Update cmake modules to match new OpenBabel, MySQL and MariaDB versions

[merkys]

I attempted building on Ubuntu 20.04 with system-provided packages (OpenBabel 3.0.0 and MariaDB 10.3.25). I used commands

CFLAGS=-DSTANDARD cmake ..
make

First of all, I stumbled upon

Scanning dependencies of target mychem-lib
[  3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /home/andrius/src/mychem-code/src/conversion.c:30:
/home/andrius/src/mychem-code/src/conversion.h:48:10: fatal error: m_ctype.h: No such file or directory
   48 | #include <m_ctype.h>
      |          ^~~~~~~~~~~
compilation terminated.
make[2]: *** [src/CMakeFiles/mychem-lib.dir/build.make:63: src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:162: src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [Makefile:130: all] Error 2

I did the following change to get around it:

diff --git a/src/conversion.h b/src/conversion.h
index 453d398..6d2ebbc 100644
--- a/src/conversion.h
+++ b/src/conversion.h
@@ -45,8 +45,6 @@ typedef long long longlong;
 #include <my_sys.h>
 #endif /* STANDARD */
 #include <mysql.h>
-#include <m_ctype.h>
-#include <m_string.h>          /* To get strmov() */

After that, building failed with OpenBabel:

/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp: In member function ‘virtual bool OpenBabel::fingerprint2::GetFingerprint(OpenBabel::OBBase*, std::vector<unsigned int>&, int)’:
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:106:9: error: ‘OBNodeBase’ was not declared in this scope; did you mean ‘OBBase’?
  106 |  vector<OBNodeBase*>::iterator i;
      |         ^~~~~~~~~~
      |         OBBase
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:106:20: error: template argument 1 is invalid
  106 |  vector<OBNodeBase*>::iterator i;
      |                    ^
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:106:20: error: template argument 2 is invalid
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:106:32: error: qualified-id in declaration before ‘i’
  106 |  vector<OBNodeBase*>::iterator i;
      |                                ^
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:107:31: error: ‘i’ was not declared in this scope
  107 |  for (patom = pmol->BeginAtom(i);patom;patom = pmol->NextAtom(i))
      |                               ^
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:109:11: error: invalid use of incomplete type ‘class OpenBabel::OBAtom’
  109 |   if(patom->IsHydrogen()) continue;
      |           ^~

[skip]

In file included from /home/andrius/src/mychem-code/src/conversion_wrapper.cpp:39:
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp: In member function ‘void OpenBabel::fingerprint2::DoReverses()’:
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:207:3: error: ‘reverse’ was not declared in this scope; did you mean ‘DoReverses’?
  207 |   reverse(t1.begin()+1, t1.end()); //(leave 0 at front alone)
      |   ^~~~~~~
      |   DoReverses
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp: In member function ‘void OpenBabel::fingerprint2::DoRings()’:
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:235:4: error: ‘rotate’ was not declared in this scope
  235 |    rotate(t1.begin(),t1.begin()+2,t1.end());
      |    ^~~~~~
/home/andrius/src/mychem-code/src/fingerprints/finger2.cpp:247:4: error: ‘reverse’ was not declared in this scope; did you mean ‘DoReverses’?
  247 |    reverse(t2.begin()+1, t2.end());
      |    ^~~~~~~
      |    DoReverses
In file included from /home/andrius/src/mychem-code/src/conversion_wrapper.cpp:40:
/home/andrius/src/mychem-code/src/fingerprints/finger3.cpp: At global scope:
/home/andrius/src/mychem-code/src/fingerprints/finger3.cpp:38:5: error: ‘OBSmartsPattern’ does not name a type
   38 |     OBSmartsPattern obsmarts;
      |     ^~~~~~~~~~~~~~~

Maybe I am missing something?

[merkys]

Nevertheless, new OpenBabel and MariaDB libraries and headers are successfully found with this PR!

[fredrikw]

An alternative solution to the m_ctype-problem is to install libmariadbclient-dev-compat, at least that worked for me but that was before this PR.

[merkys]

An alternative solution to the m_ctype-problem is to install libmariadbclient-dev-compat, at least that worked for me but that was before this PR.

libmariadbclient-dev-compat has been dropped in Debian 10 and Ubuntu 20.04. It seems that MariaDB 10.1 was the last release supporting this sort of compatibility.

[merkys]

I confirm that 5b6f95fe859c66d9cffb9033b05c5d7bff3b8af7 fixes all my issues and I finally am able to use the functions. Thanks a lot!

Tested on Ubuntu 18.04, with system-provided OpenBabel v2.3.2 and MySQL v5.7.36. I did not need any specific CMake flags, it just went very smoothly. I had to adjust AppArmor configuration as described. I will also test it with MariaDB when I have time.

[merkys]

I have as well successfully built 5b6f95f on:

• Debian 9 with system-provided OpenBabel v2.3.2 and MariaDB v10.1.45
• Debian 10 with system-provided OpenBabel v2.4.1 and MariaDB v10.3.31 I have not run the tests, though. On later Debian/Ubuntu releases OpenBabel is of v3.1.1, which needs migration (#23).

[studur]

@merkys I am trying to install the stack on a debian 10+ AWS EC2 but somehow I have some problem with the installation procedure. I always end up with a NULL value when testing the SELECT EXACTMASS(SMILES_TO_MOLECULE('c1ccccc1')); after all the installation. Could you (or anyone else) provide an updated procedure please ? Thank you

[merkys]

@studur I will try to reproduce, will get back to you.

[merkys]

@studur I have built and installed this PR on Debian 10 and ran into the same issue with all calls returning NULL. I have no idea why. What is even worse, I do not recall whether I got any non-NULL values testing on Debian 10 before.

[studur]

@merkys thank you for trying. I hope that this will be fixed. Have a great day

[Pansanel]

Hi, I will try to run it on Debian 10 (I have access to an OpenStack cloud providing such image). I will let you know ASAP. Best, Jerome

[Pansanel]

Can you check again? It works now on my side with debian 10 and Openbabel v2.4.1.

[merkys]

@Pansanel I just tried with 532eb6abfa768e62cf8a08dd73f1d9183df035f6 and got NULL for select smiles_to_molecule("c1ccccc1");. Are you using system-provided Open Babel, or have you installed it yourself?

[Pansanel]

I am using the system-provided Open Babel. Did you try to enable the test mode?

[studur]

Hi, I will try to run it on Debian 10 (I have access to an OpenStack cloud providing such image). I will let you know ASAP. Best, Jerome

Thank you for looking in to this. Could this be due to a difference between the Openstack image and the AWS Marketplace AMI Debian 10 image ? I tried with the later.

[Pansanel]

Hi, there should be no difference between the images. Is your installation directory: /usr/lib/x86_64-linux-gnu/mariadb19/plugin? What gives: ldd /usr/lib/x86_64-linux-gnu/mariadb19/plugin/libmychem.so.2.0.0

[studur]

I will check this the next time I spin up an AWS EC2 but I noticed the plugin directory change for mariadb.

Meanwhile, I would not be surprised that I don't use the right client libs for mariadb.

Could you paste in the comments the mariadb and openbabel installations please? Specifically the section that replace the lines 81-85 in the following installation doc. https://github.com/mychem/mychem-code/commit/8ac73f6eddbb9ef8294a041a7f37c0a69ddbb9fe

[Pansanel]

For openbabel and mariadb, I am just using the default debian packages:

apt install openbabel libopenbabel-dev
apt install libmariadbclient-dev mariadb-server

[studur]

Thanks @Pansanel , it works now. I executed the following commands as a new user authenticated with ssh and member of the sudo group in Debian 10

# Install Openbabel and MariaDB

sudo apt install -y openbabel libopenbabel-dev libmariadb-dev-compat libmariadbclient-dev mariadb-server python3-mysqldb cmake g++ zip git

sudo systemctl start mariadb
sudo systemctl enable mariadb

# Configure MySQL
sudo mysql_secure_installation

mysql -u root -p 
create user 'USER'@'localhost' identified by '**********';
grant all  on *.* to 'USER'@'localhost' with grant option;
flush privileges;
exit;

# Logout MySQL and login back again
mysql -u USER -p
CREATE DATABASE mychem;
exit;

cd ~
git clone https://github.com/Pansanel/mychem-code.git
cd mychem-code
# the master branch contains the code for debian 10 / mariadb 10.3 compatibility.

mkdir build
cd build
cmake ..
make
sudo make install

# Create missing symlink
sudo mkdir -p /usr/lib/mysql/plugin/
cd /usr/lib/mysql/plugin/
sudo ln -s /usr/lib/x86_64-linux-gnu/mariadb19/plugin/libmychem.so libmychem.so

# Install Mychem extension
cd ~/mychem-code
mysql -u USER -p < src/mychemdb.sql

# Test
mysql -u USER -p
use mychem;
SELECT EXACTMASS(SMILES_TO_MOLECULE('c1ccccc1'));

Should get ...
+-------------------------------------------+
| EXACTMASS(SMILES_TO_MOLECULE('c1ccccc1')) |
+-------------------------------------------+
|                                 78.046950 |
+-------------------------------------------+

@merkys Do you want to confirm on your end ?

[Pansanel]

It is a good news :-) I have to find a way to have a generic build system that can work with all the most recent OpenBabel releases. In particular, the src/descriptors/* and src/fingerprints/* files are directly copied from OpenBabel source code. I will try to fix this by downloading during CMake configuration the right files.