debugging dask - failed to detect client - debugging

My dask groupby script is failing (Memory Error) so I set off to debug the script. I'm running on a stand-alone computer .
I've updated the logging in the config.yaml file with
logging:
distributed: debug
bokeh: debug
tornado: info
I'm running the dask distributed example computation with the following updates:
from distributed import LocalCluster
c=LocalCluster()
and an updated script with the range amended to range(10000) .
While the script runs (and successfully completes) I see the following logs in the Jupyter Notebook which repeats itself until the script completes.
bokeh.server.tornado - DEBUG - [pid 3088] 0 clients connected
bokeh.server.tornado - DEBUG - [pid 3088] /system has 0 sessions
with 0 unused bokeh.server.tornado - DEBUG - [pid 3088] /stealing
has 0 sessions with 0 unused bokeh.server.tornado - DEBUG - [pid 3088]
/workers has 0 sessions with 0 unused bokeh.server.tornado - DEBUG -
[pid 3088] /events has 0 sessions with 0 unused bokeh.server.tornado
- DEBUG - [pid 3088] /counters has 0 sessions with 0 unused bokeh.server.tornado - DEBUG - [pid 3088] /tasks has 0 sessions with
0 unused bokeh.server.tornado - DEBUG - [pid 3088] /status has 0
sessions with 0 unused
Why don't I see any workers that are running?
I get the following log when running the c = LocalCluster()
bokeh.server.server - INFO - Starting Bokeh server version 0.12.4
bokeh.server.server - WARNING - Host wildcard '' can expose the
application to HTTP host header attacks. Host wildcard should only be
used for testing purpose. bokeh.server.server - WARNING - Host
wildcard '' can expose the application to HTTP host header attacks.
Host wildcard should only be used for testing purpose.
bokeh.server.tornado - DEBUG - Allowed Host headers: ['']
bokeh.server.tornado - DEBUG - These host origins can connect to the
websocket: [''] bokeh.server.tornado - DEBUG - Patterns are:
bokeh.server.tornado - DEBUG - [('/system/?', bokeh.server.tornado -
DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/system/ws'}), bokeh.server.tornado - DEBUG -
('/system/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/system/ws'}), bokeh.server.tornado - DEBUG -
('/system/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/system/ws'}), bokeh.server.tornado - DEBUG -
('/stealing/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/stealing/ws'}), bokeh.server.tornado - DEBUG
- ('/stealing/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/stealing/ws'}), bokeh.server.tornado - DEBUG
- ('/stealing/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/stealing/ws'}), bokeh.server.tornado - DEBUG
- ('/workers/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/workers/ws'}), bokeh.server.tornado - DEBUG
- ('/workers/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/workers/ws'}), bokeh.server.tornado - DEBUG
- ('/workers/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/workers/ws'}), bokeh.server.tornado - DEBUG
- ('/events/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/events/ws'}), bokeh.server.tornado - DEBUG -
('/events/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/events/ws'}), bokeh.server.tornado - DEBUG -
('/events/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/events/ws'}), bokeh.server.tornado - DEBUG -
('/counters/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/counters/ws'}), bokeh.server.tornado - DEBUG
- ('/counters/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/counters/ws'}), bokeh.server.tornado - DEBUG
- ('/counters/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/counters/ws'}), bokeh.server.tornado - DEBUG
- ('/tasks/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/tasks/ws'}), bokeh.server.tornado - DEBUG -
('/tasks/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/tasks/ws'}), bokeh.server.tornado - DEBUG -
('/tasks/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/tasks/ws'}), bokeh.server.tornado - DEBUG -
('/status/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/status/ws'}), bokeh.server.tornado - DEBUG -
('/status/ws', bokeh.server.tornado - DEBUG - , bokeh.server.tornado - DEBUG -
{'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/status/ws'}), bokeh.server.tornado - DEBUG -
('/status/autoload.js', bokeh.server.tornado - DEBUG - ,
bokeh.server.tornado - DEBUG - {'application_context':
, bokeh.server.tornado - DEBUG -
'bokeh_websocket_path': '/status/ws'}), bokeh.server.tornado - DEBUG -
('/?', bokeh.server.tornado - DEBUG - , bokeh.server.tornado -
DEBUG - {'applications': {'/counters':
, bokeh.server.tornado - DEBUG -
'/events': , bokeh.server.tornado - DEBUG -
'/status': , bokeh.server.tornado - DEBUG -
'/stealing': , bokeh.server.tornado - DEBUG -
'/system': , bokeh.server.tornado - DEBUG -
'/tasks': , bokeh.server.tornado - DEBUG -
'/workers': }, bokeh.server.tornado - DEBUG -
'prefix': '', bokeh.server.tornado - DEBUG - 'use_redirect':
True}), bokeh.server.tornado - DEBUG - ('/static/(.*)',
bokeh.server.tornado - DEBUG - )]


The logging messages that you're seeing are from the Bokeh diagnostic dashboard. They're essentially saying that no one is looking at the diagnostic webpage. You might want to decrease the verbosity of your Bokeh logging. I don't think that these messages concern you.
Debug level logging is almost always too verbose for any user. It tends to be used by developers when debugging.

Related

Keycloak 400 bad request when [state] is old

I have a Spring Boot application protected by Keycloak (15.0.2).
Let's say that I have a browser with two tabs opened for the same user and that user is authenticated.
Now I logout in tab 1 and I get the Keycloak login form with the following Url:
http://localhost:8180/auth/realms/AUTOTEST_PG/protocol/openid-connect/auth?response_type=code&client_id=mcd-client&state=e01b8a88-6945-4c56-9ee1-46fb156d33be&login=true&scope=openid
Now I logout in tab 2 and I get the Keycloak login form with the following Url:
http://localhost:8180/auth/realms/AUTOTEST_PG/protocol/openid-connect/auth?response_type=code&client_id=mcd-client&state=b9607387-7a05-4226-8313-4c5c80a1b145&login=true&scope=openid
Next, I tried to login in tab 1 and I get a 400 Bad Request response.
Looking at the Spring Boot log I get the following:
14554520 2021-12-14 00:02:06,100 [ajp-nio-0.0.0.0-8009-exec-8] DEBUG sample.controller.filters.MyKeycloakAuthenticationProcessingFilter ?:? - - - - - attemptAuthentication
14554520 2021-12-14 00:02:06,100 [ajp-nio-0.0.0.0-8009-exec-8] DEBUG sample.security.RealmProvider ?:? - - - - - getRealmName - requestUri: https://10.161.54.36/sso/login?redirect_url=/sctools/&state=e01b8a88-6945-4c56-9ee1-46fb156d33be&session_state=4fe8d159-5ada-4522-a422-07c5a0ce9d15&code=c5dda8ef-0fd9-4323-9922-fa5c73b28f89.4fe8d159-5ada-4522-a422-07c5a0ce9d15.442a440e-6df0-40c7-b8cb-3a52123430a0
14554520 2021-12-14 00:02:06,100 [ajp-nio-0.0.0.0-8009-exec-8] WARN org.keycloak.adapters.OAuthRequestAuthenticator ?:? - - - - - state parameter invalid
14554520 2021-12-14 00:02:06,100 [ajp-nio-0.0.0.0-8009-exec-8] WARN org.keycloak.adapters.OAuthRequestAuthenticator ?:? - - - - - cookie: b9607387-7a05-4226-8313-4c5c80a1b145
14554520 2021-12-14 00:02:06,100 [ajp-nio-0.0.0.0-8009-exec-8] WARN org.keycloak.adapters.OAuthRequestAuthenticator ?:? - - - - - queryParam: e01b8a88-6945-4c56-9ee1-46fb156d33be
14554521 2021-12-14 00:02:06,101 [ajp-nio-0.0.0.0-8009-exec-8] DEBUG sample.controller.filters.MyKeycloakAuthenticationProcessingFilter ?:? - - - - - unsuccessfulAuthentication - committed: true
14554521 2021-12-14 00:02:06,101 [ajp-nio-0.0.0.0-8009-exec-8] DEBUG sample.security.MyKeycloakAuthenticationFailureHandler ?:? - - - - - onAuthenticationFailure org.keycloak.adapters.springsecurity.KeycloakAuthenticationException: Invalid authorization header, see WWW-Authenticate header for details
14554521 2021-12-14 00:02:06,101 [ajp-nio-0.0.0.0-8009-exec-8] DEBUG sample.security.MyKeycloakAuthenticationFailureHandler ?:? - - - - - onAuthenticationFailure - response isCommitted - Status: 400
It seems that the cookie sent and the state value doesn't match and that is the reason why I get a bad request.
How can I login from any of the tabs without getting the Bad Request ?
Note: If I go to the tab2 and login, then I get a message telling me that the user is already login.
UPDATE
When doing the same operation on the Keycloak console, if the user logout from one tab the second tab is automatically logout and the Url doesn't get an state variable it gets a challenge variable, something like:
http://10.161.54.36:8180/auth/realms/master/protocol/openid-connect/auth?client_id=security-admin-console&redirect_uri=http%3A%2F%2F10.161.54.36%3A8180%2Fauth%2Fadmin%2Fmaster%2Fconsole%2F%23%2Frealms&state=c3015df8-4c50-4454-be8d-0555f25e3bd0&response_mode=fragment&response_type=code&scope=openid&nonce=acb2a07d-c4a3-4cd3-8a7a-e23580a97d14&code_challenge=2W6-09eeD_WEwtWct3a5MojpIQJMe-9brcOH-7fbT6A&code_challenge_method=S256
How is it done ?

create conda env from yaml (conflict)

I'm running into an issue where my conda env isn't being created from a .yaml file. I think it's failing because this yaml file was made on centos6, but I have since upgraded to a new centos7 AMI on AWS.
conda env create --name html_ribo_report --file=html_ribo_report.yaml
No errors, seems to complete after finding conflicts (takes about an hour to run). I can paste the output if needed.
Here are the contents of html_ribo_report.yaml:
name: eclipsebio
channels:
- https://repo.continuum.io/pkgs/free
- defaults
- conda-forge
- bioconda
dependencies:
- _libgcc_mutex=0.1=main
- _r-mutex=1.0.0=anacondar_1
- aioeasywebdav=2.2.0=py36_0
- aiohttp=2.2.5=py36h3a1b670_0
- altair=3.0.1=py36_0
- appdirs=1.4.3=py36_0
- argcomplete=1.8.2=py36_0
- argh=0.26.2=py36_1
- asn1crypto=0.22.0=py36h265ca7c_1
- async-timeout=2.0.0=py36h92a791d_0
- backports=1.0=py36hfa02d7e_1
- backports.functools_lru_cache=1.4=py36_1
- bamtools=2.4.0=3
- bcftools=1.6=0
- bedtools=2.26.0=0
- bioawk=1.0=1
- bioconductor-annotate=1.56.0=r3.4.1_0
- bioconductor-annotationdbi=1.40.0=r3.4.1_0
- bioconductor-biobase=2.38.0=r3.4.1_0
- bioconductor-biocgenerics=0.24.0=r3.4.1_0
- bioconductor-biocinstaller=1.28.0=r3.4.1_0
- bioconductor-biocparallel=1.12.0=r3.4.1_0
- bioconductor-biocstyle=2.6.0=r3.4.1_0
- bioconductor-biomart=2.34.0=r3.4.1_0
- bioconductor-biostrings=2.46.0=r3.4.1_0
- bioconductor-bsgenome=1.46.0=r3.4.1_0
- bioconductor-bumphunter=1.20.0=r3.4.1_0
- bioconductor-delayedarray=0.4.1=r3.4.1_0
- bioconductor-derfinder=1.12.0=r3.4.1_0
- bioconductor-derfinderhelper=1.12.0=r3.4.1_0
- bioconductor-edger=3.20.1=r3.4.1_0
- bioconductor-genefilter=1.60.0=r3.4.1_0
- bioconductor-geneplotter=1.56.0=r3.4.1_0
- bioconductor-genomeinfodb=1.14.0=r3.4.1_0
- bioconductor-genomeinfodbdata=1.1.0=r341_0
- bioconductor-genomicalignments=1.14.0=r3.4.1_0
- bioconductor-genomicfeatures=1.26.4=r3.4.1_0
- bioconductor-genomicfiles=1.14.0=r3.4.1_0
- bioconductor-genomicranges=1.30.0=r3.4.1_0
- bioconductor-glimma=1.6.0=r3.4.1_0
- bioconductor-iranges=2.12.0=r3.4.1_0
- bioconductor-limma=3.34.1=r3.4.1_0
- bioconductor-qvalue=2.10.0=r3.4.1_0
- bioconductor-rsamtools=1.30.0=r3.4.1_0
- bioconductor-rtracklayer=1.38.0=r3.4.1_0
- bioconductor-s4vectors=0.16.0=r3.4.1_0
- bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
- bioconductor-tximport=1.6.0=r3.4.1_0
- bioconductor-variantannotation=1.20.3=r3.4.1_0
- bioconductor-xvector=0.18.0=r3.4.1_0
- bioconductor-zlibbioc=1.24.0=r3.4.1_0
- biopython=1.69=np113py36_0
- blas=1.0=mkl
- bleach=2.1.1=py36hd521086_0
- boto=2.48.0=py36h6e4cd66_1
- boto3=1.4.7=py36h4cc92d5_0
- botocore=1.7.20=py36h085fff1_0
- bowtie=1.2.3=py36hc9558a2_0
- bowtie2=2.3.5=py36he860b03_0
- bzip2=1.0.6=h0376d23_1
- ca-certificates=2017.08.26=h1d4fec5_0
- cairo=1.14.8=0
- certifi=2016.9.26=py36_0
- cffi=1.10.0=py36had8d393_1
- chardet=3.0.4=py36h0f667ec_1
- click=6.7=py36h5253387_0
- configargparse=0.12.0=py36_0
- cookies=2.2.1=py36_0
- cryptography=2.0.3=py36ha225213_1
- curl=7.52.1=0
- cutadapt=2.7=py36h516909a_0
- cycler=0.10.0=py36h93f1223_0
- cython=0.28.5=py36hf484d3e_0
- dbus=1.10.20=0
- decorator=4.1.2=py36hd076ac8_0
- dicttoxml=1.7.4=py36_0
- dnaio=0.4.1=py36h516909a_0
- docopt=0.6.2=py36_0
- docutils=0.14=py36hb0f60f5_0
- dropbox=7.3.1=py36_0
- entrypoints=0.2.3=py36h1aec115_2
- expat=2.2.4=h6ea4f2b_2
- fastqc=0.11.6=2
- filechunkio=1.8=py36_1
- flask=0.12.2=py36hb24657c_0
- font-ttf-dejavu-sans-mono=2.37=h6964260_0
- font-ttf-inconsolata=2.001=hcb22688_0
- font-ttf-source-code-pro=2.030=h7457263_0
- fontconfig=2.12.1=3
- freetype=2.5.5=2
- ftputil=3.3.1=py36_0
- future=0.16.0=py36_1
- gettext=0.19.8.1=hd7bead4_3
- gffutils=0.9=py36_0
- glib=2.50.2=1
- gmp=6.1.2=h6c8ec71_1
- graphite2=1.3.10=hc526e54_0
- gsl=2.2.1=h0c605f7_3
- gst-plugins-base=1.8.0=0
- gstreamer=1.8.0=0
- harfbuzz=0.9.39=2
- homer=4.10=pl526hc9558a2_0
- html5lib=0.999999999=py36h2cfc398_0
- htseq=0.9.1=py36_0
- htslib=1.6=0
- icu=54.1=0
- idna=2.6=py36h82fb2a8_1
- intel-openmp=2018.0.0=h15fc484_7
- ipykernel=4.6.1=py36hbf841aa_0
- ipython=6.2.1=py36h88c514a_1
- ipython_genutils=0.2.0=py36hb52b0d5_0
- itsdangerous=0.24=py36h93cc618_1
- jbig=2.1=hdba287a_0
- jedi=0.11.0=py36hf290c5b_0
- jinja2=2.9.6=py36h489bce4_1
- jmespath=0.9.3=py36hd3948f9_0
- jpeg=9b=h024ee3a_2
- jsonschema=2.6.0=py36h006f8b5_0
- jupyter_client=5.1.0=py36h614e9ea_0
- jupyter_core=4.4.0=py36h7c827e3_0
- krb5=1.14.2=hcdc1b81_6
- libedit=3.1.20170329=0
- libffi=3.2.1=hd88cf55_4
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=8.2.0=hdf63c60_1
- libgfortran-ng=7.2.0=h9f7466a_2
- libiconv=1.14=0
- libpng=1.6.36=hbc83047_0
- libsodium=1.0.15=hf101ebd_0
- libssh2=1.8.0=h2d05a93_3
- libstdcxx-ng=9.1.0=hdf63c60_0
- libtiff=4.0.9=h28f6b97_0
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.12=h84ff03f_3
- libxml2=2.9.4=0
- markupsafe=1.0=py36hd9260cd_1
- matplotlib=2.0.2=np113py36_0
- matplotlib-venn=0.11.5=py_1
- mistune=0.8.1=py36h3d5977c_0
- mkl=2018.0.0=hb491cac_4
- mock=2.0.0=py36h3c5bf6c_0
- moto=1.1.1=py36_0
- multidict=3.2.0=py36h97a4c74_0
- mysql=5.5.24=0
- mysql-connector-c=6.1.6=0
- nbconvert=5.3.1=py36hb41ffb7_0
- nbformat=4.4.0=py36h31c9010_0
- ncurses=5.9=10
- notebook=5.2.2=py36h40a37e6_0
- numpy=1.13.3=py36ha12f23b_0
- openjdk=8.0.121=1
- openssl=1.0.2r=h7b6447c_0
- pandas=0.21.0=py36h78bd809_1
- pandoc=1.19.2.1=hea2e7c5_1
- pandocfilters=1.4.2=py36ha6701b7_1
- pango=1.40.3=1
- paramiko=2.1.2=py36_0
- parso=0.1.0=py36h2b61f4d_0
- patsy=0.4.1=py36ha3be15e_0
- pbr=3.1.1=py36hb5f6b33_0
- pcre=8.39=1
- perl=5.26.2=h14c3975_0
- perl-common-sense=3.74=pl526_2
- perl-json=4.02=pl526_0
- perl-json-xs=2.34=pl526h6bb024c_3
- perl-types-serialiser=1.0=pl526_2
- pexpect=4.3.0=py36h673ed17_0
- pickleshare=0.7.4=py36h63277f8_0
- pigz=2.3=0
- pip=9.0.1=py36h6c6f9ce_4
- pixman=0.34.0=hceecf20_3
- prompt_toolkit=1.0.15=py36h17d85b1_0
- psutil=5.4.0=py36h84c53db_0
- ptyprocess=0.5.2=py36h69acd42_0
- pyaml=17.10.0=py_0
- pyasn1=0.3.7=py36h0f28794_0
- pybedtools=0.7.10=py36_1
- pycparser=2.18=py36hf9f622e_1
- pyfaidx=0.5.0=py36_0
- pygments=2.2.0=py36h0d3125c_0
- pyopenssl=17.2.0=py36h5cc804b_0
- pyparsing=2.2.0=py36hee85983_1
- pyqt=5.6.0=py36_2
- pysam=0.11.2.2=py36_1
- pysftp=0.2.9=py36_0
- pysocks=1.6.7=py36hd97a5b1_1
- python=3.6.3=h1284df2_4
- python-dateutil=2.6.1=py36h88d3b88_1
- pytz=2017.2=py36hc2ccc2a_1
- pyyaml=3.12=py36hafb9ca4_1
- pyzmq=16.0.3=py36he2533c7_0
- qt=5.6.2=5
- qualimap=2.2.2a=1
- r-acepack=1.4.1=r3.4.1_0
- r-assertthat=0.2.0=r3.4.1_0
- r-backports=1.1.0=r3.4.1_0
- r-base=3.4.1=0
- r-base64enc=0.1_3=r3.4.1_0
- r-bh=1.62.0_1=r3.4.1_0
- r-bitops=1.0_6=r3.4.1_2
- r-bookdown=0.4=r3.4.1_0
- r-catools=1.17.1=r3.4.1_2
- r-checkmate=1.8.2=r3.4.1_0
- r-cluster=2.0.6=r3.4.1_0
- r-codetools=0.2_15=r3.4.1_0
- r-colorspace=1.3_2=r3.4.1_0
- r-data.table=1.10.4=r3.4.1_0
- r-dbi=0.6_1=r3.4.1_0
- r-dichromat=2.0_0=r3.4.1_2
- r-digest=0.6.12=r3.4.1_0
- r-dorng=1.6.6=r3.4.1_0
- r-evaluate=0.10=r3.4.1_0
- r-foreach=1.4.3=r3.4.1_0
- r-foreign=0.8_68=r3.4.1_0
- r-formula=1.2_1=r3.4.1_0
- r-futile.logger=1.4.3=r3.4.1_0
- r-futile.options=1.0.0=r3.4.1_0
- r-gdata=2.18.0=r3.4.1_0
- r-getopt=1.20.0=r3.4.1_0
- r-ggplot2=2.2.1=r3.4.1_0
- r-gplots=3.0.1=r3.4.1_0
- r-gridextra=2.2.1=r3.4.1_0
- r-gtable=0.2.0=r3.4.1_0
- r-gtools=3.5.0=r3.4.1_0
- r-highr=0.6=r3.4.1_0
- r-hmisc=4.0_3=r3.4.1_0
- r-htmltable=1.9=r3.4.1_0
- r-htmltools=0.3.6=r3.4.1_0
- r-htmlwidgets=0.8=r3.4.1_1
- r-iterators=1.0.8=r3.4.1_0
- r-jsonlite=1.5=r3.4.1_0
- r-kernsmooth=2.23_15=r3.4.1_0
- r-knitr=1.16=r3.4.1_0
- r-knitrbootstrap=1.0.1=r3.4.1_0
- r-labeling=0.3=r3.4.1_2
- r-lambda.r=1.1.9=r3.4.1_0
- r-lattice=0.20_35=r3.4.1_0
- r-latticeextra=0.6_28=r3.4.1_0
- r-lazyeval=0.2.0=r3.4.1_0
- r-locfit=1.5_9.1=r3.4.1_0
- r-magrittr=1.5=r3.4.1_2
- r-markdown=0.8=r3.4.1_0
- r-mass=7.3_47=r3.4.1_0
- r-matrix=1.2_10=r3.4.1_0
- r-matrixstats=0.52.2=r3.4.1_0
- r-memoise=1.1.0=r3.4.1_0
- r-mime=0.5=r3.4.1_0
- r-munsell=0.4.3=r3.4.1_0
- r-nnet=7.3_12=r3.4.1_0
- r-pkgmaker=0.22=r3.4.1_0
- r-plogr=0.1_1=r3.4.1_0
- r-plyr=1.8.4=r3.4.1_0
- r-prettyunits=1.0.2=r3.4.1_0
- r-progress=1.1.2=r3.4.1_0
- r-r6=2.2.1=r3.4.1_0
- r-rcolorbrewer=1.1_2=r3.4.1_3
- r-rcpp=0.12.11=r3.4.1_0
- r-rcpparmadillo=0.7.900.2.0=r3.4.1_0
- r-rcurl=1.95_4.8=r3.4.1_0
- r-registry=0.3=r3.4.1_0
- r-reshape2=1.4.2=r3.4.1_0
- r-rjson=0.2.15=r3.4.1_0
- r-rlang=0.1.1=r3.4.1_0
- r-rmarkdown=1.5=r3.4.1_0
- r-rngtools=1.2.4=r3.4.1_0
- r-rpart=4.1_11=r3.4.1_0
- r-rprojroot=1.2=r3.4.1_0
- r-rsqlite=1.1_2=r3.4.1_0
- r-scales=0.4.1=r3.4.1_0
- r-snow=0.4_2=r3.4.1_0
- r-stringi=1.1.5=r3.4.1_0
- r-stringr=1.2.0=r3.4.1_0
- r-survival=2.41_3=r3.4.1_0
- r-tibble=1.3.3=r3.4.1_0
- r-viridis=0.4.0=r3.4.1_0
- r-viridislite=0.2.0=r3.4.1_0
- r-xml=3.98_1.7=r3.4.1_0
- r-xtable=1.8_2=r3.4.1_0
- r-yaml=2.1.14=r3.4.1_0
- ratelimiter=1.2.0=py36_0
- readline=7.0=hb321a52_4
- regex=2017.09.23=py36h2527052_0
- requests=2.14.2=py36_0
- s3transfer=0.1.10=py36h0257dcc_1
- samtools=1.5=1
- scikit-learn=0.19.1=py36h7aa7ec6_0
- scipy=1.0.0=py36hbf646e7_0
- seaborn=0.8.0=py36h197244f_0
- seqtk=1.3=hed695b0_2
- setuptools=36.5.0=py36he42e2e1_0
- setuptools-git=1.2=py36_0
- simplegeneric=0.8.1=py36h2cb9092_0
- simplejson=3.11.1=py36_0
- sip=4.18.1=py36h51ed4ed_2
- six=1.11.0=py36h372c433_1
- snakemake=4.3.0=py36_0
- sqlite=3.20.1=hb898158_2
- star=2.6.0c=1
- statsmodels=0.8.0=py36h8533d0b_0
- system=5.8=2
- tbb=2019.8=hc9558a2_0
- terminado=0.6=py36ha25a19f_0
- testpath=0.3.1=py36h8cadb63_0
- tk=8.6.7=hc745277_3
- toolz=0.9.0=py36_0
- tornado=4.5.2=py36h1283b2a_0
- traitlets=4.3.2=py36h674d592_0
- ucsc-bedclip=377=h199ee4e_0
- ucsc-bedgraphtobigwig=332=0
- ucsc-bedtobigbed=332=0
- ucsc-twobittofa=357=1
- umi_tools=0.5.1=py36_0
- urllib3=1.22=py36hbe7ace6_0
- wcwidth=0.1.7=py36hdf4376a_0
- webencodings=0.5.1=py36h800622e_1
- werkzeug=0.12.2=py36hc703753_0
- wget=1.19.1=he4ec0ba_0
- wheel=0.29.0=py36he7f4e38_1
- wrapt=1.10.11=py36h28b7045_0
- xmltodict=0.11.0=py36_0
- xopen=0.8.4=py36_0
- xz=5.2.3=h55aa19d_2
- yaml=0.1.7=h014fa73_2
- yarl=0.13.0=py36h21e4b6b_0
- zeromq=4.2.2=hbedb6e5_2
- zlib=1.2.11=ha838bed_2
- pip:
- pillow==8.3.2
prefix: /home/ec2-user/anaconda3/envs/eclipsebio

At a glance there could be many issues with this environment. Some of the most obvious things are:
You may need channel_priority set to flexible, i.e.,
conda config --set channel_priority flexible
Otherwise, higher priority channels might be masking packages in the other channels.
The channel order is substandard. The free channel should always be last, and Bioconda has very specific channel order requirements to ensure their packages work. Change the order to:
channels:
- conda-forge
- bioconda
- defaults
- free
Switch to Mamba.
conda install -n base conda-forge::mamba
mamba env create -n html_ribo_report -f html_ribo_report.yaml
Otherwise, I'd consider breaking the environment up into more modular (i.e., manageable) components that fit to different tasks. Personally, I avoid mixing Python and R in the same environment, and keep Snakemake in its own dedicated environment.

Accept retrieving less fields than requested in MARS Web API?

I'm trying to download a 25 day ahead forecast from the ECMWF MARS Web API for all of 2018. These forecasts (WAEF Control Forecast) are only published on mondays and thursdays, and here I'm running into problems fetching the data using the MARS Web API.
I tried requesting the intuitive 2018-01-01/to/2018-12-31, but since there are 5 days a week where there aren't any fields to retrieve, the request fails.
My MARS request file is as follows:
retrieve,
class=od,
date=2018-01-01/to/2018-12-31,
expver=1,
param=229.140/245.140,
step=600/624/648/672,
stream=waef,
time=00:00:00,
type=cf,
target="output.grib"
Which results in the following response:
...
mars - INFO - 20190215.100826 - Welcome to MARS
mars - INFO - 20190215.100826 - MARS Client build stamp: 20190130224336
mars - INFO - 20190215.100826 - MARS Client version: 6.23.3
mars - INFO - 20190215.100826 - MIR version: 1.1.2
mars - INFO - 20190215.100826 - Using ecCodes version 2.10.1
mars - INFO - 20190215.100826 - Using odb_api version: 0.15.9 (file format version: 0.5)
mars - INFO - 20190215.100826 - Maximum retrieval size is 30.00 G
retrieve,target="output.grib",stream=waef,param=229.140/245.140,padding=0,step=600/624/648/672,expver=1,time=00:00:00,date=2018-01-01/to/2018-12-31,type=cf,class=odmars - WARN - 20190215.100826 - For wave data, LEVTYPE forced to Surface
mars - INFO - 20190215.100826 - Automatic split by date is on
mars - INFO - 20190215.100826 - Request has been split into 12 monthly retrievals
mars - INFO - 20190215.100826 - Processing request 1
RETRIEVE,
CLASS = OD,
TYPE = CF,
STREAM = WAEF,
EXPVER = 0001,
REPRES = SH,
LEVTYPE = SFC,
PARAM = 229.140/245.140,
TIME = 0000,
STEP = 600/624/648/672,
DOMAIN = G,
TARGET = "output.grib",
PADDING = 0,
DATE = 20180101/20180102/20180103/20180104/20180105/20180106/20180107/20180108/20180109/20180110/20180111/20180112/20180113/20180114/20180115/20180116/20180117/20180118/20180119/20180120/20180121/20180122/20180123/20180124/20180125/20180126/20180127/20180128/20180129/20180130/20180131
mars - INFO - 20190215.100826 - Web API request id: xxx
mars - INFO - 20190215.100826 - Requesting 248 fields
mars - INFO - 20190215.100826 - Calling mars on 'marsod', callback on 36551
mars - INFO - 20190215.100827 - Server task is 228 [marsod]
mars - INFO - 20190215.100827 - Request cost: 72 fields, 17.2754 Mbytes on 1 tape, nodes: hpss [marsod]
2019-02-15 11:08:59 Request is active
mars - INFO - 20190215.102300 - Transfering 18114554 bytes
mars - WARN - 20190215.102301 - Visiting database marsod : expected 248, got 72
mars - ERROR - 20190215.102301 - Expected 248, got 72.
mars - ERROR - 20190215.102301 - Request failed
...
Is there any way to allow receiving less fields than requested or any other elegant solution to this problem other than only requesting the correct dates for mondays and thursdays?

I managed to find the answer in the MARS documentation after all. Using expect = any in the control section solved the issue. More information can be found here: https://confluence.ecmwf.int/pages/viewpage.action?pageId=43521134
retrieve,
class=od,
date=2018-01-01/to/2018-12-31,
expver=1,
param=229.140/245.140,
step=600/624/648/672,
stream=waef,
time=00:00:00,
type=cf,
expect=any,
target="output.grib"

Deploying dash app with gdal dependency fails on heroku

I'm using a conda for package management and including an environment.yml file and requirements.txt file for deployment with help from this post. I've gotten simple dash apps to deploy this way, but for a more complex task which requires GDAL, the build 'succeeds' but the app crashes with the following log:
Starting process with command `gunicorn app:server --log-file=-
heroku[web.1]: Process exited with status 127
app[web.1]: bash: gunicorn: command not found
app[api]: Build succeeded
My environment.yml file calls for:
name: dashpilot
channels:
- conda-forge
- anaconda-fusion
- defaults
dependencies:
- asn1crypto=0.24.0=py36_1003
- attrs=18.2.0=py_0
- bzip2=1.0.6=1
- ca-certificates=2018.10.15=ha4d7672_0
- certifi=2018.10.15=py36_1000
- cffi=1.11.5=py36h5e8e0c9_1
- chardet=3.0.4=py36_1003
- click=7.0=py_0
- cryptography-vectors=2.3.1=py36_1000
- dash=0.30.0=py_0
- dash-core-components=0.38.0=py_0
- dash-html-components=0.13.2=py_0
- dash-renderer=0.15.0=py_0
- decorator=4.3.0=py_0
- flask=1.0.2=py_2
- flask-compress=1.4.0=py_0
- geojson=2.4.1=py_0
- idna=2.7=py36_1002
- ipython_genutils=0.2.0=py_1
- itsdangerous=1.1.0=py_0
- jinja2=2.10=py_1
- jsonschema=3.0.0a3=py36_1000
- jupyter_core=4.4.0=py_0
- markupsafe=1.1.0=py36h470a237_0
- nbformat=4.4.0=py_1
- openssl=1.0.2p=h470a237_1
- plotly=3.4.1=py_0
- pycparser=2.19=py_0
- pyopenssl=18.0.0=py36_1000
- pyrsistent=0.14.7=py36h470a237_0
- pysocks=1.6.8=py36_1002
- pytz=2018.7=py_0
- requests=2.20.1=py36_1000
- retrying=1.3.3=py_2
- six=1.11.0=py36_1001
- traitlets=4.3.2=py36_1000
- urllib3=1.23=py36_1001
- werkzeug=0.14.1=py_0
- blas=1.0=mkl
- cairo=1.14.12=hc4e6be7_4
- click-plugins=1.0.4=py36_0
- cligj=0.5.0=py36_0
- cryptography=2.3.1=py36hdbc3d79_0
- curl=7.61.1=ha441bb4_0
- cycler=0.10.0=py36hfc81398_0
- descartes=1.1.0=py36_0
- expat=2.2.6=h0a44026_0
- fiona=1.7.12=py36h0dff353_0
- fontconfig=2.13.0=h5d5b041_1
- freetype=2.9.1=hb4e5f40_0
- freexl=1.0.5=h1de35cc_0
- gdal=2.2.4=py36h6440ff4_1
- geopandas=0.3.0=py36_0
- geos=3.6.2=h5470d99_2
- gettext=0.19.8.1=h15daf44_3
- giflib=5.1.4=h1de35cc_1
- glib=2.56.2=hd9629dc_0
- gunicorn=19.9.0=py36_0
- hdf4=4.2.13=h39711bb_2
- hdf5=1.10.2=hfa1e0ec_1
- icu=58.2=h4b95b61_1
- intel-openmp=2019.1=144
- jpeg=9b=he5867d9_2
- json-c=0.13.1=h3efe00b_0
- kealib=1.4.7=h40e48e4_6
- kiwisolver=1.0.1=py36h0a44026_0
- krb5=1.16.1=h24a3359_6
- libboost=1.67.0=hebc422b_4
- libcurl=7.61.1=hf30b1f0_0
- libcxx=4.0.1=hcfea43d_1
- libcxxabi=4.0.1=hcfea43d_1
- libdap4=3.19.1=h3d3e54a_0
- libedit=3.1.20170329=hb402a30_2
- libffi=3.2.1=h475c297_4
- libgdal=2.2.4=h7b1ea53_1
- libgfortran=3.0.1=h93005f0_2
- libiconv=1.15=hdd342a3_7
- libkml=1.3.0=hbe12b63_4
- libnetcdf=4.6.1=h4e6abe9_2
- libpng=1.6.35=ha441bb4_0
- libpq=10.5=hf30b1f0_0
- libspatialindex=1.8.5=h2c08c6b_2
- libspatialite=4.3.0a=ha12ebda_19
- libssh2=1.8.0=h322a93b_4
- libtiff=4.0.9=hcb84e12_2
- libuuid=1.0.3=h6bb4b03_2
- libxml2=2.9.8=hab757c2_1
- matplotlib=3.0.1=py36h54f8f79_0
- mkl=2018.0.3=1
- mkl_fft=1.0.6=py36hb8a8100_0
- mkl_random=1.0.1=py36h5d10147_1
- munch=2.3.2=py36_0
- ncurses=6.1=h0a44026_0
- numpy=1.15.4=py36h6a91979_0
- numpy-base=1.15.4=py36h8a80b8c_0
- openjpeg=2.3.0=hb95cd4c_1
- pandas=0.23.4=py36h6440ff4_0
- pcre=8.42=h378b8a2_0
- pip=18.1=py36_0
- pixman=0.34.0=hca0a616_3
- poppler=0.65.0=ha097c24_1
- poppler-data=0.4.9=0
- proj4=5.0.1=h1de35cc_0
- psycopg2=2.7.5=py36hdbc3d79_0
- pyparsing=2.3.0=py36_0
- pyproj=1.9.5.1=py36h833a5d7_1
- pysal=1.14.4.post1=py36_1
- python=3.6.6=hc167b69_0
- python-dateutil=2.7.5=py36_0
- readline=7.0=h1de35cc_5
- rtree=0.8.3=py36_0
- scipy=1.1.0=py36h28f7352_1
- setuptools=40.6.2=py36_0
- shapely=1.6.4=py36h20de77a_0
- sqlalchemy=1.2.14=py36h1de35cc_0
- sqlite=3.25.3=ha441bb4_0
- tk=8.6.8=ha441bb4_0
- tornado=5.1.1=py36h1de35cc_0
- wheel=0.32.3=py36_0
- xerces-c=3.2.2=h44e365a_0
- xz=5.2.4=h1de35cc_4
- zlib=1.2.11=h1de35cc_3
- pip:
- dash-table==3.1.6
prefix: /Applications/anaconda3/envs/dashpilot
My requirements.txt file calls for:
asn1crypto==0.24.0
attrs==18.2.0
certifi==2018.10.15
cffi==1.11.5
chardet==3.0.4
Click==7.0
click-plugins==1.0.4
cligj==0.5.0
cryptography==2.3.1
cryptography-vectors==2.3.1
cycler==0.10.0
dash==0.30.0
dash-core-components==0.38.0
dash-html-components==0.13.2
dash-renderer==0.15.0
dash-table==3.1.6
decorator==4.3.0
descartes==1.1.0
Fiona==1.7.12
Flask==1.0.2
Flask-Compress==1.4.0
GDAL==2.2.4
geojson==2.4.1
geopandas==0.3.0
gunicorn==19.7.1
idna==2.7
ipython-genutils==0.2.0
itsdangerous==1.1.0
Jinja2==2.10
jsonschema==3.0.0a3
jupyter-core==4.4.0
kiwisolver==1.0.1
MarkupSafe==1.1.0
matplotlib==3.0.1
mkl-fft==1.0.6
mkl-random==1.0.1
munch==2.3.2
nbformat==4.4.0
numpy==1.15.4
pandas==0.23.4
plotly==3.4.1
psycopg2==2.7.5
pycparser==2.19
pyOpenSSL==18.0.0
pyparsing==2.3.0
pyproj==1.9.5.1
pyrsistent==0.14.7
PySAL==1.14.4.post1
PySocks==1.6.8
python-dateutil==2.7.5
pytz==2018.7
requests==2.20.1
retrying==1.3.3
Rtree==0.8.3
scipy==1.1.0
Shapely==1.6.4.post1
six==1.11.0
SQLAlchemy==1.2.14
tornado==5.1.1
traitlets==4.3.2
urllib3==1.23
Werkzeug==0.14.1
I've tried all sorts of combinations of buildpacks (heroku's python build pack and the gdal buildpack recommended in heroku's docs). The app works when running 'heroku local' on my mac when solely using the recommended gdal buildpack. I'm new to the the deployment process, so unclear where I might be going astray.
Will add that my config vars are currently these:
BUILD_WITH_GEO_LIBRARIES=1
GDAL_LIBRARY_PATH=os.environ.get('GDAL_LIBRARY_PATH')
GEOS_LIBRARY_PATH=os.environ.get('GEOS_LIBRARY_PATH')
WEB_CONCURRENCY=3

Strange logs when vaadin page opened in osgi

I have following logs when opening a vaadin page.
The strange logs stop when I close my webpage.
[qtp948395645-39] DEBUG org.eclipse.jetty.http.HttpParser - filled 447/447
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.Server - REQUEST / on AsyncHttpConnection#5444c658,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-5,l=48,c=0},r=11
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/ -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-39 - /] DEBUG org.eclipse.jetty.server.Server - RESPONSE / 200 handled=true
[qtp948395645-39] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#11dfd090{l(/10.221.137.111:56461)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#5444c658,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=0},r=11}
[qtp948395645-39] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[qtp948395645-36] DEBUG org.eclipse.jetty.http.HttpParser - filled 474/474
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.Server - REQUEST /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js on AsyncHttpConnection#5444c658,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-5,l=48,c=0},r=12
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-36 - /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js?1443457921853] DEBUG org.eclipse.jetty.server.Server - RESPONSE /VAADIN/widgetsets/com.vaadin.DefaultWidgetSet/com.vaadin.DefaultWidgetSet.nocache.js 200 handled=true
[qtp948395645-36] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#11dfd090{l(/10.221.137.111:56461)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#5444c658,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=0},r=12}
[qtp948395645-40] DEBUG org.eclipse.jetty.http.HttpParser - filled 731/731
[qtp948395645-36] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.Server - REQUEST / on AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=2,l=48,c=246},r=3
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/ -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-40 - /?v-1443457921854] INFO com.bekaert.handling.ui.core - Rebuilding session from cookie for user 'admin'
[qtp948395645-40 - /?v-1443457921854] WARN com.bekaert.handling.ui.core.main.ErrorView - Entered in error view:
[qtp948395645-40 - /?v-1443457921854] DEBUG org.eclipse.jetty.server.Server - RESPONSE / 200 handled=true
[qtp948395645-40] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=246},r=3}
[qtp948395645-40] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[qtp948395645-42] DEBUG org.eclipse.jetty.http.HttpParser - filled 695/695
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.Server - REQUEST /UIDL/ on AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=2,l=48,c=200},r=4
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/UIDL/ -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-42 - /UIDL/?v-wsver=7.5.5&v-uiId=1] DEBUG org.eclipse.jetty.server.Server - RESPONSE /UIDL/ 200 handled=true
[qtp948395645-42] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=200},r=4}
[qtp948395645-42] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[qtp948395645-37] DEBUG org.eclipse.jetty.http.HttpParser - filled 607/607
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.Server - REQUEST /UIDL/ on AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=2,l=48,c=126},r=5
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/UIDL/ -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-37 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.Server - RESPONSE /UIDL/ 200 handled=true
[qtp948395645-37] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=126},r=5}
[qtp948395645-37] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[DefaultQuartzScheduler_Worker-10] DEBUG com.bekaert.handling.order.location.sap.connector.impl - Start search for new SAP orders
[qtp948395645-39] DEBUG org.eclipse.jetty.http.HttpParser - filled 607/607
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.Server - REQUEST /UIDL/ on AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=2,l=48,c=126},r=6
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - scope null||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.handler.ContextHandler - context=||/UIDL/ # o.e.j.s.ServletContextHandler{/,null}
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - Got Session ID 1mddljaq8cpy11l0btqfs6p34s from cookie
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - sessionManager=org.eclipse.jetty.server.session.HashSessionManager#19868320
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.session - session=org.eclipse.jetty.server.session.HashedSession:1mddljaq8cpy11l0btqfs6p34s#1806836909
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - servlet ||/UIDL/ -> org.apache.felix.http.base.internal.DispatcherServlet-158d255c
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.servlet.ServletHandler - chain=null
[qtp948395645-39 - /UIDL/?v-uiId=1] DEBUG org.eclipse.jetty.server.Server - RESPONSE /UIDL/ 200 handled=true
[qtp948395645-39] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Enabled read interest SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=4,h=0,b=0,c=-1},p=HttpParser{s=0,l=48,c=126},r=6}
[qtp948395645-39] DEBUG org.eclipse.jetty.http.HttpParser - filled 0/0
[qtp948395645-36] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - ishut SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-14,l=0,c=-3},r=6}
[qtp948395645-36] DEBUG org.eclipse.jetty.http.HttpParser - filled -1/0
[qtp948395645-36] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Disabled read interest while writing response SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=-3},r=6}
[qtp948395645-36] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - close SCEP#61bf045{l(/10.221.137.111:56462)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=-3},r=6}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.io.nio - destroyEndPoint SCEP#61bf045{l(null)<->r(0.0.0.0/0.0.0.0:80),s=0,open=false,ishut=true,oshut=true,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=-3},r=6}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.server.AbstractHttpConnection - closed AsyncHttpConnection#34d39e39,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=-3},r=6
[qtp948395645-37] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - ishut SCEP#5534412c{l(/10.221.137.111:56463)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#cf40a17,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-14,l=0,c=0},r=0}
[qtp948395645-37] DEBUG org.eclipse.jetty.http.HttpParser - filled -1/0
[qtp948395645-37] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Disabled read interest while writing response SCEP#5534412c{l(/10.221.137.111:56463)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#cf40a17,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-37] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - close SCEP#5534412c{l(/10.221.137.111:56463)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#cf40a17,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - ishut SCEP#1dcb12a9{l(/10.221.137.111:56464)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#6a011d1d,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-14,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.http.HttpParser - filled -1/0
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.io.nio - destroyEndPoint SCEP#5534412c{l(null)<->r(0.0.0.0/0.0.0.0:80),s=0,open=false,ishut=true,oshut=true,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#cf40a17,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Disabled read interest while writing response SCEP#1dcb12a9{l(/10.221.137.111:56464)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#6a011d1d,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.server.AbstractHttpConnection - closed AsyncHttpConnection#cf40a17,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0
[qtp948395645-42] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - close SCEP#1dcb12a9{l(/10.221.137.111:56464)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#6a011d1d,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - ishut SCEP#6d491226{l(/10.221.137.111:56466)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#2c01d086,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-14,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.http.HttpParser - filled -1/0
[qtp948395645-42] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Disabled read interest while writing response SCEP#6d491226{l(/10.221.137.111:56466)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#2c01d086,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-42] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - close SCEP#6d491226{l(/10.221.137.111:56466)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#2c01d086,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.io.nio - destroyEndPoint SCEP#1dcb12a9{l(null)<->r(0.0.0.0/0.0.0.0:80),s=0,open=false,ishut=true,oshut=true,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#6a011d1d,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.server.AbstractHttpConnection - closed AsyncHttpConnection#6a011d1d,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.io.nio - destroyEndPoint SCEP#6d491226{l(null)<->r(0.0.0.0/0.0.0.0:80),s=0,open=false,ishut=true,oshut=true,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#2c01d086,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.server.AbstractHttpConnection - closed AsyncHttpConnection#2c01d086,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0
[qtp948395645-37] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - ishut SCEP#387f2edf{l(/10.221.137.111:56465)<->r(/10.224.129.14:80),s=1,open=true,ishut=false,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#574b3210,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=-14,l=0,c=0},r=0}
[qtp948395645-37] DEBUG org.eclipse.jetty.http.HttpParser - filled -1/0
[qtp948395645-37] DEBUG org.eclipse.jetty.server.AsyncHttpConnection - Disabled read interest while writing response SCEP#387f2edf{l(/10.221.137.111:56465)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1r}-{AsyncHttpConnection#574b3210,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-37] DEBUG org.eclipse.jetty.io.nio.ChannelEndPoint - close SCEP#387f2edf{l(/10.221.137.111:56465)<->r(/10.224.129.14:80),s=1,open=true,ishut=true,oshut=false,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#574b3210,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.io.nio - destroyEndPoint SCEP#387f2edf{l(null)<->r(0.0.0.0/0.0.0.0:80),s=0,open=false,ishut=true,oshut=true,rb=false,wb=false,w=true,i=1!}-{AsyncHttpConnection#574b3210,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0}
[qtp948395645-35 Selector0] DEBUG org.eclipse.jetty.server.AbstractHttpConnection - closed AsyncHttpConnection#574b3210,g=HttpGenerator{s=0,h=-1,b=-1,c=-1},p=HttpParser{s=0,l=0,c=0},r=0
[Timer-2] INFO org.jinterop.dcom.core.JIComOxidRuntime - Running ClientPingTimerTask !
[Timer-2] INFO org.jinterop.dcom.core.JIComOxidRuntime - Within ClientPingTimerTask: holder.currentSetOIDs, current size of which is 2
[Timer-2] INFO org.jinterop.dcom.core.PingObject - Simple Ping going for setId: 00000: 00 00 00 05 65 74 29 12 |....et). |
[Timer-2] INFO org.jinterop -
Sending REQUEST
[Timer-2] INFO org.jinterop -
Recieved RESPONSE
[Timer-2] INFO org.jinterop.dcom.core.PingObject - Simple Ping Succeeded
[Timer-2] INFO org.jinterop.dcom.core.JIComOxidRuntime - Within ClientPingTimerTask: holder.seqNum 1
I don't know what all this means.
Also, it doesn't happen always. If I restart my osgi program, there is a 1/2 change I have this problem.

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