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Add Storage location if not exists: see this section
Step-by-step instruction here
This clip below is show the process of adding a new chemical from suppliers:
For custom chemicals or chemical that cannot be found from suppliers list, use Method below.
This is procedure to backup Open Enventory database and restore it later on the same server or migrating to a different server
This guide is for Linux environment with Apache2, PHP and MariaDB (MySQL) (LAMP) stack:
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)
[database]: use the name of the database that you want to backup
[Path] and [backup_filename] : any path and filename
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
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 and :
For example usage of xz
, see this .
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
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)
[Path]
and [backup_filename]
: any path and filename
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)
Step 1: transfer both files (database and users, if you want to keep the same users and passwords) to the new system/server
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:
-v
: verbose, give more info
k
: to keep the compressed file, this will generated the uncompressed file .sql
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
[/path/backup-database]
and [/path/backup-user]
: any path and filename
Step 5: go to OE on web browser and login with mysql root
account.
Step 6: go to Settings
and then click on Recreate users
. That should reactivate all users and their passwords.
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:
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).
[database]: use the name of the database that you want to backup
[Path] and [backup_filename] : any path and filename
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
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).
[Path] and [user_backup_filename] : any path and filename
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
Step 1: transfer both files (database and users, if you want to keep the same users and passwords) to the new system/server
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.
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).
[database]: use the name of the database that you want to backup
[Path] and [backup_filename] : any path and filename
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
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).
[Path] and [user_backup_filename] : any path and filename
2. Type in password for the user above and then Enter (nothing will show when you are typing the password)
Step 1: transfer both files (database and users, if you want to keep the same users and passwords) to the new system/server
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.
Step 2: if you have not done so.
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 .
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 .
Step 2: if you have not done so.
If you don't know the old mysql root
password, follow this tutorial to .
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 .
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 .
Step 2: if you have not done so.
If you don't know the old mysql root
password, follow this tutorial to .
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 .
Login into OE and extract the list of chemical containers that need to be move. You don't need all of the details for each container, just: - CAS number - Names - Chemical container barcode: most important thing as this is the lookup point
Open and add a new column with the name of the new location for each container. New LOCATION NAME MUST BE EXACT or OE would create a new storage location.
Skip this step if you want to move all of the chemical containers into the exact same location.
Login into OE with an admin account if you have not done so in step 1
Go to Settings
> Import and Edit via text file
If you don't see Import and Edit via text file
, you might not use the OE version by KV. If you did, you might need to enable it. See more at: Turn On Import and Edit function for Chemical Containers
Follow the process that is laid out in Edit Multiple Chemical Containers .
In Step 5 of Edit Multiple Chemical Containers , you would only need to choose the column for CAS number
, Name
and most importantly, chemical container barcode
and **chose the correct column for the new location for the storage_name
If you want to change all chemical container into the same new storage, simply typing the EXACT STORAGE NAME in the input instead of choosing the column for the storage_name
Make sure “Chemical Search” mode is on
Step 1: choose what type of search: e.g “names, cas, supplier #”
Step 2: choose options: e.g. all words, contain (~ similar to), 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:
Note: when Suppliers search mode is on (see add chemical via suppliers), Open Enventory search includes chemicals from the local database(s) first
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, similar to, 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
TO DO: to be constructed
This guide is for KV's version of OE that is newer than 2020-02-01. If you use an older version of Felix Rudolphi (FR)'s original version, please see the guide here.
Update (2020-02-01): KV's version of OE (on and after 2020-02-01) now accepts:
Excel files (*.xlsx and *.xls)
Comma-separated files (csv)
Tab-separated files (*.txt).
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.
2. Login into your database using root user or any users with admin permission
3. Go to Settings
4. Go to Import Tab-separated text file (or Import in KV's version)
5. 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
6. Click green check mark
7. Screens as below should show up, you can scroll down to see if they show up correctly (info appear correctly in each row)
8. 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 #
Name: not too important
Empirical formula: do not import this since OE will use this to find the closest chemicals if CAS# is not present or wrong.
Amount: = size of the bottle + unit (format should be #+space+unit, for example: 5 g, 125 ml, 1 kg, etc)
Still available: the amount that left in the bottles (OK if not imported)
Locations: important. Note: Each location will have its own barcode
Compartments: = sub-location. Note: each compartment does NOT have its own barcode
Barcode: if you already have an existing barcode system, add it here.
Suppliers: = suppliers
Date open: could be in European style (dd.mm.yyyy) or American style (mm/dd/yy, etc.)
9. 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.
10. Depend of how many chemical containers are imported, this might take a long time, so please be patient.
Author: Nathanyal Truax, Baylor University. You can check out his Youtube channel for other useful videos.
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:
Click on Edit button () to edit the info. (Or double click on any fields inside the Edit package area.
Click on Edit button () to edit the info. (or double click on any where around these info)