…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

… with ERROR (qiita-spots#3413)

* 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