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I have pink tiles in the image browser

The core container didn't start. It's often a consequence of a previous problem (postgis or postgis_data not launched).

Do you have distinct URL for Core, IMS & Upload ?

We will route the requests by checking the URL. If all the services have the same URL, we cannot redirect the HTTP requests. 

Example :

CORE_URL=cytomine.university.edu
IMS_URLS="[cytomine-ims1.university.edu,cytomine-ims2.university.edu]"
UPLOAD_URL=cytomine-upload.university.edu

All of theses URL must be pointing on the IP of the host machine.

Does your browser have access to your IMS ?

We will be able to check it by browsing the IMS_URLS into your browser. If you have a "Grails page", go to the next point.
If you don't have the Grails page, run the reporting script and send us an email with the generated archive.

Does your IMS have access to your IIP ?

If the commands

  1. sudo docker exec -i -t ims /bin/bash
  2. apt-get update -y && apt-get install -y curl
  3. curl $IIP_OFF_URL/fcgi-bin/iipsrv.fcgi

(where $IIP_OFF_URL must by remplaced by the value of this variable in your configuration file) returns "Could not resolve host" and the file /etc/hosts doesn't contains your IIP_URLs,

Set the IS_LOCAL variable to true and run restart_keep_data.sh

Error : no such container: core

The core container didn't start. It's often a consequence of a previous problem (postgis or postgis_data not launched).

Be sure than sudo sh create_docker_images.sh return no error (every command is in cache).

An error often happens with the compilation of postgres or postgis image. In this case, change the Cytomine-bootstrap/postgres/Dockerfile by this version :

https://github.com/cytomine/Cytomine-bootstrap/blob/49618d62a80fec5f1e6da1aefea3fc4c746ea79f/postgres/Dockerfile

Then run the create_docker_images script.

Error : postgis_data not found/not started

Open the Cytomine-bootstrap/data_containers/postgis/Dockerfile files and change its content by the content of this version : 

https://github.com/cytomine/Cytomine-bootstrap/blob/ed1d06a4b375a11993570eb41c73c3393bd54cba/data_containers/postgis/Dockerfile

Create a new file Cytomine-bootstrap/data_containers/postgis/deploy.sh with this content

https://github.com/cytomine/Cytomine-bootstrap/blob/ed1d06a4b375a11993570eb41c73c3393bd54cba/data_containers/postgis/deploy.sh

Then run the create_docker_images script.

Error : image cytomine/software_router not found

 The software_router image depends on scipy, numpy & scikit-learn which are known to not have a "backward compatible philosophy".

Some minor releases can broke the automatic installation.

Here is the list of the modifications to do before running again the create_docker_images script to fix the software_router image

 

Images on Annotation Panel are not displayed

Check the logs of the application into the core container

  • sudo docker exec -i -t core /bin/bash
  • tail -f /var/lib/tomcat7/logs/catalina.out

If you have this warning

"WARN Sql - Failed to execute: SELECT kmeans, count(*), st_astext(ST_ConvexHull(ST_Collect(location)))
FROM (
SELECT kmeans(ARRAY[ST_X(st_centroid(location)), ST_Y(st_centroid(location))], 5) OVER (), location
FROM user_annotation a  LEFT OUTER JOIN annotation_term at ON a.id = at.user_annotation_id
WHERE true
AND a.image_id = 8817106
AND a.user_id = 8242800
AND ST_Intersects(a.location,ST_GeometryFromText('POLYGON ((-80727.357421875 -30742.401367187, -80727.357421875 60905.598632813, 133032.64257813 60905.598632813, 133032.64257813 -30742.401367187, -80727.357421875 -30742.401367187))',0))

) AS ksub
GROUP BY kmeans
ORDER BY kmeans; because: ERROR: f*unction kmean*s(double precision[], integer) does not exist
   Hint: No function matches the given name and argument types. You might need to add explicit type casts.
   Position: 88
08-04-2016 08:58:48,077 ERROR GrailsExceptionResolver - PSQLException occurred when processing request: [GET] /api/annotation.jsonp
ERROR: function kmeans(double precision[], integer) does not exist
   Hint: No function matches the given name and argument types. You might need to add explicit type casts.
   Position: 88. Stacktrace follows:
org.postgresql.util.PSQLException: ERROR: function kmeans(double precision[], integer) does not exist
   Hint: No function matches the given name and argument types. You might need to add explicit type casts.
   Position: 88
     at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2102)
"

Then you need to install the kmeans library for postgres as here

Be carefull. To enable this library, you will need to remove the data_postgis container. So, your data will be destroyed. Don't forget to do a backup before ! 

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