From 57d1b146729223da9daa286a1cc75db6f2923746 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 29 Jan 2024 12:35:46 -0700 Subject: [PATCH 1/2] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1756c7238..24ad9a78a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ Deployed on January 8th, 2024 * Workflow definitions can now use sample or preparation information columns/values to differentiate between them. * Updated the Adapter and host filtering plugin (qp-fastp-minimap2) to v2023.12 addressing a bug in adapter filtering; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/qp-fastp-minimap2.html). * Other fixes: [3334](https://github.com/qiita-spots/qiita/pull/3334), [3338](https://github.com/qiita-spots/qiita/pull/3338). Thank you @sjanssen2. -* The internal Sequence Processing Pipeline is now using the human pan-genome reference, together with the GRCh38 genome + PhiX and CHM13 genome for human host filtering. +* The internal Sequence Processing Pipeline is now using the human pan-genome reference, together with the GRCh38 genome + PhiX and T2T-CHM13v2.0 genome for human host filtering. Version 2023.10 From 0b82ec20d2a7b23f5fcc777069391be01147c9e9 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Fri, 22 Mar 2024 13:38:47 +0100 Subject: [PATCH 2/2] add trailing/separating whitespace got the error `Error running SQL: SYNTAX_ERROR. MSG: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ ` on my test instance log says ``` ==> bcf_qiita/Logs/qiita_21174.log <== [E 240322 13:35:00 web:1669] Uncaught exception GET /study/description/1 (127.0.0.1) HTTPServerRequest(protocol='https', host='qiita.jlab.bio', method='GET', uri='/study/description/1', version='HTTP/1.0', remote_ip='127.0.0.1') Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 256, in _execute cur.execute(sql, sql_args) File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/psycopg2/extras.py", line 146, in execute return super().execute(query, vars) psycopg2.errors.SyntaxError: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 199, in _raise_execution_error raise ValueError( ValueError: Error running SQL: SYNTAX_ERROR. MSG: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/tornado/web.py", line 1590, in _execute result = method(*self.path_args, **self.path_kwargs) File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/tornado/web.py", line 3006, in wrapper return method(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_pet/handlers/study_handlers/base.py", line 28, in get study_info = study_get_req(study, self.current_user.id) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_pet/handlers/api_proxy/studies.py", line 120, in study_get_req study.artifacts(artifact_type='BIOM')) != 0 File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/study.py", line 1108, in artifacts for aid in qdb.sql_connection.TRN.execute_fetchflatten()] File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 389, in execute_fetchflatten return list(chain.from_iterable(self.execute()[idx])) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 313, in execute return self._execute() File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 260, in _execute self._raise_execution_error(sql, sql_args, e) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 205, in _raise_execution_error raise ValueError("Error running SQL query: %s" % str(error)) ValueError: Error running SQL query: Error running SQL: SYNTAX_ERROR. MSG: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ [E 240322 13:35:00 web:2161] 500 GET /study/description/1 (127.0.0.1) 159.63ms [E 240322 13:35:00 web:1114] Uncaught exception in write_error Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 256, in _execute cur.execute(sql, sql_args) File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/psycopg2/extras.py", line 146, in execute return super().execute(query, vars) psycopg2.errors.SyntaxError: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 199, in _raise_execution_error raise ValueError( ValueError: Error running SQL: SYNTAX_ERROR. MSG: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/tornado/web.py", line 1590, in _execute result = method(*self.path_args, **self.path_kwargs) File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/tornado/web.py", line 3006, in wrapper return method(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_pet/handlers/study_handlers/base.py", line 28, in get study_info = study_get_req(study, self.current_user.id) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_pet/handlers/api_proxy/studies.py", line 120, in study_get_req study.artifacts(artifact_type='BIOM')) != 0 File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/study.py", line 1108, in artifacts for aid in qdb.sql_connection.TRN.execute_fetchflatten()] File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 389, in execute_fetchflatten return list(chain.from_iterable(self.execute()[idx])) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 313, in execute return self._execute() File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 260, in _execute self._raise_execution_error(sql, sql_args, e) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 205, in _raise_execution_error raise ValueError("Error running SQL query: %s" % str(error)) ValueError: Error running SQL query: Error running SQL: SYNTAX_ERROR. MSG: trailing junk after numeric literal at or near "1A" LINE 6: WHERE study_id = 1AND artifact_type = '... ^ During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 256, in _execute cur.execute(sql, sql_args) File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/psycopg2/extras.py", line 146, in execute return super().execute(query, vars) psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "pk_logging" DETAIL: Key (logging_id)=(294) already exists. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 199, in _raise_execution_error raise ValueError( ValueError: Error running SQL: UNIQUE_VIOLATION. MSG: duplicate key value violates unique constraint "pk_logging" DETAIL: Key (logging_id)=(294) already exists. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/homes/sjanssen/bcf_qiita/envs/qiita/lib/python3.9/site-packages/tornado/web.py", line 1112, in send_error self.write_error(status_code, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_pet/handlers/base_handlers.py", line 69, in write_error LogEntry.create( File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/logger.py", line 103, in create return cls(qdb.sql_connection.TRN.execute_fetchlast()) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 336, in execute_fetchlast return self.execute()[-1][0][0] File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 49, in wrapper return func(self, *args, **kwargs) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 313, in execute return self._execute() File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 260, in _execute self._raise_execution_error(sql, sql_args, e) File "/homes/sjanssen/bcf_qiita/qiita-spots/qiita/qiita_db/sql_connection.py", line 205, in _raise_execution_error raise ValueError("Error running SQL query: %s" % str(error)) ValueError: Error running SQL query: Error running SQL: UNIQUE_VIOLATION. MSG: duplicate key value violates unique constraint "pk_logging" DETAIL: Key (logging_id)=(294) already exists. ``` --- qiita_db/study.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qiita_db/study.py b/qiita_db/study.py index 3c4989f3b..98ddc1ed6 100644 --- a/qiita_db/study.py +++ b/qiita_db/study.py @@ -1092,7 +1092,7 @@ def artifacts(self, dtype=None, artifact_type=None): if artifact_type: sql_args.append(artifact_type) - sql_where += "AND artifact_type = %s" + sql_where += " AND artifact_type = %s" sql = """SELECT artifact_id FROM qiita.artifact