Postgresql schema does not match data after upgrade
kmuw opened this issue · 0 comments
kmuw commented
Hi @geektortoise,
when upgrading from cytomine v3.0.3 to v3.2.3 some table schemas of the postgresql database change which prevent existing data from being loaded properly. The cytomine core component then fails to startup and launch its data migration scripts.
If the docker volumes containing the databases are removed before install of v3.2.3, a new and empty cytomine instance works without issue.
System:
- Debian 10
- Docker 20.10.18
- one single VM
Tried approaches:
- official upgrade procedure (https://doc.cytomine.org/admin-guide/upgrade) plus removing images/containers (not volumes) before upgrade -> fail to startup
core - install empty cytomine instance and restore postgresql backup -> fail to startup
core - install v3.2.3 without prepopulated DB -> works (albeit results in an empty cytomine instance)
- install v3.0.3 and restore DB backup -> works
Attached are log files from core and postgresql containers as well as configuration.sh
Thanks in advance!
Christopher
log from postgresql container after upgrade without clearing the database in the docker volume (resembling the original upgrade proc
edure):
Comparing database dumps of both cytomine versions confirm schema differences:
--- cytomine-v303-tables.txt
+++ cytomine-v323-tables.txt
@@ -1,10 +1,10 @@
-
-COPY public.abstract_image (id, version, created, deleted, filename, height, magnification, mime_id, original_filename, path, resolution, sample_id, scanner_id, updated, user_id, width) FROM stdin;
+COPY public.abstract_image (id, version, bit_depth, channels, colorspace, created, deleted, depth, duration, fps, height, magnification, original_filename, physical_size_x, physical_size_y, physical_size_z, sample_id, scanner_id, updated, uploaded_file_id, user_id, width) FROM stdin;
+COPY public.abstract_slice (id, version, channel, created, deleted, image_id, mime_id, "time", updated, uploaded_file_id, z_stack) FROM stdin;
COPY public.acl_class (id, class) FROM stdin;
COPY public.acl_entry (id, ace_order, acl_object_identity, audit_failure, audit_success, granting, mask, sid) FROM stdin;
COPY public.acl_object_identity (id, object_id_class, entries_inheriting, object_id_identity, owner_sid, parent_object) FROM stdin;
COPY public.acl_sid (id, principal, sid) FROM stdin;
-COPY public.algo_annotation (id, version, area, area_unit, count_comments, count_reviewed_annotations, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, updated, user_id, wkt_location) FROM stdin;
+COPY public.algo_annotation (id, version, area, area_unit, count_comments, count_reviewed_annotations, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, slice_id, updated, user_id, wkt_location) FROM stdin;
COPY public.algo_annotation_term (id, version, annotation_class_name, annotation_ident, created, deleted, expected_term_id, project_id, rate, term_id, updated, user_job_id) FROM stdin;
COPY public.amqp_queue (id, version, created, deleted, exchange, host, name, updated) FROM stdin;
COPY public.amqp_queue_config (id, version, created, default_value, deleted, index, is_in_map, name, type, updated) FROM stdin;
@@ -12,12 +12,14 @@
COPY public.annotation_filter (id, version, created, deleted, name, project_id, updated, user_id) FROM stdin;
COPY public.annotation_filter_sec_user (annotation_filter_users_id, sec_user_id) FROM stdin;
COPY public.annotation_filter_term (annotation_filter_terms_id, term_id) FROM stdin;
-COPY public.annotation_index (id, version, count_annotation, count_reviewed_annotation, image_id, user_id) FROM stdin;
+COPY public.annotation_index (id, version, count_annotation, count_reviewed_annotation, slice_id, user_id) FROM stdin;
COPY public.annotation_term (id, version, created, deleted, term_id, updated, user_id, user_annotation_id) FROM stdin;
-COPY public.attached_file (id, version, created, data, deleted, domain_class_name, domain_ident, filename, updated) FROM stdin;
+COPY public.annotation_track (id, version, annotation_class_name, annotation_ident, created, deleted, slice_id, track_id, updated) FROM stdin;
+COPY public.attached_file (id, version, created, data, deleted, domain_class_name, domain_ident, filename, key, updated) FROM stdin;
COPY public.auth_with_token (id, version, expiry_date, token_key, user_id) FROM stdin;
COPY public.command (id, version, action_message, created, data, deleted, print_message, project_id, refuse_undo, save_on_undo_redo_stack, service_name, transaction_id, updated, user_id, class, link_project) FROM stdin;
COPY public.command_history (id, version, command_id, created, deleted, message, prefix_action, project_id, updated, user_id) FROM stdin;
+COPY public.companion_file (id, version, created, deleted, filename, image_id, original_filename, progress, type, updated, uploaded_file_id) FROM stdin;
COPY public.configuration (id, version, created, deleted, key, reading_role, updated, value) FROM stdin;
COPY public.description (id, version, created, data, deleted, domain_class_name, domain_ident, updated) FROM stdin;
COPY public.discipline (id, version, created, deleted, name, updated) FROM stdin;
@@ -27,13 +29,13 @@
COPY public.image_filter_project (id, version, created, deleted, image_filter_id, project_id, updated) FROM stdin;
COPY public.image_group (id, version, created, deleted, name, project_id, updated) FROM stdin;
COPY public.image_grouphdf5 (id, version, created, deleted, filename, group_id, progress, status, updated) FROM stdin;
-COPY public.image_instance (id, version, base_image_id, channel, count_image_annotations, count_image_job_annotations, count_image_reviewed_annotations, created, deleted, instance_filename, magnification, project_id, resolution, review_start, review_stop, review_user_id, updated, user_id, z_index, class, parent_id, x, y) FROM stdin;
+COPY public.image_instance (id, version, base_image_id, count_image_annotations, count_image_job_annotations, count_image_reviewed_annotations, created, deleted, fps, instance_filename, magnification, physical_size_x, physical_size_y, physical_size_z, project_id, review_start, review_stop, review_user_id, updated, user_id, class, parent_id, x, y) FROM stdin;
COPY public.image_sequence (id, version, channel, created, deleted, image_id, image_group_id, slice, "time", updated, z_stack) FROM stdin;
-COPY public.image_server (id, version, available, class_name, created, deleted, name, service, updated, url) FROM stdin;
+COPY public.image_server (id, version, available, base_path, created, deleted, name, updated, url) FROM stdin;
COPY public.image_server_storage (id, version, image_server_id, storage_id) FROM stdin;
COPY public.imaging_server (id, version, created, deleted, updated, url) FROM stdin;
COPY public.instrument (id, version, brand, created, deleted, model, updated) FROM stdin;
-COPY public.job (id, version, created, data_deleted, deleted, number, processing_server_id, progress, project_id, rate, software_id, status, status_comment, updated, class, name) FROM stdin;
+COPY public.job (id, version, created, data_deleted, deleted, favorite, number, processing_server_id, progress, project_id, rate, software_id, status, status_comment, updated, class, name) FROM stdin;
COPY public.job_data (id, version, created, deleted, dir, filename, job_id, key, size, updated, value_id) FROM stdin;
COPY public.job_data_binary_value (id, version, data) FROM stdin;
COPY public.job_parameter (id, version, created, deleted, job_id, software_parameter_id, updated, value) FROM stdin;
@@ -42,7 +44,6 @@
COPY public.message_broker_server (id, version, created, deleted, host, name, port, updated) FROM stdin;
COPY public.mime (id, version, created, deleted, extension, mime_type, updated) FROM stdin;
COPY public.mime_image_server (id, version, created, deleted, image_server_id, mime_id, updated) FROM stdin;
-COPY public.nested_file (id, version, abstract_image_id, data, filename, original_filename, size) FROM stdin;
COPY public.news (id, version, added, created, deleted, text, updated, user_id) FROM stdin;
COPY public.ontology (id, version, created, deleted, name, updated, user_id) FROM stdin;
COPY public.parameter_constraint (id, version, created, data_type, deleted, expression, name, updated) FROM stdin;
@@ -56,16 +57,17 @@
COPY public.relation (id, version, created, deleted, name, updated) FROM stdin;
COPY public.relation_term (id, version, created, deleted, relation_id, term1_id, term2_id, updated) FROM stdin;
COPY public.retrieval_server (id, version, created, deleted, description, password, path, port, updated, url, username) FROM stdin;
-COPY public.reviewed_annotation (id, version, area, area_unit, count_comments, created, deleted, geometry_compression, image_id, location, parent_class_name, parent_ident, perimeter, perimeter_unit, project_id, review_user_id, status, updated, user_id, wkt_location) FROM stdin;
+COPY public.reviewed_annotation (id, version, area, area_unit, count_comments, created, deleted, geometry_compression, image_id, location, parent_class_name, parent_ident, perimeter, perimeter_unit, project_id, review_user_id, slice_id, status, updated, user_id, wkt_location) FROM stdin;
COPY public.reviewed_annotation_term (reviewed_annotation_terms_id, term_id) FROM stdin;
-COPY public.roi_annotation (id, version, area, area_unit, count_comments, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, updated, user_id, wkt_location) FROM stdin;
+COPY public.roi_annotation (id, version, area, area_unit, count_comments, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, slice_id, updated, user_id, wkt_location) FROM stdin;
COPY public.sample (id, version, created, deleted, name, updated) FROM stdin;
COPY public.search_engine_filter (id, version, created, deleted, filters, name, updated, user_id) FROM stdin;
COPY public.sec_role (id, version, authority, created, deleted, updated) FROM stdin;
-COPY public.sec_user (id, version, account_expired, account_locked, created, deleted, enabled, origin, password, password_expired, private_key, public_key, updated, username, class, color, user_id, email, firstname, language, lastname, job_id, rate) FROM stdin;
+COPY public.sec_user (id, version, account_expired, account_locked, created, deleted, enabled, origin, password, password_expired, private_key, public_key, updated, username, class, color, user_id, email, firstname, is_developer, language, lastname, job_id, rate) FROM stdin;
COPY public.sec_user_sec_role (id, version, created, deleted, sec_role_id, sec_user_id, updated) FROM stdin;
COPY public.shared_annotation (id, version, annotation_class_name, annotation_ident, comment, created, deleted, sender_id, updated) FROM stdin;
COPY public.shared_annotation_user (shared_annotation_receivers_id, user_id) FROM stdin;
+COPY public.slice_instance (id, version, base_slice_id, created, deleted, image_id, project_id, updated) FROM stdin;
COPY public.software (id, version, created, default_processing_server_id, deleted, deprecated, execute_command, name, pulling_command, result_name, software_user_repository_id, software_version, source_path, updated) FROM stdin;
COPY public.software_parameter (id, version, command_line_flag, created, default_value, deleted, human_name, index, name, required, server_parameter, set_by_server, software_id, type, updated, uri, uri_print_attribut, uri_sort_attribut, value_key) FROM stdin;
COPY public.software_parameter_constraint (id, version, created, deleted, parameter_constraint_id, software_parameter_id, updated, value) FROM stdin;
@@ -73,17 +75,17 @@
COPY public.software_user_repository (id, version, created, deleted, docker_username, prefix, provider, updated, username) FROM stdin;
COPY public.source (id, version, created, deleted, name, sample_id, updated) FROM stdin;
COPY public.spatial_ref_sys (srid, auth_name, auth_srid, srtext, proj4text) FROM stdin;
-COPY public.storage (id, version, base_path, created, deleted, name, updated, user_id) FROM stdin;
+COPY public.storage (id, version, created, deleted, name, updated, user_id) FROM stdin;
COPY public.storage_abstract_image (id, version, abstract_image_id, created, deleted, storage_id, updated) FROM stdin;
COPY public.tag (id, version, created, deleted, name, updated, user_id) FROM stdin;
COPY public.tag_domain_association (id, version, created, deleted, domain_class_name, domain_ident, tag_id, updated) FROM stdin;
COPY public.task (id, progress, project_id, user_id, print_in_activity) FROM stdin;
COPY public.task_comment (task_id, comment, "timestamp") FROM stdin;
COPY public.term (id, version, color, comment, created, deleted, name, ontology_id, updated) FROM stdin;
+COPY public.track (id, version, color, created, deleted, image_id, name, project_id, updated) FROM stdin;
COPY public.transaction (id, version, created, deleted, updated) FROM stdin;
COPY public.undo_stack_item (id, version, command_id, created, deleted, is_from_redo, transaction_id, updated, user_id) FROM stdin;
-COPY public.uploaded_file (id, version, content_type, converted, created, deleted, ext, filename, image_id, l_tree, original_filename, parent_id, path, projects, size, status, storages, updated, user_id) FROM stdin;
-COPY public.user_annotation (id, version, area, area_unit, count_comments, count_reviewed_annotations, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, updated, user_id, wkt_location) FROM stdin;
+COPY public.uploaded_file (id, version, content_type, created, deleted, ext, filename, image_server_id, l_tree, original_filename, parent_id, projects, size, status, storage_id, updated, user_id) FROM stdin;
+COPY public.user_annotation (id, version, area, area_unit, count_comments, count_reviewed_annotations, created, deleted, geometry_compression, image_id, location, perimeter, perimeter_unit, project_id, slice_id, updated, user_id, wkt_location) FROM stdin;
COPY public.user_group (id, version, created, deleted, group_id, updated, user_id) FROM stdin;
COPY public.version (nid, deployed, major, minor, patch) FROM stdin;
Postgres log
Excerpt of docker logs -f postgresql after trying to restore a backup from v303 to v323 database:
multiple ERROR: relation " ... " already exists
psql:/BU.sql:2623: ERROR: column "filename" of relation "abstract_image" does not exist
psql:/BU.sql:2624: invalid command \N
psql:/BU.sql:2625: invalid command \N
psql:/BU.sql:3711: ERROR: column "image_id" of relation "annotation_index" does not exist
psql:/BU.sql:3785: invalid command \.
psql:/BU.sql:3792: ERROR: syntax error at or near "1508289"
LINE 1: 1508289 2 0 0 37653 208594
psql:/BU.sql:42405: ERROR: duplicate key value violates unique constraint "command_pkey"
DETAIL: Key (id)=(188) already exists.
CONTEXT: COPY command, line 6
psql:/BU.sql:76990: ERROR: duplicate key value violates unique constraint "command_history_pkey"
DETAIL: Key (id)=(189) already exists.
CONTEXT: COPY command_history, line 6
psql:/BU.sql:77005: ERROR: duplicate key value violates unique constraint "uk_5wejhym1uspe4klluscbwo9r"
DETAIL: Key (key)=(WELCOME) already exists.
CONTEXT: COPY configuration, line 1
psql:/BU.sql:77157: ERROR: duplicate key value violates unique constraint "description_pkey"
DETAIL: Key (id)=(204) already exists.
CONTEXT: COPY description, line 1
DETAIL: Key (user_id)=(1404) is not present in table "sec_user".
COPY 0
psql:/BU.sql:77221: ERROR: duplicate key value violates unique constraint "image_filter_pkey"
DETAIL: Key (id)=(8) already exists.
CONTEXT: COPY image_filter, line 1
psql:/BU.sql:77249: ERROR: insert or update on table "image_filter_project" violates foreign key constraint
"fk_q2eaays0nr0a00cdkahiekobh"
DETAIL: Key (project_id)=(1562) is not present in table "project".
COPY 0
COPY 0
psql:/BU.sql:77272: ERROR: column "channel" of relation "image_instance" does not exist
psql:/BU.sql:77273: invalid command \N
psql:/BU.sql:77274: invalid command \N
Core log
External configuration file : [file:/root/.grails/cytomineconfig.groovy]
Found configuration file ? true
Log4j consoleLevel
External configuration file : [file:/root/.grails/cytomineconfig.groovy]
Found configuration file ? true
15-09-2022 13:52:47,763 INFO HibernatePluginSupport - Set db generation strategy to 'update' for datasource DEFAULT
Configuring Spring Security Core ...
... finished configuring Spring Security Core
Configuring Spring Security ACL ...
... finished configuring Spring Security ACL
15-09-2022 13:52:50,314 INFO CacheBeanPostProcessor - postProcessBeanDefinitionRegistry start
15-09-2022 13:52:50,325 INFO CacheBeanPostProcessor - postProcessBeanFactory
15-09-2022 13:53:00,623 ERROR ConnectionPool - Unable to create initial connections of pool.
org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:297)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49)
at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:217)
at org.postgresql.Driver.makeConnection(Driver.java:458)
at org.postgresql.Driver.connect(Driver.java:260)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
Caused by: java.net.UnknownHostException: postgresql
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:607)
at org.postgresql.core.PGStream.<init>(PGStream.java:81)
at org.postgresql.core.v3.ConnectionFactoryImpl.tryConnect(ConnectionFactoryImpl.java:93)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:197)
... 9 more
15-09-2022 13:53:00,646 ERROR ConnectionPool - Unable to create initial connections of pool.
org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:297)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49)
at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:217)
at org.postgresql.Driver.makeConnection(Driver.java:458)
at org.postgresql.Driver.connect(Driver.java:260)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
Caused by: java.net.UnknownHostException: postgresql
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:607)
at org.postgresql.core.PGStream.<init>(PGStream.java:81)
at org.postgresql.core.v3.ConnectionFactoryImpl.tryConnect(ConnectionFactoryImpl.java:93)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:197)
... 9 more
15-09-2022 13:53:01,305 ERROR ConnectionPool - Unable to create initial connections of pool.
org.postgresql.util.PSQLException: The connection attempt failed.
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:297)
at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:49)
at org.postgresql.jdbc.PgConnection.<init>(PgConnection.java:217)
at org.postgresql.Driver.makeConnection(Driver.java:458)
at org.postgresql.Driver.connect(Driver.java:260)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
Caused by: java.net.UnknownHostException: postgresql
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:607)
at org.postgresql.core.PGStream.<init>(PGStream.java:81)
at org.postgresql.core.v3.ConnectionFactoryImpl.tryConnect(ConnectionFactoryImpl.java:93)
at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:197)
... 9 more
External configuration file : [file:/root/.grails/cytomineconfig.groovy]
Found configuration file ? true
Log4j consoleLevel
External configuration file : [file:/root/.grails/cytomineconfig.groovy]
Found configuration file ? true
15-09-2022 14:38:00,477 INFO HibernatePluginSupport - Set db generation strategy to 'update' for datasource DEFAULT
Configuring Spring Security Core ...
... finished configuring Spring Security Core
Configuring Spring Security ACL ...
... finished configuring Spring Security ACL
15-09-2022 14:38:03,017 INFO CacheBeanPostProcessor - postProcessBeanDefinitionRegistry start
15-09-2022 14:38:03,026 INFO CacheBeanPostProcessor - postProcessBeanFactory
15-09-2022 14:38:08,115 WARN ConfigurationFactory - No configuration found. Configuring ehcache from ehcache-failsafe.xml
found in the classpath: jar:file:/usr/local/tomcat/webapps/ROOT/WEB-INF/lib/ehcache-core-2.4.8.jar!/ehcache-failsafe.xml
15-09-2022 14:38:14,288 INFO DatabaseMetaData - HHH000262: Table not found: abstract_slice
15-09-2022 14:38:14,549 INFO DatabaseMetaData - HHH000262: Table not found: annotation_track
15-09-2022 14:38:14,623 INFO DatabaseMetaData - HHH000262: Table not found: companion_file
15-09-2022 14:38:15,454 INFO DatabaseMetaData - HHH000262: Table not found: slice_instance
15-09-2022 14:38:15,607 INFO DatabaseMetaData - HHH000262: Table not found: track
15-09-2022 14:38:15,734 INFO DatabaseMetaData - HHH000262: Table not found: abstract_slice
15-09-2022 14:38:15,736 INFO DatabaseMetaData - HHH000262: Table not found: annotation_track
15-09-2022 14:38:15,739 INFO DatabaseMetaData - HHH000262: Table not found: companion_file
15-09-2022 14:38:15,741 INFO DatabaseMetaData - HHH000262: Table not found: slice_instance
15-09-2022 14:38:15,743 INFO DatabaseMetaData - HHH000262: Table not found: track
15-09-2022 14:38:15,744 INFO DatabaseMetaData - HHH000262: Table not found: abstract_slice
15-09-2022 14:38:15,746 INFO DatabaseMetaData - HHH000262: Table not found: annotation_track
15-09-2022 14:38:15,748 INFO DatabaseMetaData - HHH000262: Table not found: companion_file
15-09-2022 14:38:15,751 INFO DatabaseMetaData - HHH000262: Table not found: slice_instance
15-09-2022 14:38:15,752 INFO DatabaseMetaData - HHH000262: Table not found: track
15-09-2022 14:39:23,342 WARN ConfigurationFactory - No configuration found. Configuring ehcache from ehcache-failsafe.xml
found in the classpath: jar:file:/usr/local/tomcat/webapps/ROOT/WEB-INF/lib/ehcache-core-2.4.8.jar!/ehcache-failsafe.xml
15-09-2022 14:39:23,372 WARN CacheManager - Creating a new instance of CacheManager using the diskStorePath "/usr/local/to
mcat/temp" which is already used by an existing CacheManager.
The source of the configuration was net.sf.ehcache.config.generator.ConfigurationSource$DefaultConfigurationSource@463a4521
.
The diskStore path for this CacheManager will be set to /usr/local/tomcat/temp/ehcache_auto_created_1663252763372.
To avoid this warning consider using the CacheManager factory methods to create a singleton CacheManager or specifying a se
parate ehcache configuration (ehcache.xml) for each CacheManager instance.
15-09-2022 14:39:24,098 INFO StdSchedulerFactory - Using default implementation for ThreadExecutor
15-09-2022 14:39:24,124 INFO SchedulerSignalerImpl - Initialized Scheduler Signaller of type: class org.quartz.core.Schedu
lerSignalerImpl
15-09-2022 14:39:24,125 INFO QuartzScheduler - Quartz Scheduler v.2.2.1 created.
15-09-2022 14:39:24,128 INFO RAMJobStore - RAMJobStore initialized.
15-09-2022 14:39:24,129 INFO QuartzScheduler - Scheduler meta-data: Quartz Scheduler (v2.2.1) 'quartzScheduler' with insta
nceId 'NON_CLUSTERED'
Scheduler class: 'org.quartz.core.QuartzScheduler' - running locally.
NOT STARTED.
Currently in standby mode.
Number of jobs executed: 0
Using thread pool 'org.quartz.simpl.SimpleThreadPool' - with 10 threads.
Using job-store 'org.quartz.simpl.RAMJobStore' - which does not support persistence. and is not clustered.
15-09-2022 14:39:24,129 INFO StdSchedulerFactory - Quartz scheduler 'quartzScheduler' initialized from an externally provi
ded properties instance.
15-09-2022 14:39:24,130 INFO StdSchedulerFactory - Quartz scheduler version: 2.2.1
15-09-2022 14:39:24,131 INFO QuartzScheduler - JobFactory set to: grails.plugins.quartz.GrailsJobFactory@2c763e41
15-09-2022 14:39:30,791 INFO ResourceProcessor - Performing a full reload
15-09-2022 14:39:30,964 INFO ResourceProcessor - Loading resource declarations...
15-09-2022 14:39:30,965 INFO ResourceProcessor - Forgetting all known modules...
15-09-2022 14:39:30,966 INFO ResourceProcessor - Forgetting all known resources...
15-09-2022 14:39:31,084 WARN ModuleDeclarationsFactory - 'grails.resources.modules' in config does not define any modules
15-09-2022 14:39:31,256 WARN ResourceProcessor - There is a dependency on module [bootstrap] by module [scaffolding] but n
o such module has been defined
15-09-2022 14:39:31,699 ERROR ResourceMeta - Resource not found: /css/scaffolding.css
15-09-2022 14:39:31,711 WARN ResourceProcessor - Cannot locate resource [/css/scaffolding.css]
15-09-2022 14:39:31,712 INFO ResourceProcessor - Finished full reload
15-09-2022 14:39:34,580 INFO MigrationRunner - updateOnStart disabled for dataSource; not running migrations
15-09-2022 14:39:34,982 INFO GrailsConfigUtils - [GrailsContextLoader] Grails application loaded.
15-09-2022 14:39:35,276 INFO QuartzScheduler - Scheduler quartzScheduler_$_NON_CLUSTERED started.
15-09-2022 14:39:37,547 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,547 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,547 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,548 INFO BootStrap -
_____ _ _
/ ____| | | (_)
| | _ _| |_ ___ _ __ ___ _ _ __ ___
| | | | | | __/ _ \| '_ ` _ \| | '_ \ / _ \
| |___| |_| | || (_) | | | | | | | | | | __/
\_____\__, |\__\___/|_| |_| |_|_|_| |_|\___|
| _ \ __/ | | | | |
| |_) ||___/ ___ | |_ ___| |_ _ __ __ _ _ __
| _ < / _ \ / _ \| __/ __| __| '__/ _` | '_ \
| |_) | (_) | (_) | |_\__ \ |_| | | (_| | |_) |
|____/ \___/ \___/ \__|___/\__|_| \__,_| .__/
| |
|_|
15-09-2022 14:39:37,548 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,548 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,548 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,549 INFO BootStrap - Current version 3.2.3
15-09-2022 14:39:37,549 INFO BootStrap - Force version [:]
15-09-2022 14:39:37,597 INFO BootStrap - ##### Environment = production
15-09-2022 14:39:37,597 INFO BootStrap - ##### Server URL = [REDACTED]
15-09-2022 14:39:37,597 INFO BootStrap - ##### Current directory = /usr/local/tomcat/.
15-09-2022 14:39:37,597 INFO BootStrap - ##### HeadLess: = true
15-09-2022 14:39:37,597 INFO BootStrap - ##### SQL = [url:jdbc:postgresql://postgresql:5432/docker, user:docker, password:
docker, driver:org.postgresql.Driver]
15-09-2022 14:39:37,598 INFO BootStrap - ##### NOSQL = [host:mongodb, port:27017, databaseName:cytomine]
15-09-2022 14:39:37,603 INFO BootStrap - ##### Datasource properties = [driverClassName:org.postgresql.Driver, removeAband
oned:false, propagateInterruptState:false, abandonWhenPercentageFull:0, minIdle:50, useEquals:true, defaultReadOnly:false,
timeBetweenEvictionRunsMillis:5000, poolProperties:ConnectionPool[defaultAutoCommit=null; defaultReadOnly=false; defaultTra
nsactionIsolation=-1; defaultCatalog=null; driverClassName=org.postgresql.Driver; maxActive=500; maxIdle=500; minIdle=50; i
nitialSize=50; maxWait=30000; testOnBorrow=false; testOnReturn=false; timeBetweenEvictionRunsMillis=5000; numTestsPerEvicti
onRun=0; minEvictableIdleTimeMillis=60000; testWhileIdle=false; testOnConnect=false; password=********; url=jdbc:postgresql
://postgresql:5432/docker; username=docker; validationQuery=null; validationQueryTimeout=-1; validatorClassName=null; valid
ationInterval=30000; accessToUnderlyingConnectionAllowed=true; removeAbandoned=false; removeAbandonedTimeout=60; logAbandon
ed=false; connectionProperties=null; initSQL=null; jdbcInterceptors=null; jmxEnabled=true; fairQueue=true; useEquals=true;
abandonWhenPercentageFull=0; maxAge=300000; useLock=false; dataSource=null; dataSourceJNDI=null; suspectTimeout=0; alternat
eUsernameAllowed=false; commitOnReturn=false; rollbackOnReturn=false; useDisposableConnectionFacade=true; logValidationErro
rs=false; propagateInterruptState=false; ignoreExceptionOnPreLoad=false; , loginTimeout:30, dbProperties:[user:docker, pass
word:docker], validationInterval:30000, rollbackOnReturn:false, initSQL:null, maxWait:30000, useDisposableConnectionFacade:
true, testOnBorrow:false, suspectTimeout:0, size:50, fairQueue:true, active:0, alternateUsernameAllowed:false, connection:P
roxyConnection[PooledConnection[org.postgresql.jdbc.PgConnection@254a0c7c]], class:class org.apache.tomcat.jdbc.pool.DataSo
urce, testOnReturn:false, pool:org.apache.tomcat.jdbc.pool.ConnectionPool@7f950457, poolName:Tomcat Connection Pool[1-95269
9520], numTestsPerEvictionRun:0, validator:null, dataSource:null, logAbandoned:false, numIdle:49, validatorClassName:null,
removeAbandonedTimeout:60, defaultCatalog:null, minEvictableIdleTimeMillis:60000, poolSweeperEnabled:true, initialSize:50,
jdbcInterceptorsAsArray:[], maxIdle:500, username:docker, url:jdbc:postgresql://postgresql:5432/docker, pooledConnection:Pr
oxyConnection[PooledConnection[org.postgresql.jdbc.PgConnection@5f72e4d6]], connectionAsync:org.apache.tomcat.jdbc.pool.Con
nectionPool$ConnectionFuture@640e861, testOnConnect:false, name:Tomcat Connection Pool[1-952699520], numActive:3, defaultTr
ansactionIsolation:-1, maxActive:500, accessToUnderlyingConnectionAllowed:true, logWriter:null, waitCount:0, password:Passw
ord not available as DataSource/JMX operation., maxAge:300000, validationQueryTimeout:-1, testWhileIdle:false, idle:47, val
idationQuery:null, useLock:false, connectionProperties:null, jdbcInterceptors:null, jmxEnabled:true, logValidationErrors:fa
lse, commitOnReturn:false, poolSize:50, defaultAutoCommit:null, ignoreExceptionOnPreLoad:false, dataSourceJNDI:null]
15-09-2022 14:39:37,604 INFO BootStrap - ##### JVM Args = [-Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.
properties, -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager, -Djava.awt.headless=true, -Xms512m, -Xmx4096
m, -XX:MaxPermSize=512M, -XX:+UseConcMarkSweepGC, -Djavax.servlet.request.encoding=UTF-8, -Dfile.encoding=UTF-8, -Djdk.tls.
ephemeralDHKeySize=2048, -Djava.protocol.handler.pkgs=org.apache.catalina.webresources, -Dorg.apache.catalina.security.Secu
rityListener.UMASK=0027, -Dignore.endorsed.dirs=, -Dcatalina.base=/usr/local/tomcat, -Dcatalina.home=/usr/local/tomcat, -Dj
ava.io.tmpdir=/usr/local/tomcat/temp]
15-09-2022 14:39:37,604 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,604 INFO BootStrap - #############################################################################
15-09-2022 14:39:37,605 INFO BootStrap - #############################################################################
15-09-2022 14:39:38,471 INFO BootStrap - init marshaller...
15-09-2022 14:39:38,631 INFO BootStrap - init sequences...
15-09-2022 14:39:38,727 INFO BootStrap - init trigger...
15-09-2022 14:39:39,135 INFO BootStrap - init index...
15-09-2022 14:39:42,251 INFO BootStrap - init grant...
15-09-2022 14:39:42,268 INFO BootStrap - init table...
15-09-2022 14:39:42,793 INFO BootStrap - init term service...
15-09-2022 14:39:42,944 INFO BootStrap - init retrieve errors hack...
15-09-2022 14:39:42,978 INFO BootStrap - fill with data...
15-09-2022 14:39:42,978 INFO BootStrap - [REDACTED]
15-09-2022 14:39:43,327 INFO BootStrap - init change for old version...
15-09-2022 14:39:43,382 INFO BootstrapOldVersionService - Skip code for initv1_2_1
15-09-2022 14:39:43,383 INFO BootstrapOldVersionService - Skip code for initv2_0_0
15-09-2022 14:39:43,383 INFO BootstrapOldVersionService - Skip code for initv2_1_0
15-09-2022 14:39:43,384 INFO BootstrapOldVersionService - Skip code for initv3_0_0
15-09-2022 14:39:43,384 INFO BootstrapOldVersionService - Skip code for initv3_0_2
15-09-2022 14:39:43,385 INFO BootstrapOldVersionService - Run code for v3.2.0 update
15-09-2022 14:39:43,385 INFO BootstrapOldVersionService - Migration to V3.2.0
15-09-2022 14:39:43,385 INFO BootstrapOldVersionService - Migration of users
15-09-2022 14:39:43,385 INFO BootstrapOldVersionService - Users: Add new column isDeveloper
15-09-2022 14:39:43,431 INFO BootstrapOldVersionService - Migration of jobs
15-09-2022 14:39:43,432 INFO BootstrapOldVersionService - Jobs: Update attached files names of job logs to be displayed in
webUI
15-09-2022 14:39:43,497 INFO BootstrapOldVersionService - Migration of storages
15-09-2022 14:39:43,503 INFO BootstrapOldVersionService - Storage: Update storage references in uploaded_file
15-09-2022 14:39:44,344 INFO BootstrapOldVersionService - Storage: Remove no more used column
15-09-2022 14:39:44,346 INFO BootstrapOldVersionService - Migration of image servers
15-09-2022 14:39:44,346 INFO BootstrapOldVersionService - Image server: Update image server reference in uploaded_file
15-09-2022 14:39:44,710 INFO BootstrapOldVersionService - Image server: Update base path in image_server with known base p
ath
15-09-2022 14:39:44,722 INFO BootstrapOldVersionService - Image server: Remove no more used columns
15-09-2022 14:39:44,730 INFO BootstrapOldVersionService - Migration of uploaded files (1)
15-09-2022 14:39:44,730 INFO BootstrapOldVersionService - Set uploaded files with valid images and status to 'uploaded' as
'deployed'
15-09-2022 14:39:44,732 INFO BootstrapOldVersionService - Remove erroneous uploaded files (filename duplicates)
15-09-2022 14:39:44,749 INFO BootstrapOldVersionService - Migration of abstract slice
15-09-2022 14:39:44,750 INFO BootstrapOldVersionService - Abstract slice: Add (0,0,0) abstract slice for all abstract imag
es
15-09-2022 14:39:44,911 INFO BootstrapOldVersionService - - Inserted 0 elements (0 / 1)
15-09-2022 14:39:44,919 INFO BootstrapOldVersionService - Migration of slice instances
15-09-2022 14:39:44,920 INFO BootstrapOldVersionService - Slice instance: Add (0,0,0) slice instance for all image instanc
es which are not in an image group
15-09-2022 14:39:45,091 INFO BootstrapOldVersionService - - Inserted 0 elements (0 / 1)
15-09-2022 14:39:45,091 INFO BootstrapOldVersionService - Migration of abstract images
15-09-2022 14:39:45,881 ERROR SqlExceptionHelper - ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759
15-09-2022 14:39:45,891 INFO BootstrapOldVersionService - Migration of image instances
15-09-2022 14:39:45,900 INFO JobRunShell - Job GRAILS_JOBS.be.cytomine.job.ExtractImageMetadataJob threw a JobExecutionExc
eption:
org.quartz.JobExecutionException: org.springframework.dao.DeadlockLoserDataAccessException: Hibernate operation: could not
extract ResultSet; SQL [n/a]; ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759; nested exception is org.postgresql.util.PSQLException: ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759 [See nested exception: org.springframework.dao.DeadlockLoserDataAccessException: Hibernate operation: coul
d not extract ResultSet; SQL [n/a]; ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759; nested exception is org.postgresql.util.PSQLException: ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759]
at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:111)
at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:573)
Caused by: org.springframework.dao.DeadlockLoserDataAccessException: Hibernate operation: could not extract ResultSet; SQL
[n/a]; ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759; nested exception is org.postgresql.util.PSQLException: ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759
at org.grails.datastore.gorm.GormStaticApi.methodMissing(GormStaticApi.groovy:104)
at be.cytomine.job.ExtractImageMetadataJob.execute(ExtractImageMetadataJob.groovy:35)
at grails.plugins.quartz.GrailsJobFactory$GrailsJob.execute(GrailsJobFactory.java:104)
... 2 more
Caused by: org.postgresql.util.PSQLException: ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2532)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2267)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:312)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:153)
at org.postgresql.jdbc.PgPreparedStatement.executeQuery(PgPreparedStatement.java:103)
... 5 more
15-09-2022 14:39:45,903 ERROR ExceptionPrinterJobListener - Exception occurred in job: Grails Job
org.quartz.JobExecutionException: org.springframework.dao.DeadlockLoserDataAccessException: Hibernate operation: could not
extract ResultSet; SQL [n/a]; ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759; nested exception is org.postgresql.util.PSQLException: ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
Process 61 waits for AccessExclusiveLock on relation 24763 of database 16385; blocked by process 62.
Hint: See server log for query details.
Position: 1759 [See nested exception: org.springframework.dao.DeadlockLoserDataAccessException: Hibernate operation: coul
d not extract ResultSet; SQL [n/a]; ERROR: deadlock detected
Detail: Process 62 waits for AccessShareLock on relation 25257 of database 16385; blocked by process 61.
after restart of containers:
5-09-2022 14:52:25,541 INFO BootStrap - init change for old version...
15-09-2022 14:52:25,594 INFO BootstrapOldVersionService - Skip code for initv1_2_1
15-09-2022 14:52:25,595 INFO BootstrapOldVersionService - Skip code for initv2_0_0
15-09-2022 14:52:25,596 INFO BootstrapOldVersionService - Skip code for initv2_1_0
15-09-2022 14:52:25,596 INFO BootstrapOldVersionService - Skip code for initv3_0_0
15-09-2022 14:52:25,596 INFO BootstrapOldVersionService - Skip code for initv3_0_2
15-09-2022 14:52:25,597 INFO BootstrapOldVersionService - Run code for v3.2.0 update
15-09-2022 14:52:25,598 INFO BootstrapOldVersionService - Migration to V3.2.0
15-09-2022 14:52:25,598 INFO BootstrapOldVersionService - Migration of users
15-09-2022 14:52:25,598 INFO BootstrapOldVersionService - Users: Add new column isDeveloper
15-09-2022 14:52:25,609 INFO BootstrapOldVersionService - Migration of jobs
15-09-2022 14:52:25,609 INFO BootstrapOldVersionService - Jobs: Update attached files names of job logs to be displayed in
webUI
15-09-2022 14:52:25,611 INFO BootstrapOldVersionService - Migration of storages
15-09-2022 14:52:25,616 INFO BootstrapOldVersionService - Storage: Update storage references in uploaded_file
15-09-2022 14:52:26,068 INFO BootstrapOldVersionService - Storage: Remove no more used column
15-09-2022 14:52:26,071 INFO BootstrapOldVersionService - Migration of image servers
15-09-2022 14:52:26,071 INFO BootstrapOldVersionService - Image server: Update image server reference in uploaded_file
15-09-2022 14:52:26,361 INFO BootstrapOldVersionService - Image server: Update base path in image_server with known base p
ath
15-09-2022 14:52:26,374 INFO BootstrapOldVersionService - Image server: Remove no more used columns
15-09-2022 14:52:26,382 INFO BootstrapOldVersionService - Migration of uploaded files (1)
15-09-2022 14:52:26,383 INFO BootstrapOldVersionService - Set uploaded files with valid images and status to 'uploaded' as
'deployed'
15-09-2022 14:52:26,385 INFO BootstrapOldVersionService - Remove erroneous uploaded files (filename duplicates)
15-09-2022 14:52:26,399 INFO BootstrapOldVersionService - Migration of abstract slice
15-09-2022 14:52:26,400 INFO BootstrapOldVersionService - Abstract slice: Add (0,0,0) abstract slice for all abstract imag
es
15-09-2022 14:52:26,521 INFO BootstrapOldVersionService - - Inserted 0 elements (0 / 1)
15-09-2022 14:52:26,526 INFO BootstrapOldVersionService - Migration of slice instances
15-09-2022 14:52:26,526 INFO BootstrapOldVersionService - Slice instance: Add (0,0,0) slice instance for all image instanc
es which are not in an image group
15-09-2022 14:52:26,648 INFO BootstrapOldVersionService - - Inserted 0 elements (0 / 1)
15-09-2022 14:52:26,649 INFO BootstrapOldVersionService - Migration of abstract images
15-09-2022 14:52:26,666 INFO BootstrapOldVersionService - Migration of image instances
15-09-2022 14:52:26,721 INFO BootstrapOldVersionService - Abstract image: update new fields depth, duration and channels
15-09-2022 14:52:26,811 INFO BootstrapOldVersionService - Abstract image: remove no more used columns
15-09-2022 14:52:26,829 INFO BootstrapOldVersionService - Abstract image: Remove no more used DB cached thumbs
15-09-2022 14:52:26,865 INFO BootstrapOldVersionService - Migration of image instances
15-09-2022 14:52:26,972 INFO BootstrapOldVersionService - Migration of uploaded files (2)
15-09-2022 14:52:26,980 INFO BootstrapOldVersionService - Uploaded file: Change direction of UF - AI relation and use the
root as AI uploaded file
15-09-2022 14:52:26,997 WARN Sql - Failed to execute: update abstract_image set uploaded_file_id = cast(ltree2text(subltre
e(uploaded_file.l_tree, 0, 1)) as bigint) from uploaded_file where abstract_image.id = image_id and uploaded_file_id is nul
l and cast(ltree2text(subltree(uploaded_file.l_tree, 0, 1)) as bigint) IN (SELECT id FROM uploaded_file); because: ERROR: i
nvalid positions
15-09-2022 14:52:27,018 ERROR GrailsContextLoaderListener - Error initializing the application: null
java.lang.reflect.UndeclaredThrowableException
at BootStrap$_closure1.doCall(BootStrap.groovy:205)
at grails.util.Environment.evaluateEnvironmentSpecificBlock(Environment.java:327)
at grails.util.Environment.executeForEnvironment(Environment.java:320)
at grails.util.Environment.executeForCurrentEnvironment(Environment.java:296)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
Caused by: org.postgresql.util.PSQLException: ERROR: invalid positions
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2532)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2267)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:312)
at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
configuration.sh
#URLs
CORE_URL=[REDACTED]
IMS_URL1=[REDACTED]
IMS_URL2=[REDACTED]
UPLOAD_URL=[REDACTED]
#Mail
ADMIN_EMAIL=[REDACTED]
# SENDER_EMAIL, SENDER_EMAIL_PASS, SENDER_EMAIL_SMTP : email params of the sending account
SENDER_EMAIL_PASS='passwd'
SENDER_EMAIL_SMTP_HOST='smtp.gmail.com'
SENDER_EMAIL_SMTP_PORT='587'
SENDER_EMAIL='your.email@gmail.com'
# RECEIVER_EMAIL : email adress of the receiver
RECEIVER_EMAIL='receiver@XXX.com'
#Paths
IMS_STORAGE_PATH=/cm/data/images
IMS_BUFFER_PATH=/cm/data/images/_buffer
BACKUP_PATH=/cm/data/backup
ALGO_PATH=/cm/data/algo/
#middlewares
RABBITMQ_LOGIN="router"
RABBITMQ_PASSWORD="router"
# You don't have to change the datas below this line instead of advanced customization
# ---------------------------
NB_IIP_PROCESS=10
IIP_OFF_URL=localhost-iip-base
IIP_CYTO_URL=localhost-iip-cyto
IIP_JP2_URL=localhost-iip-jp2000
MEMCACHED_PASS="mypass"
BIOFORMAT_ENABLED=true
BIOFORMAT_ALIAS="bioformat"
BIOFORMAT_PORT="4321"
#keys
ADMIN_PWD=$(cat /proc/sys/kernel/random/uuid)
ADMIN_PUB_KEY=$(cat /proc/sys/kernel/random/uuid)
ADMIN_PRIV_KEY=$(cat /proc/sys/kernel/random/uuid)
SUPERADMIN_PUB_KEY=$(cat /proc/sys/kernel/random/uuid)
SUPERADMIN_PRIV_KEY=$(cat /proc/sys/kernel/random/uuid)
RABBITMQ_PUB_KEY=$(cat /proc/sys/kernel/random/uuid)
RABBITMQ_PRIV_KEY=$(cat /proc/sys/kernel/random/uuid)
IMS_PUB_KEY=$(cat /proc/sys/kernel/random/uuid)
IMS_PRIV_KEY=$(cat /proc/sys/kernel/random/uuid)
SERVER_ID=$(cat /proc/sys/kernel/random/uuid)