enventory-updates Mailing List for open enventory

Dear Felix:

Thanks for the detailed message.
I will be on vacation next week. Week after that would be earliest we can have this call.

Thanks,
Sudhakar.

From: "Dr. Felix Rudolphi" <in...@sc...>
Date: Friday, May 28, 2021 at 4:23 AM
To: "Gress, Marshal" <mg...@iu...>, Open Enventory Users <env...@li...>
Subject: [External] Re: [Enventory-updates] MySQL Error

This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources.

Dear Marshal,

sorry for my late reply. Of course you can add features to open enventory, we are particularly happy if they make open enventory more useful for more people in the scientific community. If features are interesting only for smaller groups, it would be good if these features are not distracting - or be disabled by default and easily enabled on demand.

Your proposal uncovers a weak spot of the current development of OE, it happens mostly on my local PC, and I have not taken enough care to update the source code repositories at
https://sourceforge.net/p/enventory/code/ci/master/tree/ (super-outdated)
https://github.com/rudolphi/open_enventory (outdated)
The code offered for download at https://sourceforge.net/projects/enventory/files/ is updated regularly, it is compatible with MariaDB 10.4 (probably even 10.5) and actively maintained. On the weekend, I will take care of the repos, by removing the very old code at Sourceforge and updating the one at Github. Using the code of the current release version will be the best starting point: https://sourceforge.net/projects/enventory/files/open_enventory_2021-05-06.zip/download
On this basis, you will be successful installing OE, it used the mysqli extension to access the database. Merging your existing changes into this (current) codebase will hopefully not be too complicated.

If it is ok for you, it might make sense to discuss the proposed changes in a Zoom call next week, to make sure the solution is consistent with the current product and users' expectations. Let me know if/when it would fit for you. I am looking forward to meeting with you and see OE grow.

Best regards,

Felix
Am 27.05.21 um 00:50 schrieb Marshal Gress:
Hello:

My name is Marshal Gress; I'm an intern at Indiana University Bloomington working on debugging and adding features to IU's version of the Open Enventory website.  My supervisor is Sudhakar Pamidighantam, whom I believe you've been in contact with before.  Previously, we've been updating just the IU version of OE, which is built on the 2020-07-27 release version.  What we'd like to do now is fork the current version of OE on SourceForge and eventually create a merge request which showcases the changes and additional features we've made.  The main thing we've done so far (to IU's version) is add additional tabs to the Inventory table that allow users to view fluorophore data for molecules.

I've managed to fork the repository on SourceForge, but I've run into an issue with developing on my local machine.  If I try to log in using root and my mysql password, the screen goes blank with this error appearing:
The extension mysql is required for open enventory and not yet installed.

We've managed to trace the error to the checkExtensions() function in lib_global_funcs.php.  It appears the extension_loaded function returns false (line 299) when getting to "mysql" in the for loop.  However, we're not sure where to go from here as far as fixing this issue.  Developing on the 2020-07-27 version hasn't caused this problem.  For reference, I am working with a Windows laptop using XAMPP, the PHP version is 7.3.27, and the MariaDB version is 10.4.18.  Do you know what should be done so that this error doesn't appear?

Thank you very much,
Marshal Gress




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Dear Marshal,

sorry for my late reply. Of course you can add features to open
enventory, we are particularly happy if they make open enventory more
useful for more people in the scientific community. If features are
interesting only for smaller groups, it would be good if these features
are not distracting - or be disabled by default and easily enabled on
demand.

Your proposal uncovers a weak spot of the current development of OE, it
happens mostly on my local PC, and I have not taken enough care to
update the source code repositories at
https://sourceforge.net/p/enventory/code/ci/master/tree/ (super-outdated)
https://github.com/rudolphi/open_enventory (outdated)
The code offered for download at
https://sourceforge.net/projects/enventory/files/ is updated regularly,
it is compatible with MariaDB 10.4 (probably even 10.5) and actively
maintained. On the weekend, I will take care of the repos, by removing
the very old code at Sourceforge and updating the one at Github. Using
the code of the current release version will be the best starting point:
https://sourceforge.net/projects/enventory/files/open_enventory_2021-05-06.zip/download
On this basis, you will be successful installing OE, it used the mysqli
extension to access the database. Merging your existing changes into
this (current) codebase will hopefully not be too complicated.

If it is ok for you, it might make sense to discuss the proposed changes
in a Zoom call next week, to make sure the solution is consistent with
the current product and users' expectations. Let me know if/when it
would fit for you. I am looking forward to meeting with you and see OE
grow.

Best regards,

Felix

Am 27.05.21 um 00:50 schrieb Marshal Gress:
> Hello:
>
> My name is Marshal Gress; I'm an intern at Indiana University
> Bloomington working on debugging and adding features to IU's version
> of the Open Enventory website.  My supervisor is Sudhakar
> Pamidighantam, whom I believe you've been in contact with before. 
> Previously, we've been updating just the IU version of OE, which is
> built on the 2020-07-27 release version.  What we'd like to do now is
> fork the current version of OE on SourceForge and eventually create a
> merge request which showcases the changes and additional features
> we've made.  The main thing we've done so far (to IU's version) is add
> additional tabs to the Inventory table that allow users to view
> fluorophore data for molecules.
>
> I've managed to fork the repository on SourceForge, but I've run into
> an issue with developing on my local machine.  If I try to log in
> using root and my mysql password, the screen goes blank with this
> error appearing:
> The extension mysql is required for open enventory and not yet installed.
>
> We've managed to trace the error to the checkExtensions() function in
> lib_global_funcs.php.  It appears the extension_loaded function
> returns false (line 299) when getting to "mysql" in the for loop. 
> However, we're not sure where to go from here as far as fixing this
> issue.  Developing on the 2020-07-27 version hasn't caused this
> problem.  For reference, I am working with a Windows laptop using
> XAMPP, the PHP version is 7.3.27, and the MariaDB version is 10.4.18. 
> Do you know what should be done so that this error doesn't appear?
>
> Thank you very much,
> Marshal Gress
>
>
> _______________________________________________
> Enventory-updates mailing list
> Env...@li...
> https://lists.sourceforge.net/lists/listinfo/enventory-updates

Hello:

My name is Marshal Gress; I'm an intern at Indiana University Bloomington
working on debugging and adding features to IU's version of the Open
Enventory website.  My supervisor is Sudhakar Pamidighantam, whom I believe
you've been in contact with before.  Previously, we've been updating just
the IU version of OE, which is built on the 2020-07-27 release version.
What we'd like to do now is fork the current version of OE on SourceForge
and eventually create a merge request which showcases the changes and
additional features we've made.  The main thing we've done so far (to IU's
version) is add additional tabs to the Inventory table that allow users to
view fluorophore data for molecules.

I've managed to fork the repository on SourceForge, but I've run into an
issue with developing on my local machine.  If I try to log in using root
and my mysql password, the screen goes blank with this error appearing:
The extension mysql is required for open enventory and not yet installed.

We've managed to trace the error to the checkExtensions() function in
lib_global_funcs.php.  It appears the extension_loaded function returns
false (line 299) when getting to "mysql" in the for loop.  However, we're
not sure where to go from here as far as fixing this issue.  Developing on
the 2020-07-27 version hasn't caused this problem.  For reference, I am
working with a Windows laptop using XAMPP, the PHP version is 7.3.27, and
the MariaDB version is 10.4.18.  Do you know what should be done so that
this error doesn't appear?

Thank you very much,
Marshal Gress

Hi:
Is there a complete user guide for all the features available.

Thanks,
Sudhakar.

Dear friends of open enventory,

recently, many people may have updated their computers to Ubuntu 16.04
or Mint 18, which include PHP7 by default. In PHP7, the old mysql PHP
extension used by OE was phased out - OE became inoperatable. A few days
ago, I have changed the respective function calls and constants to their
mysqli equivalents, and I would ask you to test the updated version,
which you can download here:
https://sourceforge.net/projects/enventory/files/open_enventory_2016-08-xx-mysqli_beta.zip/download

Please report any problems to me, providing information like system
architecture, software versions and logfiles or error messages. This
will help me to create a stable update soon. Thanks for using OE and for
helping to make it better (or keep it working in this case).

Felix

Dear Open Enventory Community,

after many delays, I have just released an update of OE, which is still 
flagged as beta due to the numerous changes and improvements:
- first of all, Mathias Weklak has greatly improved and extended the 
depiction of analytical data - his Master thesis at LMU Munich:
-- better visual appearance
-- new converters for
--- Bruker/Stoe X-Ray powder diffraction
--- Sadtler and Galactic SPC format (mainly IR)
--- Hamamatsu PL
--- NIST MS
-- interactive graph viewer
-- clean object-oriented code

I have meanwhile tried to address smaller bugs and annoyances - thanks 
to everyone for telling and explaining to me instead of just suffering:
- possible SQL injection for logged-in users fixed
- problem on Windows-based servers when copying experiments (duplicate 
components overwriting others) fixed, uniqid was not unique. Now using 
PHP 5.6.x should be fine on Windows/Xampp
- labels for chemicals adjusted to GHS requirements (if you liked the 
old style more, there is a backup called labels.php.old
- access to catalogs fixed: Activate Scientific, apollo, Fisher Scientific
- field "order date" added to chemicals
- added option to output lists in JSON format
- barcode terminal now allows to add log entries
- many small fixes

Due to the number of changes, this release is still beta. Make backup 
copies and preliminary tests, please report any problems or difficulties 
to me.

All the best

Felix

Dear friends of open enventory,

a few hours ago, I have uploaded a small update, basically two files
were changed:
- one is a bugfix for a problem that reaction components appeared
multiple times if using the "working instructions" feature
- second is a new robot for Carl Roth, as they have changed their website
If these two things do not affect you, just wait for the next "real"
update, otherwise just replace these two files and you are done.

Currently, a student of LMU Munich is reworking the modules used to
process and depict raw analytical data files, creating more modular and
readable code, more beautiful and customizable imagery. He will also add
some file formats that were only supported in Sciformation ELN so far. I
expect Matthias' project to be complete in Spring 2016, the outcome will
be included in one of the next releases.

All the best for you and your research in 2016!!

Felix

Dear friends of open enventory,

yesterday, I uploaded a small update for open enventory, which brings
you the following improvements:
- a personal CMR report based on the experiments in the lab notebook
(developed for Heliatek GmbH)
- fixed the literature scraping for Wiley-VCH, and added some smaller
ones as well (all based on the meta tags in the HTML head)
- slightly extended the inventory import function, added some database
fields
- fixed some suppliers and catalog scraping tests (partly reported by
MK, Fraunhofer IME)
- removed the rounding of purities of chemicals (like 99.99999%, which
should of course stay that way)
- added the QDBS barcode terminal system, contributed by Dr. Konstantin
Troshin (UC Berkeley). If you want to try/activate it, just unzip the
included qdbs.zip, activate the constant "QDBS" in
lib_global_settings.php and open [server]/qdbs/qdbs.php

Special thanks to Konstantin for his accurate work and patience with me!

Have fun, please let me know if you come across any unexpected problems!

Felix

Dear OE community,

this is the first information posted on this mailing list, to inform you
about a recent update of OE published. I hope it will be useful for you,
and I would like to explain a bit what you will get:
improved installation guide. Please report any missing aspects, hints or
any mistakes.
- for LMU Munich, I added a tool to create substance-specific safety
instructions, may be a German specialty, I don't know. The feature will
be extended to further automate the document creation.
- for Heliatek GmbH, I have added HTML-formatted text modules that can
be used in ELN.
- screenscraping is a neverending story, the safety data from
Sigma-Aldrich is back, Fluorochem currently gives only search results if
not asking for prices
- on the login screen, there was a cross-site scripting flaw, which is
now fixed (reported by NM, University of Toronto)
- a problem introduced in the previous update, affecting PHP versions
below 5.5, is now fixed
- new parameters in lib_global_settings.php: tempDirPath (if the regular
temp folder is not writable, which may be the case in some cloud
environments, developed for AL and SM of Jacobs University) and
allowLocalhostLink (to use localhost instead of 127.0.0.1 for
cross-database access, may affect CentOS servers, developed for KT of UC
Berkeley)
- to reflect the differences between old and new Marvin versions, users
can choose "Marvin new" to get the additional parameters that qweee
asked for (better template support), while others will avoid
compatibility problems (changed for DS of University of Dresden)
- automatic linking of databases works more reliably now (many affected)
- minor bugfixes and Javascript performance tuning

Please note that:
a) the database format changed (see UPDATE for instructions on how to
solve that, in most cases, just login as root), and
b) users will have to clear the browser cache after applying the update
(or you install to a different directory and forward queries from the
old to the new one)

Like always, you can get the update via
http://sourceforge.net/projects/enventory/
I will wait a few days until I make the new version default download.
Please report any problems/bugs/etc. Hopefully, it is a step forward. A
good weekend to everyone!

Felix

P.S.: I posted the more or less same text also in the Facebook group, to
give you the choice of your preferred platform.