From c5466fbadc05aac98d9196e894ea50a25be9824f Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 06:52:12 +0000 Subject: [PATCH 01/12] Add pre-commit hook to check scripts with shebangs are executable --- .pre-commit-config.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fc003198..fdf2474e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,12 +2,13 @@ # See https://pre-commit.com/hooks.html for more hooks repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v3.2.0 + rev: v4.5.0 hooks: - id: check-added-large-files - id: check-json - - id: check-yaml + - id: check-shebang-scripts-are-executable - id: check-xml + - id: check-yaml - repo: https://github.com/psf/black rev: 22.8.0 hooks: From 8c08bb6c32002a3ca19edb5747e9251306a50d1f Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 06:53:08 +0000 Subject: [PATCH 02/12] Use same versions in setup.py and pre-commit --- .pre-commit-config.yaml | 2 ++ setup.py | 4 ++-- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fdf2474e..dd76fe46 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -10,12 +10,14 @@ repos: - id: check-xml - id: check-yaml - repo: https://github.com/psf/black + # Use same version as in setup.py rev: 22.8.0 hooks: - id: black args: - --line-length=79 - repo: https://github.com/PyCQA/flake8 + # Use same version as in setup.py rev: 5.0.4 hooks: - id: flake8 diff --git a/setup.py b/setup.py index edf17a7c..e71c5e38 100644 --- a/setup.py +++ b/setup.py @@ -143,9 +143,9 @@ # ------------------------------------------------------------------------- # For development only: # ------------------------------------------------------------------------- - "black==22.3.0", # auto code formatter + "black==22.8.0", # auto code formatter "faker==13.3.1", # test data creation - "flake8==3.8.4", # code checks + "flake8==5.0.4", # code checks "docutils==0.17", # documentation, 0.18 not compatible with Sphinx "mistune<2.0.0", # API documentation, 2.0.0 not compatible "pre-commit==2.20.0", # development only, various sanity checks on code From 41a7425e42a6b1483ed1ee0ace738f7e9725e178 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 10:25:19 +0000 Subject: [PATCH 03/12] Remove shebangs from python scripts that do not need them --- crate_anon/__init__.py | 2 -- crate_anon/ancillary/timely_project/dd_criteria.py | 2 -- crate_anon/ancillary/timely_project/timely_filter.py | 2 -- crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py | 2 -- crate_anon/ancillary/timely_project/timely_filter_systmone.py | 2 -- crate_anon/anonymise/__init__.py | 2 -- crate_anon/anonymise/altermethod.py | 2 -- crate_anon/anonymise/anonregex.py | 2 -- crate_anon/anonymise/anonymise.py | 2 -- crate_anon/anonymise/config.py | 2 -- crate_anon/anonymise/config_singleton.py | 2 -- crate_anon/anonymise/constants.py | 2 -- crate_anon/anonymise/dbholder.py | 2 -- crate_anon/anonymise/dd.py | 2 -- crate_anon/anonymise/ddr.py | 2 -- crate_anon/anonymise/eponyms.py | 2 -- crate_anon/anonymise/models.py | 2 -- crate_anon/anonymise/patient.py | 2 -- crate_anon/anonymise/scrub.py | 2 -- crate_anon/anonymise/tests/scrub_tests.py | 2 -- crate_anon/common/__init__.py | 2 -- crate_anon/common/argparse_assist.py | 2 -- crate_anon/common/bugfix_flashtext.py | 2 -- crate_anon/common/constants.py | 2 -- crate_anon/common/dockerfunc.py | 2 -- crate_anon/common/exceptions.py | 2 -- crate_anon/common/extendedconfigparser.py | 2 -- crate_anon/common/file_io.py | 2 -- crate_anon/common/formatting.py | 2 -- crate_anon/common/inputfunc.py | 4 +--- crate_anon/common/logfunc.py | 2 -- crate_anon/common/memsize.py | 2 -- crate_anon/common/parallel.py | 2 -- crate_anon/common/profiling.py | 2 -- crate_anon/common/regex_helpers.py | 2 -- crate_anon/common/spreadsheet.py | 2 -- crate_anon/common/sql.py | 2 -- crate_anon/common/stringfunc.py | 2 -- crate_anon/common/tests/regex_helper_tests.py | 2 -- crate_anon/common/tests/spreadsheet_tests.py | 2 -- crate_anon/common/tests/sql_tests.py | 2 -- crate_anon/common/tests/stringfunc_tests.py | 2 -- crate_anon/conftest.py | 2 -- crate_anon/crateweb/__init__.py | 2 -- crate_anon/crateweb/anonymise_api/__init__.py | 2 -- crate_anon/crateweb/config/__init__.py | 2 -- crate_anon/crateweb/config/apps.py | 2 -- crate_anon/crateweb/config/constants.py | 2 -- crate_anon/crateweb/config/settings.py | 2 -- crate_anon/crateweb/config/test_settings.py | 2 -- crate_anon/crateweb/config/urls.py | 2 -- crate_anon/crateweb/config/wsgi.py | 2 -- crate_anon/crateweb/consent/__init__.py | 2 -- crate_anon/crateweb/consent/celery.py | 2 -- crate_anon/crateweb/consent/constants.py | 2 -- crate_anon/crateweb/consent/forms.py | 2 -- crate_anon/crateweb/consent/lookup.py | 2 -- crate_anon/crateweb/consent/lookup_common.py | 2 -- crate_anon/crateweb/consent/lookup_crs.py | 2 -- crate_anon/crateweb/consent/lookup_dummy.py | 2 -- crate_anon/crateweb/consent/lookup_rio.py | 2 -- crate_anon/crateweb/consent/lookup_systmone.py | 2 -- crate_anon/crateweb/consent/management/__init__.py | 2 -- crate_anon/crateweb/consent/management/commands/__init__.py | 2 -- crate_anon/crateweb/consent/management/commands/email_rdbm.py | 2 -- .../crateweb/consent/management/commands/fetch_optouts.py | 2 -- .../crateweb/consent/management/commands/make_ethics_pack.py | 2 -- crate_anon/crateweb/consent/management/commands/populate.py | 2 -- .../consent/management/commands/resubmit_unprocessed_tasks.py | 2 -- crate_anon/crateweb/consent/management/commands/test_email.py | 2 -- crate_anon/crateweb/consent/migrations/0001_initial.py | 2 -- .../crateweb/consent/migrations/0002_auto_20160621_1511.py | 2 -- .../crateweb/consent/migrations/0003_auto_20160628_1301.py | 2 -- .../crateweb/consent/migrations/0004_auto_20160703_1530.py | 2 -- .../crateweb/consent/migrations/0005_auto_20170203_1348.py | 2 -- .../crateweb/consent/migrations/0006_auto_20170206_1617.py | 2 -- .../crateweb/consent/migrations/0007_auto_20170228_1052.py | 2 -- .../crateweb/consent/migrations/0008_auto_20170507_1218.py | 2 -- .../crateweb/consent/migrations/0009_auto_20180629_1132.py | 2 -- .../crateweb/consent/migrations/0010_auto_20180629_1238.py | 2 -- .../crateweb/consent/migrations/0011_auto_20181022_0801.py | 2 -- crate_anon/crateweb/consent/migrations/__init__.py | 2 -- crate_anon/crateweb/consent/models.py | 2 -- crate_anon/crateweb/consent/storage.py | 2 -- crate_anon/crateweb/consent/tasks.py | 2 -- crate_anon/crateweb/consent/teamlookup.py | 2 -- crate_anon/crateweb/consent/teamlookup_dummy.py | 2 -- crate_anon/crateweb/consent/teamlookup_rio.py | 2 -- crate_anon/crateweb/consent/teamlookup_systmone.py | 2 -- crate_anon/crateweb/consent/utils.py | 2 -- crate_anon/crateweb/consent/views.py | 2 -- crate_anon/crateweb/core/__init__.py | 2 -- crate_anon/crateweb/core/admin.py | 2 -- crate_anon/crateweb/core/auth_views.py | 2 -- crate_anon/crateweb/core/constants.py | 2 -- crate_anon/crateweb/core/context_processors.py | 2 -- crate_anon/crateweb/core/management/__init__.py | 2 -- crate_anon/crateweb/core/management/commands/__init__.py | 2 -- .../crateweb/core/management/commands/ensuresuperuser.py | 2 -- crate_anon/crateweb/core/middleware.py | 2 -- crate_anon/crateweb/core/utils.py | 2 -- crate_anon/crateweb/core/views.py | 2 -- crate_anon/crateweb/extra/__init__.py | 2 -- crate_anon/crateweb/extra/admin.py | 2 -- crate_anon/crateweb/extra/pdf.py | 2 -- crate_anon/crateweb/extra/salutation.py | 2 -- crate_anon/crateweb/research/__init__.py | 2 -- crate_anon/crateweb/research/archive_backend.py | 2 -- crate_anon/crateweb/research/archive_func.py | 2 -- crate_anon/crateweb/research/errors.py | 2 -- crate_anon/crateweb/research/forms.py | 2 -- crate_anon/crateweb/research/html_functions.py | 2 -- crate_anon/crateweb/research/migrations/0001_initial.py | 2 -- .../crateweb/research/migrations/0002_auto_20170203_1348.py | 2 -- .../migrations/0003_patientexplorer_patientexploreraudit.py | 2 -- .../crateweb/research/migrations/0004_auto_20170212_0137.py | 2 -- .../crateweb/research/migrations/0005_query_sql_hash.py | 2 -- .../research/migrations/0006_patientexplorer_pmq_hash.py | 2 -- crate_anon/crateweb/research/migrations/0007_sitewidequery.py | 2 -- crate_anon/crateweb/research/migrations/0008_query_display.py | 2 -- crate_anon/crateweb/research/migrations/__init__.py | 2 -- crate_anon/crateweb/research/models.py | 2 -- crate_anon/crateweb/research/research_db_info.py | 2 -- crate_anon/crateweb/research/sql_writer.py | 2 -- crate_anon/crateweb/research/views.py | 2 -- crate_anon/crateweb/userprofile/__init__.py | 2 -- crate_anon/crateweb/userprofile/forms.py | 2 -- crate_anon/crateweb/userprofile/migrations/0001_initial.py | 2 -- .../userprofile/migrations/0002_userprofile_sql_scratchpad.py | 2 -- .../userprofile/migrations/0003_auto_20160628_1301.py | 2 -- .../migrations/0004_userprofile_patients_per_page.py | 2 -- .../0005_userprofile_patient_multiquery_scratchpad.py | 2 -- .../userprofile/migrations/0006_auto_20170212_0137.py | 2 -- .../userprofile/migrations/0007_auto_20170507_1218.py | 2 -- crate_anon/crateweb/userprofile/migrations/__init__.py | 2 -- crate_anon/crateweb/userprofile/models.py | 2 -- crate_anon/crateweb/userprofile/views.py | 2 -- crate_anon/linkage/__init__.py | 2 -- crate_anon/linkage/comparison.py | 2 -- crate_anon/linkage/constants.py | 2 -- crate_anon/linkage/frequencies.py | 2 -- crate_anon/linkage/helpers.py | 2 -- crate_anon/linkage/identifiers.py | 2 -- crate_anon/linkage/matchconfig.py | 2 -- crate_anon/linkage/matchresult.py | 2 -- crate_anon/linkage/people.py | 2 -- crate_anon/linkage/person.py | 2 -- crate_anon/linkage/person_io.py | 2 -- crate_anon/linkage/tests/fuzzy_id_match_tests.py | 2 -- crate_anon/nlp_manager/__init__.py | 2 -- crate_anon/nlp_manager/all_processors.py | 2 -- crate_anon/nlp_manager/base_nlp_parser.py | 2 -- crate_anon/nlp_manager/cloud_config.py | 2 -- crate_anon/nlp_manager/cloud_parser.py | 2 -- crate_anon/nlp_manager/cloud_request.py | 2 -- crate_anon/nlp_manager/cloud_request_sender.py | 2 -- crate_anon/nlp_manager/cloud_run_info.py | 2 -- crate_anon/nlp_manager/constants.py | 2 -- crate_anon/nlp_manager/input_field_config.py | 2 -- crate_anon/nlp_manager/models.py | 2 -- crate_anon/nlp_manager/nlp_definition.py | 2 -- crate_anon/nlp_manager/number.py | 2 -- crate_anon/nlp_manager/output_user_config.py | 2 -- crate_anon/nlp_manager/parse_biochemistry.py | 2 -- crate_anon/nlp_manager/parse_clinical.py | 2 -- crate_anon/nlp_manager/parse_cognitive.py | 2 -- crate_anon/nlp_manager/parse_gate.py | 2 -- crate_anon/nlp_manager/parse_haematology.py | 2 -- crate_anon/nlp_manager/parse_medex.py | 2 -- crate_anon/nlp_manager/parse_substance_misuse.py | 2 -- crate_anon/nlp_manager/regex_func.py | 2 -- crate_anon/nlp_manager/regex_numbers.py | 2 -- crate_anon/nlp_manager/regex_parser.py | 2 -- crate_anon/nlp_manager/regex_read_codes.py | 2 -- crate_anon/nlp_manager/regex_units.py | 2 -- crate_anon/nlp_manager/tests/all_processors_tests.py | 2 -- crate_anon/nlp_manager/tests/cloud_request_process_tests.py | 2 -- crate_anon/nlp_manager/tests/cloud_request_sender_tests.py | 2 -- crate_anon/nlp_manager/tests/nlp_parser_tests.py | 2 -- crate_anon/nlp_manager/tests/parse_biochemistry_tests.py | 2 -- crate_anon/nlp_manager/tests/parse_clinical_tests.py | 2 -- crate_anon/nlp_manager/tests/parse_cognitive_tests.py | 2 -- crate_anon/nlp_manager/tests/parse_haematology_tests.py | 2 -- crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py | 2 -- crate_anon/nlp_manager/tests/regex_numbers_tests.py | 2 -- crate_anon/nlp_manager/tests/regex_parser_tests.py | 2 -- crate_anon/nlp_manager/tests/regex_read_codes_tests.py | 2 -- crate_anon/nlp_manager/tests/regex_test_helperfunc.py | 2 -- crate_anon/nlp_manager/tests/regex_units_tests.py | 2 -- crate_anon/nlp_webserver/__init__.py | 2 -- crate_anon/nlp_webserver/constants.py | 2 -- crate_anon/nlp_webserver/models.py | 2 -- crate_anon/nlp_webserver/procs.py | 2 -- crate_anon/nlp_webserver/security.py | 2 -- crate_anon/nlp_webserver/settings.py | 2 -- crate_anon/nlp_webserver/tasks.py | 2 -- crate_anon/nlp_webserver/tests/settings_tests.py | 2 -- crate_anon/nlp_webserver/views.py | 2 -- crate_anon/nlp_webserver/wsgi_app.py | 2 -- crate_anon/nlp_webserver/wsgi_launchers.py | 2 -- crate_anon/nlprp/__init__.py | 4 +--- crate_anon/nlprp/api.py | 2 -- crate_anon/nlprp/constants.py | 2 -- crate_anon/nlprp/errors.py | 2 -- crate_anon/nlprp/version.py | 2 -- crate_anon/preprocess/__init__.py | 2 -- crate_anon/preprocess/constants.py | 2 -- crate_anon/preprocess/ddhint.py | 2 -- crate_anon/preprocess/rio_constants.py | 2 -- crate_anon/preprocess/rio_ddgen.py | 2 -- crate_anon/preprocess/rio_pk.py | 2 -- crate_anon/preprocess/rio_view_func.py | 2 -- crate_anon/preprocess/rio_views.py | 2 -- crate_anon/preprocess/systmone_ddgen.py | 2 -- crate_anon/preprocess/tests/systmone_ddgen_tests.py | 2 -- crate_anon/testdocs_for_text_extraction/__init__.py | 2 -- crate_anon/tools/__init__.py | 2 -- crate_anon/version.py | 2 -- 218 files changed, 2 insertions(+), 438 deletions(-) diff --git a/crate_anon/__init__.py b/crate_anon/__init__.py index 5f09b399..2451010f 100644 --- a/crate_anon/__init__.py +++ b/crate_anon/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/__init__.py diff --git a/crate_anon/ancillary/timely_project/dd_criteria.py b/crate_anon/ancillary/timely_project/dd_criteria.py index be74ae9f..ad96f275 100644 --- a/crate_anon/ancillary/timely_project/dd_criteria.py +++ b/crate_anon/ancillary/timely_project/dd_criteria.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/ancillary/timely_project/dd_criteria.py diff --git a/crate_anon/ancillary/timely_project/timely_filter.py b/crate_anon/ancillary/timely_project/timely_filter.py index 1b94664f..140430b2 100644 --- a/crate_anon/ancillary/timely_project/timely_filter.py +++ b/crate_anon/ancillary/timely_project/timely_filter.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/ancillary/timely_project/timely_filter.py diff --git a/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py b/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py index bef5b666..43ed19ef 100644 --- a/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py +++ b/crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/ancillary/timely_project/timely_filter_cpft_rio.py diff --git a/crate_anon/ancillary/timely_project/timely_filter_systmone.py b/crate_anon/ancillary/timely_project/timely_filter_systmone.py index 913a8e01..307d522d 100644 --- a/crate_anon/ancillary/timely_project/timely_filter_systmone.py +++ b/crate_anon/ancillary/timely_project/timely_filter_systmone.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/ancillary/timely_project/timely_filter_systmone.py diff --git a/crate_anon/anonymise/__init__.py b/crate_anon/anonymise/__init__.py index c23fed0e..c36cf676 100644 --- a/crate_anon/anonymise/__init__.py +++ b/crate_anon/anonymise/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/__init__.py diff --git a/crate_anon/anonymise/altermethod.py b/crate_anon/anonymise/altermethod.py index 554f681c..17ca205b 100644 --- a/crate_anon/anonymise/altermethod.py +++ b/crate_anon/anonymise/altermethod.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/altermethod.py diff --git a/crate_anon/anonymise/anonregex.py b/crate_anon/anonymise/anonregex.py index 46b8bbca..04209fde 100755 --- a/crate_anon/anonymise/anonregex.py +++ b/crate_anon/anonymise/anonregex.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/anonregex.py diff --git a/crate_anon/anonymise/anonymise.py b/crate_anon/anonymise/anonymise.py index c119e404..91ead476 100644 --- a/crate_anon/anonymise/anonymise.py +++ b/crate_anon/anonymise/anonymise.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/anonymise.py diff --git a/crate_anon/anonymise/config.py b/crate_anon/anonymise/config.py index 66474b00..c87ddb2c 100644 --- a/crate_anon/anonymise/config.py +++ b/crate_anon/anonymise/config.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/config.py diff --git a/crate_anon/anonymise/config_singleton.py b/crate_anon/anonymise/config_singleton.py index a79c63ec..a7a2acec 100644 --- a/crate_anon/anonymise/config_singleton.py +++ b/crate_anon/anonymise/config_singleton.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/config_singleton.py diff --git a/crate_anon/anonymise/constants.py b/crate_anon/anonymise/constants.py index 41283f7b..fb5fbe19 100644 --- a/crate_anon/anonymise/constants.py +++ b/crate_anon/anonymise/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/constants.py diff --git a/crate_anon/anonymise/dbholder.py b/crate_anon/anonymise/dbholder.py index 078deb7e..8f680ff1 100644 --- a/crate_anon/anonymise/dbholder.py +++ b/crate_anon/anonymise/dbholder.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/dbholder.py diff --git a/crate_anon/anonymise/dd.py b/crate_anon/anonymise/dd.py index bd930549..f6bbfba5 100644 --- a/crate_anon/anonymise/dd.py +++ b/crate_anon/anonymise/dd.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/dd.py diff --git a/crate_anon/anonymise/ddr.py b/crate_anon/anonymise/ddr.py index 902af499..483eb53e 100644 --- a/crate_anon/anonymise/ddr.py +++ b/crate_anon/anonymise/ddr.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/ddr.py diff --git a/crate_anon/anonymise/eponyms.py b/crate_anon/anonymise/eponyms.py index af9855db..52b4973b 100644 --- a/crate_anon/anonymise/eponyms.py +++ b/crate_anon/anonymise/eponyms.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/eponyms.py diff --git a/crate_anon/anonymise/models.py b/crate_anon/anonymise/models.py index d1a58002..32fb2e2c 100644 --- a/crate_anon/anonymise/models.py +++ b/crate_anon/anonymise/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/models.py diff --git a/crate_anon/anonymise/patient.py b/crate_anon/anonymise/patient.py index ddd19ffd..896c2a23 100644 --- a/crate_anon/anonymise/patient.py +++ b/crate_anon/anonymise/patient.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/patient.py diff --git a/crate_anon/anonymise/scrub.py b/crate_anon/anonymise/scrub.py index 4f90a16f..86aed9d9 100644 --- a/crate_anon/anonymise/scrub.py +++ b/crate_anon/anonymise/scrub.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/scrub.py diff --git a/crate_anon/anonymise/tests/scrub_tests.py b/crate_anon/anonymise/tests/scrub_tests.py index a1e85963..538730c9 100644 --- a/crate_anon/anonymise/tests/scrub_tests.py +++ b/crate_anon/anonymise/tests/scrub_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/anonymise/tests/scrub_tests.py diff --git a/crate_anon/common/__init__.py b/crate_anon/common/__init__.py index a79c561c..2b367977 100644 --- a/crate_anon/common/__init__.py +++ b/crate_anon/common/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/__init__.py diff --git a/crate_anon/common/argparse_assist.py b/crate_anon/common/argparse_assist.py index a82d306e..6a0fcebe 100644 --- a/crate_anon/common/argparse_assist.py +++ b/crate_anon/common/argparse_assist.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/argparse_assist.py diff --git a/crate_anon/common/bugfix_flashtext.py b/crate_anon/common/bugfix_flashtext.py index 5dcfede6..0c60d11d 100644 --- a/crate_anon/common/bugfix_flashtext.py +++ b/crate_anon/common/bugfix_flashtext.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/bugfix_flashtext.py diff --git a/crate_anon/common/constants.py b/crate_anon/common/constants.py index 3f11aa45..412af248 100644 --- a/crate_anon/common/constants.py +++ b/crate_anon/common/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/constants.py diff --git a/crate_anon/common/dockerfunc.py b/crate_anon/common/dockerfunc.py index 6f2bc103..04014734 100644 --- a/crate_anon/common/dockerfunc.py +++ b/crate_anon/common/dockerfunc.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/dockerfunc.py diff --git a/crate_anon/common/exceptions.py b/crate_anon/common/exceptions.py index 22977dcb..7b6b3d34 100644 --- a/crate_anon/common/exceptions.py +++ b/crate_anon/common/exceptions.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/exceptions.py diff --git a/crate_anon/common/extendedconfigparser.py b/crate_anon/common/extendedconfigparser.py index 8f98294d..a29d53b9 100644 --- a/crate_anon/common/extendedconfigparser.py +++ b/crate_anon/common/extendedconfigparser.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/extendedconfigparser.py diff --git a/crate_anon/common/file_io.py b/crate_anon/common/file_io.py index fd8c2fd6..1ad86bc7 100644 --- a/crate_anon/common/file_io.py +++ b/crate_anon/common/file_io.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/file_io.py diff --git a/crate_anon/common/formatting.py b/crate_anon/common/formatting.py index 06639c67..be00c384 100644 --- a/crate_anon/common/formatting.py +++ b/crate_anon/common/formatting.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/formatting.py diff --git a/crate_anon/common/inputfunc.py b/crate_anon/common/inputfunc.py index 953fe497..a99b584b 100644 --- a/crate_anon/common/inputfunc.py +++ b/crate_anon/common/inputfunc.py @@ -1,7 +1,5 @@ -#!/usr/bin/env python - """ -crate_anon/nlp_manager/run_crate_nlp_demo.py +crate_anon/common/inputfunc.py =============================================================================== diff --git a/crate_anon/common/logfunc.py b/crate_anon/common/logfunc.py index 71375943..c3744f6f 100644 --- a/crate_anon/common/logfunc.py +++ b/crate_anon/common/logfunc.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/common/logfunc.py diff --git a/crate_anon/common/memsize.py b/crate_anon/common/memsize.py index a6ab03c3..129caf82 100644 --- a/crate_anon/common/memsize.py +++ b/crate_anon/common/memsize.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/memsize.py diff --git a/crate_anon/common/parallel.py b/crate_anon/common/parallel.py index f3cc117f..4d7e4b1e 100644 --- a/crate_anon/common/parallel.py +++ b/crate_anon/common/parallel.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/parallel.py diff --git a/crate_anon/common/profiling.py b/crate_anon/common/profiling.py index d3f8739e..4059fa72 100644 --- a/crate_anon/common/profiling.py +++ b/crate_anon/common/profiling.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/profiling.py diff --git a/crate_anon/common/regex_helpers.py b/crate_anon/common/regex_helpers.py index 0cf96374..82d9e94e 100644 --- a/crate_anon/common/regex_helpers.py +++ b/crate_anon/common/regex_helpers.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/regex_helpers.py diff --git a/crate_anon/common/spreadsheet.py b/crate_anon/common/spreadsheet.py index ebb5d324..99a8dad3 100644 --- a/crate_anon/common/spreadsheet.py +++ b/crate_anon/common/spreadsheet.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/spreadsheet.py diff --git a/crate_anon/common/sql.py b/crate_anon/common/sql.py index 88af62b7..fa8969c5 100644 --- a/crate_anon/common/sql.py +++ b/crate_anon/common/sql.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/sql.py diff --git a/crate_anon/common/stringfunc.py b/crate_anon/common/stringfunc.py index ca574981..04aee441 100644 --- a/crate_anon/common/stringfunc.py +++ b/crate_anon/common/stringfunc.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/stringfunc.py diff --git a/crate_anon/common/tests/regex_helper_tests.py b/crate_anon/common/tests/regex_helper_tests.py index b88fcfb5..accd3e3b 100644 --- a/crate_anon/common/tests/regex_helper_tests.py +++ b/crate_anon/common/tests/regex_helper_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/tests/regex_helper_tests.py diff --git a/crate_anon/common/tests/spreadsheet_tests.py b/crate_anon/common/tests/spreadsheet_tests.py index 5ab33ab1..a1b18816 100644 --- a/crate_anon/common/tests/spreadsheet_tests.py +++ b/crate_anon/common/tests/spreadsheet_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/tests/spreadsheet_tests.py diff --git a/crate_anon/common/tests/sql_tests.py b/crate_anon/common/tests/sql_tests.py index 8fb7e5f5..d52191ed 100644 --- a/crate_anon/common/tests/sql_tests.py +++ b/crate_anon/common/tests/sql_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/tests/sql_tests.py diff --git a/crate_anon/common/tests/stringfunc_tests.py b/crate_anon/common/tests/stringfunc_tests.py index a764c320..e9feebde 100644 --- a/crate_anon/common/tests/stringfunc_tests.py +++ b/crate_anon/common/tests/stringfunc_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/common/tests/stringfunc_tests.py diff --git a/crate_anon/conftest.py b/crate_anon/conftest.py index 5300788d..6e58a9a9 100644 --- a/crate_anon/conftest.py +++ b/crate_anon/conftest.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/conftest.py diff --git a/crate_anon/crateweb/__init__.py b/crate_anon/crateweb/__init__.py index 888660bf..0dae3607 100644 --- a/crate_anon/crateweb/__init__.py +++ b/crate_anon/crateweb/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/__init__.py diff --git a/crate_anon/crateweb/anonymise_api/__init__.py b/crate_anon/crateweb/anonymise_api/__init__.py index 760ed198..4d734be2 100644 --- a/crate_anon/crateweb/anonymise_api/__init__.py +++ b/crate_anon/crateweb/anonymise_api/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/anonymise_api/__init__.py diff --git a/crate_anon/crateweb/config/__init__.py b/crate_anon/crateweb/config/__init__.py index 73ae5767..0810f67e 100644 --- a/crate_anon/crateweb/config/__init__.py +++ b/crate_anon/crateweb/config/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/__init__.py diff --git a/crate_anon/crateweb/config/apps.py b/crate_anon/crateweb/config/apps.py index f704f651..a9e7c822 100644 --- a/crate_anon/crateweb/config/apps.py +++ b/crate_anon/crateweb/config/apps.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/apps.py diff --git a/crate_anon/crateweb/config/constants.py b/crate_anon/crateweb/config/constants.py index 2f313ed0..8b887623 100644 --- a/crate_anon/crateweb/config/constants.py +++ b/crate_anon/crateweb/config/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/constants.py diff --git a/crate_anon/crateweb/config/settings.py b/crate_anon/crateweb/config/settings.py index 79a2c896..1cbc35c0 100644 --- a/crate_anon/crateweb/config/settings.py +++ b/crate_anon/crateweb/config/settings.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/settings.py diff --git a/crate_anon/crateweb/config/test_settings.py b/crate_anon/crateweb/config/test_settings.py index 507d6836..30ed4bd3 100644 --- a/crate_anon/crateweb/config/test_settings.py +++ b/crate_anon/crateweb/config/test_settings.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/test_settings.py diff --git a/crate_anon/crateweb/config/urls.py b/crate_anon/crateweb/config/urls.py index ba570032..ba9b60c6 100644 --- a/crate_anon/crateweb/config/urls.py +++ b/crate_anon/crateweb/config/urls.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/urls.py diff --git a/crate_anon/crateweb/config/wsgi.py b/crate_anon/crateweb/config/wsgi.py index 773b60d3..6c220203 100644 --- a/crate_anon/crateweb/config/wsgi.py +++ b/crate_anon/crateweb/config/wsgi.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/config/wsgi.py diff --git a/crate_anon/crateweb/consent/__init__.py b/crate_anon/crateweb/consent/__init__.py index d8929178..d85417ad 100644 --- a/crate_anon/crateweb/consent/__init__.py +++ b/crate_anon/crateweb/consent/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/__init__.py diff --git a/crate_anon/crateweb/consent/celery.py b/crate_anon/crateweb/consent/celery.py index 3e4b276d..79275518 100644 --- a/crate_anon/crateweb/consent/celery.py +++ b/crate_anon/crateweb/consent/celery.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/celery.py diff --git a/crate_anon/crateweb/consent/constants.py b/crate_anon/crateweb/consent/constants.py index 3cdc2ba5..6efb6e51 100644 --- a/crate_anon/crateweb/consent/constants.py +++ b/crate_anon/crateweb/consent/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/constants.py diff --git a/crate_anon/crateweb/consent/forms.py b/crate_anon/crateweb/consent/forms.py index bb3a270e..93957ba7 100644 --- a/crate_anon/crateweb/consent/forms.py +++ b/crate_anon/crateweb/consent/forms.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/forms.py diff --git a/crate_anon/crateweb/consent/lookup.py b/crate_anon/crateweb/consent/lookup.py index c52ec382..3acbff13 100644 --- a/crate_anon/crateweb/consent/lookup.py +++ b/crate_anon/crateweb/consent/lookup.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup.py diff --git a/crate_anon/crateweb/consent/lookup_common.py b/crate_anon/crateweb/consent/lookup_common.py index f28ee1bd..2e977c53 100644 --- a/crate_anon/crateweb/consent/lookup_common.py +++ b/crate_anon/crateweb/consent/lookup_common.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup_common.py diff --git a/crate_anon/crateweb/consent/lookup_crs.py b/crate_anon/crateweb/consent/lookup_crs.py index b131f415..bec03e27 100644 --- a/crate_anon/crateweb/consent/lookup_crs.py +++ b/crate_anon/crateweb/consent/lookup_crs.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup_crs.py diff --git a/crate_anon/crateweb/consent/lookup_dummy.py b/crate_anon/crateweb/consent/lookup_dummy.py index f2e79a61..422eeeb5 100644 --- a/crate_anon/crateweb/consent/lookup_dummy.py +++ b/crate_anon/crateweb/consent/lookup_dummy.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup_dummy.py diff --git a/crate_anon/crateweb/consent/lookup_rio.py b/crate_anon/crateweb/consent/lookup_rio.py index 669e72ad..2ba222e5 100644 --- a/crate_anon/crateweb/consent/lookup_rio.py +++ b/crate_anon/crateweb/consent/lookup_rio.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup_rio.py diff --git a/crate_anon/crateweb/consent/lookup_systmone.py b/crate_anon/crateweb/consent/lookup_systmone.py index 3d220d15..d517a74e 100644 --- a/crate_anon/crateweb/consent/lookup_systmone.py +++ b/crate_anon/crateweb/consent/lookup_systmone.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/lookup_systmone.py diff --git a/crate_anon/crateweb/consent/management/__init__.py b/crate_anon/crateweb/consent/management/__init__.py index 54682fc7..52f05157 100644 --- a/crate_anon/crateweb/consent/management/__init__.py +++ b/crate_anon/crateweb/consent/management/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/__init__.py diff --git a/crate_anon/crateweb/consent/management/commands/__init__.py b/crate_anon/crateweb/consent/management/commands/__init__.py index 72a3f4aa..5a5e982e 100644 --- a/crate_anon/crateweb/consent/management/commands/__init__.py +++ b/crate_anon/crateweb/consent/management/commands/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/__init__.py diff --git a/crate_anon/crateweb/consent/management/commands/email_rdbm.py b/crate_anon/crateweb/consent/management/commands/email_rdbm.py index d3f3f9c1..a45f7d95 100644 --- a/crate_anon/crateweb/consent/management/commands/email_rdbm.py +++ b/crate_anon/crateweb/consent/management/commands/email_rdbm.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/email_rdbm.py diff --git a/crate_anon/crateweb/consent/management/commands/fetch_optouts.py b/crate_anon/crateweb/consent/management/commands/fetch_optouts.py index eb0616a3..edd36dd8 100644 --- a/crate_anon/crateweb/consent/management/commands/fetch_optouts.py +++ b/crate_anon/crateweb/consent/management/commands/fetch_optouts.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/fetch_optouts.py diff --git a/crate_anon/crateweb/consent/management/commands/make_ethics_pack.py b/crate_anon/crateweb/consent/management/commands/make_ethics_pack.py index db4f7a45..9dba0f42 100755 --- a/crate_anon/crateweb/consent/management/commands/make_ethics_pack.py +++ b/crate_anon/crateweb/consent/management/commands/make_ethics_pack.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/tools/make_ethics_pack.py diff --git a/crate_anon/crateweb/consent/management/commands/populate.py b/crate_anon/crateweb/consent/management/commands/populate.py index ab5e5e62..78dcc709 100644 --- a/crate_anon/crateweb/consent/management/commands/populate.py +++ b/crate_anon/crateweb/consent/management/commands/populate.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/populate.py diff --git a/crate_anon/crateweb/consent/management/commands/resubmit_unprocessed_tasks.py b/crate_anon/crateweb/consent/management/commands/resubmit_unprocessed_tasks.py index 818a25b2..d4524582 100644 --- a/crate_anon/crateweb/consent/management/commands/resubmit_unprocessed_tasks.py +++ b/crate_anon/crateweb/consent/management/commands/resubmit_unprocessed_tasks.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/resubmit_unprocessed_tasks.py diff --git a/crate_anon/crateweb/consent/management/commands/test_email.py b/crate_anon/crateweb/consent/management/commands/test_email.py index 4d24737e..293c508c 100644 --- a/crate_anon/crateweb/consent/management/commands/test_email.py +++ b/crate_anon/crateweb/consent/management/commands/test_email.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/management/commands/test_email.py diff --git a/crate_anon/crateweb/consent/migrations/0001_initial.py b/crate_anon/crateweb/consent/migrations/0001_initial.py index 25657f79..5eba2fdc 100644 --- a/crate_anon/crateweb/consent/migrations/0001_initial.py +++ b/crate_anon/crateweb/consent/migrations/0001_initial.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0001_initial.py diff --git a/crate_anon/crateweb/consent/migrations/0002_auto_20160621_1511.py b/crate_anon/crateweb/consent/migrations/0002_auto_20160621_1511.py index b0a5017c..003027bc 100644 --- a/crate_anon/crateweb/consent/migrations/0002_auto_20160621_1511.py +++ b/crate_anon/crateweb/consent/migrations/0002_auto_20160621_1511.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0002_auto_20160621_1511.py diff --git a/crate_anon/crateweb/consent/migrations/0003_auto_20160628_1301.py b/crate_anon/crateweb/consent/migrations/0003_auto_20160628_1301.py index ea7e477f..e2d7bc69 100644 --- a/crate_anon/crateweb/consent/migrations/0003_auto_20160628_1301.py +++ b/crate_anon/crateweb/consent/migrations/0003_auto_20160628_1301.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0003_auto_20160628_1301.py diff --git a/crate_anon/crateweb/consent/migrations/0004_auto_20160703_1530.py b/crate_anon/crateweb/consent/migrations/0004_auto_20160703_1530.py index 6f48be60..1612c364 100644 --- a/crate_anon/crateweb/consent/migrations/0004_auto_20160703_1530.py +++ b/crate_anon/crateweb/consent/migrations/0004_auto_20160703_1530.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0004_auto_20160703_1530.py diff --git a/crate_anon/crateweb/consent/migrations/0005_auto_20170203_1348.py b/crate_anon/crateweb/consent/migrations/0005_auto_20170203_1348.py index d110b08d..50a60144 100644 --- a/crate_anon/crateweb/consent/migrations/0005_auto_20170203_1348.py +++ b/crate_anon/crateweb/consent/migrations/0005_auto_20170203_1348.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0005_auto_20170203_1348.py diff --git a/crate_anon/crateweb/consent/migrations/0006_auto_20170206_1617.py b/crate_anon/crateweb/consent/migrations/0006_auto_20170206_1617.py index ba5f4577..ade27267 100644 --- a/crate_anon/crateweb/consent/migrations/0006_auto_20170206_1617.py +++ b/crate_anon/crateweb/consent/migrations/0006_auto_20170206_1617.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0006_auto_20170206_1617.py diff --git a/crate_anon/crateweb/consent/migrations/0007_auto_20170228_1052.py b/crate_anon/crateweb/consent/migrations/0007_auto_20170228_1052.py index 367af2f2..abd7897a 100644 --- a/crate_anon/crateweb/consent/migrations/0007_auto_20170228_1052.py +++ b/crate_anon/crateweb/consent/migrations/0007_auto_20170228_1052.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0007_auto_20170228_1052.py diff --git a/crate_anon/crateweb/consent/migrations/0008_auto_20170507_1218.py b/crate_anon/crateweb/consent/migrations/0008_auto_20170507_1218.py index 0f038654..d384848a 100644 --- a/crate_anon/crateweb/consent/migrations/0008_auto_20170507_1218.py +++ b/crate_anon/crateweb/consent/migrations/0008_auto_20170507_1218.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0008_auto_20170507_1218.py diff --git a/crate_anon/crateweb/consent/migrations/0009_auto_20180629_1132.py b/crate_anon/crateweb/consent/migrations/0009_auto_20180629_1132.py index 5e9dcb3b..27c76983 100644 --- a/crate_anon/crateweb/consent/migrations/0009_auto_20180629_1132.py +++ b/crate_anon/crateweb/consent/migrations/0009_auto_20180629_1132.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0009_auto_20180629_1132.py diff --git a/crate_anon/crateweb/consent/migrations/0010_auto_20180629_1238.py b/crate_anon/crateweb/consent/migrations/0010_auto_20180629_1238.py index 62a9af7f..1fe67a3e 100644 --- a/crate_anon/crateweb/consent/migrations/0010_auto_20180629_1238.py +++ b/crate_anon/crateweb/consent/migrations/0010_auto_20180629_1238.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0010_auto_20180629_1238.py diff --git a/crate_anon/crateweb/consent/migrations/0011_auto_20181022_0801.py b/crate_anon/crateweb/consent/migrations/0011_auto_20181022_0801.py index 0d21a98e..2fbe4bb1 100644 --- a/crate_anon/crateweb/consent/migrations/0011_auto_20181022_0801.py +++ b/crate_anon/crateweb/consent/migrations/0011_auto_20181022_0801.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/0011_auto_20181022_0801.py diff --git a/crate_anon/crateweb/consent/migrations/__init__.py b/crate_anon/crateweb/consent/migrations/__init__.py index 6067b4c1..772b7fea 100644 --- a/crate_anon/crateweb/consent/migrations/__init__.py +++ b/crate_anon/crateweb/consent/migrations/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/migrations/__init__.py diff --git a/crate_anon/crateweb/consent/models.py b/crate_anon/crateweb/consent/models.py index 8d264591..77b7f0d9 100644 --- a/crate_anon/crateweb/consent/models.py +++ b/crate_anon/crateweb/consent/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/models.py diff --git a/crate_anon/crateweb/consent/storage.py b/crate_anon/crateweb/consent/storage.py index 3e8ed182..cb5d92f1 100644 --- a/crate_anon/crateweb/consent/storage.py +++ b/crate_anon/crateweb/consent/storage.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/storage.py diff --git a/crate_anon/crateweb/consent/tasks.py b/crate_anon/crateweb/consent/tasks.py index 086a7a77..7da8c261 100644 --- a/crate_anon/crateweb/consent/tasks.py +++ b/crate_anon/crateweb/consent/tasks.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/tasks.py diff --git a/crate_anon/crateweb/consent/teamlookup.py b/crate_anon/crateweb/consent/teamlookup.py index 4ac2cc65..43bacc70 100644 --- a/crate_anon/crateweb/consent/teamlookup.py +++ b/crate_anon/crateweb/consent/teamlookup.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/teamlookup.py diff --git a/crate_anon/crateweb/consent/teamlookup_dummy.py b/crate_anon/crateweb/consent/teamlookup_dummy.py index 3a9e3a7b..b160b814 100644 --- a/crate_anon/crateweb/consent/teamlookup_dummy.py +++ b/crate_anon/crateweb/consent/teamlookup_dummy.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/teamlookup_dummy.py diff --git a/crate_anon/crateweb/consent/teamlookup_rio.py b/crate_anon/crateweb/consent/teamlookup_rio.py index 80898560..e4cc09cb 100644 --- a/crate_anon/crateweb/consent/teamlookup_rio.py +++ b/crate_anon/crateweb/consent/teamlookup_rio.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/teamlookup_rio.py diff --git a/crate_anon/crateweb/consent/teamlookup_systmone.py b/crate_anon/crateweb/consent/teamlookup_systmone.py index 8befd3b0..07b67fd9 100644 --- a/crate_anon/crateweb/consent/teamlookup_systmone.py +++ b/crate_anon/crateweb/consent/teamlookup_systmone.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/teamlookup_systmone.py diff --git a/crate_anon/crateweb/consent/utils.py b/crate_anon/crateweb/consent/utils.py index 670a870a..a95fc68a 100644 --- a/crate_anon/crateweb/consent/utils.py +++ b/crate_anon/crateweb/consent/utils.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/utils.py diff --git a/crate_anon/crateweb/consent/views.py b/crate_anon/crateweb/consent/views.py index f10bb678..69828dc6 100644 --- a/crate_anon/crateweb/consent/views.py +++ b/crate_anon/crateweb/consent/views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/consent/views.py diff --git a/crate_anon/crateweb/core/__init__.py b/crate_anon/crateweb/core/__init__.py index 76486610..67f75578 100644 --- a/crate_anon/crateweb/core/__init__.py +++ b/crate_anon/crateweb/core/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/__init__.py diff --git a/crate_anon/crateweb/core/admin.py b/crate_anon/crateweb/core/admin.py index 87faed63..7c319bf7 100644 --- a/crate_anon/crateweb/core/admin.py +++ b/crate_anon/crateweb/core/admin.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/admin.py diff --git a/crate_anon/crateweb/core/auth_views.py b/crate_anon/crateweb/core/auth_views.py index 4069ab62..ead2a113 100644 --- a/crate_anon/crateweb/core/auth_views.py +++ b/crate_anon/crateweb/core/auth_views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/auth_views.py diff --git a/crate_anon/crateweb/core/constants.py b/crate_anon/crateweb/core/constants.py index 71d1ee0b..ddce0f6d 100644 --- a/crate_anon/crateweb/core/constants.py +++ b/crate_anon/crateweb/core/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/constants.py diff --git a/crate_anon/crateweb/core/context_processors.py b/crate_anon/crateweb/core/context_processors.py index be90fc69..00aee864 100644 --- a/crate_anon/crateweb/core/context_processors.py +++ b/crate_anon/crateweb/core/context_processors.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/context_processors.py diff --git a/crate_anon/crateweb/core/management/__init__.py b/crate_anon/crateweb/core/management/__init__.py index 3f2398f9..1c71b39a 100644 --- a/crate_anon/crateweb/core/management/__init__.py +++ b/crate_anon/crateweb/core/management/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/management/__init__.py diff --git a/crate_anon/crateweb/core/management/commands/__init__.py b/crate_anon/crateweb/core/management/commands/__init__.py index 80d38e83..c1696402 100644 --- a/crate_anon/crateweb/core/management/commands/__init__.py +++ b/crate_anon/crateweb/core/management/commands/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/management/commands/__init__.py diff --git a/crate_anon/crateweb/core/management/commands/ensuresuperuser.py b/crate_anon/crateweb/core/management/commands/ensuresuperuser.py index 69321ead..a7de753c 100644 --- a/crate_anon/crateweb/core/management/commands/ensuresuperuser.py +++ b/crate_anon/crateweb/core/management/commands/ensuresuperuser.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/management/commands/ensuresuperuser.py diff --git a/crate_anon/crateweb/core/middleware.py b/crate_anon/crateweb/core/middleware.py index c109cf2e..bea2abed 100644 --- a/crate_anon/crateweb/core/middleware.py +++ b/crate_anon/crateweb/core/middleware.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/middleware.py diff --git a/crate_anon/crateweb/core/utils.py b/crate_anon/crateweb/core/utils.py index 72c07211..23485439 100644 --- a/crate_anon/crateweb/core/utils.py +++ b/crate_anon/crateweb/core/utils.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/utils.py diff --git a/crate_anon/crateweb/core/views.py b/crate_anon/crateweb/core/views.py index ca9da261..ba74c799 100644 --- a/crate_anon/crateweb/core/views.py +++ b/crate_anon/crateweb/core/views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/core/views.py diff --git a/crate_anon/crateweb/extra/__init__.py b/crate_anon/crateweb/extra/__init__.py index 019981e8..ccba06ba 100644 --- a/crate_anon/crateweb/extra/__init__.py +++ b/crate_anon/crateweb/extra/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/extra/__init__.py diff --git a/crate_anon/crateweb/extra/admin.py b/crate_anon/crateweb/extra/admin.py index 4a714252..0663ca0e 100644 --- a/crate_anon/crateweb/extra/admin.py +++ b/crate_anon/crateweb/extra/admin.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/extra/admin.py diff --git a/crate_anon/crateweb/extra/pdf.py b/crate_anon/crateweb/extra/pdf.py index 4ca1ac2e..0c56162c 100644 --- a/crate_anon/crateweb/extra/pdf.py +++ b/crate_anon/crateweb/extra/pdf.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/extra/pdf.py diff --git a/crate_anon/crateweb/extra/salutation.py b/crate_anon/crateweb/extra/salutation.py index eba43e53..81eabe4c 100644 --- a/crate_anon/crateweb/extra/salutation.py +++ b/crate_anon/crateweb/extra/salutation.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/extra/salutation.py diff --git a/crate_anon/crateweb/research/__init__.py b/crate_anon/crateweb/research/__init__.py index e36db3ff..2d5e6e32 100644 --- a/crate_anon/crateweb/research/__init__.py +++ b/crate_anon/crateweb/research/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/__init__.py diff --git a/crate_anon/crateweb/research/archive_backend.py b/crate_anon/crateweb/research/archive_backend.py index cb6afa0d..a7ec4916 100644 --- a/crate_anon/crateweb/research/archive_backend.py +++ b/crate_anon/crateweb/research/archive_backend.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/archive_backend.py diff --git a/crate_anon/crateweb/research/archive_func.py b/crate_anon/crateweb/research/archive_func.py index c748403e..9f2f09db 100644 --- a/crate_anon/crateweb/research/archive_func.py +++ b/crate_anon/crateweb/research/archive_func.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/archive_func.py diff --git a/crate_anon/crateweb/research/errors.py b/crate_anon/crateweb/research/errors.py index e2b2ce40..1cc88fbc 100644 --- a/crate_anon/crateweb/research/errors.py +++ b/crate_anon/crateweb/research/errors.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/crateweb/research/errors.py diff --git a/crate_anon/crateweb/research/forms.py b/crate_anon/crateweb/research/forms.py index 5af5f86e..d865b9bc 100644 --- a/crate_anon/crateweb/research/forms.py +++ b/crate_anon/crateweb/research/forms.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/forms.py diff --git a/crate_anon/crateweb/research/html_functions.py b/crate_anon/crateweb/research/html_functions.py index 338ad074..a6a80bce 100644 --- a/crate_anon/crateweb/research/html_functions.py +++ b/crate_anon/crateweb/research/html_functions.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/html_functions.py diff --git a/crate_anon/crateweb/research/migrations/0001_initial.py b/crate_anon/crateweb/research/migrations/0001_initial.py index ab57c496..24c6b0ad 100644 --- a/crate_anon/crateweb/research/migrations/0001_initial.py +++ b/crate_anon/crateweb/research/migrations/0001_initial.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0001_initial.py diff --git a/crate_anon/crateweb/research/migrations/0002_auto_20170203_1348.py b/crate_anon/crateweb/research/migrations/0002_auto_20170203_1348.py index 091583fa..00769f4d 100644 --- a/crate_anon/crateweb/research/migrations/0002_auto_20170203_1348.py +++ b/crate_anon/crateweb/research/migrations/0002_auto_20170203_1348.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0002_auto_20170203_1348.py diff --git a/crate_anon/crateweb/research/migrations/0003_patientexplorer_patientexploreraudit.py b/crate_anon/crateweb/research/migrations/0003_patientexplorer_patientexploreraudit.py index 8e9d1dce..4079cac3 100644 --- a/crate_anon/crateweb/research/migrations/0003_patientexplorer_patientexploreraudit.py +++ b/crate_anon/crateweb/research/migrations/0003_patientexplorer_patientexploreraudit.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0003_patientexplorer_patientexploreraudit.py diff --git a/crate_anon/crateweb/research/migrations/0004_auto_20170212_0137.py b/crate_anon/crateweb/research/migrations/0004_auto_20170212_0137.py index c8f60ce2..9b22d361 100644 --- a/crate_anon/crateweb/research/migrations/0004_auto_20170212_0137.py +++ b/crate_anon/crateweb/research/migrations/0004_auto_20170212_0137.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0004_auto_20170212_0137.py diff --git a/crate_anon/crateweb/research/migrations/0005_query_sql_hash.py b/crate_anon/crateweb/research/migrations/0005_query_sql_hash.py index c8535102..4a55bf89 100644 --- a/crate_anon/crateweb/research/migrations/0005_query_sql_hash.py +++ b/crate_anon/crateweb/research/migrations/0005_query_sql_hash.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0005_query_sql_hash.py diff --git a/crate_anon/crateweb/research/migrations/0006_patientexplorer_pmq_hash.py b/crate_anon/crateweb/research/migrations/0006_patientexplorer_pmq_hash.py index 2b1b3995..ff661300 100644 --- a/crate_anon/crateweb/research/migrations/0006_patientexplorer_pmq_hash.py +++ b/crate_anon/crateweb/research/migrations/0006_patientexplorer_pmq_hash.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0006_patientexplorer_pmq_hash.py diff --git a/crate_anon/crateweb/research/migrations/0007_sitewidequery.py b/crate_anon/crateweb/research/migrations/0007_sitewidequery.py index 47d78785..7c24c0a5 100644 --- a/crate_anon/crateweb/research/migrations/0007_sitewidequery.py +++ b/crate_anon/crateweb/research/migrations/0007_sitewidequery.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0007_sitewidequery.py diff --git a/crate_anon/crateweb/research/migrations/0008_query_display.py b/crate_anon/crateweb/research/migrations/0008_query_display.py index 04a968f4..2de287e4 100644 --- a/crate_anon/crateweb/research/migrations/0008_query_display.py +++ b/crate_anon/crateweb/research/migrations/0008_query_display.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/0008_query_display.py diff --git a/crate_anon/crateweb/research/migrations/__init__.py b/crate_anon/crateweb/research/migrations/__init__.py index 4bd7ab57..caaa0039 100644 --- a/crate_anon/crateweb/research/migrations/__init__.py +++ b/crate_anon/crateweb/research/migrations/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/migrations/__init__.py diff --git a/crate_anon/crateweb/research/models.py b/crate_anon/crateweb/research/models.py index 4608f24a..61ab8bce 100644 --- a/crate_anon/crateweb/research/models.py +++ b/crate_anon/crateweb/research/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/models.py diff --git a/crate_anon/crateweb/research/research_db_info.py b/crate_anon/crateweb/research/research_db_info.py index 1cad8ed7..08ae4b0e 100644 --- a/crate_anon/crateweb/research/research_db_info.py +++ b/crate_anon/crateweb/research/research_db_info.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/research_db_info.py diff --git a/crate_anon/crateweb/research/sql_writer.py b/crate_anon/crateweb/research/sql_writer.py index 99198521..269fb65d 100644 --- a/crate_anon/crateweb/research/sql_writer.py +++ b/crate_anon/crateweb/research/sql_writer.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/sql_writer.py diff --git a/crate_anon/crateweb/research/views.py b/crate_anon/crateweb/research/views.py index 11cda645..bedb4b90 100644 --- a/crate_anon/crateweb/research/views.py +++ b/crate_anon/crateweb/research/views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/research/views.py diff --git a/crate_anon/crateweb/userprofile/__init__.py b/crate_anon/crateweb/userprofile/__init__.py index 70a8e15f..85b0062c 100644 --- a/crate_anon/crateweb/userprofile/__init__.py +++ b/crate_anon/crateweb/userprofile/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/__init__.py diff --git a/crate_anon/crateweb/userprofile/forms.py b/crate_anon/crateweb/userprofile/forms.py index 470f9099..6ba3d950 100644 --- a/crate_anon/crateweb/userprofile/forms.py +++ b/crate_anon/crateweb/userprofile/forms.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/forms.py diff --git a/crate_anon/crateweb/userprofile/migrations/0001_initial.py b/crate_anon/crateweb/userprofile/migrations/0001_initial.py index e0944ced..29c5966a 100644 --- a/crate_anon/crateweb/userprofile/migrations/0001_initial.py +++ b/crate_anon/crateweb/userprofile/migrations/0001_initial.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0001_initial.py diff --git a/crate_anon/crateweb/userprofile/migrations/0002_userprofile_sql_scratchpad.py b/crate_anon/crateweb/userprofile/migrations/0002_userprofile_sql_scratchpad.py index ab84f4b7..c48d1200 100644 --- a/crate_anon/crateweb/userprofile/migrations/0002_userprofile_sql_scratchpad.py +++ b/crate_anon/crateweb/userprofile/migrations/0002_userprofile_sql_scratchpad.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0002_userprofile_sql_scratchpad.py diff --git a/crate_anon/crateweb/userprofile/migrations/0003_auto_20160628_1301.py b/crate_anon/crateweb/userprofile/migrations/0003_auto_20160628_1301.py index fb62cdc3..79fb1759 100644 --- a/crate_anon/crateweb/userprofile/migrations/0003_auto_20160628_1301.py +++ b/crate_anon/crateweb/userprofile/migrations/0003_auto_20160628_1301.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0003_auto_20160628_1301.py diff --git a/crate_anon/crateweb/userprofile/migrations/0004_userprofile_patients_per_page.py b/crate_anon/crateweb/userprofile/migrations/0004_userprofile_patients_per_page.py index 84a555f3..153e9508 100644 --- a/crate_anon/crateweb/userprofile/migrations/0004_userprofile_patients_per_page.py +++ b/crate_anon/crateweb/userprofile/migrations/0004_userprofile_patients_per_page.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0004_userprofile_patients_per_page.py diff --git a/crate_anon/crateweb/userprofile/migrations/0005_userprofile_patient_multiquery_scratchpad.py b/crate_anon/crateweb/userprofile/migrations/0005_userprofile_patient_multiquery_scratchpad.py index 044f39e0..a6fa0e0b 100644 --- a/crate_anon/crateweb/userprofile/migrations/0005_userprofile_patient_multiquery_scratchpad.py +++ b/crate_anon/crateweb/userprofile/migrations/0005_userprofile_patient_multiquery_scratchpad.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0005_userprofile_patient_multiquery_scratchpad.py diff --git a/crate_anon/crateweb/userprofile/migrations/0006_auto_20170212_0137.py b/crate_anon/crateweb/userprofile/migrations/0006_auto_20170212_0137.py index f787f368..55001c37 100644 --- a/crate_anon/crateweb/userprofile/migrations/0006_auto_20170212_0137.py +++ b/crate_anon/crateweb/userprofile/migrations/0006_auto_20170212_0137.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0006_auto_20170212_0137.py diff --git a/crate_anon/crateweb/userprofile/migrations/0007_auto_20170507_1218.py b/crate_anon/crateweb/userprofile/migrations/0007_auto_20170507_1218.py index 5c810576..cfd0ce8f 100644 --- a/crate_anon/crateweb/userprofile/migrations/0007_auto_20170507_1218.py +++ b/crate_anon/crateweb/userprofile/migrations/0007_auto_20170507_1218.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/0007_auto_20170507_1218.py diff --git a/crate_anon/crateweb/userprofile/migrations/__init__.py b/crate_anon/crateweb/userprofile/migrations/__init__.py index b6617048..fbb44d83 100644 --- a/crate_anon/crateweb/userprofile/migrations/__init__.py +++ b/crate_anon/crateweb/userprofile/migrations/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/migrations/__init__.py diff --git a/crate_anon/crateweb/userprofile/models.py b/crate_anon/crateweb/userprofile/models.py index 57fa4f18..8e58e024 100644 --- a/crate_anon/crateweb/userprofile/models.py +++ b/crate_anon/crateweb/userprofile/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/models.py diff --git a/crate_anon/crateweb/userprofile/views.py b/crate_anon/crateweb/userprofile/views.py index e027c488..ab57ed9a 100644 --- a/crate_anon/crateweb/userprofile/views.py +++ b/crate_anon/crateweb/userprofile/views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/crateweb/userprofile/views.py diff --git a/crate_anon/linkage/__init__.py b/crate_anon/linkage/__init__.py index 5203744a..1d412625 100644 --- a/crate_anon/linkage/__init__.py +++ b/crate_anon/linkage/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/linkage/__init__.py diff --git a/crate_anon/linkage/comparison.py b/crate_anon/linkage/comparison.py index d230f2d5..1663228f 100644 --- a/crate_anon/linkage/comparison.py +++ b/crate_anon/linkage/comparison.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/comparison.py diff --git a/crate_anon/linkage/constants.py b/crate_anon/linkage/constants.py index 20ee9b3d..eb8bbcf0 100644 --- a/crate_anon/linkage/constants.py +++ b/crate_anon/linkage/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/constants.py diff --git a/crate_anon/linkage/frequencies.py b/crate_anon/linkage/frequencies.py index e4202976..695aea7e 100644 --- a/crate_anon/linkage/frequencies.py +++ b/crate_anon/linkage/frequencies.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/frequencies.py diff --git a/crate_anon/linkage/helpers.py b/crate_anon/linkage/helpers.py index 762a477c..db164141 100644 --- a/crate_anon/linkage/helpers.py +++ b/crate_anon/linkage/helpers.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/helpers.py diff --git a/crate_anon/linkage/identifiers.py b/crate_anon/linkage/identifiers.py index 0cf2f877..bc982e3a 100644 --- a/crate_anon/linkage/identifiers.py +++ b/crate_anon/linkage/identifiers.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/identifiers.py diff --git a/crate_anon/linkage/matchconfig.py b/crate_anon/linkage/matchconfig.py index 2f0b352b..a68f761a 100644 --- a/crate_anon/linkage/matchconfig.py +++ b/crate_anon/linkage/matchconfig.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/matchconfig.py diff --git a/crate_anon/linkage/matchresult.py b/crate_anon/linkage/matchresult.py index 9229d348..a47636ca 100644 --- a/crate_anon/linkage/matchresult.py +++ b/crate_anon/linkage/matchresult.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/matchresult.py diff --git a/crate_anon/linkage/people.py b/crate_anon/linkage/people.py index bda02388..6249720c 100644 --- a/crate_anon/linkage/people.py +++ b/crate_anon/linkage/people.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/people.py diff --git a/crate_anon/linkage/person.py b/crate_anon/linkage/person.py index 12d040c6..e15be3ee 100644 --- a/crate_anon/linkage/person.py +++ b/crate_anon/linkage/person.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/person.py diff --git a/crate_anon/linkage/person_io.py b/crate_anon/linkage/person_io.py index ea12f8c0..adb12288 100644 --- a/crate_anon/linkage/person_io.py +++ b/crate_anon/linkage/person_io.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/linkage/person_io.py diff --git a/crate_anon/linkage/tests/fuzzy_id_match_tests.py b/crate_anon/linkage/tests/fuzzy_id_match_tests.py index f14d1978..a54074c5 100644 --- a/crate_anon/linkage/tests/fuzzy_id_match_tests.py +++ b/crate_anon/linkage/tests/fuzzy_id_match_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/linkage/tests/fuzzy_id_match_tests.py diff --git a/crate_anon/nlp_manager/__init__.py b/crate_anon/nlp_manager/__init__.py index b1b7a2a1..a77df6a2 100644 --- a/crate_anon/nlp_manager/__init__.py +++ b/crate_anon/nlp_manager/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/__init__.py diff --git a/crate_anon/nlp_manager/all_processors.py b/crate_anon/nlp_manager/all_processors.py index 87685280..9ac84628 100644 --- a/crate_anon/nlp_manager/all_processors.py +++ b/crate_anon/nlp_manager/all_processors.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/all_processors.py diff --git a/crate_anon/nlp_manager/base_nlp_parser.py b/crate_anon/nlp_manager/base_nlp_parser.py index c5422a72..ac56a4a8 100644 --- a/crate_anon/nlp_manager/base_nlp_parser.py +++ b/crate_anon/nlp_manager/base_nlp_parser.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/base_nlp_parser.py diff --git a/crate_anon/nlp_manager/cloud_config.py b/crate_anon/nlp_manager/cloud_config.py index 587a2cc1..854bd16e 100644 --- a/crate_anon/nlp_manager/cloud_config.py +++ b/crate_anon/nlp_manager/cloud_config.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/cloud_config.py diff --git a/crate_anon/nlp_manager/cloud_parser.py b/crate_anon/nlp_manager/cloud_parser.py index bd3f92e3..670fbab2 100644 --- a/crate_anon/nlp_manager/cloud_parser.py +++ b/crate_anon/nlp_manager/cloud_parser.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/cloud_parser.py diff --git a/crate_anon/nlp_manager/cloud_request.py b/crate_anon/nlp_manager/cloud_request.py index f085f1a9..0926c124 100644 --- a/crate_anon/nlp_manager/cloud_request.py +++ b/crate_anon/nlp_manager/cloud_request.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/cloud_request.py diff --git a/crate_anon/nlp_manager/cloud_request_sender.py b/crate_anon/nlp_manager/cloud_request_sender.py index 3032be60..8a0b7107 100644 --- a/crate_anon/nlp_manager/cloud_request_sender.py +++ b/crate_anon/nlp_manager/cloud_request_sender.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/cloud_request_sender.py diff --git a/crate_anon/nlp_manager/cloud_run_info.py b/crate_anon/nlp_manager/cloud_run_info.py index 019b9678..f936e747 100644 --- a/crate_anon/nlp_manager/cloud_run_info.py +++ b/crate_anon/nlp_manager/cloud_run_info.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/cloud_run_info.py diff --git a/crate_anon/nlp_manager/constants.py b/crate_anon/nlp_manager/constants.py index 0f3a2dfc..50ff1436 100644 --- a/crate_anon/nlp_manager/constants.py +++ b/crate_anon/nlp_manager/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/constants.py diff --git a/crate_anon/nlp_manager/input_field_config.py b/crate_anon/nlp_manager/input_field_config.py index 25c0f1ff..a01b440b 100644 --- a/crate_anon/nlp_manager/input_field_config.py +++ b/crate_anon/nlp_manager/input_field_config.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/input_field_config.py diff --git a/crate_anon/nlp_manager/models.py b/crate_anon/nlp_manager/models.py index 84df1bda..0cff2036 100644 --- a/crate_anon/nlp_manager/models.py +++ b/crate_anon/nlp_manager/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/models.py diff --git a/crate_anon/nlp_manager/nlp_definition.py b/crate_anon/nlp_manager/nlp_definition.py index a3acf5c0..8a932866 100644 --- a/crate_anon/nlp_manager/nlp_definition.py +++ b/crate_anon/nlp_manager/nlp_definition.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/nlp_definition.py diff --git a/crate_anon/nlp_manager/number.py b/crate_anon/nlp_manager/number.py index 267be829..62bdab28 100644 --- a/crate_anon/nlp_manager/number.py +++ b/crate_anon/nlp_manager/number.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/number.py diff --git a/crate_anon/nlp_manager/output_user_config.py b/crate_anon/nlp_manager/output_user_config.py index 7b81e17a..8b2766fa 100644 --- a/crate_anon/nlp_manager/output_user_config.py +++ b/crate_anon/nlp_manager/output_user_config.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/output_user_config.py diff --git a/crate_anon/nlp_manager/parse_biochemistry.py b/crate_anon/nlp_manager/parse_biochemistry.py index 176ff5db..ebf19088 100644 --- a/crate_anon/nlp_manager/parse_biochemistry.py +++ b/crate_anon/nlp_manager/parse_biochemistry.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_biochemistry.py diff --git a/crate_anon/nlp_manager/parse_clinical.py b/crate_anon/nlp_manager/parse_clinical.py index f4250090..af931e79 100644 --- a/crate_anon/nlp_manager/parse_clinical.py +++ b/crate_anon/nlp_manager/parse_clinical.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_clinical.py diff --git a/crate_anon/nlp_manager/parse_cognitive.py b/crate_anon/nlp_manager/parse_cognitive.py index c69a5aea..8f11cc4b 100644 --- a/crate_anon/nlp_manager/parse_cognitive.py +++ b/crate_anon/nlp_manager/parse_cognitive.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_cognitive.py diff --git a/crate_anon/nlp_manager/parse_gate.py b/crate_anon/nlp_manager/parse_gate.py index 5fdcfc39..7e887f77 100644 --- a/crate_anon/nlp_manager/parse_gate.py +++ b/crate_anon/nlp_manager/parse_gate.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_gate.py diff --git a/crate_anon/nlp_manager/parse_haematology.py b/crate_anon/nlp_manager/parse_haematology.py index 26235390..5468823c 100644 --- a/crate_anon/nlp_manager/parse_haematology.py +++ b/crate_anon/nlp_manager/parse_haematology.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_haematology.py diff --git a/crate_anon/nlp_manager/parse_medex.py b/crate_anon/nlp_manager/parse_medex.py index 91b5cbe3..128105ab 100644 --- a/crate_anon/nlp_manager/parse_medex.py +++ b/crate_anon/nlp_manager/parse_medex.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_manager/parse_medex.py diff --git a/crate_anon/nlp_manager/parse_substance_misuse.py b/crate_anon/nlp_manager/parse_substance_misuse.py index 4b640878..abb24465 100644 --- a/crate_anon/nlp_manager/parse_substance_misuse.py +++ b/crate_anon/nlp_manager/parse_substance_misuse.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/parse_substance_misuse.py diff --git a/crate_anon/nlp_manager/regex_func.py b/crate_anon/nlp_manager/regex_func.py index 69fdd8d1..f4f0bdd0 100644 --- a/crate_anon/nlp_manager/regex_func.py +++ b/crate_anon/nlp_manager/regex_func.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/regex_func.py diff --git a/crate_anon/nlp_manager/regex_numbers.py b/crate_anon/nlp_manager/regex_numbers.py index b16b0d00..e6232f93 100644 --- a/crate_anon/nlp_manager/regex_numbers.py +++ b/crate_anon/nlp_manager/regex_numbers.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/regex_numbers.py diff --git a/crate_anon/nlp_manager/regex_parser.py b/crate_anon/nlp_manager/regex_parser.py index 9c5d40c4..9cb86286 100644 --- a/crate_anon/nlp_manager/regex_parser.py +++ b/crate_anon/nlp_manager/regex_parser.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/regex_parser.py diff --git a/crate_anon/nlp_manager/regex_read_codes.py b/crate_anon/nlp_manager/regex_read_codes.py index e8b04822..1d34d1e3 100644 --- a/crate_anon/nlp_manager/regex_read_codes.py +++ b/crate_anon/nlp_manager/regex_read_codes.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/regex_read_codes.py diff --git a/crate_anon/nlp_manager/regex_units.py b/crate_anon/nlp_manager/regex_units.py index 5254225e..79ac3ff7 100644 --- a/crate_anon/nlp_manager/regex_units.py +++ b/crate_anon/nlp_manager/regex_units.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/regex_units.py diff --git a/crate_anon/nlp_manager/tests/all_processors_tests.py b/crate_anon/nlp_manager/tests/all_processors_tests.py index 7a610dfb..50f14e61 100644 --- a/crate_anon/nlp_manager/tests/all_processors_tests.py +++ b/crate_anon/nlp_manager/tests/all_processors_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/all_processors_tests.py diff --git a/crate_anon/nlp_manager/tests/cloud_request_process_tests.py b/crate_anon/nlp_manager/tests/cloud_request_process_tests.py index dabf8740..679d1937 100644 --- a/crate_anon/nlp_manager/tests/cloud_request_process_tests.py +++ b/crate_anon/nlp_manager/tests/cloud_request_process_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/cloud_request_process_tests.py diff --git a/crate_anon/nlp_manager/tests/cloud_request_sender_tests.py b/crate_anon/nlp_manager/tests/cloud_request_sender_tests.py index 57c5d2c6..8142ec4b 100644 --- a/crate_anon/nlp_manager/tests/cloud_request_sender_tests.py +++ b/crate_anon/nlp_manager/tests/cloud_request_sender_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/cloud_request_sender_tests.py diff --git a/crate_anon/nlp_manager/tests/nlp_parser_tests.py b/crate_anon/nlp_manager/tests/nlp_parser_tests.py index 68a71373..48fdfe82 100644 --- a/crate_anon/nlp_manager/tests/nlp_parser_tests.py +++ b/crate_anon/nlp_manager/tests/nlp_parser_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/nlp_parser_tests.py diff --git a/crate_anon/nlp_manager/tests/parse_biochemistry_tests.py b/crate_anon/nlp_manager/tests/parse_biochemistry_tests.py index 79349d46..e8fd1889 100644 --- a/crate_anon/nlp_manager/tests/parse_biochemistry_tests.py +++ b/crate_anon/nlp_manager/tests/parse_biochemistry_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/parse_biochemistry_tests.py diff --git a/crate_anon/nlp_manager/tests/parse_clinical_tests.py b/crate_anon/nlp_manager/tests/parse_clinical_tests.py index 10e8050d..cd012dcf 100644 --- a/crate_anon/nlp_manager/tests/parse_clinical_tests.py +++ b/crate_anon/nlp_manager/tests/parse_clinical_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/parse_clinical_tests.py diff --git a/crate_anon/nlp_manager/tests/parse_cognitive_tests.py b/crate_anon/nlp_manager/tests/parse_cognitive_tests.py index 56eead2a..481e19e5 100644 --- a/crate_anon/nlp_manager/tests/parse_cognitive_tests.py +++ b/crate_anon/nlp_manager/tests/parse_cognitive_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/parse_cognitive_tests.py diff --git a/crate_anon/nlp_manager/tests/parse_haematology_tests.py b/crate_anon/nlp_manager/tests/parse_haematology_tests.py index 2cc18fb6..e9238ce4 100644 --- a/crate_anon/nlp_manager/tests/parse_haematology_tests.py +++ b/crate_anon/nlp_manager/tests/parse_haematology_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/parse_haematology_tests.py diff --git a/crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py b/crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py index ce801eee..a08f902f 100644 --- a/crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py +++ b/crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/parse_substance_misuse_tests.py diff --git a/crate_anon/nlp_manager/tests/regex_numbers_tests.py b/crate_anon/nlp_manager/tests/regex_numbers_tests.py index e76fc77d..056fab53 100644 --- a/crate_anon/nlp_manager/tests/regex_numbers_tests.py +++ b/crate_anon/nlp_manager/tests/regex_numbers_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/regex_numbers_tests.py diff --git a/crate_anon/nlp_manager/tests/regex_parser_tests.py b/crate_anon/nlp_manager/tests/regex_parser_tests.py index 324bc275..9808e5a6 100644 --- a/crate_anon/nlp_manager/tests/regex_parser_tests.py +++ b/crate_anon/nlp_manager/tests/regex_parser_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/regex_parser_tests.py diff --git a/crate_anon/nlp_manager/tests/regex_read_codes_tests.py b/crate_anon/nlp_manager/tests/regex_read_codes_tests.py index c53bb794..80fad9f0 100644 --- a/crate_anon/nlp_manager/tests/regex_read_codes_tests.py +++ b/crate_anon/nlp_manager/tests/regex_read_codes_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/regex_read_codes_tests.py diff --git a/crate_anon/nlp_manager/tests/regex_test_helperfunc.py b/crate_anon/nlp_manager/tests/regex_test_helperfunc.py index 04440ffa..2f4d1684 100644 --- a/crate_anon/nlp_manager/tests/regex_test_helperfunc.py +++ b/crate_anon/nlp_manager/tests/regex_test_helperfunc.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/regex_test_helperfunc.py diff --git a/crate_anon/nlp_manager/tests/regex_units_tests.py b/crate_anon/nlp_manager/tests/regex_units_tests.py index 54519a59..d263e027 100644 --- a/crate_anon/nlp_manager/tests/regex_units_tests.py +++ b/crate_anon/nlp_manager/tests/regex_units_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlp_manager/tests/regex_units_tests.py diff --git a/crate_anon/nlp_webserver/__init__.py b/crate_anon/nlp_webserver/__init__.py index 2ab76c88..6aef96ad 100644 --- a/crate_anon/nlp_webserver/__init__.py +++ b/crate_anon/nlp_webserver/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/__init__.py diff --git a/crate_anon/nlp_webserver/constants.py b/crate_anon/nlp_webserver/constants.py index b08cd8ed..f126eba5 100644 --- a/crate_anon/nlp_webserver/constants.py +++ b/crate_anon/nlp_webserver/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/constants.py diff --git a/crate_anon/nlp_webserver/models.py b/crate_anon/nlp_webserver/models.py index aec8f62a..b75aea72 100644 --- a/crate_anon/nlp_webserver/models.py +++ b/crate_anon/nlp_webserver/models.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/models.py diff --git a/crate_anon/nlp_webserver/procs.py b/crate_anon/nlp_webserver/procs.py index f53f1a7c..77cb837d 100644 --- a/crate_anon/nlp_webserver/procs.py +++ b/crate_anon/nlp_webserver/procs.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/procs.py diff --git a/crate_anon/nlp_webserver/security.py b/crate_anon/nlp_webserver/security.py index 36c34b2f..5277eebf 100644 --- a/crate_anon/nlp_webserver/security.py +++ b/crate_anon/nlp_webserver/security.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/security.py diff --git a/crate_anon/nlp_webserver/settings.py b/crate_anon/nlp_webserver/settings.py index 7709bc0d..3c76de37 100644 --- a/crate_anon/nlp_webserver/settings.py +++ b/crate_anon/nlp_webserver/settings.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/settings.py diff --git a/crate_anon/nlp_webserver/tasks.py b/crate_anon/nlp_webserver/tasks.py index 523207d0..cc1157e9 100644 --- a/crate_anon/nlp_webserver/tasks.py +++ b/crate_anon/nlp_webserver/tasks.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/tasks.py diff --git a/crate_anon/nlp_webserver/tests/settings_tests.py b/crate_anon/nlp_webserver/tests/settings_tests.py index 8bccec9e..064e7146 100644 --- a/crate_anon/nlp_webserver/tests/settings_tests.py +++ b/crate_anon/nlp_webserver/tests/settings_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/tests/settings_tests.py diff --git a/crate_anon/nlp_webserver/views.py b/crate_anon/nlp_webserver/views.py index 73bc62be..9fe89669 100644 --- a/crate_anon/nlp_webserver/views.py +++ b/crate_anon/nlp_webserver/views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/views.py diff --git a/crate_anon/nlp_webserver/wsgi_app.py b/crate_anon/nlp_webserver/wsgi_app.py index 6a89e36e..7042e43c 100644 --- a/crate_anon/nlp_webserver/wsgi_app.py +++ b/crate_anon/nlp_webserver/wsgi_app.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/wsgi_app.py diff --git a/crate_anon/nlp_webserver/wsgi_launchers.py b/crate_anon/nlp_webserver/wsgi_launchers.py index b08830eb..f0a46b30 100644 --- a/crate_anon/nlp_webserver/wsgi_launchers.py +++ b/crate_anon/nlp_webserver/wsgi_launchers.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/wsgi_launchers.py diff --git a/crate_anon/nlprp/__init__.py b/crate_anon/nlprp/__init__.py index bdf47818..9c1946f9 100644 --- a/crate_anon/nlprp/__init__.py +++ b/crate_anon/nlprp/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/nlprp/__init__.py @@ -25,7 +23,7 @@ =============================================================================== -crate_anon/nlp_manager/__init__.py +crate_anon/nlprp/__init__.py The mere existence of this file makes Python treat the directory as a package. """ diff --git a/crate_anon/nlprp/api.py b/crate_anon/nlprp/api.py index 3738e6d5..199ace8c 100644 --- a/crate_anon/nlprp/api.py +++ b/crate_anon/nlprp/api.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlprp/api.py diff --git a/crate_anon/nlprp/constants.py b/crate_anon/nlprp/constants.py index 2512ff14..4c32f804 100644 --- a/crate_anon/nlprp/constants.py +++ b/crate_anon/nlprp/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlprp/constants.py diff --git a/crate_anon/nlprp/errors.py b/crate_anon/nlprp/errors.py index d96c0a5a..192b4129 100644 --- a/crate_anon/nlprp/errors.py +++ b/crate_anon/nlprp/errors.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlprp/errors.py diff --git a/crate_anon/nlprp/version.py b/crate_anon/nlprp/version.py index 41839a8a..f1570d0a 100644 --- a/crate_anon/nlprp/version.py +++ b/crate_anon/nlprp/version.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlprp/version.py diff --git a/crate_anon/preprocess/__init__.py b/crate_anon/preprocess/__init__.py index f4c7777b..fd8d14b4 100644 --- a/crate_anon/preprocess/__init__.py +++ b/crate_anon/preprocess/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/__init__.py diff --git a/crate_anon/preprocess/constants.py b/crate_anon/preprocess/constants.py index 9e78812c..887d42c4 100644 --- a/crate_anon/preprocess/constants.py +++ b/crate_anon/preprocess/constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/constants.py diff --git a/crate_anon/preprocess/ddhint.py b/crate_anon/preprocess/ddhint.py index ae76fe49..eb25d031 100644 --- a/crate_anon/preprocess/ddhint.py +++ b/crate_anon/preprocess/ddhint.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/ddhint.py diff --git a/crate_anon/preprocess/rio_constants.py b/crate_anon/preprocess/rio_constants.py index 80664456..0dd642ca 100644 --- a/crate_anon/preprocess/rio_constants.py +++ b/crate_anon/preprocess/rio_constants.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/rio_constants.py diff --git a/crate_anon/preprocess/rio_ddgen.py b/crate_anon/preprocess/rio_ddgen.py index 9520e874..7b1d1e9f 100644 --- a/crate_anon/preprocess/rio_ddgen.py +++ b/crate_anon/preprocess/rio_ddgen.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/rio_ddgen.py diff --git a/crate_anon/preprocess/rio_pk.py b/crate_anon/preprocess/rio_pk.py index 13bd2540..1eb56646 100644 --- a/crate_anon/preprocess/rio_pk.py +++ b/crate_anon/preprocess/rio_pk.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/rio_pk.py diff --git a/crate_anon/preprocess/rio_view_func.py b/crate_anon/preprocess/rio_view_func.py index 2b9f0636..2ee47858 100644 --- a/crate_anon/preprocess/rio_view_func.py +++ b/crate_anon/preprocess/rio_view_func.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/rio_view_func.py diff --git a/crate_anon/preprocess/rio_views.py b/crate_anon/preprocess/rio_views.py index 62093611..f5ea47aa 100644 --- a/crate_anon/preprocess/rio_views.py +++ b/crate_anon/preprocess/rio_views.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/rio_views.py diff --git a/crate_anon/preprocess/systmone_ddgen.py b/crate_anon/preprocess/systmone_ddgen.py index 11439e6e..4daf61e9 100644 --- a/crate_anon/preprocess/systmone_ddgen.py +++ b/crate_anon/preprocess/systmone_ddgen.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/preprocess/systmone_ddgen.py diff --git a/crate_anon/preprocess/tests/systmone_ddgen_tests.py b/crate_anon/preprocess/tests/systmone_ddgen_tests.py index 949e31e5..80d7f361 100644 --- a/crate_anon/preprocess/tests/systmone_ddgen_tests.py +++ b/crate_anon/preprocess/tests/systmone_ddgen_tests.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/preprocess/tests/systmone_ddgen_tests.py diff --git a/crate_anon/testdocs_for_text_extraction/__init__.py b/crate_anon/testdocs_for_text_extraction/__init__.py index 9c313c0b..19a9cb3c 100644 --- a/crate_anon/testdocs_for_text_extraction/__init__.py +++ b/crate_anon/testdocs_for_text_extraction/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/testdocs_for_text_extraction/__init__.py diff --git a/crate_anon/tools/__init__.py b/crate_anon/tools/__init__.py index ea4f3192..4f8aa250 100644 --- a/crate_anon/tools/__init__.py +++ b/crate_anon/tools/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/tools/__init__.py diff --git a/crate_anon/version.py b/crate_anon/version.py index 42e230b9..31b02f93 100644 --- a/crate_anon/version.py +++ b/crate_anon/version.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/version.py From 34cd2b5224c680e307ecd656a870b89b46a3c18f Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 10:31:29 +0000 Subject: [PATCH 04/12] Make nlprp_test_client.py executable --- crate_anon/nlprp/nlprp_test_client.py | 0 docs/source/nlp/_nlprp_test_client.py | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 crate_anon/nlprp/nlprp_test_client.py mode change 100644 => 100755 docs/source/nlp/_nlprp_test_client.py diff --git a/crate_anon/nlprp/nlprp_test_client.py b/crate_anon/nlprp/nlprp_test_client.py old mode 100644 new mode 100755 diff --git a/docs/source/nlp/_nlprp_test_client.py b/docs/source/nlp/_nlprp_test_client.py old mode 100644 new mode 100755 From 4bbde2019d51127861ed4a90965abfb0ad3d3b19 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 11:08:06 +0000 Subject: [PATCH 05/12] Make standalone scripts executable --- bug_reports/check_pycharm_generator_hint.py | 0 crate_anon/anonymise/anonymise_cli.py | 0 crate_anon/anonymise/check_text_extractor.py | 0 crate_anon/anonymise/demo_config.py | 0 crate_anon/anonymise/draft_dd.py | 0 crate_anon/anonymise/fetch_wordlists.py | 0 crate_anon/anonymise/launch_multiprocess_anonymiser.py | 0 crate_anon/anonymise/researcher_report.py | 0 crate_anon/anonymise/show_counts.py | 0 crate_anon/anonymise/subset_db.py | 0 crate_anon/anonymise/summarize_dd.py | 0 crate_anon/anonymise/test_anonymisation.py | 0 crate_anon/anonymise/test_extract_text.py | 0 crate_anon/anonymise/tests/anonregex_tests.py | 0 crate_anon/crateweb/consent/management/commands/lookup_consent.py | 0 crate_anon/crateweb/consent/management/commands/lookup_patient.py | 0 crate_anon/crateweb/core/management/commands/runcpserver.py | 0 crate_anon/crateweb/manage.py | 0 crate_anon/linkage/validation/analyse_fuzzy_id_match_validate2.R | 0 crate_anon/nlp_manager/build_gate_java_interface.py | 0 crate_anon/nlp_manager/build_medex_itself.py | 0 crate_anon/nlp_manager/build_medex_java_interface.py | 0 crate_anon/nlp_manager/launch_multiprocess_nlp.py | 0 crate_anon/nlp_manager/nlp_manager.py | 0 crate_anon/nlp_manager/prepare_umls_for_bioyodie.py | 0 crate_anon/nlp_webserver/manage_users.py | 0 crate_anon/nlp_webserver/print_demos.py | 0 crate_anon/nlprp/nlprp_test_server.py | 0 crate_anon/preprocess/postcodes.py | 0 crate_anon/preprocess/preprocess_pcmis.py | 0 crate_anon/preprocess/preprocess_rio.py | 0 crate_anon/preprocess/preprocess_systmone.py | 0 crate_anon/tools/celery_status.py | 0 crate_anon/tools/email_rdbm.py | 0 crate_anon/tools/launch_celery.py | 0 crate_anon/tools/launch_cherrypy_server.py | 0 crate_anon/tools/launch_docs.py | 0 crate_anon/tools/launch_flower.py | 0 crate_anon/tools/launch_nlp_webserver_celery.py | 0 crate_anon/tools/launch_nlp_webserver_flower.py | 0 crate_anon/tools/launch_nlp_webserver_gunicorn.py | 0 crate_anon/tools/print_crateweb_demo_config.py | 0 crate_anon/tools/winservice.py | 0 debugging/mssql_without_transaction.py | 0 docs/__init__.py | 0 docs/source/conf.py | 0 docs/source/introduction/images/convert_images.py | 0 docs/source/linkage/fetch_name_frequencies.sh | 0 docs/source/preprocessing/crate_fetch_wordlists_specimen_usage.sh | 0 setup.py | 0 tools/install_virtualenv.py | 0 tools/install_wkhtmltopdf.py | 0 52 files changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 bug_reports/check_pycharm_generator_hint.py mode change 100644 => 100755 crate_anon/anonymise/anonymise_cli.py mode change 100644 => 100755 crate_anon/anonymise/check_text_extractor.py mode change 100644 => 100755 crate_anon/anonymise/demo_config.py mode change 100644 => 100755 crate_anon/anonymise/draft_dd.py mode change 100644 => 100755 crate_anon/anonymise/fetch_wordlists.py mode change 100644 => 100755 crate_anon/anonymise/launch_multiprocess_anonymiser.py mode change 100644 => 100755 crate_anon/anonymise/researcher_report.py mode change 100644 => 100755 crate_anon/anonymise/show_counts.py mode change 100644 => 100755 crate_anon/anonymise/subset_db.py mode change 100644 => 100755 crate_anon/anonymise/summarize_dd.py mode change 100644 => 100755 crate_anon/anonymise/test_anonymisation.py mode change 100644 => 100755 crate_anon/anonymise/test_extract_text.py mode change 100644 => 100755 crate_anon/anonymise/tests/anonregex_tests.py mode change 100644 => 100755 crate_anon/crateweb/consent/management/commands/lookup_consent.py mode change 100644 => 100755 crate_anon/crateweb/consent/management/commands/lookup_patient.py mode change 100644 => 100755 crate_anon/crateweb/core/management/commands/runcpserver.py mode change 100644 => 100755 crate_anon/crateweb/manage.py mode change 100644 => 100755 crate_anon/linkage/validation/analyse_fuzzy_id_match_validate2.R mode change 100644 => 100755 crate_anon/nlp_manager/build_gate_java_interface.py mode change 100644 => 100755 crate_anon/nlp_manager/build_medex_itself.py mode change 100644 => 100755 crate_anon/nlp_manager/build_medex_java_interface.py mode change 100644 => 100755 crate_anon/nlp_manager/launch_multiprocess_nlp.py mode change 100644 => 100755 crate_anon/nlp_manager/nlp_manager.py mode change 100644 => 100755 crate_anon/nlp_manager/prepare_umls_for_bioyodie.py mode change 100644 => 100755 crate_anon/nlp_webserver/manage_users.py mode change 100644 => 100755 crate_anon/nlp_webserver/print_demos.py mode change 100644 => 100755 crate_anon/nlprp/nlprp_test_server.py mode change 100644 => 100755 crate_anon/preprocess/postcodes.py mode change 100644 => 100755 crate_anon/preprocess/preprocess_pcmis.py mode change 100644 => 100755 crate_anon/preprocess/preprocess_rio.py mode change 100644 => 100755 crate_anon/preprocess/preprocess_systmone.py mode change 100644 => 100755 crate_anon/tools/celery_status.py mode change 100644 => 100755 crate_anon/tools/email_rdbm.py mode change 100644 => 100755 crate_anon/tools/launch_celery.py mode change 100644 => 100755 crate_anon/tools/launch_cherrypy_server.py mode change 100644 => 100755 crate_anon/tools/launch_docs.py mode change 100644 => 100755 crate_anon/tools/launch_flower.py mode change 100644 => 100755 crate_anon/tools/launch_nlp_webserver_celery.py mode change 100644 => 100755 crate_anon/tools/launch_nlp_webserver_flower.py mode change 100644 => 100755 crate_anon/tools/launch_nlp_webserver_gunicorn.py mode change 100644 => 100755 crate_anon/tools/print_crateweb_demo_config.py mode change 100644 => 100755 crate_anon/tools/winservice.py mode change 100644 => 100755 debugging/mssql_without_transaction.py mode change 100644 => 100755 docs/__init__.py mode change 100644 => 100755 docs/source/conf.py mode change 100644 => 100755 docs/source/introduction/images/convert_images.py mode change 100644 => 100755 docs/source/linkage/fetch_name_frequencies.sh mode change 100644 => 100755 docs/source/preprocessing/crate_fetch_wordlists_specimen_usage.sh mode change 100644 => 100755 setup.py mode change 100644 => 100755 tools/install_virtualenv.py mode change 100644 => 100755 tools/install_wkhtmltopdf.py diff --git a/bug_reports/check_pycharm_generator_hint.py b/bug_reports/check_pycharm_generator_hint.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/anonymise_cli.py b/crate_anon/anonymise/anonymise_cli.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/check_text_extractor.py b/crate_anon/anonymise/check_text_extractor.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/demo_config.py b/crate_anon/anonymise/demo_config.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/draft_dd.py b/crate_anon/anonymise/draft_dd.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/fetch_wordlists.py b/crate_anon/anonymise/fetch_wordlists.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/launch_multiprocess_anonymiser.py b/crate_anon/anonymise/launch_multiprocess_anonymiser.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/researcher_report.py b/crate_anon/anonymise/researcher_report.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/show_counts.py b/crate_anon/anonymise/show_counts.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/subset_db.py b/crate_anon/anonymise/subset_db.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/summarize_dd.py b/crate_anon/anonymise/summarize_dd.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/test_anonymisation.py b/crate_anon/anonymise/test_anonymisation.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/test_extract_text.py b/crate_anon/anonymise/test_extract_text.py old mode 100644 new mode 100755 diff --git a/crate_anon/anonymise/tests/anonregex_tests.py b/crate_anon/anonymise/tests/anonregex_tests.py old mode 100644 new mode 100755 diff --git a/crate_anon/crateweb/consent/management/commands/lookup_consent.py b/crate_anon/crateweb/consent/management/commands/lookup_consent.py old mode 100644 new mode 100755 diff --git a/crate_anon/crateweb/consent/management/commands/lookup_patient.py b/crate_anon/crateweb/consent/management/commands/lookup_patient.py old mode 100644 new mode 100755 diff --git a/crate_anon/crateweb/core/management/commands/runcpserver.py b/crate_anon/crateweb/core/management/commands/runcpserver.py old mode 100644 new mode 100755 diff --git a/crate_anon/crateweb/manage.py b/crate_anon/crateweb/manage.py old mode 100644 new mode 100755 diff --git a/crate_anon/linkage/validation/analyse_fuzzy_id_match_validate2.R b/crate_anon/linkage/validation/analyse_fuzzy_id_match_validate2.R old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/build_gate_java_interface.py b/crate_anon/nlp_manager/build_gate_java_interface.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/build_medex_itself.py b/crate_anon/nlp_manager/build_medex_itself.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/build_medex_java_interface.py b/crate_anon/nlp_manager/build_medex_java_interface.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/launch_multiprocess_nlp.py b/crate_anon/nlp_manager/launch_multiprocess_nlp.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/nlp_manager.py b/crate_anon/nlp_manager/nlp_manager.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/prepare_umls_for_bioyodie.py b/crate_anon/nlp_manager/prepare_umls_for_bioyodie.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_webserver/manage_users.py b/crate_anon/nlp_webserver/manage_users.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_webserver/print_demos.py b/crate_anon/nlp_webserver/print_demos.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlprp/nlprp_test_server.py b/crate_anon/nlprp/nlprp_test_server.py old mode 100644 new mode 100755 diff --git a/crate_anon/preprocess/postcodes.py b/crate_anon/preprocess/postcodes.py old mode 100644 new mode 100755 diff --git a/crate_anon/preprocess/preprocess_pcmis.py b/crate_anon/preprocess/preprocess_pcmis.py old mode 100644 new mode 100755 diff --git a/crate_anon/preprocess/preprocess_rio.py b/crate_anon/preprocess/preprocess_rio.py old mode 100644 new mode 100755 diff --git a/crate_anon/preprocess/preprocess_systmone.py b/crate_anon/preprocess/preprocess_systmone.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/celery_status.py b/crate_anon/tools/celery_status.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/email_rdbm.py b/crate_anon/tools/email_rdbm.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_celery.py b/crate_anon/tools/launch_celery.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_cherrypy_server.py b/crate_anon/tools/launch_cherrypy_server.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_docs.py b/crate_anon/tools/launch_docs.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_flower.py b/crate_anon/tools/launch_flower.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_nlp_webserver_celery.py b/crate_anon/tools/launch_nlp_webserver_celery.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_nlp_webserver_flower.py b/crate_anon/tools/launch_nlp_webserver_flower.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/launch_nlp_webserver_gunicorn.py b/crate_anon/tools/launch_nlp_webserver_gunicorn.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/print_crateweb_demo_config.py b/crate_anon/tools/print_crateweb_demo_config.py old mode 100644 new mode 100755 diff --git a/crate_anon/tools/winservice.py b/crate_anon/tools/winservice.py old mode 100644 new mode 100755 diff --git a/debugging/mssql_without_transaction.py b/debugging/mssql_without_transaction.py old mode 100644 new mode 100755 diff --git a/docs/__init__.py b/docs/__init__.py old mode 100644 new mode 100755 diff --git a/docs/source/conf.py b/docs/source/conf.py old mode 100644 new mode 100755 diff --git a/docs/source/introduction/images/convert_images.py b/docs/source/introduction/images/convert_images.py old mode 100644 new mode 100755 diff --git a/docs/source/linkage/fetch_name_frequencies.sh b/docs/source/linkage/fetch_name_frequencies.sh old mode 100644 new mode 100755 diff --git a/docs/source/preprocessing/crate_fetch_wordlists_specimen_usage.sh b/docs/source/preprocessing/crate_fetch_wordlists_specimen_usage.sh old mode 100644 new mode 100755 diff --git a/setup.py b/setup.py old mode 100644 new mode 100755 diff --git a/tools/install_virtualenv.py b/tools/install_virtualenv.py old mode 100644 new mode 100755 diff --git a/tools/install_wkhtmltopdf.py b/tools/install_wkhtmltopdf.py old mode 100644 new mode 100755 From 95cf4498b4b54885ae31903769f17b2ce729bf06 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 11:09:20 +0000 Subject: [PATCH 06/12] Add main entry point to scripts that were missing it --- crate_anon/anonymise/check_text_extractor.py | 4 ++++ crate_anon/anonymise/demo_config.py | 4 ++++ crate_anon/anonymise/draft_dd.py | 4 ++++ crate_anon/anonymise/researcher_report.py | 4 ++++ crate_anon/anonymise/show_counts.py | 4 ++++ crate_anon/anonymise/subset_db.py | 4 ++++ crate_anon/anonymise/summarize_dd.py | 4 ++++ crate_anon/nlp_webserver/manage_users.py | 4 ++++ crate_anon/nlp_webserver/print_demos.py | 4 ++++ 9 files changed, 36 insertions(+) diff --git a/crate_anon/anonymise/check_text_extractor.py b/crate_anon/anonymise/check_text_extractor.py index b52835d0..a39d61e3 100755 --- a/crate_anon/anonymise/check_text_extractor.py +++ b/crate_anon/anonymise/check_text_extractor.py @@ -69,3 +69,7 @@ def main() -> None: ext = None available = is_text_extractor_available(ext) print(f"Text extractor for extension {ext} present: {available}") + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/demo_config.py b/crate_anon/anonymise/demo_config.py index aeb099e6..97d5100b 100755 --- a/crate_anon/anonymise/demo_config.py +++ b/crate_anon/anonymise/demo_config.py @@ -127,3 +127,7 @@ def main() -> None: else: contents = get_demo_config() print(contents, file=f) + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/draft_dd.py b/crate_anon/anonymise/draft_dd.py index d0496b15..f54f0def 100755 --- a/crate_anon/anonymise/draft_dd.py +++ b/crate_anon/anonymise/draft_dd.py @@ -302,3 +302,7 @@ def main() -> None: systmone_alter_loaded_rows=args.systmone_alter_loaded_rows, systmone_table_info_in_comments=args.systmone_table_info_in_comments, ) + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/researcher_report.py b/crate_anon/anonymise/researcher_report.py index 59b11617..5dde07fb 100755 --- a/crate_anon/anonymise/researcher_report.py +++ b/crate_anon/anonymise/researcher_report.py @@ -820,3 +820,7 @@ def main() -> None: ) mk_researcher_report_pdf(reportcfg) + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/show_counts.py b/crate_anon/anonymise/show_counts.py index 5905558b..ebe36db9 100755 --- a/crate_anon/anonymise/show_counts.py +++ b/crate_anon/anonymise/show_counts.py @@ -133,3 +133,7 @@ def main() -> None: from crate_anon.anonymise.config_singleton import config # delayed import show_record_counts(config) + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/subset_db.py b/crate_anon/anonymise/subset_db.py index 09a58a80..5e06ac82 100755 --- a/crate_anon/anonymise/subset_db.py +++ b/crate_anon/anonymise/subset_db.py @@ -613,3 +613,7 @@ def main() -> None: ) subsetter = Subsetter(subsetcfg) subsetter.subset_db() + + +if __name__ == "__main__": + main() diff --git a/crate_anon/anonymise/summarize_dd.py b/crate_anon/anonymise/summarize_dd.py index 765580f6..98c1bf6a 100755 --- a/crate_anon/anonymise/summarize_dd.py +++ b/crate_anon/anonymise/summarize_dd.py @@ -119,3 +119,7 @@ def main() -> None: from crate_anon.anonymise.config_singleton import config # delayed import summarize_dd(config, args.output) + + +if __name__ == "__main__": + main() diff --git a/crate_anon/nlp_webserver/manage_users.py b/crate_anon/nlp_webserver/manage_users.py index 121e3f5b..605067f8 100755 --- a/crate_anon/nlp_webserver/manage_users.py +++ b/crate_anon/nlp_webserver/manage_users.py @@ -202,3 +202,7 @@ def main() -> None: change_password(username, new_password) else: log.info("Password change aborted.") + + +if __name__ == "__main__": + main() diff --git a/crate_anon/nlp_webserver/print_demos.py b/crate_anon/nlp_webserver/print_demos.py index d5bd594f..2b561262 100755 --- a/crate_anon/nlp_webserver/print_demos.py +++ b/crate_anon/nlp_webserver/print_demos.py @@ -297,3 +297,7 @@ def main() -> None: print(demo_processors().strip()) else: log.error("One option required: '--config' or '--processors'.") + + +if __name__ == "__main__": + main() From 60c6660b483293826e86dacd55d4030bac6276fa Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 11:09:51 +0000 Subject: [PATCH 07/12] Remove shebangs from python files that don't need them --- crate_anon/nlp_webserver/server_processor.py | 2 -- docs/__init__.py | 2 -- docs/source/conf.py | 2 -- setup.py | 2 -- 4 files changed, 8 deletions(-) diff --git a/crate_anon/nlp_webserver/server_processor.py b/crate_anon/nlp_webserver/server_processor.py index be317610..c2e92af4 100644 --- a/crate_anon/nlp_webserver/server_processor.py +++ b/crate_anon/nlp_webserver/server_processor.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - r""" crate_anon/nlp_webserver/server_processor.py diff --git a/docs/__init__.py b/docs/__init__.py index 72329e89..a5faffe9 100755 --- a/docs/__init__.py +++ b/docs/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ docs/__init__.py diff --git a/docs/source/conf.py b/docs/source/conf.py index 63c5fd41..744ebdc9 100755 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ docs/source/conf.py diff --git a/setup.py b/setup.py index e71c5e38..bb65838e 100755 --- a/setup.py +++ b/setup.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ setup.py From 7c8ae8bcfd785b6b5bac909a7f1a44051cafb677 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 15 Feb 2024 16:30:29 +0000 Subject: [PATCH 08/12] Bump cryptography to fix CVE-2023-50782 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bb65838e..d7c0b37e 100755 --- a/setup.py +++ b/setup.py @@ -126,7 +126,7 @@ # Packages for cloud NLP: # ------------------------------------------------------------------------- "bcrypt==3.1.7", # bcrypt encryption - "cryptography==41.0.6", # cryptography library + "cryptography==42.0.0", # cryptography library # "mysqlclient", # database access "paste==3.4.2", # middleware; https://github.com/cdent/paste/ "pyramid==1.10.4", # Pyramid web framework From b54433004c99d8094ea26968ae7e240caf0c6a44 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 11:14:36 +0000 Subject: [PATCH 09/12] Bump cryptography to fix CVE-2024-26130 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d7c0b37e..c575f683 100755 --- a/setup.py +++ b/setup.py @@ -126,7 +126,7 @@ # Packages for cloud NLP: # ------------------------------------------------------------------------- "bcrypt==3.1.7", # bcrypt encryption - "cryptography==42.0.0", # cryptography library + "cryptography==42.0.4", # cryptography library # "mysqlclient", # database access "paste==3.4.2", # middleware; https://github.com/cdent/paste/ "pyramid==1.10.4", # Pyramid web framework From 3eb9b0054ee21daab22e2a23717db80715c170cd Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Thu, 22 Feb 2024 11:31:32 +0000 Subject: [PATCH 10/12] Ensure the python files copied to docs have the right permissions --- docs/recreate_inclusion_files.py | 19 ++++++++++++++++--- docs/source/nlp/_nlprp_test_server.py | 0 2 files changed, 16 insertions(+), 3 deletions(-) mode change 100644 => 100755 docs/source/nlp/_nlprp_test_server.py diff --git a/docs/recreate_inclusion_files.py b/docs/recreate_inclusion_files.py index b07cba47..17403f02 100755 --- a/docs/recreate_inclusion_files.py +++ b/docs/recreate_inclusion_files.py @@ -165,6 +165,19 @@ def make_command_line_index_help(filename: str) -> None: f.write(full_content) +def copy_file_wth_permissions(source: str, dest: str) -> None: + """ + Copy a file and set the permissions to be the same on the destination. + + https://docs.python.org/3/library/shutil.html + Warning: Even the higher-level file copying functions (shutil.copy(), + shutil.copy2()) cannot copy all file metadata. + """ + shutil.copy(source, dest) + st = os.stat(source) + os.chmod(dest, st.st_mode) + + # ============================================================================= # main # ============================================================================= @@ -450,7 +463,7 @@ def main(): [CrateCommand.SHOW_CRATE_MEDEX_PIPELINE_OPTIONS], join(DevPath.DOCS_NLP_DIR, "_CrateMedexPipeline_help.txt"), ) - shutil.copy( + copy_file_wth_permissions( join(CratePath.NLP_MANAGER_DIR, "specimen_gate_plugin_file.ini"), join(DevPath.DOCS_NLP_DIR, "_specimen_gate_plugin_file.ini"), ) @@ -599,11 +612,11 @@ def main(): join(DevPath.DOCS_NLP_DIR, "_crate_nlp_webserver_pserve_help.txt"), ) - shutil.copy( + copy_file_wth_permissions( join(CratePath.NLPRP_DIR, "nlprp_test_client.py"), join(DevPath.DOCS_NLP_DIR, "_nlprp_test_client.py"), ) - shutil.copy( + copy_file_wth_permissions( join(CratePath.NLPRP_DIR, "nlprp_test_server.py"), join(DevPath.DOCS_NLP_DIR, "_nlprp_test_server.py"), ) diff --git a/docs/source/nlp/_nlprp_test_server.py b/docs/source/nlp/_nlprp_test_server.py old mode 100644 new mode 100755 From 3ac61a5f5fe0e5778977ed93b4cf527740c59370 Mon Sep 17 00:00:00 2001 From: Martin Burchell Date: Tue, 23 Jan 2024 11:07:47 +0000 Subject: [PATCH 11/12] Pin down a bunch of Sphinx modules Otherwise newer versions are loaded that require sphinx >= 5.0 --- setup.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/setup.py b/setup.py index c575f683..9a1ad0ad 100755 --- a/setup.py +++ b/setup.py @@ -153,6 +153,11 @@ # when resolving crate_anon.anonymise.patient.Patient in # crate_anon.anonymise.altermethod.py "sphinx==4.2.0", # documentation + "sphinxcontrib-applehelp==1.0.4", # development only + "sphinxcontrib-devhelp==1.0.2", # development only + "sphinxcontrib-htmlhelp==2.0.1", # development only + "sphinxcontrib-serializinghtml==1.1.5", # development only + "sphinxcontrib-qthelp==1.0.3", # development only "sphinx_rtd_theme==1.0.0", # documentation # --------------------------------------------------------------------- # For database connections (see manual): install manually From cf09a06b9693574786dbaf6038350585427461a7 Mon Sep 17 00:00:00 2001 From: Rudolf Cardinal Date: Mon, 26 Feb 2024 11:49:34 +0000 Subject: [PATCH 12/12] cosmetic tweak --- crate_anon/nlprp/__init__.py | 1 - 1 file changed, 1 deletion(-) diff --git a/crate_anon/nlprp/__init__.py b/crate_anon/nlprp/__init__.py index 9c1946f9..6c297c98 100644 --- a/crate_anon/nlprp/__init__.py +++ b/crate_anon/nlprp/__init__.py @@ -23,7 +23,6 @@ =============================================================================== -crate_anon/nlprp/__init__.py The mere existence of this file makes Python treat the directory as a package. """