Getting server error: (503) Service Unavailable from NBLAST on the fly GAL4

Margaret H

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Apr 28, 2017, 7:00:02 PM4/28/17

to nat-user

Hi there,

I noticed the NBLAST on the fly service for finding GAL4 drivers doesn't seem to be working. When I enter the FlyCircuit Neuron ID and try to query for GAL4 drivers, I get this error. I have used it in the past (a few months ago) and it was working, but as of last week the server seems to be down. Is there anything someone can do to restart and check the server? Thank you!

server error: (503) Service Unavailable

server error: (503) Service Unavailable

Margaret

Gregory Jefferis

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Apr 28, 2017, 11:38:47 PM4/28/17

to Margaret H, nat-user, Court Robert

Dear Margaret,

Thank you for the report. I think the problem is with a second server that it calls to get the scores (@Rob this looks like the VFB R service).

VFB will soon put the whole NBLAST service on a larger dedicated server of its own, which should give improved stability/speed.

Best,

Greg.

Sent from my iPhone

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Margaret Ho

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May 1, 2017, 10:29:14 AM5/1/17

to R Court, nat-user, jeff...@gmail.com

Sorry to bother you guys again, but the error is now a 400 (Bad Request) error for searching for GAL4 lines with a FlyCircuit neuron query. I pasted the error that I get below. I searched using"TH-F-200064" as the search term.

Thank you!

Margaret

*******************

NBLAST results

Query neuron: TH-F-200064

Top hits

client error: (400) Bad Request

On Sun, Apr 30, 2017 at 1:59 PM, Margaret Ho <margi...@gmail.com> wrote:

Great, thank you!
Margaret

On Apr 30, 2017 1:18 PM, "R Court" <r.c...@ed.ac.uk> wrote:
Sorry about that, the service has now moved to it's new home and should be back up now.

Thanks,

Rob

On Sat, 29 Apr 2017 at 04:38 Gregory Jefferis <jeff...@gmail.com> wrote:

Dear Margaret,

Thank you for the report. I think the problem is with a second server that it calls to get the scores (@Rob this looks like the VFB R service).

VFB will soon put the whole NBLAST service on a larger dedicated server of its own, which should give improved stability/speed.

Best,

Greg.

Sent from my iPhone

On 29 Apr 2017, at 00:00, Margaret H <margi...@gmail.com> wrote:

Hi there,

I noticed the NBLAST on the fly service for finding GAL4 drivers doesn't seem to be working. When I enter the FlyCircuit Neuron ID and try to query for GAL4 drivers, I get this error. I have used it in the past (a few months ago) and it was working, but as of last week the server seems to be down. Is there anything someone can do to restart and check the server? Thank you!

server error: (503) Service Unavailable
server error: (503) Service Unavailable

Margaret

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Margaret Ho

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May 3, 2017, 5:36:13 PM5/3/17

to R Court, nat-user, Greg Jefferis

Hi Dr. Court and Dr. Jefferis,

Did you figure out what was wrong with the NBLAST on the fly server?

I tried to install a local version of NBLAST on the fly on my linux workstation according to your instructions, but I seem to have a problem with downloading and installing the flycircuit data, since I get this weird error that says Error : package ‘nat’ 1.7.2 was found, but >= 1.8.8 is required by ‘flycircuit’. However, upon trying to download the latest version of nat, and seeing if I could download nat version 1.8.8 from your github server I find that the version doesn't exist.

Do you have a suggestion as to how to resolve this error? thanks!

Margaret

> packageVersion("nat")
[1] ‘1.7.2’
> install_github("jefferis/flycircuit", dependencies=TRUE)
Downloading GitHub repo jefferis/flycircuit@master
from URL https://api.github.com/repos/jefferis/flycircuit/zipball/master
Installing flycircuit
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
'/tmp/RtmpMgQfkA/devtools4aa656ef9b1c/jefferis-flycircuit-78415bb' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘flycircuit’ ...
** R
** data
*** moving datasets to lazyload DB
** tests
** preparing package for lazy loading
Error : package ‘nat’ 1.7.2 was found, but >= 1.8.8 is required by ‘flycircuit’
ERROR: lazy loading failed for package ‘flycircuit’
* removing ‘/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/flycircuit’
Error: Command failed (1)

> devtools::install_github("jefferis/nat",ref="1.8.8")
Downloading GitHub repo jefferis/n...@1.8.8
from URL https://api.github.com/repos/jefferis/nat/zipball/1.8.8
Error in stop(github_error(request)) : 404: Not Found
(404)

> devtools::install_github("jefferis/n...@v1.8.8")
Downloading GitHub repo jefferis/n...@v1.8.8
from URL https://api.github.com/repos/jefferis/nat/zipball/v1.8.8
Error in stop(github_error(request)) : 404: Not Found
(404)

On Mon, May 1, 2017 at 10:31 AM, R Court <r.c...@ed.ac.uk> wrote:

No problem, thanks for letting us know. I'll take a look.

Margaret Ho

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May 3, 2017, 5:38:43 PM5/3/17

to R Court, nat-user, Greg Jefferis

The latest version of nat I was able to find is 1.8.6, so I installed it, but I still get the error, which is now:
"Error : package ‘nat’ 1.8.6 was found, but >= 1.8.8 is required by ‘flycircuit’

ERROR: lazy loading failed for package ‘flycircuit’
* removing ‘/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/flycircuit’
Error: Command failed (1)"

Margaret Ho

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May 3, 2017, 6:12:43 PM5/3/17

to R Court, nat-user, Greg Jefferis

In order to resolve the "nat" version issue when installing flycircuit, I downloaded the flycircuit tarball, found the DESCRIPTION file changed the requirement from 1.8.8 to 1.8.6, then ran R CMD INSTALL to get it to install, and it is fine now, in that I am able to install flycircuit data. Probably should fix it in the github if 1.8.6 is in fact the latest version.

However, when I run Shiny according to the instructions:

library(shiny)
runGitHub("jefferislab/NBLAST_on-the-fly")

I get a really weird error

> library(shiny)
> runGitHub("jefferislab/NBLAST_on-the-fly")
Downloading https://github.com/jefferislab/NBLAST_on-the-fly/archive/master.tar.gz

Listening on http://127.0.0.1:7854
Warning: Error in library: there is no package called ‘nat.nblast’
Stack trace (innermost first):
    42: library
     3: runApp
     2: runUrl
     1: runGitHub
Error in library(nat.nblast) : there is no package called ‘nat.nblast’

So then I went to the nat.nblast github and followed instructions for installing nat.nblast:

> if (!require("devtools")) install.packages("devtools")
Loading required package: devtools

> devtools::install_github(c("jefferis/nat", "jefferislab/nat.nblast"))
Downloading GitHub repo jefferis/nat@master
from URL https://api.github.com/repos/jefferis/nat/zipball/master
Installing nat

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/tmp/RtmpOyhUM5/devtools7ac245521d66/jefferis-nat-fdf6eee' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘nat’ ...

** R
** data
*** moving datasets to lazyload DB

** inst

** tests
** preparing package for lazy loading

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nat)
Reloading installed nat
unloadNamespace("nat") not successful, probably because another loaded package depends on it.Forcing unload. If you encounter problems, please restart R.
Downloading GitHub repo jefferislab/nat.nblast@master
from URL https://api.github.com/repos/jefferislab/nat.nblast/zipball/master
Installing nat.nblast
trying URL 'https://cran.rstudio.com/src/contrib/dendroextras_0.2.1.tar.gz'
Content type 'application/x-gzip' length 8280 bytes
==================================================
downloaded 8280 bytes

Installing dendroextras

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/tmp/RtmpOyhUM5/devtools7ac23baa01f/dendroextras' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘dendroextras’ ...
** package ‘dendroextras’ successfully unpacked and MD5 sums checked
** R
** inst

** tests
** preparing package for lazy loading

** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (dendroextras)
trying URL 'https://cran.rstudio.com/src/contrib/spam_1.4-0.tar.gz'
Content type 'application/x-gzip' length 1286352 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

Installing spam

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/tmp/RtmpOyhUM5/devtools7ac252b7f7c4/spam' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘spam’ ...
** package ‘spam’ successfully unpacked and MD5 sums checked
** libs
gfortran   -fpic -g -O2 -fstack-protector-strong -c bckslvmodified.f -o bckslvmodified.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c cholmodified.f -o cholmodified.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c dist.f -o dist.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c fromsparsekit.f -o fromsparsekit.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c kronecker.f -o kronecker.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c permutation.f -o permutation.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c rowcolstats.f -o rowcolstats.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c spamown.f -o spamown.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c spamown2.f -o spamown2.o
gfortran   -fpic -g -O2 -fstack-protector-strong -c xybind.f -o xybind.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o spam.so bckslvmodified.o cholmodified.o dist.o fromsparsekit.o kronecker.o permutation.o rowcolstats.o spamown.o spamown2.o xybind.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/margaret/R/x86_64-pc-linux-gnu-library/3.4/spam/libs

** R
** data
*** moving datasets to lazyload DB

** demo
** inst

** tests
** preparing package for lazy loading

Creating a generic function for ‘diag’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘diag<-’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘norm’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘rowMeans’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘colMeans’ from package ‘base’ in package ‘spam’
Creating a new generic function for ‘backsolve’ in package ‘spam’
Creating a new generic function for ‘forwardsolve’ in package ‘spam’
Creating a generic function for ‘chol2inv’ from ‘base’ in package ‘spam’
(from the saved implicit definition)
Creating a generic function for ‘chol2inv’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘crossprod’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘tcrossprod’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘rbind’ from package ‘base’ in package ‘spam’
Creating a generic function for ‘cbind’ from package ‘base’ in package ‘spam’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (spam)

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/tmp/RtmpOyhUM5/devtools7ac2b3ff73b/jefferislab-nat.nblast-29f67b4' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘nat.nblast’ ...

** R
** data
*** moving datasets to lazyload DB
** tests
** preparing package for lazy loading

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nat.nblast)

Everything seemed ok, and so I tried to run Shiny again, but then get a weird error that I have no idea what to do about. I also checked the package version of "nat" installed on the machine and now it says "1.8.9" but I can't load "nat" or "nat.nblast" using library(). Trying to reinstall continues to give me errors that say "Error in dev_meta(pkg$package) : Namespace not found for nat. Is it loaded?"

> library(shiny)
> runGitHub("jefferislab/NBLAST_on-the-fly")
Downloading https://github.com/jefferislab/NBLAST_on-the-fly/archive/master.tar.gz

Listening on http://127.0.0.1:7854
Warning in get(Info[i, 1], envir = env) :
internal error -3 in R_decompress1
Warning: Error in : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
Stack trace (innermost first):
    46: value[[3L]]
    45: tryCatchOne
    44: tryCatchList
    43: tryCatch
    42: library
     3: runApp
     2: runUrl
     1: runGitHub
Error : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt

> library(nat.nblast)
Error: package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1
> library(shiny)
> runGitHub("jefferislab/NBLAST_on-the-fly")
Downloading https://github.com/jefferislab/NBLAST_on-the-fly/archive/master.tar.gz

Listening on http://127.0.0.1:7854
Warning in get(Info[i, 1], envir = env) :
internal error -3 in R_decompress1
Warning: Error in : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
Stack trace (innermost first):
    46: value[[3L]]
    45: tryCatchOne
    44: tryCatchList
    43: tryCatch
    42: library
     3: runApp
     2: runUrl
     1: runGitHub
Error : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
ERROR: [on_request_read] connection reset by peer

> packageVersion("nat")
[1] ‘1.8.9’

> library(shiny)
> runGitHub("jefferislab/NBLAST_on-the-fly")
Downloading https://github.com/jefferislab/NBLAST_on-the-fly/archive/master.tar.gz

Listening on http://127.0.0.1:7854
Warning in get(Info[i, 1], envir = env) :
internal error -3 in R_decompress1
Warning: Error in : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
Stack trace (innermost first):
    46: value[[3L]]
    45: tryCatchOne
    44: tryCatchList
    43: tryCatch
    42: library
     3: runApp
     2: runUrl
     1: runGitHub
Error : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt

devtools::install_github(c("jefferis/nat", "jefferislab/nat.nblast"), force=TRUE)
Downloading GitHub repo jefferis/nat@master
from URL https://api.github.com/repos/jefferis/nat/zipball/master
Installing nat

'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \

'/tmp/RtmpOyhUM5/devtools7ac2452f8c4c/jefferis-nat-fdf6eee' \
--library='/home/margaret/R/x86_64-pc-linux-gnu-library/3.4' --install-tests

* installing *source* package ‘nat’ ...

** R
** data
*** moving datasets to lazyload DB

** inst

** tests
** preparing package for lazy loading

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nat)
Reloading installed nat
Error in dev_meta(pkg$package) :
Namespace not found for nat. Is it loaded?

When I try to run Shiny the window comes up and almost looks like the NBLAST server is starting, but it gets to "loading" and then the window immediately shuts and the program hangs with errors:

> library(shiny)
> runGitHub("jefferislab/NBLAST_on-the-fly")
Downloading https://github.com/jefferislab/NBLAST_on-the-fly/archive/master.tar.gz

Listening on http://127.0.0.1:7854
Warning in get(Info[i, 1], envir = env) :
internal error -3 in R_decompress1
Warning: Error in : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
Stack trace (innermost first):
    46: value[[3L]]
    45: tryCatchOne
    44: tryCatchList
    43: tryCatch
    42: library
     3: runApp
     2: runUrl
     1: runGitHub
Error : package or namespace load failed for ‘nat.nblast’ in get(Info[i, 1], envir = env):
lazy-load database '/home/margaret/R/x86_64-pc-linux-gnu-library/3.4/nat/R/nat.rdb' is corrupt
ERROR: [on_request_read] connection reset by peer

Sorry for the huge error dump, but I figured it may be easier to get help if I provide some of the errors I am getting.

I have used NBLAST in the past and it has been really really useful, so I want to be able to use it!

Thank you!

Margaret

Gregory Jefferis

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May 4, 2017, 4:55:05 PM5/4/17

to R Court, Margare...@gmail.com, nat-user

Hi Margaret,

I'm sorry that you have had all these install difficulties. That said I am not quite sure which install instructions you were trying to follow (link?) as the ones I see do not seem consistent with your original install errors. The NBLAST on the fly instructions have superfluous installs but should still work. If you install the flycircuit package as recommended here

https://github.com/jefferis/flycircuit/blob/master/README.md

you should find that it installs just fine. In fact this one line version should now work

devtools::install_github("jefferis/flycircuit", dependencies=TRUE)

If it does not you have probably borked your R package directory with your rather ingenious attempts to fool it into thinking that the nat package is up to date! In that case you would have to uninstall all packages and start again. Also when doing R installs it is best to start a clean R session.

Best wishes,

Greg.

Sent from my iPhone

On 4 May 2017, at 21:07, R Court <r.c...@ed.ac.uk> wrote:

Hi Margret,

Just wanted to keep you up to date:

I'm still resolving some issues on the production deployment of the NBLAST server, almost there fingers crossed.

I think Greg is going to take a look at the install notes as you shouldn't have been all that hassle for you.

Will let you know when the server is back online,

Rob

Great, thank you!
Margaret

To unsubscribe from this group and stop receiving emails from it, send an email to nat-user+u...@googlegroups.com.

Margaret Ho

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May 4, 2017, 4:59:59 PM5/4/17

to R Court, nat-user, Greg Jefferis

Hi Rob,

Thanks for letting me know! Hope it is able to work again soon.

I was able to get the nblast and nblast-on-the-fly local installations up and running finally on my machine, but I guess it still somehow depends on connecting to the NBLAST server though, because I keep getting server/client errors when I try the GAL4 function.

I tried to run it again this morning using the instructions on https://github.com/jefferislab/NBLAST_on-the-fly

The only thing I had to do was resolve this error after all.
Error in read.neuronlistfh(file.path(getOption("flycircuit.datadir"), :
Unable to locate data directory at: /Users/jefferis/projects/ChiangReanalysis/data/data or: /home/margaret/.local/share/rpkg-flycircuit/data/data

I went into /home/margaret/.local/share/rpkg-flycircuit/data/ and created another empty folder named data and made sure all the data was downloaded into /home/margaret/.local/share/rpkg-flycircuit/data/ (just one folder above) using the commands:

library(flycircuit)

allbyall=load_si_data("allbyallblastcanon_f9dc90ce5b2ffb74af37db1e3a2cb35b.desc")
dps=load_si_data("dpscanon_f9dc90ce5b2ffb74af37db1e3a2cb35b.rds")
apres16k.p0=load_si_data("apres16k.p0.rds")

Then the shiny server loads but I guess its a webapp so it still depends on the NBLAST server to work? When I search for a neuron to find suitable matching GAL4 lines I get 400 server errors.

For "One against All" when I input a neuron I get the following error "unable to obtain value for key '8b907a1c5d030af7c278d67878013ba2'"

3D view
Loading...Loading...
unable to obtain value for key '8b907a1c5d030af7c278d67878013ba2'

I'm not sure how to resolve this one. In order to run the GAL4 search, I need to use NBLAST on the fly and not regular NBLAST, correct?

Thanks!

Margaret

Gregory Jefferis

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May 5, 2017, 12:19:34 PM5/5/17

to Margaret Ho, Court Robert, nat-user, Rachel Wilson

Dear Margaret (and also Rachel),

1. First of all the GAL4 NBLAST is working again after a lot of wrangling by Rob Court to get the VFB server supplying GAL4 scores up to date. I hope that this means the rest of this email is largely moot.

2. Thanks for the update on this and well done for getting through the install. The only thing I wanted to check was the data download part. In theory running:

library(flycircuit)

allbyall=load_si_data("allbyallblastcanon_f9dc90ce5b2ffb74af37db1e3a2cb35b.desc")
dps=load_si_data("dpscanon_f9dc90ce5b2ffb74af37db1e3a2cb35b.rds")
apres16k.p0=load_si_data("apres16k.p0.rds")

should create the required directory. Did it not?

3. However as you concluded the local version still relies on a remote server to provide GAL4 scores. It would be possible to override this with some small code additions but I will assume this is not necessary given 1.

All the best,

Greg.

--

Gregory Jefferis, PhD

Division of Neurobiology

MRC Laboratory of Molecular Biology

Francis Crick Avenue

Cambridge Biomedical Campus

Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis

http://jefferislab.org

http://flybrain.stanford.edu

Margaret Ho

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May 5, 2017, 2:30:23 PM5/5/17

to Gregory Jefferis, Court Robert, nat-user, Rachel Wilson

Hi Greg and Rob,

Sorry but I just tried it (this URL: http://flybrain.mrc-lmb.cam.ac.uk:8080/NBLAST_on-the-fly/) and still keep getting the

Error: client error: (400) Bad Request

Am I using the correct URL?

thanks!

Margaret

Margaret Ho

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May 9, 2017, 10:58:06 AM5/9/17

to R Court, Rachel Wilson, nat-user, Greg Jefferis

Thank you for getting it up and running again! I was able to get the information I needed to do some new experiments

Margaret

On May 6, 2017 7:24 AM, "R Court" <r.c...@ed.ac.uk> wrote:

Yep sorry, it stopped working due to one more (sporadically) conflicting library. I've replaced them all now and put health checks to check a full query rather than just the health of the openCPU servicer itself.

Thanks for all your help in resolving this,

Rob

Kyunghee Koh

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Jun 21, 2017, 4:07:38 PM6/21/17

to nat-user, r.c...@ed.ac.uk, rachel...@hms.harvard.edu, jeff...@gmail.com, Margare...@gmail.com

NBLAST Gal4 search gives me client error: (400) Bad Request. From the email trail, I see that this was a problem solved in May. Is it still working for everyone?

Thanks,

Kyunghee

Tatsuo Okubo

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Jun 21, 2017, 4:57:44 PM6/21/17

to nat-user, r.c...@ed.ac.uk, rachel...@hms.harvard.edu, jeff...@gmail.com, Margare...@gmail.com

Hi Kyunghee,

I am also getting the same error message: client error: (400) Bad Request

Best,
Tatsuo

Margaret Ho

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Jun 21, 2017, 5:08:02 PM6/21/17

to Kyunghee Koh, nat-user, R Court, Rachel Wilson, Greg Jefferis

Nope, it doesn't work for me either.

Gregory Jefferis

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Jun 21, 2017, 6:22:53 PM6/21/17

to R Court, Margaret Ho, Kyunghee Koh, nat-user, Rachel Wilson

Thanks a lot, Rob. It was a call in in vfbr::vfb_nblast.

https://rdrr.io/github/jefferis/vfbr/src/R/vfb_nblast.R

Best, Greg.

Sent from my iPhone

On 21 Jun 2017, at 23:04, R Court <r.c...@ed.ac.uk> wrote:

Restarting the service now (takes a few hours) to check nothing has got locked up.

I'll take a look at the health checks so this is automatic in future to that end do we know what api requests specially were failing?

Thanks,

Rob

Marta Costa

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Jun 22, 2017, 3:56:05 PM6/22/17

to Gregory Jefferis, R Court, Margaret Ho, Kyunghee Koh, nat-user, Rachel Wilson

Dear all,

The NBLAST-on-the-fly GAL4 search is now back up. Thanks Rob!

Please empty the cache and do a hard reload of any tabs you might have open.

Best wishes,

Marta Costa

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Kyunghee Koh

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Jun 22, 2017, 4:51:54 PM6/22/17

to Marta Costa, Gregory Jefferis, R Court, Margaret Ho, nat-user, Rachel Wilson

It's working now. I already found a Gal4 line I was looking for. It's a wonderful tool!

Thanks for taking care of it promptly.

Best,

Kyunghee

----------
Kyunghee Koh

Associate Professor, Department of Neuroscience
Co-director, Neuroscience Graduate Program
Thomas Jefferson University
900 Walnut, Room 411
Philadelphia, PA 19107
215-955-5905

kyungheekohlab.net

Gregory Jefferis

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Jun 22, 2017, 5:34:09 PM6/22/17

to Kyunghee Koh, Marta Costa, R Court, nat-user

Dear Rob,

Many thanks for fixing the vfb R server!

Dear Kyunghee,

I'm very pleased to hear you found something successfully - I hope you're able to use this for future experiments. When you are ready you can thank us by citing our NBLAST paper!

Best wishes,

Greg.

Sent from my iPhone

Kyunghee Koh

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Jun 22, 2017, 5:37:23 PM6/22/17

to Gregory Jefferis, Marta Costa, R Court, nat-user

Dear all,

Thanks for generating and maintaining this fantastic tool! Of course, I will cite your paper when the time comes.

Best,

Kyunghee

----------
Kyunghee Koh

Associate Professor, Department of Neuroscience
Co-director, Neuroscience Graduate Program
Thomas Jefferson University
900 Walnut, Room 411
Philadelphia, PA 19107
215-955-5905

kyungheekohlab.net

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Getting server error: (503) Service Unavailable from NBLAST on the fly GAL4

Margaret H

Gregory Jefferis

Margaret Ho

Sorry to bother you guys again, but the error is now a 400 (Bad Request) error for searching for GAL4 lines with a FlyCircuit neuron query. I pasted the error that I get below. I searched using"TH-F-200064" as the search term.Thank you!

*******************

NBLAST results

Top hits

Margaret Ho

Margaret Ho

Margaret Ho

Gregory Jefferis

Margaret Ho

Gregory Jefferis

Margaret Ho

Margaret Ho

Kyunghee Koh

Tatsuo Okubo

Margaret Ho

Gregory Jefferis

Marta Costa

Kyunghee Koh

Gregory Jefferis

Kyunghee Koh

Sorry to bother you guys again, but the error is now a 400 (Bad Request) error for searching for GAL4 lines with a FlyCircuit neuron query. I pasted the error that I get below. I searched using"TH-F-200064" as the search term.

Thank you!