Inject user tracking code #8
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…ots#3384) * Update CHANGELOG.md * make help email address configurable instead of hard coding * codestyle * don't default with email addresses but raise Errors * set mail addresses in example configuration, which is also used for testing * addessing Antonios issues + switch to a non deprecated read fct. * updating dummy help email address in tests --------- Co-authored-by: Antonio Gonzalez <[email protected]>
* Initial commmit to resource allocation plots * Update to util.py and tests * Update test_util.py * revert 072023.ipynb * Debug test_util * testing plot based on № failures * Addressed Antonio's comments * Updates according to @charles-cowart comments * define functions as const @charles-cowart
* Update CHANGELOG.md
* 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.
```
---------
Co-authored-by: Antonio Gonzalez <[email protected]>
* Update CHANGELOG.md * let user configure the center point for the stats world map --------- Co-authored-by: Antonio Gonzalez <[email protected]>
* Update CHANGELOG.md * add db changes including fix qiita-spots#3368
* Update CHANGELOG.md * PacBio_SMRT new instruments
* Update CHANGELOG.md * adding current_human_filtering to PrepTemplate
* Update CHANGELOG.md * fix qiita-spots#3352
* Update CHANGELOG.md * fix qiita-spots#3387
* Update CHANGELOG.md * fix qiita-spots#3376
* Update CHANGELOG.md * updating QiitaPrepTemp06182020.xlsx
* Update CHANGELOG.md * add reprocess_job_id to PrepTemplate
* Update CHANGELOG.md * clean plugins * patch 54.sql * fix Internal Qiita jobs * sample_template.generate_files * rm extra filepath * qiita.filepath_filepath_id_seq * basedir_len * basedir_len * 2 * basedir_len * 3 * get_db_files_base_dir * address @charles-cowart comment
* Update CHANGELOG.md * clean plugins * patch 54.sql * fix Internal Qiita jobs * sample_template.generate_files * rm extra filepath * qiita.filepath_filepath_id_seq * basedir_len * basedir_len * 2 * basedir_len * 3 * get_db_files_base_dir * adding test_db_sql * missing ` * echo $QIITA_CONFIG_FP * -p 32768 * -l localhost * pgport * testing 1 * testing 2 * localhost * testing 3 * -h localhost * -W * PGPASSWORD * doc * flake8 * mods after chatting with @charles-cowart * exit 1 * "$row_counts" * # * `echo $row_counts` * full tests
* Update CHANGELOG.md * Note about missing mod_zip As I wasted too much time in figuring out what's wrong with anonymous link downloads, I thought it would be handy to summarize my lessons learned for others * add git "secretly" adding git as an Ubuntu package to be installed in a fresh system. Git later referred to for obtaining the Qiita sources. --------- Co-authored-by: Antonio Gonzalez <[email protected]>
* Update CHANGELOG.md * fix qiita-spots#3381 * fallback * rm qiimp from test
* Update to DB qiita.slurm_resource_allocations * connected tests to database * Update util.py * debugging changes to test * Update test_util.py * Update test_util.py * Tests update * Update test_meta_util.py * Updates to @antgonza comments * Updates to @charles-cowart comments
* Update CHANGELOG.md * fix admin processing_job msg None * update keys
* user profile can now also store social handles from google scholar, ORCID and ResearchGate * set DEFAULT NULL to new qiita.qiita_user columns * extending existing test * extending tests * add tests for validator functions for WTform StringFields * operate on str instead of field.data
* Update to DB qiita.slurm_resource_allocations * connected tests to database * Update util.py * debugging changes to test * Update test_util.py * Update test_util.py * Tests update * Update test_meta_util.py * Updates to @antgonza comments * Updates to @charles-cowart comments * Resource Allocation Insertion into DB - Added functionality of updating resource allocation data into db in qiita_db/util.py - Added tests for the added functionality in qiita_db/test/test_util.py - Moved MaxRSS_helper function from qiita_core/util.py to qiita_db/util.py. - Moved MaxRSS_helper test from qiita_core/tests/test_util.py to qiita_db/test/test_util.py * Debug Memory Model * Update test_util.py * Added columns to slurm_resource_allocation table * Update test_processing_job.py * Update test_util.py * Automatic date adjustment in utill.py * Update util.py
* use SQL's NOW() fct to log creation of a new user account (validated or not). * at -> on * add new col * use patch for DB changes * forgot to remove addition of comment here * moving changes to patch 92 * move adding date from populate_test_db.sql to here * revert changes, see patch * adding table name :-/ * order in DB changed due to UPDATE of creation_timestamp for user [email protected] * fix test
* use SQL's NOW() fct to log creation of a new user account (validated or not). * at -> on * add new col * adding a new page for admins to easily list all users not yet validated and offer means to delete those * flake8 * fix tests * move DB changes to patch * revert file * no change here * execute merge manually * moving data insertion to test_db_sql patch * account for additional test users
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This PR adds the ability to define some JavaScript code for visitor tracking of Qiita. Raw code, i.e. contents of variable JS_CODE in config section user_tracking is injected as top element in of the sitebase.html template.
We, i.e. NFDI4Microbiota will use this mechanism to measure performance indicators.