categoryID=u.category AND l.status='ACTIVE'"
)
result = cursor.fetchone()
if result:
uid = int(result[0])
username = result[1]
firstname = result[2]
lastname = result[3]
category = result[4]
labID = int(result[5])
labname = result[6]
email = result[7]
password = result[8]
newLab = Laboratory(labID, labname)
newUser = User(uid, username, firstname, lastname, descr, newLab,
category, email, password)
return newUser
else:
# Nov. 15/07: Retry, just select userID and category and labID - other attributes may be omitted - for ACTIVE users only
cursor.execute(
"SELECT u.userID, c.category FROM Users_tbl u, UserCategories_tbl c WHERE u.description="
+ ` descr ` +
" AND c.categoryID=u.category AND u.status='ACTIVE'")
result = cursor.fetchone()
if result:
uid = int(result[0])
category = result[1]
newUser = User(uid, "", "", "", descr, None, category, "", "")
return newUser
def addLab(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
lHandler = LabHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Get form values
labName = form.getvalue("labName")
labHeadTitle = form.getvalue("titles")
labHeadName = form.getvalue("labHead")
labHead = labHeadTitle + " " + labHeadName
labCode = form.getvalue("labCode").upper()
labDescr = form.getvalue("labDescription")
labAddress = form.getvalue("labAddress")
labAccess = form.getvalue("system_access_level")
defaultLabAccessLevel = category_Name_ID_Map[
labAccess] # map to database ID
try:
newLabID = lHandler.insertLab(labName, labDescr, labAddress,
defaultLabAccessLevel, labHead,
labCode)
#print `newLabID`
newLab = Laboratory(newLabID, labName, labDescr, labAccess,
labAddress, labHead, labCode)
self.printLabInfo('view', newLab)
except DuplicateLabCodeException:
d = DuplicateLabCodeException()
utils.redirect(hostname + "User.php?View=3&labName=" + labName +
"&title=" + labHeadTitle + "&labHead=" +
labHeadName + "&labCode=" + labCode + "&labDescr=" +
labDescr + "&locn=" + labAddress + "&access=" +
labAccess + "&ErrCode=" + ` d.err_code() `)
def __init__(self,
cType="",
cSize=0,
nRows=0,
nCols=0,
cName=0,
cLab=0,
cDesc="",
c_props=[]):
self.__cont_type = cType
self.__cont_size = cSize
self.__rows = nRows
self.__cols = nCols
self.__num_wells = nRows * nCols
self.__cont_name = cName
self.__cont_desc = cDesc
self.__cont_lab = Laboratory(cLab)
# Assign properties based on container type
if cType == 'Vector':
self.__properties = ['Method ID', 'Concentration']
elif cType == 'Glycerol Stocks':
self.__properties = ['Bacteria Strain']
elif cType == 'Oligo':
self.__properties = ['Concentration', 'Reagent Source']
elif cType == 'Insert':
self.__properties = [
'Concentration', 'Alternate ID', "5' digest/3' Digest"
]
elif cType == 'Cell Line':
self.__properties = [
'Isolate Name', 'Plates/Vial', 'Date', 'Person', 'Passage'
]
# Jan. 3/10
else:
self.__properties = c_props
def getUserByID(self, uid):
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
db = self.db # make local copies of global variables for easy access
cursor = self.cursor
newUser = None
# ATT'N: Removed 'user status=ACTIVE' clause, since this function may be called to retrieve a project owner, who may be gone, but his/her packet is still active
#print "SELECT u.username, u.firstname, u.lastname, u.description, c.category, u.labID, l.lab_name, u.email, u.password FROM Users_tbl u, LabInfo_tbl l, UserCategories_tbl c WHERE u.userID=" + `uid` + " AND u.labID=l.labID AND c.categoryID=u.category AND l.status='ACTIVE'"
cursor.execute(
"SELECT u.username, u.firstname, u.lastname, u.description, c.category, u.labID, l.lab_name, u.email, u.password FROM Users_tbl u, LabInfo_tbl l, UserCategories_tbl c WHERE u.userID="
+ ` uid ` +
" AND u.labID=l.labID AND c.categoryID=u.category AND l.status='ACTIVE'"
)
result = cursor.fetchone()
if result:
username = result[0]
firstname = result[1]
lastname = result[2]
description = result[3]
category = result[4]
labID = int(result[5])
labname = result[6]
email = result[7]
password = result[8]
newLab = Laboratory(labID, labname)
newUser = User(uid, username, firstname, lastname, description,
newLab, category, email, password)
return newUser
def findProjectMembers(self, projectID, role):
db = self.db
cursor = self.cursor
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
uHandler = UserHandler(db, cursor)
members = []
# include status='ACTIVE' clause; otherwise a DEP member might be selected causing an error
cursor.execute("SELECT p.memberID, u.firstname, u.lastname, u.description, u.category, u.labID, l.lab_name, l.description FROM ProjectMembers_tbl p, Users_tbl u, LabInfo_tbl l WHERE p.packetID=" + `projectID` + " AND p.role=" + `role` + " AND u.userID=p.memberID AND l.labID=u.labID AND p.status='ACTIVE' AND u.status='ACTIVE' AND l.status='ACTIVE'")
results = cursor.fetchall()
for result in results:
memberID = int(result[0])
# removed, more efficient and accurate to rewrite query here and include 'status=ACTIVE' clause
#member = uHandler.getUserByID(memberID)
memberFirstName = result[1]
memberLastName = result[2]
memberFullName = result[3]
memberCategory = int(result[4])
memberLabID = result[5]
labName = result[6]
labDescr = result[7]
tempLab = Laboratory(memberLabID, labName, labDescr)
member = User(memberID, "", memberFirstName, memberLastName, memberFullName, tempLab, memberCategory)
members.append(member)
return members
def findAllMembersInCategory(self, category, active, oper='=', labID=0):
db = self.db
cursor = self.cursor
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
ucMapper = UserCategoryMapper(db,
cursor) # for category name/id mapping
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
members = [] # list of User **objects**
# When we include 'status=ACTIVE' restriction in the query, a DEP owner of an active project is not shown in project view. However, we should not add DEP members to a project.
# Therefore, the calling function should specify whether it wants to restrict query by status.
# If 'active' parameter is True, add 'status=ACTIVE' clause
# In any case, **remember to fill in 'category' column for DEP users before the launch**
if labID == 0:
if active:
cursor.execute(
"SELECT userID, firstname, lastname, description FROM Users_tbl u, UserCategories_tbl c WHERE c.categoryID "
+ oper + " " + ` category_Name_ID_Map[category] ` +
" AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>'' AND u.status='ACTIVE'"
)
else:
cursor.execute(
"SELECT userID, firstname, lastname, description FROM Users_tbl u, UserCategories_tbl c WHERE c.categoryID "
+ oper + " " + ` category_Name_ID_Map[category] ` +
" AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>''"
)
else:
if active:
cursor.execute(
"SELECT u.userID, u.firstname, u.lastname, u.description, l.lab_name FROM Users_tbl u, UserCategories_tbl c, LabInfo_tbl l WHERE c.categoryID "
+ oper + " " + ` category_Name_ID_Map[category] ` +
" AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.labID="
+ ` labID ` + " AND l.labID=u.labID AND u.status='ACTIVE'")
else:
cursor.execute(
"SELECT u.userID, u.firstname, u.lastname, u.description, l.lab_name FROM Users_tbl u, UserCategories_tbl c, LabInfo_tbl l WHERE c.categoryID "
+ oper + " " + ` category_Name_ID_Map[category] ` +
" AND c.categoryID=u.category AND u.firstname <> '' AND u.lastname <> '' AND u.description <>'' AND u.labID="
+ ` labID ` + " AND l.labID=u.labID")
results = cursor.fetchall()
for result in results:
userID = int(result[0])
firstName = result[1]
lastName = result[2]
description = result[3]
tmpLab = Laboratory(labID)
if len(result) == 5:
labName = result[4]
tmpLab.setName(labName)
# create a User object
tmpUser = User(userID, "", firstName, lastName, description,
tmpLab, category, "", "")
members.append(tmpUser)
return members
def saveLab(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
# print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
# print # DITTO
# print `form`
# Handlers and mappers
lHandler = LabHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
# Get form values
labID = int(form.getvalue("labID"))
lab = Laboratory(
labID
) # here need to use the default constructor and not findLabByID, because lab is being updated and need a fresh instance and set its attributes to new values
newName = form.getvalue("labName")
newLabHead = form.getvalue("labHead")
newLabCode = form.getvalue("labCode").upper()
newDescr = form.getvalue("description")
newAddr = form.getvalue("address")
newAccess = form.getvalue("system_access_level")
newAccLev = category_Name_ID_Map[newAccess]
# change database values
try:
lHandler.setLabName(labID, newName)
lHandler.setLabHead(labID, newLabHead)
lHandler.setLabCode(labID, newLabCode)
lHandler.setLabDescription(labID, newDescr)
lHandler.setLabAccessLevel(labID, newAccLev)
lHandler.setLocation(labID, newAddr)
#######################
# update members!
#######################
newMembers = form.getlist("labMembers")
lHandler.updateLabMembers(labID, newMembers)
# change object values
lab.setName(newName)
lab.setLabHead(newLabHead)
lab.setLabCode(newLabCode)
lab.setDescription(newDescr)
lab.setAddress(newAddr)
lab.setDefaultAccessLevel(newAccess)
# return to detailed view
self.printLabInfo("view", lab)
# utils.redirect(hostname + "User.php?View=5&Lab=" + `labID` + "&fd=" + filename)
except DuplicateLabCodeException:
newLab = Laboratory(labID, newName, newDescr, newAccess, newAddr, newLabHead, newLabCode)
d = DuplicateLabCodeException()
self.printLabInfo("edit", newLab, d.err_code())
def setContainerLab(self, cLab):
newLab = Laboratory(cLab)
self.__cont_lab = newLab
def saveLab(self, form):
db = self.__db
cursor = self.__cursor
hostname = self.__hostname
#print "Content-type:text/html" # TEMPORARY, REMOVE AFTER DEBUGGING TO HAVE SCRIPT REDIRECT PROPERLY!!!!!!
#print # DITTO
#print `form`
# Handlers and mappers
lHandler = LabHandler(db, cursor)
ucMapper = UserCategoryMapper(db, cursor)
category_Name_ID_Map = ucMapper.mapCategoryNameToID()
# Get form values
labID = int(form.getvalue("labID"))
lab = Laboratory(
labID
) # here need to use the default constructor and not findLabByID, because lab is being updated and need a fresh instance and set its attributes to new values
newName = form.getvalue("labName")
newLabHead = form.getvalue("labHead")
newLabCode = form.getvalue("labCode").upper()
newDescr = form.getvalue("description")
newAddr = form.getvalue("address")
newAccess = form.getvalue("system_access_level")
newAccLev = category_Name_ID_Map[newAccess]
# change database values
try:
lHandler.setLabName(labID, newName)
lHandler.setLabHead(labID, newLabHead)
lHandler.setLabCode(labID, newLabCode)
lHandler.setLabDescription(labID, newDescr)
lHandler.setLabAccessLevel(labID, newAccLev)
lHandler.setLocation(labID, newAddr)
#######################
# update members!
#######################
newMembers = form.getlist("labMembers")
lHandler.updateLabMembers(labID, newMembers)
# change object values
lab.setName(newName)
lab.setLabHead(newLabHead)
lab.setLabCode(newLabCode)
lab.setDescription(newDescr)
lab.setAddress(newAddr)
lab.setDefaultAccessLevel(newAccess)
# return to detailed view
self.printLabInfo('view', lab)
#utils.redirect(hostname + "User.php?View=5&Lab=" + `labID` + "&fd=" + filename)
except DuplicateLabCodeException:
newLab = Laboratory(labID, newName, newDescr, newAccess, newAddr,
newLabHead, newLabCode)
d = DuplicateLabCodeException()
self.printLabInfo('edit', newLab, d.err_code())
import dash
from laboratory import Laboratory
import dash_bootstrap_components as dbc
from flask_caching import Cache
from laboratory.processing import Sample
lab = Laboratory()
stylesheets = [
{
'href': 'https://use.fontawesome.com/releases/v5.15.1/css/all.css',
'rel': 'stylesheet',
'integrity':
'sha384-vp86vTRFVJgpjF9jiIGPEEqYqlDwgyBgEF109VFjmqGmIY/Y4HV4d3Gp2irVfcrp',
'crossorigin': 'anonymous'
},
"assets\css\sb-admin-2.css",
dbc.themes.DARKLY,
]
external_scripts = [
"assets\js\jquery.min.js",
"assets\js\\bootstrap.bundle.min.js",
"assets\js\jquery.easing.min.js",
"assets\js\sb-admin-2.js",
]
app = dash.Dash(
__name__,
external_stylesheets=stylesheets,
external_scripts=external_scripts,