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Dmitry Mozzherin
@dimus
@abusalehmdtayeen I updated gnrd to use only gnfinder now, name detection should become much faster now
I tried my best not to change API much http://gnrd.globalnames.org/api
but there is no more NetiNeti or TaxonFinder. There are only 2 engines now: gnfinder and gnfinder_no_bayes, and they cannot happen at the same time, so there is no 3rd engine
let me know if you have any problems with API, I will help ASAP
Dmitry Mozzherin
@dimus
@abusalehmdtayeen for the time being while you migrate your code you can use https://gnrdbhl.globalnames.org instead of https://gnrd.globalnames.org for old API. Only you and BHL would use it for now, so let me know when you do not need it anymore, I will migrate it when both your and BHL are done with old API
abu saleh
@abusalehmdtayeen
Hi @bomeara, I was able to create a docker for the ETE tree viewer service. You can find it here: https://github.com/phylotastic/phylo_webservices/tree/master/Phylo_Dockers/tree_viewer. With this one, now we have all the core phylotastic services necessary for the portal and can deploy easily. If you can give me access to a machine, I can test those dockers and create a second version of services running.
Enrico Pontelli
@epontell
Has the paper been accepted? I did not see any notifications
Dmitry Mozzherin
@dimus
@epontell yes, @arlin said it was, I am not sure about final DOI yet. This is one from biorchive preprint: https://doi.org/10.1101/419143
Thanh Nguyen
@thanhnh-infinity
@dimus : I think it is preprint for our old submission in MEE, not the accepted one in Evolutionary Bioinformatics
Dmitry Mozzherin
@dimus
do we have an update about the paper?
Brian O'Meara
@bomeara
datelife server is currently down -- I don't know what happened
Brian O'Meara
@bomeara
I got it back up this morning. University disconnected it from the network.
Enrico Pontelli
@epontell
Annual reporting time - any updates on the manuscript?
Brian O'Meara
@bomeara
Screen Shot 2020-04-11 at 5.10.30 PM.jpg
The certificate has expired again.
ndvan
@ducvan0212
@abusalehmdtayeen Can you check what happen with the certificate? Will that be related to the automatic deployment using docker for the portal?
abu saleh
@abusalehmdtayeen
@ducvan0212 , No, its not relevant to docker deployment. The automatic renew certificate command did not work because the command has to be executed using sudo password. I have renewed the certificate. It should be working now.
Brian O'Meara
@bomeara
Thanks!
abu saleh
@abusalehmdtayeen
@bomeara , I can't access your machine anymore. Is it still online? Are the dockers for the services running? The only thing left was to deploy the portal in that machine and I was not able to finish because I became busy with another project. If you could give me access to that machine again, I can try to finish that by this month.
Brian O'Meara
@bomeara
One of my computers was hacked -- not the one you were using, but I took them all offline and am wiping and reinstalling everything (using ansible, so it's not that bad) as a precaution. But I'm quarantined at home, so I have a few here, but they're not readily available online. I can try debugging here locally if you give me stuff to run (or wait until the covid-19 thing is over so I can get to my other ones, but who knows how long that will be).
btw, I hope everyone is doing well at this time!
Mark T. Holder
@mtholder
oof. sorry to hear that @bomeara . I'd much rather be having a beer at the Evolution meetings with you rather than being hacked twins with you - 2020 is not trying to go down in anyone's memory as "the best of times".
Jim Allman
@jimallman
oh no! by any chance, was your hacker also running hammer.py for DDOS attacks?
if so, it might help us to narrow down the vulnerability that allowed this on OpenTree servers. was your server running any web2py instances, perchance?
@bomeara ^
Brian O'Meara
@bomeara
Mine wasn't -- ubuntu with docker, htcondor, and nfs
Benjamin Redelings
@bredelings
Did your hacker get root access?
Ours ended up running scripts as a normal user.
Brian O'Meara
@bomeara
Not sure -- our IT said that it was being used in a DDOS (so presumably wouldn't need root), so I took all my computers offline until I could wipe them
The beauty of ansible is that setting them back up again isn't too bad
But I also then didn't do forensics to try to see what happened
Benjamin Redelings
@bredelings
Ah! Makes sense, thanks for clarifying! I always worry more about root hacks, since they could point to bugs in parts of the infrastructure that are harder to replace.
Brian O'Meara
@bomeara
My daughter had a homework assignment to make a tree for her 100 species she identified in her field journal this year. She uploaded to phylotastic and.... it didn't work: came back with a tree with higher level names, only a couple of species, and many "mrcaott" style names. So she looked for alternatives, found https://phylot.biobyte.de/, which required every name to match NCBI (which took some wrangling), and which, after she got it all working, told her that given over 10 species, she would have to either pay for tokens or register for info and go to partner companies for tokens -- she registered, and then she was asked to give her gender, go to companies offering credit cards or whatever, and then she'd get a few tokens to let phyloT give her a pruned NCBI taxonomy tree). She was never asked age or consent, no GDPR warning -- seems really scammy. So I vetoed that. So she tried phylotastic again but with spaces after commas for input, and voila, it worked! Got a tree, downloaded newick, put into itol for better viz. She also tried datelife, but it was slow for all her species (worked for ~10) -- so I'll be playing with speed for that.
Dmitry Mozzherin
@dimus
we are the champions, at least after struggle :)
who would think that phylotree generator can be as schetchy as https://phylot.biobyte.de
Enrico Pontelli
@epontell
how do we make that a a less painful experience?
Brian O'Meara
@bomeara
Easiest would be automatically adding a space after every comma if there isn't one -- it can probably handle extra spaces ok, so just substituting comma space for every comma as a default could work
Enrico Pontelli
@epontell
@ducvan0212 @abusalehmdtayeen is this somehting we could easily do?
abu saleh
@abusalehmdtayeen
@epontell @bomeara I will check whether the services already handle this issue. If not, it should be easy to fix.
ndvan
@ducvan0212
please let me know if there is anything needed to change in the server
Brian O'Meara
@bomeara
All the work we've done together would not have been possible without this team assembled from people around the world. I'm sorry the US government is continuing and expanding its anti-immigration stance. If these changes affect any of you, please let me and others know if we can help.
ndvan
@ducvan0212
Thank you Brian. As a student, I haven't affected by the policy, but I think the anti-immigration policy is short-sighted. There are a lot of talented people from all around the world studying and working in the US, and that high-skilled workforce is wanted by a lot of countries. I think suspending the H1B visa simply won't solve the US citizen unemployment problem. Personally, as a foreigner, I respect American in general, and I really don't want to be targeted as stealing American's job if I am employed by an American company.
Enrico Pontelli
@epontell
Brian, very kind words. thank you. We are living very difficult times...
Arlin Stoltzfus
@arlin
@bomeara, @epontell, did you submit a final "outcomes" report for NSF? I still have to do this. If you have some something, I would like to review it, and if not, I would like to get some text from you.
Brian O'Meara
@bomeara
I haven't yet
Arlin Stoltzfus
@arlin
That makes me feel strangely good. I thought I was procrastinating outrageously.
I did a final report, however. That's when I realized I needed to do this "outcomes" thing also.
BTW, I want to emphasize what a great experience @jwiggi18 created for a group of 20 educators last summer, with a lot of help from @LunaSare, along with @bomeara @hyanwong (OneZoom) @jhammock (EOL) Louise Mead (BEACON) Lisa White (UCMP). The lessons they developed are here https://jwiggi18.github.io/phyloEd/
Many of them were used in the classroom for the 2019-2020 school year.
Arlin Stoltzfus
@arlin
The educators really appreciated the opportunity to interact with experts to get advice and also to modify tools.