metawatt / Discussion / General Discussion: download Databases?

Maria Pachiadaki - 2016-08-29

Hello Marc,

I get the following error when I am trying to download the metawatt databases.
wget http://coe30.coe.ucalgary.ca/~mstrous/metawatt-databases.tar.gz

--2016-08-29 10:08:42-- http://coe30.coe.ucalgary.ca/~mstrous/metawatt-databases.tar.gz
Resolving coe30.coe.ucalgary.ca... failed: nodename nor servname provided, or not known.
wget: unable to resolve host address 'coe30.coe.ucalgary.ca'

Any suggestions?

Best,
Maria

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- Marc Strous - 2016-08-29
  
  Hi Maria,
  
  Indeed, this doesn't work anymore, but metawatt will create a database
  for you during first run...
  
  Best wishes,
  
  Marc
  
  On 08/29/2016 08:31 AM, Maria Pachiadaki wrote:
  
  Hello Marc,
  
  I get the following error when I am trying to download the metawatt
  databases.
  wget http://coe30.coe.ucalgary.ca/~mstrous/metawatt-databases.tar.gz
  http://coe30.coe.ucalgary.ca/%7Emstrous/metawatt-databases.tar.gz
  
  --2016-08-29 10:08:42--
  http://coe30.coe.ucalgary.ca/~mstrous/metawatt-databases.tar.gz
  http://coe30.coe.ucalgary.ca/%7Emstrous/metawatt-databases.tar.gz
  Resolving coe30.coe.ucalgary.ca... failed: nodename nor servname
  provided, or not known.
  wget: unable to resolve host address 'coe30.coe.ucalgary.ca'
  
  Any suggestions?
  
  Best,
  Maria
  
  download Databases?
  https://sourceforge.net/p/metawatt/discussion/general/thread/8f4398bd/?limit=25#708c
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/metawatt/discussion/general/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  --
  Marc Strous
  Engineer, Ecologist, Entrepreneur
  Energy Bioengineering Group
  
  www.ucalgary.ca/ebg
  www.solarbiocells.com
  www.fixingtheatmosphere.com
  www.linkedin.com/in/strous
  www.twitter.com/marc_strous
  
  Department of Geoscience
  University of Calgary
  tel: (403) 220 6604
  2500 University Drive NW
  Calgary, AB, Canada T2N 1N4
  Energy Environment and Experiental Learning (EEEL) Building
  Room 509
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Michal Kaminski - 2016-11-18

Hello Marc,

Any suggestions what should I do if the Update Database module doesn't create any database?

I guess the problem is somewhere here:

"Metawatt [INFO|4:43:56] Processing NCBI queries for database update...
Metawatt [INFO|4:43:56] (1/1) Processing "Bacteria"...
Metawatt [INFO|4:43:56] Polling NCBI for new assemblies for superkingdom "Bacteria" unique at rank "genus"...
Metawatt [INFO|4:43:57] Warning: Search at NCBI unsuccessful!"

Best wishes,
Michal

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- Marc Strous - 2016-11-21
  
  Hi Michal,
  
  I uploaded a new version - check it out...
  
  Best wishes,
  
  Marc
  
  On 11/18/2016 08:57 AM, Michal Kaminski wrote:
  
  Hello Marc,
  
  Any suggestions what should I do if the Update Database module doesn't
  create any database?
  
  I guess the problem is somewhere here:
  
  "Metawatt [INFO|4:43:56] Processing NCBI queries for database update...
  Metawatt [INFO|4:43:56] (1/1) Processing "Bacteria"...
  Metawatt [INFO|4:43:56] Polling NCBI for new assemblies for
  superkingdom "Bacteria" unique at rank "genus"...
  Metawatt [INFO|4:43:57] Warning: Search at NCBI unsuccessful!"
  
  Best wishes,
  Michal
  
  download Databases?
  https://sourceforge.net/p/metawatt/discussion/general/thread/8f4398bd/?limit=25#dec1
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/metawatt/discussion/general/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  --
  Marc Strous
  Engineer, Ecologist, Entrepreneur
  Energy Bioengineering Group
  
  www.ucalgary.ca/ebg
  www.solarbiocells.com
  www.fixingtheatmosphere.com
  www.linkedin.com/in/strous
  www.twitter.com/marc_strous
  
  Department of Geoscience
  University of Calgary
  tel: (403) 220 6604
  2500 University Drive NW
  Calgary, AB, Canada T2N 1N4
  Energy Environment and Experiental Learning (EEEL) Building
  Room 509
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Yu Bin Wang - 2016-11-19

Hello Marc,

I also got this problem like Michal said, so I take a look into the src of metawatt. After trace some java files, I think the problem is "DatabaseMaker" settings[line:44].

BASE_URL is assigned as "http://eutils.ncbi.nlm.nih.gov/entrez/eutils", but recently NCBI change its web protocol into "https", so "esearch.fcgi" can not get correct xml in {processQuery}.

Then metawatt can not poll genome orf from NCBI because esearch report "nothing" based on default "setNCBIdatabaseQuery".

I try to re-compile metawatt to fix the error, but some svg (apache) lib can be found.

Maybe you can check the problem, thanks.

Yu Bin

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- Marc Strous - 2016-11-21
  
  Hi Yu Bin,
  
  thanks for exploring this issue.... I uploaded a new version of metawatt
  that addresses this issue - so if you're right, it should work...
  
  Best wishes,
  
  Marc
  
  On 11/18/2016 11:40 PM, Yu Bin Wang wrote:
  
  Hello Marc,
  
  I also got this problem like Michal said, so I take a look into the
  src of metawatt. After trace some java files, I think the problem is
  "DatabaseMaker" settings[line:44].
  
  BASE_URL is assigned as
  "http://eutils.ncbi.nlm.nih.gov/entrez/eutils", but recently NCBI
  change its web protocol into "https", so "esearch.fcgi" can not get
  correct xml in {processQuery}.
  
  Then metawatt can not poll genome orf from NCBI because esearch report
  "nothing" based on default "setNCBIdatabaseQuery".
  
  I try to re-compile metawatt to fix the error, but some svg (apache)
  lib can be found.
  
  Maybe you can check the problem, thanks.
  
  Yu Bin
  
  download Databases?
  https://sourceforge.net/p/metawatt/discussion/general/thread/8f4398bd/?limit=25#98ea
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/metawatt/discussion/general/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  --
  Marc Strous
  Engineer, Ecologist, Entrepreneur
  Energy Bioengineering Group
  
  www.ucalgary.ca/ebg
  www.solarbiocells.com
  www.fixingtheatmosphere.com
  www.linkedin.com/in/strous
  www.twitter.com/marc_strous
  
  Department of Geoscience
  University of Calgary
  tel: (403) 220 6604
  2500 University Drive NW
  Calgary, AB, Canada T2N 1N4
  Energy Environment and Experiental Learning (EEEL) Building
  Room 509
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Yu Bin Wang - 2016-11-22
    
    Hi Marc,
    Thanks, I can't wait to try.
    Regards,
    Yu Bin
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

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download Databases?