Ideas, guides, comments are welcomed.

For this gitbook User guides or the modified version of OE:

You can contact Dr. Khoi Van (modified version of OE), at this email: knv88@pm.me or Twitter

For the original Open Enventory:

you can contact Felix Rudolphi, the creator: info@sciformation.com

Introduction

This is a User Guide (wiki) for Open Enventory. The links to the software (original version by FR, and forked version by KV) are on the top bar.

About Open Enventory

• Open Enventory is a free, open-source (AGPL v3) programs for chemical inventory and electronic lab notebook. It combines:

  • a lab notebook,

  • a database for all spectroscopic data,

  • a chemical inventory and

  • a literature database.

• It is designed for the requirements of university groups and small companies, focuses primarily in Chemistry research.

• It is operated in the web browser (Edge, Firefox, Opera, Apple Safari, Google Chrome) and is therefore platform-independent. The integration means that physical data and safety information from the inventory can be used automatically in the laboratory journal. The automatic query of freely accessible substance data from online chemical catalogs saves manual data entry and catalog searches. Access to the catalog data also enables a price overview to be created with a click of the mouse.

• The laboratory journal uses the data from inventory management and makes the results accessible to all members of the working group. Both inventory and laboratory journal allow the data to be shared with other working groups for the purpose of collaboration.

The goals of Open Enventory are:

• to make unnecessary and boring tasks in the laboratory obsolete: searching for chemicals, price surveys.

• to make knowledge accessible inside and outside (if access is granted) the workgroup, for longer periods.

• to improve working safety be easily accessible safety instructions.

• to reduce waste amounts and unnecessary costs by an easily searchable inventory database.

Currently, Open Enventory can be used in German, English, French, Spanish, Italian, and Portuguese. Additional language files and modifications can be created with little effort.

• Sources:

  • http://www.open-enventory.de/index_en.html

  • http://sciformation.com/open_enventory.html?lang=en

Why would you want to use Open Enventory?

Please see the following presentation for a brief intro into Open Enventory, why you would want to use it and some of its functions:

• Link to online presentation.

• Click the link below to download the presentation:

Screenshots

Demo page

Official demo site for: - Chemical inventory - Electronic Lab notebook (ELN)

Contribution

This guide will be updated periodically.

If you want to contribute, you can create an account to generate or edit this guide. Please follow this link.

If you have some documents or guide or videos and want to contribute and do not want to make the page yourself, please feel free to send it over to KV using the contact page:

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)

vim mariadb_user_backup.sh

Step 2: Paste in the content of the file as follow:

#!/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}

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:

chmod u+x mariadb_user_backup.sh

Step 4: Execute the script file to obtain the user backup file

./mariadb_user_backup.sh

Restore Users

Similar to the guide here.

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:

mysql_upgrade    # Upgrade MySQL data
systemctl restart mariadb   # Restart mariadb

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.

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.

Done! You can now search chemicals in other database(s) in the search page

Searching Chemicals in Existing Database(s)

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:

Searching Chemicals in Supplier Mode

Search Chemicals using Structure

Step 1: choose search with Structures

Step 2: draw structure

Step 3: choose options: contain, similar to, exact, etc.

Step 4: click search

Step 1: Search chemical in the database:

Step 2: Click on the structure

Step 3: Depends on the type of info you want to edit, choose the corresponding tab below:

Download site

You have 2 versions to choose from:

. Improvements or changes in this version compared to Felix Rudolphi version is .

Installation instruction

Please see the Installation section:

Step-wise guide

1. 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.

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.

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.

Demo video

Author: Nathanyal Truax, Baylor University. You can check out his for other useful videos.

Step 1:

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

Step 2

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.

Step 3

Login into OE with an admin account if you have not done so in step 1

Step 4

Go to Settings > Import and Edit via text file

Step 5

Follow the process that is laid out in Edit Multiple Chemical Containers .

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

If your institution has this option turned on, you can edit a list of chemicals automatically.

To turn on this function, please see this page:

Instruction

then:

Step 1: Choose Settings

Step 2: choose Import and Edit via Text File

Step 3: on the Import page:

• Choose package in the table field:

• Click on Choose file button to choose your prepared file

• Choose the number of Lines to preview

• Choose number of lines to skip (header lines)

Step 4: click the green check mark to start uploading the file

Step 5: match the appropriate column for each info

• Most importantly: match Barcode for chemical container with the correct column on your prepared file. This is how Open Enventory use as ID of the container.

• Match the rest of the info in the red rectangle area as desired:

• Preview of the data:

Step 6: click the green check mark

User Permissions

Create a New User

Create multiple users

Change user password

Modify user's permissions, information

Delete a user

Inactivate a user

For chemicals from existing database

Step-by-step instruction here

For chemicals from suppliers

Step 1: change to supplier search and search chemical

Step 2: choose Create new molecule based on data

Step 3: add more info: amount, person responsible, etc.

This clip below is show the process of adding a new chemical from suppliers:

Add a single chemical from scratch

Step 1: choose New

Step 2: use CAS number (if exists) to pull info from suppliers

Step 3: add more info

Change user password using an admin account

Step 1: Choose Settings

Step 2: Choose Users

Step 3: click on Details button ( ) on the same row of the user you need to change password

Step 4: click on Edit button () (or double click anywhere on the info window)

Step 5: type in the new password and repeat

Step 6: Click on the green check mark: ✅

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.

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:

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:

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):

Step 4: use ssh and terminal, login as terminal root and run:

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.

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:

In Inventory Mode

Borrow a chemical

Step 1: search for the chemical of interest (see Search chemicals section)

Step 2: click Borrow button

Return a chemical

Step 1: go to Borrowed chemicals

Step 2: click Return button

In Terminal Mode

Borrow a chemical for users of that database

This function only works for users and chemical containers in the same database. For cross-databases (guest) borrowing, please see the guest borrowing guide below.

Step 1: scan your own barcode

Step 2: scan chemical barcode

Borrow a chemical for guest users

Step 1: Follow the following guide to create a guest account

Step 2: Follow the step above in Borrow a chemical for users of that database

Return a chemical

Action: scan borrowed chemical barcode

If you want to create multiple new users, please see:

Step 1: Choose Settings

Step 2: Choose Users

Step 3: Click on the plus side button ➕

Step 4: Add info such as username, password.

Step 5: add additional info such as name, locations

Step 6: Choose the appropriate permission

• Choose one of the predefined permissions or "User defined" for customized permission

Step 7: Click on the green check mark: ✅

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:

Details

The idea is each group should have one ‘user’ account designated for external users (users from outside of the group, guests). When someone outside of the group comes and borrows chemical containers, this account barcode should be scanned and following by the container barcode. This specific account (made by turning on a specific permission setting External borrow in Predefined permission) is set so that during checking out of a chemical container by this account, a pop-up window would open and ask for the specific info (borrower’s name, group, contact info, and the group member assisting during checkout). This info is then saved into the history entry of that exact checkout event.

Guide

Step 1: Create a new user, ‘guests_<database_name>’ for example.

• While creating this user, choose the following ‘External borrow’ in the ‘Predefined permissions’

Step 2: Use this new account barcode in the OE barcode terminal. During checkout, a popup window like this should open to ask for more info:

The provided info will be appended to the history entry for that particular checking out event. Example:

Step 1: Choose Settings

Step 2: Choose Users

Step 3: click on Details button ( ) on the same row of the user you need to change password

Step 4: click on Edit button () (or double click anywhere on the info window)

Step 5: change desired info or permission

Step 6: Click on the green check mark: ✅

Step 1: Choose Settings

Step 2: Choose Users

Step 3: click on Delete button ( ) on the same row of the user of interes

Step 4: choose OK to confirm deletion

Different than , this will not remove the user from the database. It only disable the user from logging into the database

Step 1: Choose Settings

Step 2: Choose Users

Step 3: click on Details button ( ) on the same row of the user of interest

Step 4: click on Edit button () (or double click anywhere on the info window)

Step 5: check Account disabled

Step 6: Click on the green check mark: ✅

Go to an active Terminal on your Open Enventory page. It should look similar to the following page.

Without any user logging in, scanning a chemical container barcode will bring up that chemical info.

SETTING FOR BARCODE TERMINAL USER

1. To have a barcode terminal client (stand-alone computer), create a user with permission as below and log in into OE using this user.

To create a new user, please see the following link:

Step 1: Choose Settings

Step 2: Choose Import

Step 3: download the User template and fill out the sheet according to the instruction.

• This is a copy of the Excel User Import template. It is better to download the template from Step 2 above

Step 4: on the Import page:

• Choose user in the table field:

• Click on Choose file button to choose your prepared excel user import file from step 3

• Choose the number of Lines to preview

• Choose number of lines to skip (header lines)

Step 5: click the green check mark to start uploading the file

Step 6: match the appropriate column for each info

Step 7: click the green check mark

Create a storage location

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

Modify a single storage's information, permissions

Modify info for a list of storage

Merge two storage locations

Delete a storage

See Borrow and Return Chemicals in Terminal Mode

These are not hard-setting but might be adapted to specific usage. All pages in this section are for guiding purpose.

This guide is created for new unmanaged VPS from A2hosting.com

• OS: CentOS 7

• Ram: 1GB

• Hard drive: 20 GB

• Bandwidth: 2 TB

INITIAL SETUP

1. Login into A2 account, service to find the following info:

• IP or hostname (if the domain name has been set up/registered)

• Ssh username

• SSH password

• SSH port

2. Connect to server using ssh. If you are on a Mac, use Terminal and type in the following command. If you are on a Window, you can use CMD (if CMD does not work, google “connecting to ssh on Window” to find the program

ssh -p xxxx yy@ zz.zz.zz.zz

Select “Yes” if asked to continue connecting

If there is a problem, follow this link: https://www.a2hosting.com/kb/getting-started-guide/accessing-your-account/using-ssh-secure-shell

3. To secure your ssh and your server, set up new user and deactivate root login via SSH by following steps 2, 3, and 5 in this tutorial:

https://www.digitalocean.com/community/tutorials/initial-server-setup-with-centos-7

Install sudo by:

yum –y install sudo

4. Optional: Setting up time by following this link: https://www.tecmint.com/set-time-timezone-and-synchronize-time-using-timedatectl-command/

5. Following this link to set up LAMP stack:

with:

yum –y install firewalld
systemctl start firewalld
firewall-cmd --permanent --zone=public --add-service=http
firewall-cmd --permanent --zone=public --add-service=https
firewall-cmd --permanent --zone=public --add-port=7822/tcp
firewall-cmd –reload
systemctl enable firewalld

In step 4: choose PHP7.2

Follow this tutorial from steps 1-5, make sure instruction for specific steps as indicated above

https://www.howtoforge.com/tutorial/centos-lamp-server-apache-mysql-php/

6. Install the following packages to prepare for Open enventory

yum -y install php-mysql php-gd php-mbstring php-pear zlib-devel ghostscript ImageMagick libreoffice
systemctl restart httpd

7. Create a “download” folder; download OE (get the exact link from website: https://sourceforge.net/projects/enventory/files/?source=navbar ); unzip OE and copy to the right location:

mkdir download
cd download
wget https://sourceforge.net/projects/enventory/files/open_enventory_2018-02-21.zip
unzip open_enventory_2018-02-21.zip
cp -rp open_enventory_2018-02-21/. /var/www/html/oe

8. Go to http://xx.xx.xx.xx/oe

9. The OE website should load like screenshot below

10. If successful, this page will load:

11. Modify .htaccess file

vi /var/www/html/oe/.htaccess

Modify the content of the file as in this screenshot. Important: these setting is for the server with configuration as indicated in the top of this tutorial

Save the file (hit Esc, type “:wq” and then Enter) and restart httpd service

systemctl restart httpd

12. Modify mysqld config:

vi /etc/my.cnf.d/server.cnf

Right after [mysqld], add:

sql_mode = NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION 
max_allowed_packet = 64M # (or higher) 
innodb_buffer_pool_size = 1024M # to about 50% of the available memory

Save the file (hit Esc, type “:wq” and then Enter) and restart httpd and mariadb services

systemctl restart httpd mariadb

Goal: Setting for adding prefix Ctrl-A. This is to remove all pre-existing data inside an input field

Reference: https://www.honeywellaidc.com/en/-/media/en/files-public/technical-publications/multi-product/00-02544.pdf

Instruction: scan every single barcode on the first column in this order from top to bottom

Explanation:

• 1st Configurable Prefix = 175 : Left Crtl + 1 character

• 2nd Configurable Prefix = 065 : Letter “A”

• Scanner will transmit <left CRTL Make> “A” <Left CRTL Break>

Go to an active Terminal on your Open Enventory page. It should look similar to the following page.

1. Scan user barcode (will say you are logged in)

2. Scan chemical container (will now show chemical information)

3. 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).

Go to an active Terminal on your Open Enventory page. It should look similar to the following page.

Moving one single chemical

1. Scan user barcode (will say you are logged in)

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

1. 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”

A brief tutorial of creating a new laboratory notebook and creating a reaction entry.

1. Create new notebook.

   If you do not see the + button ask your admin to give you administrator journal privileges.

2. Generate reaction from scratch.

3. Generate reaction by copying existing reaction.

4. Add a new empty notebook page

CHANGING TIMEOUT FOR WRONG PASSWORD

Edit file lib_global_setting.php: from

to

ADDING MORE OPTIONS FOR # OF RESULTS PER PAGE & DEFAULT CURRENCY TO USD

Edit file lib_global_setting.php

from

to

ADDING MORE MEMORY IN ORDER TO EXPORT (IN OE) TO EXCEL OF LARGE AMOUNT OF CHEMICALS

1. edit filephp.ini (in Linux, /etc/php.ini)

with xxx = desired memory in megabytes

2. edit file.htaccess (in the folder install oe)

with xxx = desired memory in megabytes

SETTING FOR BARCODE SCANNER

1. For OE original barcode, add Prefix ESC

2. For existing barcode, (specifically for Tao Tronic scanner: ) add Prefix: [l_shift_on]+[Home]+[l_shift_off]

TO FIX ISSUE WITH IMPORT TEXT-SEPARATED TEXT FILE NOT LOADING

• If you find a blank page after clicking the check mark ✅:

• Chance is you miss php-mbstring and php-gd packages

• Install these packaged and restart apache (httpd in CentOS 7) should fix this issue

• In CentOS 7, you can install the two above packages by running :

• Restart your server (in Centos 7):

TO KEEP THE CURSOR ALWAYS IN THE FIRST TEXTBOX IN BARCODE TERMINAL FUNCTION

1. Go to OE folder, change …/lib/barcode_terminal.js, line 174-185, content:

From

To:

CHANGE LOGIN DEFAULT DATABASE TO NONE

1. Edit lib_global_funcs.php

Change:

to:

2. Restart server

TO AUTO FOCUS ON THE DATABASE TEXT BOX ON THE LOGIN PAGE

1. Edit lib_global_funcs.php by adding autofocus after id=\"db_name\". Around line ~1180

Original:

to:

UPGRADING OE

1. Backup current OE files

2. Download the appropriate files from:

3. Unzip the file

4. Copy the content of the folder into your current [OE_folder] and overwrite the old files

5. Copy the “List of files that have been modified to specific need (different than the original files of oe)” from the backed up OE to the new [OE_folder]

6. Restart httpd and mariadb (or mysqld) services

7. Go to web browser and access OE url

8. Login as root into a database of interest and perform upgrade if necessary (you will have to do this again for all of the databases if major upgrade is required

MULTIPLE LABEL STYLES

This will create n number of window for different styles of label when click on this Print Dymo Label button (). Also, this code will close these pop-up windows automatically after 30 seconds (30000 miliseconds)

1. Create the label by re-design the original file chemical_storage.label (in /oe/forms/dymo/). You can open and edit ".label" files by using Dymo software:

2. Name these files as chemical_storage1.label, chemical_storage2.label, etc.

3. Save these files in the same location: /oe/forms/dymo/

4. Edit file edit.js (in /oe/lib/)

From:

To:

Pic:

Original file:

Modified file:

2. Restart the apache service: in CentOS7 use this in the command line:

HAVING THE “PRINT DYMO LABEL” BUTTON ALWAYS SHOW UP REGARDLESS OF DYMO PLUGINS INTALLED

This will make this button () always show up even if the dymo plugin for browser is not detected.

1. Edit file lib_edit.php (in /oe/)

From:

Pic:

To (remove style=\"display:none\")

2. Restart the http/apache service

CHANGING LOCATION OF MULTIPLE CONTAINERS

1. Install phpMyAdmin by following the instruction from:

2. Log in into phpMyAdmin using Web browser: (or https://) with root user

3. Choose the Database in which the containers belong to:

For example in this case, I choose Database storage

4. Create new storage location in OE as usual, see:

5. Identify the storage_id of the new and old locations by choosing Table storage in Database “xyz”.

Another way of doing this is to use “Console” function in phpMyAdmin

Type in:

You should see similar to:

With the screen above, you should be able to see the storage_name and the corresponding storage_id

The next few steps is demonstration for changing all of the chemical in “315-R (Personal)” (storage_id=1) into “305-test” (storage_id=9)

In the Console:

6. To check how many chemical, type:

7. To change, type:

Done

CHANGING INFO OF MULTIPLE CHEMICALS

Install phpMyAdmin (See above)

To return all chemicals borrow by somebody (borrowed_by_person_id)

1. Look up person_id by going into [Database]/person

2. Show chemical borrow by that person (i.e. a person with person_id=8)

3. Return by:

To change the owner info of a chemical (owner_person_id)

1. Look up person_id by going into [Database]/person

2. Show chemical owned by that person (i.e. a person with person_id=7)

3. Change, in this case, to no owner (NULL)

Find person_id using Console command line in PHPMyAdmin

In the following example, show person_id of user with username=julia

Find storage ID using Console Command line in PHPMyAdmin

1. First choose the desired database on the tree folder from the left

2. Use:

Explain:

• LIKE 'FH-2206%' : show the storage_id of the storage location with name starting with FH-2206

• LIKE '%FH-2206%' would mean find anything with storage name containing FH-2206

• LIKE 'FH-2206%' would mean find anything with storage name ending with FH-2206

Show chemicals with multiple criteria

Explain: the above command is used to

• Select all of the chemical in the database that match: owner_person_id=15 AND with storage_id is NOT 18

Change Responsible person for chemicals with multiple criteria

Explain: see above for explanation of the criteria.

Show storage_name and storage_id using username

Explain:

GROUP BY storage_name : is added so that duplicates are only shown once

Update responsible person for chemicals in many location (storage)

Explain: the command above change responsible people to no one for all of the chemicals being owned by person_id=13 AND in all of the storage_id listed

Search for barcodes that are duplicated

The below command will search for all the barcode that is assigned to more than 1 container (chemical_storage). This search ignores disposed container as well as container without barcodes (chemical_storage_disabled IS NULL AND chemical_storage_barcode != "")

Update/Get extra info for containers with duplicated barcode (continued from “Search for barcodes that are duplicated”)

To select info from the list of duplicated barcodes. In this case, created by a specific user and created after some specific timestamp

REMOVE ALL CONTAINERS (BOTTLES) OF CHEMICALS

This will remove all of the containers, including info about manufactures, order date, barcode, owner, location, etc. However, info about molecule (MW, structures, safety, etc) and database related such as users will be reserved.

This is particularly helpful when you need to update a large amount of chemicals via text import.

1. Login into your server via ssh

2. Login into myswl using root account or user account with administrator priviledge for the database that you want to change. Replace “root” with the username if desired

3. Show database and then choose the database of interest. test is the name of the database in this example

4. Remove the chemical container by running the following command

5. (Optional): Run the command below if you want to reset the id counter (chemical_storage_id as well as autogenerated barcode)

6. Log out of mysql, restart httpd and mariadb services

7. Go back to OE website and import new tab-separated text file

SETTINGS FOR OE TO USE WITH EXISTING CONTAINER BARCODES

If you have existing barcodes for your chemical containers, use the following settings

1. Login into OE with the database that you want to modify, using an admin account, (or root account, or an account with sufficient permission)

2. Navigate to Settings/Global Settings/Inventory

Important: when switching to this setting, you have to generate your own storage(locations) barcodes as well as user barcodes. See below for way to automatically generate location and user barcodes.

TO FIX EXISTING BARCODE IMPORTED ISSUE: Removing trailing “\n” in existing barcodes

Issue: if the existing barcode column is the last column in the tab-separated text file, when imported into OE, the “\n” will also be imported as part of the barcode. This lead to terminal window does not work with existing barcode. Use the following methods to remove this trailing “\n” character

1. Login into your server via ssh

2. Login into mysql using root account or user account with administrator priviledge for the database that you want to change. Replace “root” with the username if desired

3. Show database and then choose the database of interest. “test” is the name of the database in this example:

4. Remove the chemical container by running the following command

5. Log out of mysql, restart httpd and mariadb services

TO AUTOMATICALLY ADD STORAGE BARCODE WHEN USING “USE EXISTING BARCODES”

Issue: when switching to using pre-existing barcode instead of using OE-generated barcodes, the system won’t work well if no existing barcode for storages and users are added. Use the code below in mysql to automatically add barcodes for storage using OE-generated code.

While these barcodes look the same, they have to be generated in order for terminal to work

1. Login into your server via ssh

2. Login into mysql using root account or user account with administrator privilege for the database that you want to change. Replace “root” with the username if desired

3. Show database and then choose the database of interest. “test” is the name of the database in this example:

4. You can check if the new generated barcode first by running this in phpMyAdmin (easier to see result). See explanation below for the complicated function. Compared the “new_barcode” with the autogenerated barcode to make sure the function work well.

5. Update the “storage” table, by setting “storage_barcode” field. “storage_barcode” field is a binary so cast() was used. Note, this whole function inside cast() is to convert “storage_id” field to EAN8 barcode. See here for more info on how to make EAN8 barcode:

Explain: default in OE, the barcode for storage is “92xxxxxy” with the last digit “y” (digit number 8 on 1-based) is the check sum of the first 7 digits. The “xxxxx” labeled in red is the “storage_id” left padded with “0” (number zero).

For example: if “storage_id”=1 => “storage_barcode”=92000018

1. Exit mysql:

TO AUTOMATICALLY ADD PERSON BARCODE WHEN USING “USE EXISTING BARCODES”

Issue: when switching to using pre-existing barcode instead of using OE-generated barcodes, the system won’t work well if no existing barcode for storages and users are added. Use the code below in mysql to automatically add barcodes for USER using OE-generated barcode.

While these barcodes look the same, they have to be generated in order for terminal to work

1. Login into your server via ssh

2. Login into mysql using root account or user account with administrator privilege for the database that you want to change. Replace “root” with the username if desired

3. Show database and then choose the database of interest. “test” is the name of the database in this example:

4. You can check if the new generated barcode first by running this in phpMyAdmin (easier to see result). See explanation below for the complicated function. Compared the “new_barcode” with the autogenerated barcode to make sure the function work well.

5. Update the “storage” table, by setting storage_barcode field. storage_barcode field is a binary so cast() was used. Note, this whole function inside cast() is to convert storage_id field to EAN8 barcode. See here for more info on how to make EAN8 barcode:

Explain: default in OE, the barcode for PERSON is “91xxxxxy” with the last digit “y” (digit number 8 on 1-based) is the check sum of the first 7 digits. The “xxxxx” labeled in red is the “person_id” left padded with “0” (number zero).

For example: if “person_id”=1 => “person_barcode”=91000019

6. Exit mysql:

SETTING TO ALLOW SEEING LOCATION OF CHEMICAL OUTSIDE YOUR OWN GROUP

In the default setting of OE, the exact location of a chemical belonging to a different group is masked. This setting will help you to allow some specific person or everyone to be able to see locations of chemicals outside of your own groups

1. Login into the server via ssh and then convert to root user or use sudo command. The following is using sudo command

2. It is a good idea to save an original copy of this file first. Modify the file lib_output.php inside open enventory folder. In this example, the open enventory folder is named “oe”. The specific location of your folder might change. Change the path accordingly.

3. Change the content of the file as follow. Note, this is on line 2584 so google to search for some term in vi; otherwise you will need to scroll a lot.

Original content:

To let EVERYONE see the locations:

To let a specific user to see the location, change the content as follow. In this example, the person name is “special_person”

UPLOADING EXISTING LOCATION BARCODES

Below guide is referenced from:

Prepare the excel file with one column as storage with the same name as those found in OE. Export to csv file, csv file does not have to have the same column but it is best to have the first 2 columns is the storage name and barcode

Use mysql command line. ( if you use phpMyAdmin console, see section below)

1. Login into mysql as root user using:

2. Show all databases and choose the correct database to modify (in this example “test” is the name of the database):

3. Create a temporary table (in this example temp_storage is the name of the database, storage and barcode are the 2 headlines of the 2 columns):

4. Load csv data file into temp_storage table (in this example test is the name of the database; “ignore 1 lines” because the csv file head 1 line headline):

5. Update storage table

6. Remove the temporary table

If you want to use phpMyAdmin,

1. Copy csv files into /var/lib/mysql

2. Open phpMyAdmin console.

3. Choose the right databases

4. Run ALL of these commands AT ONCE (Ctrl-Enter to run command(s) in phpMyAdmin console)

This guide is to create a working Open enventory running on OS Raspbian on a Raspberry pi 3B (see for information on the RPi 3B)

• Quad Core 1.2GHz Broadcom BCM2837 64bit CPU

• 1GB RAM

• Using as boot and home drive

Initial Setup

1. Flash a fresh copy of Raspbian onto the micro SD card. (A guide for completing this task can be found here .

• Raspbian image found at We used "" zip file

• use zip file with to flash to micro SD

2. Once flashed insert micro SD into the RPi 3B and boot the device with monitor connected. If install completed you should now see the Raspbian desktop as shown below.

3. The first thing that should be done is to update the OS

• open a terminal window by clicking on terminal icon on top bar or by pressing ctl+alt+t

• run the following commands

4. After the update has completed we will create a LAMP server on the pi. This was completed following this guide ()

• Complete the steps to set up the Apache server, install PHP, and install MYSQL mysql is outdated trying the command in the above link will give you an error use the following instead to setup the mariadb and mysql (NOTE: Wordpress does not need to be installed)

5. Install the following packages to prepare for Open enventory

6. Create MYSQL root pwd by entering the following command in terminal the default password is blank. We will subsequently set it up so sudo is not required so that we can login online to create our databases for oe. When asked for a password after command 4, use the password we just set up for mysql_secure_installation.

7. Download Open Enventory image and set up on apache server (exact link to download can be found at ) (NOTE: in terminal commands below, the open_enventory_2019-07-24.zipshould be replaced with the version you wish to use) - Once downloaded unzip and copy to the right location which we will need to make.

8. Now go to the

To find the ip address of your raspberry pi on your local network run the following command. The result will yield many things we only care about the ip address number directly following inet

going to servers address in a browser on a device on the local network will look like the following

9. If successful after clicking inventory you should see the following page

10. Modify .htaccess file

Modify the content of the file as in this screenshot. Important: these settings are for the server with configuration as indicated in the top of this tutorial

Save the file by typing ctrl+o then hitting the enter key then exit by typing ctrl+x. You will then have to tell the raspberry pi to use the settings in the .htaccess file. Navigate to 000-default.conf and add add the Directory lines so that the file is identical to the image below.

Then restart the apache server

11. Note this can only be accessed on the local server if you wish to access the OE database on any network you can set up ngrok. If you sign up you can use the given link indefinitely, and using you can make a DNS to access the database easily.

12. Install ngrok (see for more details)

13. Start the ngrok server

the output should look as follows (note if you close the terminal window the session will be closed

by navigating to the link provided by your output in a web browser with the directory oe for this example it would be http://2057a4d3.ngrok.io/oe should get you to the open enventory login page from any device on any network.

This is for this scanner:

1. For OE original barcode, add Prefix ESC

2. For existing barcode, add Prefix: [l_shift_on]+[Home]+[l_shift_off]

Step 1: Install this XAMPP from

Step 2: Copy/extract Open Enventory files into C://XAMPP/htdocs/ . Write down the folder name because this will be the web address. In this case the folder is named ‘enventory’

Step 3: Start XAMPP and start Apache and MySQL

Step 4: setting up root password for MySQL. This changes with XAMPP version so consult this for specific details.

Step 5: Change php.ini content by clicking on Config button on the same row with Apache on XAMPP panel to match the following:

• error_reporting = E_ALL & ~E_WARNING & ~E_NOTICE & ~E_STRICT & ~E_DEPRECATED (otherwise some warnings being displayed will break the functionality)

• safe_mode=Off

• magic_quotes_gpc=Off

• upload_max_filesize=64M # (or higher)

• post_max_size=64M # (or higher)

If still warnings appear in the generated HTML code (breaking open enventory), you should set:

• display_errors=Off # (especially on PHP 7+)

Step 6: Change my.cnf (or my.ini) content by clicking on Config button on the same row with MySQL on XAMPP panel to match the following under [mysqld] section:

Step 7: Restart both Apache and MySQL service by clicking on Stop and then Start for each service.

Step 8: Open this link in your web browser: and log in with the following info:

• "Database": <database-name> "database-name" can be whatever you choose but should not have blank space and unique; I suggest short name is better as well.

• "Username": root (It has to be the exact word "root" for this set up first)

• "Password": the root password that we set in the step above

• Then click on "Inventory".

Step 9: If successful, it will bring up something similar to this page:

Installation

1. Install XAMPP: https://www.apachefriends.org/index.html

2. Copy/extract Open Enventory into Applications/XAMPP/htdocs/ . Write down the folder name because this will be the web address. In this case the folder is named ‘open_enventory’

3. Open Applications/XAMPP manager. Start MySQL and Apache.

4. Change mysql root password by following these steps:

1. Ensure that the MySQL/MariaDB server is running. (see step 3)

2. Open a new terminal.

3. Use the mysqladmin command-line utility to alter the MySQL/MariaDB password, using the following syntax: mysqladmin --user=root password "newpassword"

4. The mysqladmin command-line utility is located within the bin/ subdirectory of the XAMPP installation directory, typically /Applications/XAMPP.

5. For example, to change the MySQL/MariaDB root password from its default empty value to the password gue55me, you would execute:/Applications/XAMPP/bin/mysqladmin --user=root password "gue55me"

6. Or, if a password has already been previously set and you’d like to change it to a new one, you can use the following syntax: mysqladmin --user=root --password=oldpassword password "newpassword"

7. For example, to change the root password from 12345 to gue55me, you would execute: /Applications/XAMPP/bin/mysqladmin --user=root --password=12345 password "gue55me"

5. Test that your password change has been accepted, by attempting to connect to the MySQL/MariaDB server using the mysqlcommand-line client in the same directory. For example, you could use the command below to connect to the server and return the results of a calculation: (make sure you use your own password instead of “gue55me”)

/Applications/XAMPP/bin/mysql --user=root --password=gue55me -e "SELECT 1+1"

8. Using a web browser, go to: http://localhost/open_enventory/

• In Database: put in the name for your database server

• Log in with username ‘root’ and set password Notice the error messages

9. Under Warning above notice the place of the temp folder (in this case /var/folders/87/…)

10. Go to that folder containing the openenv.log (in this case: T with the path as following in Finder (file maybe hidden): /var/folders/87/b98_ym4x1r91ldysmq8r29kc0000gn/T/

11. Set permission for everyone to Read&Write for this folder (e.g. “T”)

12. Look-up file php.ini. Should be in Applications/XAMPP/xamppfiles/etc/

And change to: error_reporting=E_ALL & ~E_NOTICE

13. Restart Apache and SQL in XAMPP manager

14. Restart the web browser and go the server website at: http://localhost/open_enventory/ - In Database: put in the name for your database server - Log in with username ‘root’ and set password

CHANGE TIME ZONE

1. Edit php.ini with TextEdit: Path: /Applications/XAMPP/xamppfiles/etc/php.ini Change: date.timezone=Europe/Berlin to: date.timezone=America/Chicago

2. Restart server

CHANGE LOGIN DEFAULT DATABASE TO NONE

1. Edit lib_global_funcs.php with TextEdit: Path: /Applications/XAMPP/xamppfiles/htdocs/open_enventory/ Change: if ($db_name=="") { $db_name="storage";

   to: if ($db_name=="") { $db_name="";

2. Restart server

SAVE/ BACK-UP and RESTORE DATABASE

See this page:

This program is designed specifically for Open Enventory to fix issue with molecule missing sds (could not be extracted through "Read data from supplier") This programs does:

CHANGE TIME ZONE

1. Edit php.ini file (/Applications/XAMPP/xamppfiles/etc/php.ini if you use XAMPP in MacOS)

Change:

date.timezone=Europe/Berlin

to:

date.timezone=America/Chicago

2. Restart server

SETTING UP HTTPS (SECURED HTTP) FOR OE (RECOMMENDED)

This is optional but recommend for any site that requires user login

This specifically apply to:

• CentOS 7

1. Follow the instruction in this website to install and enable ssl: http://wiki.centos.org/HowTos/Https#head-35299da4f7078eeba5f5f62b0222acc8c5f2db5f

2. Create /etc/httpd/conf.d/oe.conf (same name as the folder contain Open Enventory, in this case /var/www/html/oe)

In Terminal, type:

sudo vi /etc/httpd/conf.d/oe.conf

Add the content below:

NameVirtualHost *:80
<VirtualHost *:80>
    ServerName your_url.net
    DocumentRoot /var/www/html/oe
    Redirect permanent / https://your_url.net
</VirtualHost>

NameVirtualHost *:443
<VirtualHost *:443>
    SSLEngine on
    SSLCertificateFile /etc/pki/tls/certs/ca.crt
    SSLCertificateKeyFile /etc/pki/tls/private/ca.key
    <Directory /var/www/html/oe>
        AllowOverride All
    </Directory>
    DocumentRoot /var/www/html/oe
    ServerName your_url.net
</VirtualHost>

2. Restart apache service, in Terminal:

sudo systemctl restart httpd.service

SETTING UP CRONTAB TO AUTOMATICALLY BACKUP YOUR DATABASE

This is optional but recommend for auto back up the OE database as well as the user’s info and password

This specifically apply to: CentOS 7 (Apache version: Apache/2.4.6 (CentOS) OpenSSL/1.0.1e-fips PHP/5.5.25 PHP version: 5.5.25 MySQL server version: 5.5.41-MariaDB)

1. Set up sshpass to automatically pass the password. Note: this is not ultrasafe but it is simple. Check out this link: http://www.server-world.info/en/note?os=CentOS_7&p=ssh&f=7 (only need to follow how to install, step 1)

2. Go into Terminal in your server and log in as root user (type: “su” and then password at the command line

Note: you can do the rest of the command lines below with prefix “sudo your-command-here” if you don’t want to log in as root

3. At the command line, type:

crontab –e

4. When the file is open, insert the following. Note: everything is red can be changed to match specific details. -$(date +\%Y\%m\%d): is used to set automatic date

#This is to back up the Romo's OE database into home/khoi/OEbackup, every day at 00:05 am
5 0 * * * mysqldump -u root –pyour-password romo > /home/khoi/OEbackup/romo-backup-`date +"%Y%m%d"`.sql

#This is to back up the user table in mysql in order to save users' password, every day at 00:10 am
10 0 * * * mysqldump -u root -pyour-password mysql user > /home/khoi/OEbackup/romo-backup-user`date +"%Y%m%d"`.sql

#This is to copy the back up file to External harddrive, every day at 00:15 am
15 0 * * * sshpass -p your-password rsync -ave ssh --ignore-existing /home/khoi/OEbackup/ daniel@romomacpro.ddns.net:/Users/daniel/Documents/OEbackup/

#This is to delete the file every month
0 0 * * */4 rm -r /home/khoi/OEbackup/romo-backup-*.sql

5. More example of crontab can be read here:

OPTIMIZING CENTOS 7 PERFORMANCE

IP BLOCKING FOR SECURITY ENHANCEMENT ON CENTOS 7 SERVER

This guide to use access_log to find out some high frequent access ip and then check them manually and form a block ip if necessary

Find IP address with the most access

1. Follow this: https://stackoverflow.com/questions/18682308/sort-uniq-ip-address-in-from-apache-log , first answer

2. Specifically, ssh into the server and then log in as root user

3. Use following command:

cat /var/log/httpd/access_log | awk '{print $1}' | sort -n | uniq -c | sort -nr | head -20

change “-20” to “-xx” with “xx” is the number of result. This is sort from most to least access request

4. Google any ip lookup website and check these IPs(e.g: https://whatismyipaddress.com/ip-lookup). If find any suspicious ones, you can add a rule to block those ip network address by the next step

Setting up rule to block ip network.

Follow this guide: https://www.getpagespeed.com/server-setup/security/centos-7-ban-bad-ips-and-networks-with-firewalld

Finding info about the network list

1. Follow this guide: https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/7/html/security_guide/sec-setting_and_controlling_ip_sets_using_firewalld

2. Specifically using this command (after ssh into the server and then log in as root)

To list the IP sets known to firewalld in the permanent environment, use the following command as root:

firewall-cmd --permanent --get-ipsets

3. To get more information about the IP set, use the following command as root: (in the example below, “test” is the name of ipsets you got from the above command

firewall-cmd --permanent --info-ipset=test

Or:

To see the extended entries list of the IP set, use the following command as root:

firewall-cmd --permanent --ipset=test --get-entries

To block IP from a whole country

1. Follow this guide:

FREEING DISK SPACE IN CENTOS 7

See these references:

ADVANCE FILE AND FOLDER PERMISSION/OWNERSHIP SETTING IN CENTOS 7

See the following resources:

• Good and comprehensive: http://www.vanemery.com/Linux/ACL/linux-acl.html#default

• Simple preservation of parent folder group owernship for all files newly created: https://serverfault.com/a/361666

• https://unix.stackexchange.com/questions/115631/getting-new-files-to-inherit-group-permissions-on-linux

• https://askubuntu.com/questions/642236/how-to-make-the-newly-created-files-inherit-the-directorys-permissions

There are a lot more SQL commands in the following section:

CHANGING INFO OF MULTIPLE CHEMICALS

Install phpMyAdmin (See OE Settings)

To return all chemicals borrow by somebody (borrowed_by_person_id)

1. Look up person_id by going into [Database]/person

2. Show chemical borrow by that person (i.e. a person with person_id=8)

SELECT * FROM chemical_storage WHERE borrowed_by_person_id=8

3. Return by:

UPDATE chemical_storage SET borrowed_by_person_id=NULL WHERE borrowed_by_person_id=8

To change the owner info of a chemical (owner_person_id)

1. Look up person_id by going into [Database]/person

2. Show chemical owned by that person (i.e. a person with person_id=7)

SELECT * FROM chemical_storage WHERE owner_person_id=7

3. Change, in this case, to no owner (NULL)

UPDATE chemical_storage SET owner_person_id=NULL WHERE owner_person_id=7

Find person_id using Console command line in PHPMyAdmin

In the following example, show person_id of user with username=julia

SELECT person_id FROM person WHERE username='julia'

Find storage ID using Console Command line in PHPMyAdmin

1. First choose the desired database on the tree folder from the left

2. Use:

SELECT storage_id FROM storage WHERE storage_name LIKE 'FH-2206%'

Explain:

• LIKE 'FH-2206%' : show the storage_id of the storage location with name starting with FH-2206

• LIKE '%FH-2206%' would mean find anything with storage name containing FH-2206

• LIKE 'FH-2206%' would mean find anything with storage name ending with FH-2206

Show chemicals with multiple criteria

SELECT * FROM chemical_storage 
WHERE owner_person_id=15 AND storage_id NOT LIKE 18

Explain: the above command is used to

• Select all of the chemical in the database that match: owner_person_id=15 AND with storage_id is NOT 18

Change Responsible person for chemicals with multiple criteria

UPDATE chemical_storage 
SET owner_person_id='NULL' 
WHERE owner_person_id=15 AND storage_id NOT LIKE 18

Explain: see above for explanation of the criteria.

Show storage_name and storage_id using username

SELECT storage_name,storage_id 
FROM storage 
WHERE storage_id IN
    (SELECT storage_id 
     FROM chemical_storage 
     WHERE owner_person_id in
         (SELECT person_id FROM person WHERE username='mingzhao')
     )
GROUP BY storage_name

Explain:

GROUP BY storage_name : is added so that duplicates are only shown once

Update responsible person for chemicals in many location (storage)

UPDATE chemical_storage 
SET owner_person_id=null 
WHERE owner_person_id=13 AND storage_id IN (19,7,5,4,12,8)

Explain: the command above change responsible people to no one for all of the chemicals being owned by person_id=13 AND in all of the storage_id listed

Search for barcodes that are duplicated

The below command will search for all the barcode that is assigned to more than 1 container (chemical_storage). This search ignores disposed container as well as container without barcodes (chemical_storage_disabled IS NULL AND chemical_storage_barcode != "")

SELECT chemical_storage_barcode
FROM chemical_storage
WHERE chemical_storage_disabled IS NULL AND chemical_storage_barcode != ""
GROUP BY chemical_storage_barcode
HAVING Count(*) > 1;

Update/Get extra info for containers with duplicated barcode (continued from “Search for barcodes that are duplicated”)

To select info from the list of duplicated barcodes. In this case, created by a specific user and created after some specific timestamp

SELECT molecule_id, 
        chemical_storage_id, 
        chemical_storage_created_when, 
        chemical_storage_created_by,
        chemical_storage_barcode
FROM chemical_storage
WHERE chemical_storage_barcode IN 
    (SELECT chemical_storage_barcode
     FROM chemical_storage
     WHERE chemical_storage_disabled IS NULL AND chemical_storage_barcode != ""
     GROUP BY chemical_storage_barcode
     HAVING Count(*) > 1
    ) AND
    chemical_storage_created_by = "user1" AND 
    chemical_storage_created_when > '2019-08-16 18:00:00'
ORDER BY chemical_storage_barcode;

REMOVE ALL CONTAINERS (BOTTLES) OF CHEMICALS

This will remove all of the containers, including info about manufactures, order date, barcode, owner, location, etc. However, info about molecule (MW, structures, safety, etc) and database related such as users will be reserved.

This is particularly helpful when you need to update a large amount of chemicals via text import.

1. Login into your server via ssh

2. Login into myswl using root account or user account with administrator priviledge for the database that you want to change. Replace “root” with the username if desired

mysql –u root -p

3. Show database and then choose the database of interest. test is the name of the database in this example

show databases;
use test;

4. Remove the chemical container by running the following command

truncate table chemical_storage;
truncate table cache;
truncate table change_notify;

5. (Optional): Run the command below if you want to reset the id counter (chemical_storage_id as well as autogenerated barcode)

alter table chemical_storage auto_increment=1

6. Log out of mysql, restart httpd and mariadb services

exit

systemctl restart httpd mariadb

7. Go back to OE website and import new tab-separated text file

Find duplicated custom barcodes using SQL

This should be run on the database of interest, table chemical_storage

SELECT chemical_storage_id, chemical_storage_barcode, count(chemical_storage_barcode) as NumOccurrences
from `chemical_storage`
WHERE chemical_storage_disabled is NULL
GROUP BY chemical_storage_barcode
HAVING (COUNT(chemical_storage_barcode) > 1)

• chemical_storage_disabled is NULL : to ignored disposed containers

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SETTING UP NEW SERVER ON A2 HOSTING

A2 hosting was chosen because of:

1. Setting up LAMP stack

2. Accessing your account:

• SSH set up:

• SSH using keys:

  • Possible error while setting up ssh key:

• Disable SSH login for root (recommended):

• FTP:

• SCP:

3. Back-up data (document from A2), also should see Khoi’s document on OE:

• To make a script to delete files older than X days when there is less than XGB left, see this:

• To monitor uptime for the server, use:

• Rclone is used to automatically backup file toGoogle Drive account:

  • Install:

  • Configuration for Google Drive: or

  • Usage:

  • For Rclone filtering:

• To back up the whole VPS, follow this:

  • This is more options:

  • Modified script as this:

4. Install EPEL repository on CentOS 7:

5. Change timezone on Linux shell:

6. Set default text Editor:

7. Obtaining free SSL certificate (from Let’sEncrypt):

• First: Make sure you have the your_site.com.conf file inside /etc/httpd/conf.d. Following the following website: ; For more elaborate see:

• Optional, here is another way the step above can be set up (Note: this website set up a bit different than the one above, specifically, the above website use /etc/httpd/conf.d/ instead of /etc/httpd/sites-enabled):

• danielromogroup.com and other sites on this server has been set up using /etc/httpd/conf.d/site.com.conf

• This is a good installation for Certbot Let’sEncrypt (ignore the multiple certificate setting):

• Using Certbot (Intro):

• Doc:

• Rate limit for Let’sEncrypt:

• To test your SSL for your site:

• To read more about SSL:

• To strengthen your SSL connection:

  • Info:

  • Remove SSLv3 SSLv2:

  • HSTS Strict-Transport-Security:

  • OCSP Stapling: help with all SSL security connection a little faster:

8. Setting up owner of /var/www/html folders, to easy update website:

9. Creating groups, users; Assigning passwords:

• Assinging password and require immediate pass change after log in:

• Add Linux users to a group:

10. Force using https access using .htaccess:

11. Configure PHP to read .htaccess file on a CentOS 7 server

We need to modify the httpd.conf file:

In this file: after <Directory "/var/www/html">, modify AllowOverride None to AllowOverride Options.

Save the file (hit Esc, type :wq and then Enter)

Restart httpd service:

12. Dreamweaver:

• Creating Template:

13. Setting up firewall for CentOS 7:

• DON’T FORGET TO OPEN PORT 7822 FOR SSH WHILE USING A2 SERVER

• If forgot to open port 7822, follow this link:

14. MySQL/MariaDB

• Error that need to change packet size:

15. Installing phpMyAdmin

16. Working with tar files

17. Setting up multiple websites with multiple domains on the same server

• On current A2 hosting, the server config can be found in /etc/httpd/conf/httpd.conf

• Setting up multiple Let’sEncrypt certificates for multiple hosts on the same server: (this is for Ubuntu)

  • For CentOS, generate two #.conf files in /etc/httpd/conf.d/. For example: /etc/httpd/conf.d/site1.com.conf and /etc/httpd/conf.d/site2.com.conf. Each conf file is the apache set up for the site. Example of the content of site2.com.conf:

• • After that use “/usr/local/sbin/certbot --apache -d example.com -d ” . The content of site2.com.conf file will be automatically changed. Here is example of the content of site2.com.conf after running the “certbot-auto…”

• Read here for more info about a set up a conf file for SSL certificate:

18. Working with WordPress

• Initial Install:

  • From A2:

  • WP security, from A2 hosting:

  • UpdraftPlus Plugin is used to back up WordPress. To restore Wordpress

    • Create a fresh install of wordpress as in the link above

    • Install Updraftplus plugin

    • Load the backup files

    • Restore

    • If there is issue after restore, check here first. A common issue is the rewrite link issue (Wordpress Permanet link), follow the solution in “Using ‘Pretty’ permalinks” in this link:

  • Optimizing WP, from A2 hosting: ;

• Multiple sites (using WordPress) installation:

• Moving Wordpress site(s):

• Uninstall Wordpress:

• To use 1-click update on Wordpress, you need

  • Wordpress folder (in this case /var/www/html/baylorcpritlab.com) to be owned by apache:apache with 755 permission

  • To secure Wordpress, all folders inside the baylorcpritlab.com should have 755 persmission and all files should have 644 permission

• Wordpress login trouble:

19. Setting up Booked Scheduler

• See here for official guide:

• Note: when change the info in the config.php file, make sure to change the:

  1. Install password

  2. User: to ‘root’

  3. Password to ‘root_passowrd’

• Also see:

Overview

You can quickly have a container (virtual machine) up and running Centos 7 and LAMP stack by using this Docker Image, see link below to download the docker image and quick instruction. If you have more questions, please feel free to contact KV.

Details

In order to use this image, you need to:

1. Install Docker Community Edition (CE):

2. Go to this link and get the download link

OR download the docker image:

3. Follow the instruction in the Docker hub link above to get the container running

4. Download Open Enventory and put the content inside html folder inside the project folder created by following the instruction of the Docker image.

Requirements

Overview

"Import and Edit" option is similar to previous version of Import in which it allows admin users to import: chemical containers ("packages"), storages list, user list, and supplier offers. For chemical containers ("packages"), this function will check if the database has the chemicals based on provided barcode. If the barcode is not found, it will add new container. If the barcode is found, it will change the provided info for that container.

"Import Only": only allow importing of chemical containers AND it will NOT check for existing container.

Right now, this function will only turned on for MIT and Baylor University.

Instruction to turn on this function

• To add your own institution, you need:

  1. Creating lib_customization.your-school-name.php with your-school-name is short or abbreviation of your school name. Use lib_customization.mit.php for an example

  2. Add the following line inside lib_customization.your-school-name.php after $default_g_settings["order_system"]="fundp";:

  3. Modify lib_global_settings.php by:

     • Change this: define("customization",""); // Customization to use: f.e.: ".sample" for use of "lib_customization.sample.php", and "" for "lib_customization.php"

     • To: define("customization",".your-school-name"); // Customization to use: f.e.: ".sample" for use of "lib_customization.sample.php", and "" for "lib_customization.php". Notice there is a period (.) in front of "your-school-name".

  4. Modify sidenav.php by:

     • Right before this line: showSideLink(array("url" => "import_edit.php","text" => s("import_edit_tab_sep"), "target" => "mainpage", ));. On this line: if (in_array($g_settings["customization"], array("baylor", "mit"), true)) { add "your-school-name" (the same as "your-school-name" set in lib_customization.your-school-name.php) right at the end of the array list of institutions. For example: