Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

0.9.2 rc.1 #222

Merged
merged 3 commits into from
Aug 30, 2023
Merged

0.9.2 rc.1 #222

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
06ff503
Handle cache key not found for preprocessing setup
JoQCcoz Aug 30, 2023
a00c49c
udated static
JoQCcoz Aug 30, 2023
fd033fd
Fix entrypoint and initialdb
JoQCcoz Aug 30, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions Docker/entrypoint.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,19 +23,19 @@ fi


#Make sure that the database server is running first.
until mysqladmin ping --user=$MYSQL_USERNAME --password=$MYSQL_ROOT_PASSWORD --host=$MYSQL_HOST > /dev/null;
until mysqladmin ping --user=$MYSQL_USER --password=$MYSQL_PASSWORD --host=$MYSQL_HOST > /dev/null;
do
echo "Database server is not up. Will retryn in 2 seconds"
sleep 2
done
echo "Database server is running."

#Check that the database already exists
result=$(mysql -s -N --user=$MYSQL_USERNAME --password=$MYSQL_ROOT_PASSWORD --host=$MYSQL_HOST $DB_NAME -e "SHOW TABLES");
result=$(mysql -s -N --user=$MYSQL_USER --password=$MYSQL_PASSWORD --host=$MYSQL_HOST $DB_NAME -e "SHOW TABLES");
if [ -z "$result" ];
then
echo "DATABASE DOES NOT EXIST, INITIATING DB."
mysql --user=$MYSQL_USERNAME --password=$MYSQL_ROOT_PASSWORD --host=$MYSQL_HOST $DB_NAME < config/docker/initialdb.sql;
mysql --user=$MYSQL_USER --password=$MYSQL_PASSWORD --host=$MYSQL_HOST $DB_NAME < config/docker/initialdb.sql;
else
echo "DATABASE EXISTS"
fi
Expand Down
3 changes: 3 additions & 0 deletions Smartscope/core/cache.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,5 +9,8 @@
def save_json_from_cache(item_id, directory, file_root_name):
cached_item = cache.get(item_id)
logger.debug(f'Getting {file_root_name} from cache at id {item_id}:\n{cached_item}')
if cached_item is None:
logger.info('Could get the preprocessing settings from cache, using default pipeline.')
return
with open(Path(directory,f'{file_root_name}.json'),'w') as f:
f.write(cached_item)
Binary file removed Smartscope/mydatabase
View file
Open in desktop
Binary file not shown.
31 changes: 19 additions & 12 deletions config/docker/initialdb.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
-- MySQL dump 10.16 Distrib 10.1.48-MariaDB, for debian-linux-gnu (x86_64)
-- MySQL dump 10.19 Distrib 10.3.38-MariaDB, for debian-linux-gnu (x86_64)
--
-- Host: db Database: smartscope
-- ------------------------------------------------------
-- Server version 10.5.18-MariaDB-1:10.5.18+maria~ubu2004
-- Server version 10.5.22-MariaDB-1:10.5.22+maria~ubu2004

/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
Expand Down Expand Up @@ -159,7 +159,7 @@ CREATE TABLE `auth_user` (

LOCK TABLES `auth_user` WRITE;
/*!40000 ALTER TABLE `auth_user` DISABLE KEYS */;
INSERT INTO `auth_user` VALUES (56,'pbkdf2_sha256$320000$QgE4VdjFNhpVdEJSNd3heF$gQjO88hB6TkSGvBpuzMWsEpGUP30ID52CESg7SvRGVs=','2022-07-21 15:14:08.963283',1,'admin','','','',1,1,'2022-05-27 13:07:14.000000');
INSERT INTO `auth_user` VALUES (56,'pbkdf2_sha256$600000$P9VVxQ49PnoOWIrgHy7Pa9$uwKZYfgrnTLO/EEd42eR89xfRbxuVhTRyvk+rS0pHLQ=','2023-08-30 15:42:57.715206',1,'admin','','','',1,1,'2022-05-27 13:07:14.000000');
/*!40000 ALTER TABLE `auth_user` ENABLE KEYS */;
UNLOCK TABLES;

Expand Down Expand Up @@ -380,6 +380,7 @@ CREATE TABLE `detector` (
`frames_windows_directory` varchar(200) NOT NULL,
`atlas_to_search_offset_x` double NOT NULL,
`atlas_to_search_offset_y` double NOT NULL,
`atlas_c2_aperture` int(11) NOT NULL,
PRIMARY KEY (`id`),
KEY `detector_microscope_id_id_c62bb405_fk_microscope_microscope_id` (`microscope_id_id`),
CONSTRAINT `detector_microscope_id_id_c62bb405_fk_microscope_microscope_id` FOREIGN KEY (`microscope_id_id`) REFERENCES `microscope` (`microscope_id`)
Expand All @@ -392,7 +393,7 @@ CREATE TABLE `detector` (

LOCK TABLES `detector` WRITE;
/*!40000 ALTER TABLE `detector` DISABLE KEYS */;
INSERT INTO `detector` VALUES (3,'test_K2','K2',62,6,6,5,'alignframes',3,1,0,'h0PgRUjUq2K2Cr1CGZJq3q08il8i5n',100,'/mnt/scope/movies/','movies',0,0);
INSERT INTO `detector` VALUES (3,'test_K2','K2',62,6,6,5,'alignframes',3,1,0,'h0PgRUjUq2K2Cr1CGZJq3q08il8i5n',100,'/mnt/fake_scope/movies/','movies',0,0,70);
/*!40000 ALTER TABLE `detector` ENABLE KEYS */;
UNLOCK TABLES;

Expand All @@ -417,7 +418,7 @@ CREATE TABLE `django_admin_log` (
KEY `django_admin_log_user_id_c564eba6_fk_auth_user_id` (`user_id`),
CONSTRAINT `django_admin_log_content_type_id_c4bce8eb_fk_django_co` FOREIGN KEY (`content_type_id`) REFERENCES `django_content_type` (`id`),
CONSTRAINT `django_admin_log_user_id_c564eba6_fk_auth_user_id` FOREIGN KEY (`user_id`) REFERENCES `auth_user` (`id`)
) ENGINE=InnoDB AUTO_INCREMENT=276 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
) ENGINE=InnoDB AUTO_INCREMENT=277 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
/*!40101 SET character_set_client = @saved_cs_client */;

--
Expand All @@ -426,6 +427,7 @@ CREATE TABLE `django_admin_log` (

LOCK TABLES `django_admin_log` WRITE;
/*!40000 ALTER TABLE `django_admin_log` DISABLE KEYS */;
INSERT INTO `django_admin_log` VALUES (276,'2023-08-30 15:45:37.073664','3','test - fake_scope - test_K2',2,'[{\"changed\": {\"fields\": [\"Frames directory\"]}}]',10,56);
/*!40000 ALTER TABLE `django_admin_log` ENABLE KEYS */;
UNLOCK TABLES;

Expand Down Expand Up @@ -468,7 +470,7 @@ CREATE TABLE `django_migrations` (
`name` varchar(255) NOT NULL,
`applied` datetime(6) NOT NULL,
PRIMARY KEY (`id`)
) ENGINE=InnoDB AUTO_INCREMENT=33 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
) ENGINE=InnoDB AUTO_INCREMENT=39 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
/*!40101 SET character_set_client = @saved_cs_client */;

--
Expand All @@ -477,7 +479,7 @@ CREATE TABLE `django_migrations` (

LOCK TABLES `django_migrations` WRITE;
/*!40000 ALTER TABLE `django_migrations` DISABLE KEYS */;
INSERT INTO `django_migrations` VALUES (1,'contenttypes','0001_initial','2022-03-28 19:45:39.604977'),(2,'contenttypes','0002_remove_content_type_name','2022-03-28 19:45:39.871200'),(3,'auth','0001_initial','2022-03-28 19:45:40.690613'),(4,'auth','0002_alter_permission_name_max_length','2022-03-28 19:45:44.021735'),(5,'auth','0003_alter_user_email_max_length','2022-03-28 19:45:44.071631'),(6,'auth','0004_alter_user_username_opts','2022-03-28 19:45:44.090858'),(7,'auth','0005_alter_user_last_login_null','2022-03-28 19:45:44.313585'),(8,'auth','0006_require_contenttypes_0002','2022-03-28 19:45:44.343315'),(9,'auth','0007_alter_validators_add_error_messages','2022-03-28 19:45:44.376690'),(10,'auth','0008_alter_user_username_max_length','2022-03-28 19:45:44.438401'),(11,'auth','0009_alter_user_last_name_max_length','2022-03-28 19:45:44.521934'),(12,'auth','0010_alter_group_name_max_length','2022-03-28 19:45:44.580201'),(13,'auth','0011_update_proxy_permissions','2022-03-28 19:45:44.598903'),(14,'auth','0012_alter_user_first_name_max_length','2022-03-28 19:45:44.671816'),(15,'API','0001_initial','2022-03-28 19:45:49.766699'),(16,'admin','0001_initial','2022-03-28 19:45:55.635521'),(17,'admin','0002_logentry_remove_auto_add','2022-03-28 19:45:56.199706'),(18,'admin','0003_logentry_add_action_flag_choices','2022-03-28 19:45:56.234886'),(19,'authtoken','0001_initial','2022-03-28 19:45:56.442933'),(20,'authtoken','0002_auto_20160226_1747','2022-03-28 19:45:57.490956'),(21,'authtoken','0003_tokenproxy','2022-03-28 19:45:57.512029'),(22,'sessions','0001_initial','2022-03-28 19:45:57.662359'),(23,'API','0002_microscope_scope_path','2022-03-30 14:50:35.954750'),(24,'API','0003_detector_c2_perc','2022-03-30 15:45:54.807446'),(25,'API','0002_auto_20220608_1836','2022-07-02 11:03:11.526775'),(26,'API','0003_remove_holemodel_dist_from_center_and_more','2022-07-02 11:03:11.571192'),(27,'API','0004_v07','2022-07-21 15:57:10.854652'),(28,'API','0005_v07_2','2022-07-21 15:57:10.980773'),(29,'API','0006_detector_frames_directory_and_more','2023-02-06 19:00:42.786828'),(30,'API','0007_detector_atlas_to_search_offset_x_and_more','2023-02-06 19:00:42.834656'),(31,'API','0008_highmagmodel_selected_alter_microscope_location_and_more','2023-02-06 19:00:42.874391'),(32,'API','0009_selector_value','2023-02-06 19:00:42.887843');
INSERT INTO `django_migrations` VALUES (1,'contenttypes','0001_initial','2022-03-28 19:45:39.604977'),(2,'contenttypes','0002_remove_content_type_name','2022-03-28 19:45:39.871200'),(3,'auth','0001_initial','2022-03-28 19:45:40.690613'),(4,'auth','0002_alter_permission_name_max_length','2022-03-28 19:45:44.021735'),(5,'auth','0003_alter_user_email_max_length','2022-03-28 19:45:44.071631'),(6,'auth','0004_alter_user_username_opts','2022-03-28 19:45:44.090858'),(7,'auth','0005_alter_user_last_login_null','2022-03-28 19:45:44.313585'),(8,'auth','0006_require_contenttypes_0002','2022-03-28 19:45:44.343315'),(9,'auth','0007_alter_validators_add_error_messages','2022-03-28 19:45:44.376690'),(10,'auth','0008_alter_user_username_max_length','2022-03-28 19:45:44.438401'),(11,'auth','0009_alter_user_last_name_max_length','2022-03-28 19:45:44.521934'),(12,'auth','0010_alter_group_name_max_length','2022-03-28 19:45:44.580201'),(13,'auth','0011_update_proxy_permissions','2022-03-28 19:45:44.598903'),(14,'auth','0012_alter_user_first_name_max_length','2022-03-28 19:45:44.671816'),(15,'API','0001_initial','2022-03-28 19:45:49.766699'),(16,'admin','0001_initial','2022-03-28 19:45:55.635521'),(17,'admin','0002_logentry_remove_auto_add','2022-03-28 19:45:56.199706'),(18,'admin','0003_logentry_add_action_flag_choices','2022-03-28 19:45:56.234886'),(19,'authtoken','0001_initial','2022-03-28 19:45:56.442933'),(20,'authtoken','0002_auto_20160226_1747','2022-03-28 19:45:57.490956'),(21,'authtoken','0003_tokenproxy','2022-03-28 19:45:57.512029'),(22,'sessions','0001_initial','2022-03-28 19:45:57.662359'),(23,'API','0002_microscope_scope_path','2022-03-30 14:50:35.954750'),(24,'API','0003_detector_c2_perc','2022-03-30 15:45:54.807446'),(25,'API','0002_auto_20220608_1836','2022-07-02 11:03:11.526775'),(26,'API','0003_remove_holemodel_dist_from_center_and_more','2022-07-02 11:03:11.571192'),(27,'API','0004_v07','2022-07-21 15:57:10.854652'),(28,'API','0005_v07_2','2022-07-21 15:57:10.980773'),(29,'API','0006_detector_frames_directory_and_more','2023-02-06 19:00:42.786828'),(30,'API','0007_detector_atlas_to_search_offset_x_and_more','2023-02-06 19:00:42.834656'),(31,'API','0008_highmagmodel_selected_alter_microscope_location_and_more','2023-02-06 19:00:42.874391'),(32,'API','0009_selector_value','2023-02-06 19:00:42.887843'),(33,'API','0010_gridcollectionparams_multishot_per_hole_and_more','2023-08-30 15:42:47.337920'),(34,'API','0011_alter_screeningsession_version','2023-08-30 15:42:47.353948'),(35,'API','0012_gridcollectionparams_hardwaredark_delay_and_more','2023-08-30 15:42:47.375054'),(36,'API','0013_gridcollectionparams_afis','2023-08-30 15:42:47.387238'),(37,'API','0014_alter_holemodel_unique_together_and_more','2023-08-30 15:42:47.461040'),(38,'API','0015_detector_atlas_c2_aperture_and_more','2023-08-30 15:42:47.514252');
/*!40000 ALTER TABLE `django_migrations` ENABLE KEYS */;
UNLOCK TABLES;

Expand All @@ -503,6 +505,7 @@ CREATE TABLE `django_session` (

LOCK TABLES `django_session` WRITE;
/*!40000 ALTER TABLE `django_session` DISABLE KEYS */;
INSERT INTO `django_session` VALUES ('jj7gcq0w6hzuc2kv176lu2c57kv2rpal','.eJxVjEEOgjAQRe_StWlomU5bl-45QzOdoYIaSCisjHcXEha6fe_9_1aJtnVIW-2XNIq6Kofq8gsz8bOfDiMPmu6z5nlalzHrI9GnrbqbpX_dzvbvYKA67OviIGQroaAUCySO0ZsWoVjCwLxDEh8acNDECJxDMYARneeWjZBXny8XEDgh:1qbNLN:lUFZ_20Eb7vTr2-lh5_29NHEZnW2_hVKYZFq12o_2dU','2023-09-13 15:42:57.765024');
/*!40000 ALTER TABLE `django_session` ENABLE KEYS */;
UNLOCK TABLES;

Expand Down Expand Up @@ -566,6 +569,10 @@ CREATE TABLE `gridcollectionparams` (
`offset_distance` double NOT NULL,
`offset_targeting` tinyint(1) NOT NULL,
`force_process_from_average` tinyint(1) NOT NULL,
`multishot_per_hole` tinyint(1) NOT NULL,
`hardwaredark_delay` int(11) NOT NULL,
`afis` tinyint(1) NOT NULL,
`coldfegflash_delay` int(11) NOT NULL,
PRIMARY KEY (`params_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
Expand Down Expand Up @@ -647,7 +654,6 @@ CREATE TABLE `holemodel` (
`grid_id_id` varchar(30) NOT NULL,
`square_id_id` varchar(30) NOT NULL,
PRIMARY KEY (`hole_id`),
UNIQUE KEY `holemodel_name_square_id_id_3d66de91_uniq` (`name`,`square_id_id`),
KEY `holemodel_grid_id_id_e0af6c4d_fk_autoloadergrid_grid_id` (`grid_id_id`),
KEY `holemodel_square_id_id_b73a5e24_fk_squaremodel_square_id` (`square_id_id`),
CONSTRAINT `holemodel_grid_id_id_e0af6c4d_fk_autoloadergrid_grid_id` FOREIGN KEY (`grid_id_id`) REFERENCES `autoloadergrid` (`grid_id`),
Expand Down Expand Up @@ -759,6 +765,8 @@ CREATE TABLE `microscope` (
`windows_path` varchar(200) NOT NULL,
`scope_path` varchar(200) NOT NULL,
`vendor` varchar(30) NOT NULL,
`aperture_control` tinyint(1) NOT NULL,
`cold_FEG` tinyint(1) NOT NULL,
PRIMARY KEY (`microscope_id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
Expand All @@ -769,7 +777,7 @@ CREATE TABLE `microscope` (

LOCK TABLES `microscope` WRITE;
/*!40000 ALTER TABLE `microscope` DISABLE KEYS */;
INSERT INTO `microscope` VALUES ('fake_scope','test',200,2.7,'h0PgRUjUq2K2Cr1CGZJq3q08il8i5n',12,'localhost','smartscope.py','xxx.xxx.xxx.xxx',48888,'X:\\\\auto_screening\\','/mnt/fake_scope','TFS');
INSERT INTO `microscope` VALUES ('fake_scope','test',200,2.7,'h0PgRUjUq2K2Cr1CGZJq3q08il8i5n',12,'localhost','smartscope.py','xxx.xxx.xxx.xxx',48888,'X:\\\\auto_screening\\','/mnt/fake_scope','TFS',0,0);
/*!40000 ALTER TABLE `microscope` ENABLE KEYS */;
UNLOCK TABLES;

Expand Down Expand Up @@ -812,7 +820,7 @@ DROP TABLE IF EXISTS `screeningsession`;
CREATE TABLE `screeningsession` (
`session` varchar(30) NOT NULL,
`date` varchar(8) NOT NULL,
`version` varchar(8) NOT NULL,
`version` varchar(20) NOT NULL,
`working_dir` varchar(300) NOT NULL,
`session_id` varchar(30) NOT NULL,
`detector_id_id` int(11) DEFAULT NULL,
Expand Down Expand Up @@ -888,7 +896,6 @@ CREATE TABLE `squaremodel` (
`atlas_id_id` varchar(30) NOT NULL,
`grid_id_id` varchar(30) NOT NULL,
PRIMARY KEY (`square_id`),
UNIQUE KEY `squaremodel_name_atlas_id_id_cdc2974a_uniq` (`name`,`atlas_id_id`),
KEY `squaremodel_atlas_id_id_89647666_fk_atlasmodel_atlas_id` (`atlas_id_id`),
KEY `squaremodel_grid_id_id_775a3fee_fk_autoloadergrid_grid_id` (`grid_id_id`),
CONSTRAINT `squaremodel_atlas_id_id_89647666_fk_atlasmodel_atlas_id` FOREIGN KEY (`atlas_id_id`) REFERENCES `atlasmodel` (`atlas_id`),
Expand All @@ -914,4 +921,4 @@ UNLOCK TABLES;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;

-- Dump completed on 2023-02-06 19:04:07
-- Dump completed on 2023-08-30 15:47:17
Binary file removed ctffind
View file
Open in desktop
Binary file not shown.
61 changes: 0 additions & 61 deletions docker-compose-template.yml
View file
Open in desktop

This file was deleted.

Loading