Is it possible to get more detail on setting up SMTP in the install guide? I'm running into errors when I try to send the test email even though I've got SMTP2GO set up. I'm fairly certain that the issue is the
Sender Address: field, but that's not covered in the install guide
(I'm sure this is probably assumed knowledge for most sysadmins but it's new to me)
There could also be issues related to the University firewall (in fact there are almost certainly issues related to that), but I'm not certain without a bit more detail on the expected config
@besselfunct your first step must be to look at the error in the log instead of guessing what could be the issue. See https://doc.elabftw.net/debug.html
Hello all! I have a problem updating elab to the latest version.
We are running elabftw in Docker on ubuntu. I did the Update via elabctl update, and it was completet successfully. After that, we needed to add the SITE_URL variable to the docker yml, so that the WEB UI is working again.
The WEB UI shows, that we have to run the "bin/console db:update" command to finish the update, but when run this command on the ubuntu cli, we get the following permission denied error.
"1227 Access denied; you need (at least one of) the SUPER, SYSTEM_VARIABLES_ADMIN or SESSION_VARIABlES_ADMIN privilege(s) for this operation.
Does anyone know whats going on here? Everything is set up with default config.
We are running elabftw in Docker on ubuntu. I did the Update via elabctl update, and it was completet successfully. After that, we needed to add the SITE_URL variable to the docker yml, so that the WEB UI is working again.
The WEB UI shows, that we have to run the "bin/console db:update" command to finish the update, but when run this command on the ubuntu cli, we get the following permission denied error.
"1227 Access denied; you need (at least one of) the SUPER, SYSTEM_VARIABLES_ADMIN or SESSION_VARIABlES_ADMIN privilege(s) for this operation.
Does anyone know whats going on here? Everything is set up with default config.
I upgraded elabftw from ver 4.2.4 to 4.3.10 in Ubuntu 18.04. In this new version (not in old version), attached files with Japanese filename is downloaded as that a file with "". For example, the filename is changed to "protocol_.docx" (_ should be in Japanese). What's wrong? How can I solve the problem?
@sysopls I think you run into this: https://github.com/elabftw/elabftw/discussions/3592#discussioncomment-3268365 try the solution and report back
2 replies
@sakuraabcdef Wait, I figured out something. I was not using the filename fallback. Because only the fallback must be ASCII!!! So now the correct filename will be downloaded, and only the fallback filename is in ascii!
Regarding the error logs. I've switched to trying to use the internal SMTP server that the university runs. I get the following (anonymized) error:
2022/09/12 16:57:05 [error] 133#133: *4796 FastCGI sent in stderr: "PHP message: [2022-09-12T18:57:05.871483+02:00] elabftw.ERROR: {"exception":"[object] (Symfony\\Component\\Mailer\\Exception\\TransportException(code: 0): Unable to connect with STARTTLS: stream_socket_enable_crypto(): Peer certificate CN=`*.pphosted.com' did not match expected CN=`relay-hostname' at /elabftw/vendor/symfony/mailer/Transport/Smtp/Stream/SocketStream.php:171)"} []" while reading response header from upstream, client: IPADDRESS, server: hostname, request: "POST /app/controllers/SysconfigAjaxController.php HTTP/2.0", upstream: "fastcgi://unix:/run/php-fpm.sock:", host: "hostname"
The SMTP server the university uses for this instance is supposed to allow unauthenticated mail sending from internal IP addresses
Having trouble with letsencrypt and the yml config file. Now I get this error in the log:
2022/09/22 06:14:41 [emerg] 1462#1462: cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
nginx: [emerg] cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
2022/09/22 06:14:42 [emerg] 1464#1464: cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
Please help
2022/09/22 06:14:41 [emerg] 1462#1462: cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
nginx: [emerg] cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
2022/09/22 06:14:42 [emerg] 1464#1464: cannot load certificate "/ssl/live/lab-notebook.nobles.app/fullchain.pem": BIO_new_file() failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/ssl/live/lab-notebook.nobles.app/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
Please help
look at the example: https://github.com/elabftw/elabimg/blob/master/src/docker-compose.yml-EXAMPLE#L240
@noblelabs1 use a bind mount
/etc/letsencrypt:/ssl
@NicolasCARPi I'm finally at a point where I want to start using the server and pushing data to it, but I'm running into some organizational snags.
- Is it possible to tag uploaded files? I see that we can make comments, but is it possible to associate a file with a given type of information, say a UV-Vis spectrum from instance?
- Does information have to be within the
extra_fieldsparameter of a JSON in order to be searchable with quick search? We'd like to push metadata to the server for each experiment entry in such a way that it will be searchable, but it's not necessary that it be editable by the end user. - Is there a way to run search queries from the python api? I checked the docs and it seems like there should be, but when I check the function definitions, the
get_experiment()function doesn't seem to be able to take a search argument
@besselfunct
- no but it is an interesting idea.
- The quicksearch doesn't search in the
metadatacolumn. Searching JSON with mysql is not straightforward. Only on the search page you can search for key/value in extra_fields, and yes it needs to be in extra_fields. - Yes, look at the
searchparamater inQuery parametershttps://doc.elabftw.net/api/#api-Entity-GetExperiment
Hey @NicolasCARPi thanks for the response.
Regarding 1, it would make a lot of what I'm trying to do with elab a lot easier if this was implemented, but I think I might be able to find a workaround
Regarding 1, it would make a lot of what I'm trying to do with elab a lot easier if this was implemented, but I think I might be able to find a workaround
- If you can't search JSON, is it possible to add our own mysql columns/data for a given experiment type?
- I've tried a couple of different syntax variations, but I still can't determine what's meant by the query parameters. Would you be able to provide a syntax example? I tried the following:
exp.search("string")exp = manager.get_experiment(id=3, search="string")exp = manager.get_experiment(3, search="string")
- Absolutely not. Letting users mess the database structure is a recipe for disaster. The better approach would be to add the metadata in the searched columns, but that doesn't seem straightforward to do: https://stackoverflow.com/questions/56753870/mysql-full-text-search-on-extracted-json-column
- I'm not sure you can do it with elabapy. But it isn't difficult to bypass it and directly use requests lib to query the endpoint. After all, it really is just a simple GET request with the token as
Authorizationheader.
Hello I am trying to run elabftw on a window docker but then I try to run the container there will be an error message saying "Could not find mandatory site_url variable! Please have a look at the changelog." It will take me to the verison 4.3.0 and it say something about edit the configuration file (/etc/elabftw.yml) however I can't find the configuration file.
@NicolasCARPi One of the main goals of my thesis project is to auto-generate experimental records from instruments, with rich metadata that we can then go back to and perform large-scale analysis on. To that end, it would be nice for us to be able to execute search queries based on this rich metadata.
For example, say I want all experiments where the material is CdSe and they have a UV-Vis spectrum, and then I want to grab the UV-Vis spectrum and do some data analysis on it to get a high level understanding (extract peak position and FWHM for example).
As I understand it this is only kind of possible with the current scheme, and I have to do it in a somewhat hacky way. I think I would have to add a
Is there a better way to do this, or is this the current "best way"?
(also, to be clear, I'm not trying to say, "can you please add feature X so we can do things my way?", I'm just not a developer so I'm not sure what is and isn't possible in this system)
For example, say I want all experiments where the material is CdSe and they have a UV-Vis spectrum, and then I want to grab the UV-Vis spectrum and do some data analysis on it to get a high level understanding (extract peak position and FWHM for example).
As I understand it this is only kind of possible with the current scheme, and I have to do it in a somewhat hacky way. I think I would have to add a
material parameter, a hasSpectrum parameter, and a filename parameter to extra_fields in order to accomplish this, and then I would have to execute multiple queries, since you can only do exact matches(?) with the extra_fields query.Is there a better way to do this, or is this the current "best way"?
(also, to be clear, I'm not trying to say, "can you please add feature X so we can do things my way?", I'm just not a developer so I'm not sure what is and isn't possible in this system)
@besselfunct @NicolasCARPi Regarding recording data from instruments and rich metadata, I've come to the conclusion that, for our experimental purposes at least, a tabular format is more appropriate/intuitive as opposed to the notebook format of eLabFTW. The combination of notebook entries + spreadsheet recording of parameters and data is how most experimental research is done in labs without electronic notebooks, so combining eLabFTW with a tabular application makes sense for me at the moment. Spreadsheets are cumbersome however, so we are using a database application developed by a colleague in Russia, that allows for easy filtering and linking to data (spectra, etc). As much as I would love for eLabFTW to be able to handle this and have just one application to deal with, I haven't found a workflow that makes it possible. Using templates with fields in the 'body' or 'extra_fields', combined with API interfacing could probably solve this, but I haven't had time to test this and I think it would need quite a lot of time. So we are using eLabFTW for general notes (setup, modifications, observations) and manually referencing where in our database software we are recording the metadata and instrument data. I hope to eventually use the API to better integrate both approaches in our workflow. I hope this makes sense and that I'm not coming across as too critical/dismissive of eLab's capabilities.
@garrettcurley I'm interested in the approach you're talking about, but I'm also not sure how easy it would be to integrate into my current model. One of the main reasons that I want to switch to elabFTW with automation is to eliminate issues caused by..."non-compliance" within the laboratory. So my current vision is to use NodeRED for instrument control/UI, with several other applications on the back end, and then push all of the experimental data to a new elabFTW experiment once an
experiment_finished parameter evaluates to true. I don't strictly need all of the metadata tagging that I'm talking about, but it would be nice for facilitating ML and trend analysis on our data as no one has really done it very well in our field (datasets are much too small).
Is the database application you're talking about publicly available?
@NicolasCARPi I was messing around with the
search query using curl yesterday, and I kept getting errors. Would you be willing to provide an example of a minimum working command (something like search for experiments with Author X), and then an example of a multi-component query (Author X AND Body string)?
I'm assuming the basic format is
curl -H "Authorization: $TOKEN" https://elab.example.org/api/v1/search?author=X, but I'm not sure of the syntax and special characters
for author the key is
owner, and cat for categories (status for experiments, items types for items)
Basically the same query parameters used by the web app are applicable to the api
at least in the dev version, not sure in current stable version though
@besselfunct seminar of the 13th of october could interest you then: https://www.indiscale.com/new-linkahead-introductiory-series-online-events/
last message was for @garrettcurley
Data Integration with LinkAhead
Integrating Electronic Lab Notebooks, File Servers and other Data Sources
13.10.2022 16:00
Automation is key. Learn how the LinkAhead Crawler harvests complete file servers and how you can interconnect LinkAhead with other parts of your RDM infrastructure. We present the exemplary integration of eLabFTW.
Meeting link (BBB): https://app.bbbserver.de/de/join/9595713c-24d4-4e54-bcef-04e3433f130a