Merge branch 'master' into s3-task-chains

ucam-department-of-psychiatry · Mar 20, 2023 · e9eb03b · e9eb03b
2 parents 1ce57a9 + 6b2ee89
commit e9eb03b
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diff --git a/docs/recreate_inclusion_files.py b/docs/recreate_inclusion_files.py
@@ -206,8 +206,13 @@ def main():
     )
     log.warning("Skipping camcops_windows_service_help.txt (requires Windows)")
 
-    secret_regex = r"^(SESSION_COOKIE_SECRET = camcops_autogenerated_secret_)[\w-]+=="  # noqa: E501
-    secret_replacement = r"\g<1>YhXZQ4zVMYobWawci-zbv6nn6B6iMrZcUkGjpko4pExjwNgOpgjGh0TVzUEMt1u3DlzRGI6RJVxd8ohvKGleag=="  # noqa: E501
+    secret_regex = (
+        r"^(SESSION_COOKIE_SECRET = camcops_autogenerated_secret_)[\w-]+=="
+    )
+    secret_replacement = (
+        r"\g<1>YhXZQ4zVMYobWawci-zbv6nn6B6iMrZcUkGjpko4pEx"
+        r"jwNgOpgjGh0TVzUEMt1u3DlzRGI6RJVxd8ohvKGleag=="
+    )
 
     run_cmd(
         ["camcops_server", "demo_camcops_config"],

diff --git a/docs/source/administrator/_camcops_server_allhelp.txt b/docs/source/administrator/_camcops_server_allhelp.txt
@@ -1,5 +1,5 @@
 USAGE: camcops_server [-h] [--allhelp] [--version] [-v] [--no_log]
-                      {docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli}
+                      {docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli,list_tasks}
                       ...
 
 CamCOPS server, created by Rudolf Cardinal; version 2.4.15.
@@ -15,7 +15,7 @@ OPTIONAL ARGUMENTS:
 COMMANDS:
   Valid CamCOPS commands are as follows.
 
-  {docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli}
+  {docs,demo_camcops_config,demo_supervisor_config,demo_apache_config,upgrade_db,dev_upgrade_db,dev_downgrade_db,dev_add_dummy_data,show_db_title,show_db_schema,merge_db,create_db,ddl,reindex,check_index,make_superuser,reset_password,enable_user,export,show_export_queue,crate_dd,cris_dd,serve_cherrypy,serve_gunicorn,serve_pyramid,convert_athena_icd_snomed_to_xml,launch_workers,launch_scheduler,launch_monitor,housekeeping,purge_jobs,dev_cli,list_tasks}
                         Specify one command.
     docs                Launch the main documentation (CamCOPS manual)
     demo_camcops_config
@@ -66,6 +66,7 @@ COMMANDS:
                         jobs
     dev_cli             Developer command-line interface, with config loaded
                         as 'config'.
+    list_tasks          List supported tasks.
 
 ===============================================================================
 Help for command 'docs'
@@ -652,3 +653,16 @@ OPTIONAL ARGUMENTS:
   --config CONFIG  Configuration file (if not specified, the environment
                    variable CAMCOPS_CONFIG_FILE is checked) (default: None)
 
+===============================================================================
+Help for command 'list_tasks'
+===============================================================================
+USAGE: camcops_server list_tasks [-h] [-v] [--config CONFIG]
+
+List supported tasks.
+
+OPTIONAL ARGUMENTS:
+  -h, --help       show this help message and exit
+  -v, --verbose    Be verbose (default: False)
+  --config CONFIG  Configuration file (if not specified, the environment
+                   variable CAMCOPS_CONFIG_FILE is checked) (default: None)
+
diff --git a/docs/source/administrator/server_config_file.rst b/docs/source/administrator/server_config_file.rst
@@ -1644,10 +1644,14 @@ TRANSMISSION_METHOD
 
 One of the following methods:
 
-- ``db``: Exports tasks to a relational database.
-- ``email``: Sends tasks via e-mail.
-- ``hl7``: Sends HL7 (v2) messages across a TCP/IP network.
-- ``file``: Writes files to a local filesystem.
+- ``db``: Exports tasks to a relational database; see
+  :ref:`database exports <config_db>`.
+- ``email``: Sends tasks via e-mail; see :ref:`e-mail exports <config_email>`.
+- ``fhir``: Sends data via FHIR_; see :ref:`FHIR exports <config_fhir>`.
+- ``file``: Writes files to a local filesystem; see
+  :ref:`file exports <config_file>`.
+- ``hl7``: Sends HL7 (v2) messages across a TCP/IP network; see
+  :ref:`HL7 exports <config_hl7>`.
 - ``redcap``: :ref:`Exports tasks to REDCap <redcap>`.
 
 
@@ -1842,6 +1846,8 @@ PRIMARY_IDNUM_ is set.
   that the primary ID number must be present (as above) for *all* groups.
 
 
+.. _config_db:
+
 Options applicable to database export only
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -1902,6 +1908,8 @@ a task, or similar) add the fields ``_task_tablename`` and ``_task_pk`` as
 part of this denormalization-for-convenience.
 
 
+.. _config_email:
+
 Options applicable to e-mail export only
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -1994,6 +2002,8 @@ Keep the entire message (including attachments). Turning this option on
 consumes lots of database space! Use only for debugging.
 
 
+.. _config_hl7:
+
 Options applicable to HL7 (v2) only
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -2192,6 +2202,8 @@ There is no penalty for leaving it at ``False`` except perhaps a slight
 reduction in speed.
 
 
+.. _config_file:
+
 Options applicable to file transfers and attachments
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/docs/source/tasks/isaaq10.rst b/docs/source/tasks/isaaq10.rst
@@ -44,16 +44,24 @@ Intellectual property rights
   ISAAQ (all versions) cannot be reproduced, modified, and/or published without
   prior written permission of the copyright holders.
 
+  - Approved for inclusion in CamCOPS on the "non-commercial" basis. "I am
+    happy for the ISAAQ-10 and ISAAQ Part B to be fully public on CamCOPS for
+    those who declare the commercial “no”." (Konstantinos Ioannidis to Martin
+    Burchell and Rudolf Cardinal, and approved by Sam Chamberlain, 13 Feb
+    2023.)
 
 
 History
 ~~~~~~~
 
 - Ioannidis K, Tiego J, Lutz N, Omrawo C, Yücel M, Grant JE, Lochner C,
-  Chamberlain SR.  Internet severity and activities addiction questionnaire
-  (ISAAQ): Psychometrics of item response theory and clustering of online
-  activities.  *Comprehensive Psychiatry* 122: 152366
-  https://doi.org/10.1016/j.comppsych.2023.152366
+  Chamberlain SR (2023). Internet severity and activities addiction
+  questionnaire (ISAAQ): Psychometrics of item response theory and clustering
+  of online activities. *Comprehensive Psychiatry* 122: 152366.
+  https://pubmed.ncbi.nlm.nih.gov/36702061/;
+  https://doi.org/10.1016/j.comppsych.2023.152366.
+
+  - Defines both the original 15-item ISAAQ and the ISAAQ-10.
 
 
 Source
@@ -66,25 +74,32 @@ Source
   - Young KS (1998). Internet Addiction: The Emergence of a New Clinical
     Disorder. *CyberPsychology & Behavior* 1: 237–44.
     https://doi.org/10.1089/cpb.1998.1.237
+
   - American Psychiatric Association (2013). *Diagnostic and Statistical Manual
     of Mental Disorders: DSM-5.*
     American Psychiatric Association, Washington, DC.
+
   - Ioannidis K, Chamberlain SR, Tredder M, Kiraly F, Redden S, Stein DJ,
     Lochner C, Grant JE (2018). Problematic internet use as an age-related
     multifaceted problem: evidence from a two-site survey.
     *Addict Behav* 81: 157.166.
     https://pubmed.ncbi.nlm.nih.gov/29459201/
+
   - Chamberlain SR, Redden SA, Stein DJ, Lochner C, Grant JE (2017). Impact of
     obsessive-compulsive personality disorder symptoms in Internet users.
     *Ann Clin Psychiatry* 29: 173-181.
+    https://pubmed.ncbi.nlm.nih.gov/28738097/
+
   - Ioannidis K, Chamberlain SR, Tredder M, Kiraly F, Leppink E, Redden S,
     Stein DJ, Lochner C, Grant JE (2016). Problematic internet use (PIU):
     Associations with the impulsive-compulsive spectrum. An application of
     machine learning in psychiatry.
     *J Psych Res* 83: 94-102.
     https://pubmed.ncbi.nlm.nih.gov/27580487/
+
   - Fineberg NA, Demetrovics Z, Stein DJ, Ioannidis K, Potenza MN, Grünblatt E,
-    et al (2018). Manifesto for a European research network into Problematic
+    et al. (2018). Manifesto for a European research network into Problematic
     Usage of the Internet.
     *European Neuropsychopharmacology* 28: 1232-1246.
+    https://pubmed.ncbi.nlm.nih.gov/30509450/;
     https://doi.org/10.1016/j.euroneuro.2018.08.004
diff --git a/server/camcops_server/alembic/versions/0001_start.py b/server/camcops_server/alembic/versions/0001_start.py
@@ -376,7 +376,8 @@ def upgrade():
         sa.Column("success", sa.Boolean(), nullable=True),
         sa.Column("failure_reason", sa.Text(), nullable=True),
         # Next one altered 2018-11-09 for SQL Server:
-        # sa.Column('message', sa.UnicodeText(length=4294967295), nullable=True),  # noqa: E501
+        # sa.Column('message',
+        #           sa.UnicodeText(length=4294967295), nullable=True),
         sa.Column(
             "message",
             sa.UnicodeText().with_variant(mysql.LONGTEXT, "mysql"),

diff --git a/server/camcops_server/alembic/versions/0030_chi_t.py b/server/camcops_server/alembic/versions/0030_chi_t.py
@@ -71,7 +71,7 @@ def upgrade():
             "q1",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q1 (hate unfinished task) (0 strongly disagree - 3 strongly"
                 " agree)"
             ),
@@ -86,7 +86,7 @@ def upgrade():
             "q3",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q3 (keep doing task) (0 strongly disagree - 3 strongly agree)"
             ),
         ),
@@ -112,7 +112,7 @@ def upgrade():
             "q7",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q7 (stubborn rigid) (0 strongly disagree - 3 strongly agree)"
             ),
         ),
@@ -126,7 +126,7 @@ def upgrade():
             "q9",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q9 (rewarding things) (0 strongly disagree - 3 strongly"
                 " agree)"
             ),
@@ -143,7 +143,7 @@ def upgrade():
             "q11",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q11 (higher standards) (0 strongly disagree - 3 strongly"
                 " agree)"
             ),
@@ -166,7 +166,7 @@ def upgrade():
             "q14",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "Q14 (avoid situations) (0 strongly disagree - 3 strongly"
                 " agree)"
             ),
@@ -207,7 +207,7 @@ def upgrade():
             "clinician_professional_registration",
             sa.Text(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(CLINICIAN) Clinician's professional registration (e.g. GMC#"
                 " 12345)"
             ),
@@ -222,7 +222,7 @@ def upgrade():
             "clinician_service",
             sa.Text(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(CLINICIAN) Clinician's service (e.g. Liaison Psychiatry"
                 " Service)"
             ),
@@ -231,7 +231,7 @@ def upgrade():
             "clinician_contact_details",
             sa.Text(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(CLINICIAN) Clinician's contact details (e.g. bleep,"
                 " extension)"
             ),
@@ -256,7 +256,7 @@ def upgrade():
             "firstexit_is_finish",
             sa.Boolean(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(TASK) Was the first exit from the task because it was"
                 " finished (1)?"
             ),
@@ -265,7 +265,7 @@ def upgrade():
             "firstexit_is_abort",
             sa.Boolean(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(TASK) Was the first exit from this task because it was"
                 " aborted (1)?"
             ),
@@ -293,7 +293,7 @@ def upgrade():
             "_era",
             sa.String(length=32),
             nullable=False,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) 'NOW', or when this row was preserved and removed"
                 " from the source device (UTC ISO 8601)"
             ),
@@ -314,7 +314,7 @@ def upgrade():
             "_when_added_batch_utc",
             sa.DateTime(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) Date/time of the upload batch that added this row"
                 " (DATETIME in UTC)"
             ),
@@ -329,7 +329,7 @@ def upgrade():
             "_when_removed_exact",
             PendulumDateTimeAsIsoTextColType(length=32),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) Date/time this row was removed, i.e. made not"
                 " current (ISO 8601)"
             ),
@@ -338,7 +338,7 @@ def upgrade():
             "_when_removed_batch_utc",
             sa.DateTime(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) Date/time of the upload batch that removed this row"
                 " (DATETIME in UTC)"
             ),
@@ -359,7 +359,7 @@ def upgrade():
             "_forcibly_preserved",
             sa.Boolean(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) Forcibly preserved by superuser (rather than"
                 " normally preserved by tablet)?"
             ),
@@ -374,7 +374,7 @@ def upgrade():
             "_successor_pk",
             sa.Integer(),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(SERVER) PK of successor record  (after modification) or NULL"
                 " (whilst live, or after deletion)"
             ),
@@ -431,7 +431,7 @@ def upgrade():
             "when_last_modified",
             PendulumDateTimeAsIsoTextColType(length=32),
             nullable=True,
-            comment=(  # noqa: E501
+            comment=(
                 "(STANDARD) Date/time this row was last modified on the source"
                 " tablet device (ISO 8601)"
             ),