55 dockerize sql database again

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[jess789550]

Great work! Docker works :)

But I've got a couple of errors - one with the BED file and another with the database:

If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2. 1 Enter your search term: (e.g., R128 or pneumothorax) R128 Which genome build would you like to use? Enter 1 for GRCh37. Enter 2 for GRCh38. 1 2024-01-03 10:54:50,032 INFO: Starting PanelSearch with input type: R-code GRch37 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Ensembl_ID Mane_Select_Transcript HGNC:10593 SCN5A 3:38589548-38691164 ENSG00000183873 NM_000335.5 HGNC:6251 KCNH2 7:150642049-150675403 ENSG00000055118 NM_000238.4 HGNC:60 ABCC9 12:21950335-22094336 ENSG00000069431 NM_020297.4 HGNC:493 ANK2 4:113739265-114304896 ENSG00000145362 NM_001148.6 HGNC:1390 CACNA1C 12:2079952-2802108 ENSG00000151067 NM_000719.7 HGNC:1399 CACNA2D1 7:81575760-82073114 ENSG00000153956 NM_000722.4 HGNC:1402 CACNB2 10:18429606-18830798 ENSG00000165995 NM_201596.3 HGNC:1529 CAV3 3:8775486-8883492 ENSG00000182533 NM_033337.3 HGNC:2900 DLG1 3:196769431-197026171 ENSG00000075711 NM_001366207.1 HGNC:28956 GPD1L 3:32147181-32210205 ENSG00000152642 NM_015141.4 HGNC:16882 HCN4 15:73612200-73661605 ENSG00000138622 NM_005477.3 HGNC:6239 KCND3 1:112313284-112531777 ENSG00000171385 NM_001378969.1 HGNC:6243 KCNE3 11:74165886-74178774 ENSG00000175538 NM_005472.5 HGNC:6241 KCNE5 X:108866929-108868393 ENSG00000176076 NM_012282.4 HGNC:6269 KCNJ8 12:21917889-21928515 ENSG00000121361 NM_004982.4 HGNC:9024 PKP2 12:32943679-33049774 ENSG00000057294 NM_001005242.3 HGNC:17679 RANGRF 17:8191815-8193410 ENSG00000108961 NM_016492.5 HGNC:10582 SCN10A 3:38738293-38835501 ENSG00000185313 NM_006514.4 HGNC:10586 SCN1B 19:35521588-35531352 ENSG00000105711 NM_001037.5 HGNC:10589 SCN2B 11:118032666-118047388 ENSG00000149575 NM_004588.5 HGNC:20665 SCN3B 11:123499895-123525952 ENSG00000166257 NM_001040151.2 HGNC:16643 SLMAP 3:57741177-57914895 ENSG00000163681 NM_001377540.1 HGNC:17993 TRPM4 19:49660998-49715093 ENSG00000130529 NM_017636.4 2024-01-03 10:54:52,388 INFO: Panel data processed successfully Generate BED file? (Y/N) Y python: can't open file '/app/generate_bed.py': [Errno 2] No such file or directory 2024-01-03 10:54:53,826 INFO: BED file generation initiated Would you like to save this search against a patient ID? (Y/N) Y What patient ID would you like to save this search against? tester Brugada syndrome and cardiac sodium channel disease GRch37 GRch37 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Ensembl_ID Mane_Select_Transcript HGNC:10593 SCN5A 3:38589548-38691164 ENSG00000183873 NM_000335.5 HGNC:6251 KCNH2 7:150642049-150675403 ENSG00000055118 NM_000238.4 HGNC:60 ABCC9 12:21950335-22094336 ENSG00000069431 NM_020297.4 HGNC:493 ANK2 4:113739265-114304896 ENSG00000145362 NM_001148.6 HGNC:1390 CACNA1C 12:2079952-2802108 ENSG00000151067 NM_000719.7 HGNC:1399 CACNA2D1 7:81575760-82073114 ENSG00000153956 NM_000722.4 HGNC:1402 CACNB2 10:18429606-18830798 ENSG00000165995 NM_201596.3 HGNC:1529 CAV3 3:8775486-8883492 ENSG00000182533 NM_033337.3 HGNC:2900 DLG1 3:196769431-197026171 ENSG00000075711 NM_001366207.1 HGNC:28956 GPD1L 3:32147181-32210205 ENSG00000152642 NM_015141.4 HGNC:16882 HCN4 15:73612200-73661605 ENSG00000138622 NM_005477.3 HGNC:6239 KCND3 1:112313284-112531777 ENSG00000171385 NM_001378969.1 HGNC:6243 KCNE3 11:74165886-74178774 ENSG00000175538 NM_005472.5 HGNC:6241 KCNE5 X:108866929-108868393 ENSG00000176076 NM_012282.4 HGNC:6269 KCNJ8 12:21917889-21928515 ENSG00000121361 NM_004982.4 HGNC:9024 PKP2 12:32943679-33049774 ENSG00000057294 NM_001005242.3 HGNC:17679 RANGRF 17:8191815-8193410 ENSG00000108961 NM_016492.5 HGNC:10582 SCN10A 3:38738293-38835501 ENSG00000185313 NM_006514.4 HGNC:10586 SCN1B 19:35521588-35531352 ENSG00000105711 NM_001037.5 HGNC:10589 SCN2B 11:118032666-118047388 ENSG00000149575 NM_004588.5 HGNC:20665 SCN3B 11:123499895-123525952 ENSG00000166257 NM_001040151.2 HGNC:16643 SLMAP 3:57741177-57914895 ENSG00000163681 NM_001377540.1 HGNC:17993 TRPM4 19:49660998-49715093 ENSG00000130529 NM_017636.4 Traceback (most recent call last): File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 145, in init self._dbapi_connection = engine.raw_connection() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 3292, in raw_connection return self.pool.connect() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 452, in connect return _ConnectionFairy._checkout(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 1269, in _checkout fairy = _ConnectionRecord.checkout(pool) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 716, in checkout rec = pool._do_get() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/impl.py", line 169, in _do_get with util.safe_reraise(): File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/langhelpers.py", line 146, in exit raise exc_value.with_traceback(exc_tb) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/impl.py", line 167, in _do_get return self._create_connection() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 393, in _create_connection return _ConnectionRecord(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 678, in init self.connect() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 902, in connect with util.safe_reraise(): File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/langhelpers.py", line 146, in exit raise exc_value.with_traceback(exc_tb) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 898, in connect self.dbapi_connection = connection = pool._invoke_creator(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 637, in connect return dialect.connect(*cargs, *cparams) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 616, in connect return self.loaded_dbapi.connect(cargs, **cparams) File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 358, in init__ self.connect() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 664, in connect self._request_authentication() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 976, in _request_authentication auth_packet = _auth.caching_sha2_password_auth(self, auth_packet) File "/usr/local/lib/python3.10/site-packages/pymysql/_auth.py", line 267, in caching_sha2_password_auth pkt = _roundtrip(conn, data) File "/usr/local/lib/python3.10/site-packages/pymysql/_auth.py", line 120, in _roundtrip pkt = conn._read_packet() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 772, in _read_packet packet.raise_for_error() File "/usr/local/lib/python3.10/site-packages/pymysql/protocol.py", line 221, in raise_for_error err.raise_mysql_exception(self._data) File "/usr/local/lib/python3.10/site-packages/pymysql/err.py", line 143, in raise_mysql_exception raise errorclass(errno, errval) pymysql.err.OperationalError: (1049, "Unknown database 'panelsearch'")

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/app/./PanelSearch/main.py", line 148, in main() File "/app/./PanelSearch/main.py", line 135, in main create_sql_record(panel_name,SEARCH.genome_build, pid) File "/app/./PanelSearch/main.py", line 81, in create_sql_record PK_Parse_Data_to_SQL_cloud(pid,genome_build,PK = panel_name) File "/app/PanelSearch/API_to_SQL_cloud.py", line 23, in PK_Parse_Data_to_SQL_cloud add_new_cloud_record(pid = pid,panel_id = panel_id,panel_name = panel_name, panel_version = panel_version,GMS= GMS,gene_number= gene_number,r_code= r_code , transcript = "a really good one",genome_build = genome_build,bed_file="placeholder") File "/app/PanelSearch/SQL_Cloud_Functions.py", line 35, in add_new_cloud_record with engine.connect() as conn: File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 3268, in connect return self._connection_cls(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 147, in init Connection._handle_dbapi_exception_noconnection( File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 2430, in _handle_dbapi_exception_noconnection raise sqlalchemy_exception.with_traceback(exc_info[2]) from e File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 145, in init self._dbapi_connection = engine.raw_connection() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 3292, in raw_connection return self.pool.connect() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 452, in connect return _ConnectionFairy._checkout(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 1269, in _checkout fairy = _ConnectionRecord.checkout(pool) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 716, in checkout rec = pool._do_get() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/impl.py", line 169, in _do_get with util.safe_reraise(): File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/langhelpers.py", line 146, in exit raise exc_value.with_traceback(exc_tb) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/impl.py", line 167, in _do_get return self._create_connection() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 393, in _create_connection return _ConnectionRecord(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 678, in init self.connect() File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 902, in connect with util.safe_reraise(): File "/usr/local/lib/python3.10/site-packages/sqlalchemy/util/langhelpers.py", line 146, in exit raise exc_value.with_traceback(exc_tb) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/pool/base.py", line 898, in connect self.dbapi_connection = connection = pool._invoke_creator(self) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/create.py", line 637, in connect return dialect.connect(*cargs, *cparams) File "/usr/local/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 616, in connect return self.loaded_dbapi.connect(cargs, **cparams) File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 358, in init__ self.connect() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 664, in connect self._request_authentication() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 976, in _request_authentication auth_packet = _auth.caching_sha2_password_auth(self, auth_packet) File "/usr/local/lib/python3.10/site-packages/pymysql/_auth.py", line 267, in caching_sha2_password_auth pkt = _roundtrip(conn, data) File "/usr/local/lib/python3.10/site-packages/pymysql/_auth.py", line 120, in _roundtrip pkt = conn._read_packet() File "/usr/local/lib/python3.10/site-packages/pymysql/connections.py", line 772, in _read_packet packet.raise_for_error() File "/usr/local/lib/python3.10/site-packages/pymysql/protocol.py", line 221, in raise_for_error err.raise_mysql_exception(self._data) File "/usr/local/lib/python3.10/site-packages/pymysql/err.py", line 143, in raise_mysql_exception raise errorclass(errno, errval) sqlalchemy.exc.OperationalError: (pymysql.err.OperationalError) (1049, "Unknown database 'panelsearch'") (Background on this error at: https://sqlalche.me/e/20/e3q8)

[jess789550]

Refreshed docker - database ok but issue with BED file persists:

panelsearch app container created
running panelsearch app... If you would like to search by R-code, enter 1. If you would like to enter a disease description, enter 2. 1 Enter your search term: (e.g., R128 or pneumothorax) R128 Which genome build would you like to use? Enter 1 for GRCh37. Enter 2 for GRCh38. 1 2024-01-03 11:30:25,984 INFO: Starting PanelSearch with input type: R-code GRch37 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Ensembl_ID Mane_Select_Transcript HGNC:10593 SCN5A 3:38589548-38691164 ENSG00000183873 NM_000335.5 HGNC:6251 KCNH2 7:150642049-150675403 ENSG00000055118 NM_000238.4 HGNC:60 ABCC9 12:21950335-22094336 ENSG00000069431 NM_020297.4 HGNC:493 ANK2 4:113739265-114304896 ENSG00000145362 NM_001148.6 HGNC:1390 CACNA1C 12:2079952-2802108 ENSG00000151067 NM_000719.7 HGNC:1399 CACNA2D1 7:81575760-82073114 ENSG00000153956 NM_000722.4 HGNC:1402 CACNB2 10:18429606-18830798 ENSG00000165995 NM_201596.3 HGNC:1529 CAV3 3:8775486-8883492 ENSG00000182533 NM_033337.3 HGNC:2900 DLG1 3:196769431-197026171 ENSG00000075711 NM_001366207.1 HGNC:28956 GPD1L 3:32147181-32210205 ENSG00000152642 NM_015141.4 HGNC:16882 HCN4 15:73612200-73661605 ENSG00000138622 NM_005477.3 HGNC:6239 KCND3 1:112313284-112531777 ENSG00000171385 NM_001378969.1 HGNC:6243 KCNE3 11:74165886-74178774 ENSG00000175538 NM_005472.5 HGNC:6241 KCNE5 X:108866929-108868393 ENSG00000176076 NM_012282.4 HGNC:6269 KCNJ8 12:21917889-21928515 ENSG00000121361 NM_004982.4 HGNC:9024 PKP2 12:32943679-33049774 ENSG00000057294 NM_001005242.3 HGNC:17679 RANGRF 17:8191815-8193410 ENSG00000108961 NM_016492.5 HGNC:10582 SCN10A 3:38738293-38835501 ENSG00000185313 NM_006514.4 HGNC:10586 SCN1B 19:35521588-35531352 ENSG00000105711 NM_001037.5 HGNC:10589 SCN2B 11:118032666-118047388 ENSG00000149575 NM_004588.5 HGNC:20665 SCN3B 11:123499895-123525952 ENSG00000166257 NM_001040151.2 HGNC:16643 SLMAP 3:57741177-57914895 ENSG00000163681 NM_001377540.1 HGNC:17993 TRPM4 19:49660998-49715093 ENSG00000130529 NM_017636.4 2024-01-03 11:30:28,453 INFO: Panel data processed successfully Generate BED file? (Y/N) Y python: can't open file '/app/generate_bed.py': [Errno 2] No such file or directory 2024-01-03 11:30:29,745 INFO: BED file generation initiated Would you like to save this search against a patient ID? (Y/N) Y What patient ID would you like to save this search against? seras Brugada syndrome and cardiac sodium channel disease GRch37 GRch37 build selected. Panel ID: 13 Panel Name: Brugada syndrome and cardiac sodium channel disease GMS Sign-off Status: Signed Off Associated NGTD R-codes: R128 Gene Number: 23 Gene List: HGNC_ID Symbol Coords Ensembl_ID Mane_Select_Transcript HGNC:10593 SCN5A 3:38589548-38691164 ENSG00000183873 NM_000335.5 HGNC:6251 KCNH2 7:150642049-150675403 ENSG00000055118 NM_000238.4 HGNC:60 ABCC9 12:21950335-22094336 ENSG00000069431 NM_020297.4 HGNC:493 ANK2 4:113739265-114304896 ENSG00000145362 NM_001148.6 HGNC:1390 CACNA1C 12:2079952-2802108 ENSG00000151067 NM_000719.7 HGNC:1399 CACNA2D1 7:81575760-82073114 ENSG00000153956 NM_000722.4 HGNC:1402 CACNB2 10:18429606-18830798 ENSG00000165995 NM_201596.3 HGNC:1529 CAV3 3:8775486-8883492 ENSG00000182533 NM_033337.3 HGNC:2900 DLG1 3:196769431-197026171 ENSG00000075711 NM_001366207.1 HGNC:28956 GPD1L 3:32147181-32210205 ENSG00000152642 NM_015141.4 HGNC:16882 HCN4 15:73612200-73661605 ENSG00000138622 NM_005477.3 HGNC:6239 KCND3 1:112313284-112531777 ENSG00000171385 NM_001378969.1 HGNC:6243 KCNE3 11:74165886-74178774 ENSG00000175538 NM_005472.5 HGNC:6241 KCNE5 X:108866929-108868393 ENSG00000176076 NM_012282.4 HGNC:6269 KCNJ8 12:21917889-21928515 ENSG00000121361 NM_004982.4 HGNC:9024 PKP2 12:32943679-33049774 ENSG00000057294 NM_001005242.3 HGNC:17679 RANGRF 17:8191815-8193410 ENSG00000108961 NM_016492.5 HGNC:10582 SCN10A 3:38738293-38835501 ENSG00000185313 NM_006514.4 HGNC:10586 SCN1B 19:35521588-35531352 ENSG00000105711 NM_001037.5 HGNC:10589 SCN2B 11:118032666-118047388 ENSG00000149575 NM_004588.5 HGNC:20665 SCN3B 11:123499895-123525952 ENSG00000166257 NM_001040151.2 HGNC:16643 SLMAP 3:57741177-57914895 ENSG00000163681 NM_001377540.1 HGNC:17993 TRPM4 19:49660998-49715093 ENSG00000130529 NM_017636.4 1 Your search was saved Thank you for using PanelSearch. Goodbye.

[jess789550]

./setup.sh

Checking for docker.io: No docker.io. Setting up docker.io. Reading package lists... Done Building dependency tree... Done Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies. containerd.io : Conflicts: containerd E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. Checking for docker-buildx: No docker-buildx. Setting up docker-buildx. Reading package lists... Done Building dependency tree... Done Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation:

The following packages have unmet dependencies. containerd.io : Conflicts: containerd docker-ce : Conflicts: docker.io but 24.0.5-0ubuntu1~22.04.1 is to be installed docker-ce-cli : Conflicts: docker.io but 24.0.5-0ubuntu1~22.04.1 is to be installed E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. Docker running Checking for mysql-server: install ok installed 22d36344637c269a341ab8a0d571e8680160f7496de12fb57acef762a2c00c0d panelsearch-network created panelsearch-volume panelsearch-volume created Unable to find image 'mysql:8' locally 8: Pulling from library/mysql bce031bc522d: Pull complete cf7e9f463619: Pull complete 105f403783c7: Pull complete 878e53a613d8: Pull complete 2a362044e79f: Pull complete 6e4df4f73cfe: Pull complete 69263d634755: Pull complete fe5e85549202: Pull complete 5c02229ce6f1: Pull complete 7320aa32bf42: Pull complete Digest: sha256:4ef30b2c11a3366d7bb9ad95c70c0782ae435df52d046553ed931621ea36ffa5 Status: Downloaded newer image for mysql:8 7b08d3f385c1119e6522f8e7ccb85ea3c0bc3c47b8154b00d053589881caa236 panelsearch-database container created mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 1 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 2 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 3 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 4 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 5 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 6 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 7 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 8 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 9 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 10 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 11 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 12 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 13 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 14 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 15 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 16 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 17 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 18 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 19 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 20 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 21 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 22 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 23 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 24 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 25 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 26 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 27 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 28 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 29 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 30 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 31 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 32 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 33 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 34 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 35 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 36 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 37 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 38 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 39 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 40 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 41 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 42 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 43 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 44 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 45 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 46 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 47 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 48 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 49 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 50 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 51 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 52 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 53 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 54 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 55 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 56 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 57 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 58 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 59 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 60 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 61 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 62 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 63 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 64 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 65 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 66 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 67 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 68 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 69 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 70 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 71 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 72 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 73 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 1045 (28000): Access denied for user 'root'@'localhost' (using password: YES) Attempt 74 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2013 (HY000) at line 1: Lost connection to MySQL server during query Attempt 75 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 76 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 77 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 78 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 79 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 80 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 81 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 82 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 83 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 84 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 85 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 86 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 87 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 88 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 89 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 90 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 91 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 92 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 93 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 94 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 95 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 96 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 97 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 98 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 99 failed. Trying again... mysql: [Warning] Using a password on the command line interface can be insecure. ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) Attempt 100 failed. Trying again... The command failed after 100 attempts. panelsearch database created database tables 'searches' and 'patients' created [+] Building 32.0s (13/13) FINISHED docker:default => [internal] load .dockerignore 0.1s => => transferring context: 680B 0.0s => [internal] load build definition from Dockerfile 0.1s => => transferring dockerfile: 2.10kB 0.0s => resolve image config for docker.io/docker/dockerfile:1 1.4s => docker-image://docker.io/docker/dockerfile:1@sha256:ac85f380a63b13dfcefa89046420e1781752bab202122f8f50032edf31be0021 0.5s => => resolve docker.io/docker/dockerfile:1@sha256:ac85f380a63b13dfcefa89046420e1781752bab202122f8f50032edf31be0021 0.0s => => sha256:a17ee7fff8f5e97b974f5b48f51647d2cf28d543f2aa6c11aaa0ea431b44bb89 1.27kB / 1.27kB 0.0s => => sha256:9d9c93f4b00be908ab694a4df732570bced3b8a96b7515d70ff93402179ad232 11.80MB / 11.80MB 0.3s => => sha256:ac85f380a63b13dfcefa89046420e1781752bab202122f8f50032edf31be0021 8.40kB / 8.40kB 0.0s => => sha256:657fcc512c7369f4cb3d94ea329150f8daf626bc838b1a1e81f1834c73ecc77e 482B / 482B 0.0s => => extracting sha256:9d9c93f4b00be908ab694a4df732570bced3b8a96b7515d70ff93402179ad232 0.1s => [internal] load metadata for docker.io/library/python:3.10-slim 1.3s => [base 1/6] FROM docker.io/library/python:3.10-slim@sha256:25f03d17398b3f001e040fc951b4ee9404862f1b65c5eea1aa31c042dfdab527 3.5s => => resolve docker.io/library/python:3.10-slim@sha256:25f03d17398b3f001e040fc951b4ee9404862f1b65c5eea1aa31c042dfdab527 0.0s => => sha256:25f03d17398b3f001e040fc951b4ee9404862f1b65c5eea1aa31c042dfdab527 1.65kB / 1.65kB 0.0s => => sha256:9956522e7eafd57e3e7bb4b102d56f02882924019867cd2036c1a7c3ee56b174 1.37kB / 1.37kB 0.0s => => sha256:3e27f11955d637ad643f1ebf37168854043fbaaafa20176af0339c01d51f1c1c 6.94kB / 6.94kB 0.0s => => sha256:af107e978371b6cd6339127a05502c5eacd1e6b0e9eb7b2f4aa7b6fc87e2dd81 29.13MB / 29.13MB 0.6s => => sha256:8ce3f2b601ccac03ff1858022363c325355bafba224123a4563dade58bc8e70f 3.51MB / 3.51MB 0.3s => => sha256:64119eae2e5157ca18d0ec9b9c7865e454b09bca702c3e2f579703deb0eaaeaf 12.38MB / 12.38MB 0.5s => => sha256:a28cd3d033268c30cb986f4a0d36c4aeda4c5aeaa5c764562f323c73d1f4f771 244B / 244B 0.5s => => sha256:2c1fe8bcf114038da9146a2528b2c3b606a09873aee7122f8529d45418fcd9e9 3.36MB / 3.36MB 0.7s => => extracting sha256:af107e978371b6cd6339127a05502c5eacd1e6b0e9eb7b2f4aa7b6fc87e2dd81 0.7s => => extracting sha256:8ce3f2b601ccac03ff1858022363c325355bafba224123a4563dade58bc8e70f 0.2s => => extracting sha256:64119eae2e5157ca18d0ec9b9c7865e454b09bca702c3e2f579703deb0eaaeaf 0.9s => => extracting sha256:a28cd3d033268c30cb986f4a0d36c4aeda4c5aeaa5c764562f323c73d1f4f771 0.0s => => extracting sha256:2c1fe8bcf114038da9146a2528b2c3b606a09873aee7122f8529d45418fcd9e9 0.6s => [internal] load build context 0.1s => => transferring context: 551.41kB 0.0s => [base 2/6] WORKDIR /app 0.2s => [base 3/6] RUN adduser --disabled-password --gecos "" --home "/nonexistent" --shell "/sbin/nologin" --no-crea 0.5s => [base 4/6] RUN chown appuser:appuser -R /app 0.2s => [base 5/6] RUN --mount=type=cache,target=/root/.cache/pip --mount=type=bind,source=requirements.txt,target=requirements.txt 22.2s => [base 6/6] COPY . . 0.1s => exporting to image 1.5s => => exporting layers 1.5s => => writing image sha256:56d35c18f0dd82178de43c3be8563ae474c9f737a06ae012cff9d056c24d8773 0.0s => => naming to docker.io/library/panelsearch 0.0s panelsearch app container created
running panelsearch app... Traceback (most recent call last): File "/app/./PanelSearch/main.py", line 27, in RotatingFileHandler(log_file, maxBytes=50000, backupCount=1) File "/usr/local/lib/python3.10/logging/handlers.py", line 155, in init BaseRotatingHandler.init(self, filename, mode, encoding=encoding, File "/usr/local/lib/python3.10/logging/handlers.py", line 58, in init logging.FileHandler.init(self, filename, mode=mode, File "/usr/local/lib/python3.10/logging/init.py", line 1169, in init StreamHandler.init(self, self._open()) File "/usr/local/lib/python3.10/logging/init.py", line 1201, in _open return open_func(self.baseFilename, self.mode, PermissionError: [Errno 13] Permission denied: '/app/panel_search.log'