While the quick user backup as this one-line commandmysqldump -u [user] -p mysql > [Path]/[user_backup_filename].sql might work when you have same version for backup and restore SQL. In most cases, you want to implement something similar to the following bash script
Backup Users
Step 1: On your server, in terminal, prepare the following bash file using vi (or vim or any text-editor of choice)
Step 2: Paste in the content of the file as follow:
PASSWORD : change to your root password or the password of the user that you use for the backup process. If you don't use root then change root on line 8 to your user
Step 3: make sure you (or the user that run the mariadb_user_backup.sh file has the sufficient permission (i.e. chown) and make the script file executable:
Step 4: Execute the script file to obtain the user backup file
Restore Users
Similar to the guide .
If your new SQL server is newer than your old one, after importing both database(s) and users, you can run the following command in terminal to upgrade MySQL:
Search Chemicals
Searching Chemicals in Existing Database(s)
Make sure “Chemical Search” mode is on
vim mariadb_user_backup.sh
Delete a chemical container
TO DO: to be constructed
path : use your specified path to the output file
oe_backup-user-$(date +\%Y\%m\%d).sql : the output file will have the current date concatenated at the end of the file
This script above also not save oldroot user info or empty users. You can change it by modify the code on line 12
#!/bin/sh
# This bash script is used to save users and permission from mysql database.
# Ref: https://stackoverflow.com/a/57878326
# explanation: https://wisdmlabs.com/blog/migrate-mysql-users-one-server-another/
HOSTNAME="localhost"
logininfo="-u root -pPASSWORD"
outfile="/path/oe_backup-user-$(date +\%Y\%m\%d).sql"
# The line below will save all users except 'root', empty name and specified ones
mysql ${logininfo} -B -N -e "SELECT CONCAT('\'',user,'\'@\'',host,'\'') from user where user != 'root' AND user != '' AND user not like 'auto%'" mysql | \
while read uh
do
echo "SHOW GRANTS FOR ${uh};"
done | mysql ${logininfo} -B -N | sed -e 's/$/;/' > ${outfile}
chmod u+x mariadb_user_backup.sh
./mariadb_user_backup.sh
mysql_upgrade # Upgrade MySQL data
systemctl restart mariadb # Restart mariadb
Step 1: choose what type of search: e.g “names, cas, supplier #”
Step 2: choose options: e.g. allwords,contain(~similarto),exact
Step 3: type is your search query, this can be name, CAS, supplier #, best with CAS and name
Step 4: choose database(s): choose one, or several (holding Ctrl while Left-click, or All databases (default)
Step 5: click Search
Video demonstration:
Searching Chemicals in Supplier Mode
Note: when Supplierssearch mode is on (see add chemical via suppliers), Open Enventory search includes chemicals from the local database(s) first
Supplier search mode
Search Chemicals using Structure
The default drawing program in Sciformation Vectormol. You can choose a different program by going to: Settings/Settings/Molecule editing/ and change “Structure Drawing Program” to “ChemDoodle (Javascript)” (recommended).
Step 1: choose search with Structures
Step 2: draw structure
Step 3: choose options: contain, similarto,exact, etc.
Step 4: click search
If it appears that the search is not accurate in ChemDraw plugin, you have to active the ChemDraw plugin:
a) Right click on the background of the chemdraw drawing window
b) Help/Activate my ChemDraw Plugin
c) Input your activation info the same (from email) as what you did for installation of Chemdraw
Database Backup and Restore
This is procedure to backup Open Enventory database and restore it later on the same server or migrating to a different server
For traditional LAMP stack
This guide is for Linux environment with Apache2, PHP and MariaDB (MySQL) (LAMP) stack:
Save or Backup Database(s)
For chemicals and lab journal databases:
1. In Terminal window, type the following command:
Replace [italic_text] (including the square bracket) with specific info:
[user]: in most cases, use root (recommended)
If you want to compress the SQL backup files, you can use this command instead:
| xz was added for compressing SQL file to .xz file
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
For users info:
1. In Terminal window, type the following command:
Replace [italic_text] (including the square bracket) with specific info:
[user]: in most cases, use root (recommended)
While this approach might work well in case of same MySQL or MariaDB version, if you migrate or upgrade SQL, you want to follow the instruction here for better users backup:
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
Restore
Step 1: transfer both files (database and users, if you want to keep the same users and passwords) to the new system/server
Step 2: if you have not done so.
Step 3 (optional):
If you have compressed the SQL file as instruction above, you will need to decompress the file first.
This is for compressed file with .xz extension:
Step 4: use ssh and terminal, login as terminal root and run:
Replace [italic_text] (including the square bracket) with specific info:
[database-name]: use the name of the database that you want to backup
Step 5: go to OE on web browser and login with mysql root account.
If the mysql root user in the old database has password different than the current mysql root user, after step 3 above, the root user password will be changed to the old password.If you don't know the old mysql root password, follow this tutorial to .
Step 6: go to Settings and then click on Recreate users. That should reactivate all users and their passwords.
Again, if you have migrate from MariaDB < 10.4 to MariaDB 10.4+, it might not work and we have to change the command in step 3 above. The reason is because the mysql.user table is deprecated in MariaDB 10.4. You can read more about it .
For XAMPP users
While the general steps are similar, the exact paths to the executable command are different for Mac OS and Windows using XAMPP, please follow the corresponding guides below:
Save or Backup Database
For chemicals and lab journal databases:
Import a list of chemicals
Prepare the Excel file, an example might look similar as below. A few important things:
Columns that are highlight in blue are important info.
You don't need all of the info that show in this example.
Empty cells are OK.
The amount need to be “xx Y” with xx is the amount and Y is the unit.
For unit, it is best to have all in lower case, for example, “ML” should be either “ml” or “mL”. It is best to convert all unit to lower case (use lower() command in excel).
Double check the CAS number column, Open Enventory uses CAS number as primary source to look up chemical info from the internet.
See step 9 for more info about each column in the excel sheet.
Location column: remove all commas ( , ) if there is any. Dashes ( - ) are ok. Update (2020-02-01): for KV's version of OE, if you updated to version after 2020-02-01, this has been fixed.
Update (2020-02-01): for KV's version of OE, if you updated to version after 2020-02-01, steps 2 and 3 below are not necessary any more. KV's version OE (on and after 2020-02-01) now accepts Excel files (*.xlsx and *.xls), comma-separated files (csv) tab-separated files (*.txt). You can find the guide for newer version .
2. Copy all of the cells in this file (Ctrl-C for Windows, Cmd-C for Mac) and paste (Ctrl-V for Windows, Cmd-V for Mac) them into Notepad (Windows) or TextEdit (Mac)
3. Save this new file as your-file-name.txt. The “.txt” part is important.
Alternatively, instead of step 2 or 3, you can do the following. (Note: in some cases with some chemicals names, Excel has shown to add quotation marks (“”) around the name when exporting to text file. That is the reason why step 2&3 above is preferred.
Save As… the file using Window Formatted Text (for Mac OS)
For Windows, Office 2016 of Office 365, use “Text (Tab delimited) (*.txt)” option:
4. Login into your database using root user or any users with admin permission
5. Go to Settings
6. Go to Import Tab-separated text file (or Import in KV's version)
7. Choose Browse… and choose the exported text file.
Note: in Lines to skip, put 1 if you have a header rows, if not, choose 0
8. Click green check mark
9. Screens as below should show up, you can scroll down to see if they show up correctly (info appear correctly in each row)
10. Choose Column X for each content. If you choose None, that column will not be imported. You can also add a default value for each column that will apply for ALL items being imported.
Notes:
CAS number: most important info, OE will use this to look up other info (structures, MW, safety data, etc) from this cas #
11. Click green check mark. Screen similar as below should show. Note: line X:… will tell you which lines in the text file is being imported.
12. Depend of how many chemical containers are imported, this might take a long time, so please be patient.
Step 3: Depends on the type of info you want to edit, choose the corresponding tab below:
Click on ‘Go to molecule’ button to edit structure and structural info (MW, Formula, etc.)
To change the lab related (person responsible, amount, etc.) info, double click on any where around these info
Borrow and Return Chemicals
In Inventory Mode
Borrow a chemical
Step 1: search for the chemical of interest (see Search chemicals section)
Add a single chemical
Add Storagelocation if not exists: see
For chemicals from existing database
Terminal Mode
All of the guides in this section require you to be in an active Terminal. Please contact your site admin for specific details on how to access a terminal page on Open Enventory.
A terminal site should look similar to this:
If you are an admin and need to set up a Terminal, please see the following page:
[database]: use the name of the database that you want to backup
[Path] and [backup_filename] : any path and filename
Make sure that you have .xz at the end of the file as above.
.xz files seem to have the best compression vs bzip2 and gzip for SQL files. You can see more info here and here:
Step 3: use ssh and terminal, login as terminal root and run:
Replace [italic_text] (including the square bracket) with specific info:
[database-name]: use the name of the database that you want to backup
[/path/to/backup-database]: any path and filename
Step 4: go to OE on web browser and login with mysql root account.
If the mysql root user in the old database has password different than the current mysql root user, after step 3 above, the root user password will be changed to the old password.
Step 5: go to Settings and then click on Recreate users. That should reactivate all users and their passwords.
Again, if you have migrate from MariaDB < 10.4 to MariaDB 10.4+, it might not work and we have to change the command in step 3 above. The reason is because the mysql.user table is deprecated in MariaDB 10.4. You can read more about it here.
Save or Backup Database
For chemicals and lab journal databases:
1. Open a Window Powershell window, type the following command:
Replace [italic_text] (including the square bracket) with specific info.
[user]: in most cases, use root (recommended).
In the command above, this part is for the default XAMPP set up. If some error happens, you should find the executable file inside XAMPP folder in your system. You can try to follow this .
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
For users info:
1. In Terminal window, type the following command:
Replace [italic_text] (including the square bracket) with specific info:
[user]: in most cases, use root (recommended).
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
Restore
Step 1: transfer both files (database and users, if you want to keep the same users and passwords) to the new system/server
Step 2: if you have not done so.
Step 3: use ssh and terminal, login as terminal root and run:
Replace [italic_text] (including the square bracket) with specific info:
[database-name]: use the name of the database that you want to backup
Step 4: go to OE on web browser and login with mysql root account.
If the mysql root user in the old database has password different than the current mysql root user, after step 3 above, the root user password will be changed to the old password.
If you don't know the old mysql root password, follow this tutorial to .
Step 5: go to Settings and then click on Recreate users. That should reactivate all users and their passwords.
Again, if you have migrate from MariaDB < 10.4 to MariaDB 10.4+, it might not work and we have to change the command in step 3 above. The reason is because the mysql.user table is deprecated in MariaDB 10.4. You can read more about it .
❗Computer that connected to the scanner must be ON
❗Barcode terminal window must be ON and ACTIVE, if not log in with terminal username and pass or contact your local admin
❗ Active barcode terminal look like below:
Step 1: scan your own barcode
Step 2: scan chemical barcode
Watch the terminal window to make sure the info is transmitted/recorded.
Return a chemical
❗ Computer that connected to the scanner must be ON !!! Barcode terminal window must be ON and ACTIVE
Action: scan borrowed chemical barcode
Note: you don’t need to scan the your own barcode beforehand. The scan on a borrowed chemical will return the chemical.
Note: if the chemical is free and nobody has logged in, scanning the barcode of that chemical will bring up that chemical’s info in the system.
mysqldump -u [user] -p mysql > [Path]/[user_backup_filename].sql
unxz -vk [/path/backup-database].sql.xz
mysql -u root -p [database-name] < [/path/backup-database].sql #for database restore
mysql -u root -p mysql < [/path/backup-user].sql #for users restore, this might not work for mariabd 10.4+
c:\Programs\XAMPP\mysql\bin\mysqldump -u [user] -p mysql > [Path]/[user_backup_filename].sql
c:\Programs\XAMPP\mysql\bin\mysql -u root -p [database-name] < [/path/to/backup-database].sql #for database restore
c:\Programs\XAMPP\mysql\bin\mysql -u root -p mysql < [/path/to/backup-user].sql #for users restore, this might not work for mariabd 10.4+
2. Scan chemical container (will now show chemical information)
3. Scan new location barcode (will now say “updated and location field will show new location”)
Moving multiple containers to the same location
Check the 2 boxes “Stock-keeping mode” and “Set storage for all following containers” (the “Set storage for all following containers” will show up after you check “Stock-keeping mode”). Note: you can check by mouse or use the “Barcode for stock-keeping mode” list from Settings menu.
2. In typical terminal window of database of interest. Login by scanning user barcode
3. Scan the 1st chemical containers
4. Scan the new location. The window will show the new location and say the 1st container “… updated”
5. Scan the 2nd containers, 3rd container, 4th container, etc.
6. When Done, uncheck “Set storage for all following containers”
The following should be changed to your own setting:
- adress: your Open Enventory web address
- databasename
- username
- password
Keep in mind that the password for Terminal user will be exposed in your bookmark link above
Do NOT create a user with username starting with "auto". Any user with this kind of username will be deleted when linking databases.
Change user password
Change user password using an admin account
Change one's own password
First, open up Open Enventory in any web browsers. Your screen should look as follows.
After logging in you should see the general window for searching chemicals.
Click on the “Settings” tab top and center of the page (outlined with a red box below).
This will change the left side bar. At the top of the left side bar you should see “Change password” Click here (the button is outlined with a red box below).
Your screen should have two boxes as shown below. Fill in both boxes press the “Change password” button right next to the text fields and your password has been changed.
Create a list of users
Modify a user's information, permissions
Delete a user
Inactivate a user
Step 1: After logging into Open Enventory, click on Settings on the top bar navigation.
Step 2: click on Storages on the Left.
Step 3: click on the ➕ button
Step 4: after adding the info, click the checkmark ( ✅ ) button
Create a list of storage
TO DO: to be constructed
Modify a single storage's information, permissions
TO DO: to be constructed
Modify info for a list of storage
TO DO: to be constructed
Merge two storage locations
TODO: add line-by-line instruction
GIF image
Delete a storage
TO DO: to be constructed
Scan barcode for “Delete” (will say “data set will be deleted in 3 seconds, then deleted)
Notes: If you manually change data (not using the scanner) you will have to click “update” after changing the data manually (mouse and keyboard).
Database
Create a database
1. Go to your Open Enventory Login page on your web browser
2. On the Login page, fill in the following info:
- Database: name for the new database
- Username: root
- Password: your mysql root password
3. Open Enventory will then create a new empty database
Connect databases
This allows for users in one database to see chemicals in another database and/or vice versa.
Note: in the default setting, OE only allows user in one database to see if other databases have chemical(s) but not revealing the chemical's location.
If you want to let users in one database to be able to see location of chemicals in another database, after connecting the databases, please follow the instruction in this .
1. Go to your Open Enventory Login page on your web browser
2. Log into your database of interest using root as Username and your mysql root password as Password
3. Go to Settings on Top menus:
4. On the left side menu, choose Manage databases :
5. There are two types of connections:
2-way connections: users in one database can see/search chemicals in another database AND vice versa
1-way connection: users in one database can see/search chemicals in another database BUT NOT vice versa)
choose the desired connection and follow the instruction below.
Step 1: Choose as databases that you want to connect (hold Ctrl while choosing). You can choose more than 2. Click select all if you want to connect all databases
Step 2: Click the button Connect selected databases
Step 3: Click the green check mark ✅
Done! You can now search chemicals in other database(s) in the search page
Using the rubric table, the databases with name in the bold format and listed horizontally in the first row of the table will be able to see/search chemical in database(s) (list vertically in the first column) that has checked check box
For example:
In the picture below, users in romo database will be able to see/search chemicals in romo_test database BUT users in romo_test database will NOT be able to see/search any chemicals in romo database.
Step 1: using the info above, make the connection of interest by checking the check boxes
