diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index fc0031986..dd76fe461 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,19 +2,22 @@ # 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 + # 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/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/__init__.py b/crate_anon/__init__.py index 5f09b399c..2451010f6 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 be74ae9fc..ad96f275d 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 1b94664fb..140430b20 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 bef5b6662..43ed19ef7 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 913a8e016..307d522d3 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 c23fed0eb..c36cf676f 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 554f681c2..17ca205ba 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 46b8bbca3..04209fdea 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 c119e4043..91ead4761 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/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 index b52835d06..a39d61e32 --- 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/config.py b/crate_anon/anonymise/config.py index 66474b000..c87ddb2c6 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 a79c63ecb..a7a2acecf 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 41283f7b6..fb5fbe198 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 078deb7eb..8f680ff17 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 bd9305492..f6bbfba5f 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 902af499d..483eb53ea 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/demo_config.py b/crate_anon/anonymise/demo_config.py old mode 100644 new mode 100755 index aeb099e60..97d5100be --- 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 old mode 100644 new mode 100755 index d0496b15d..f54f0def3 --- 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/eponyms.py b/crate_anon/anonymise/eponyms.py index af9855dbd..52b4973b9 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/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/models.py b/crate_anon/anonymise/models.py index d1a58002b..32fb2e2c7 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 ddd19ffdf..896c2a231 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/researcher_report.py b/crate_anon/anonymise/researcher_report.py old mode 100644 new mode 100755 index 59b116174..5dde07fb3 --- 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/scrub.py b/crate_anon/anonymise/scrub.py index 4f90a16f6..86aed9d9e 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/show_counts.py b/crate_anon/anonymise/show_counts.py old mode 100644 new mode 100755 index 5905558ba..ebe36db9d --- 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 old mode 100644 new mode 100755 index 09a58a80f..5e06ac822 --- 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 old mode 100644 new mode 100755 index 765580f64..98c1bf6ad --- 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/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/anonymise/tests/scrub_tests.py b/crate_anon/anonymise/tests/scrub_tests.py index a1e859638..538730c9a 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 a79c561c0..2b3679773 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 a82d306ec..6a0fcebe0 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 5dcfede6e..0c60d11d3 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 3f11aa452..412af2480 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 6f2bc1030..040147345 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 22977dcb2..7b6b3d34d 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 8f98294df..a29d53b9d 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 fd8c2fd65..1ad86bc7c 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 06639c671..be00c3848 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 953fe497e..a99b584be 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 713759434..c3744f6f9 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 a6ab03c3a..129caf823 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 f3cc117f0..4d7e4b1ea 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 d3f8739e1..4059fa72e 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 0cf963742..82d9e94ee 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 ebb5d3242..99a8dad3a 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 88af62b71..fa8969c51 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 ca574981b..04aee4414 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 b88fcfb59..accd3e3bc 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 5ab33ab12..a1b188165 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 8fb7e5f59..d52191edb 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 a764c3200..e9feebde6 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 5300788d4..6e58a9a90 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 888660bf3..0dae36071 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 760ed1987..4d734be2e 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 73ae5767e..0810f67ee 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 f704f651e..a9e7c822c 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 2f313ed06..8b887623d 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 79a2c8961..1cbc35c0c 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 507d6836e..30ed4bd30 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 ba570032d..ba9b60c6d 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 773b60d36..6c220203c 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 d8929178d..d85417ad5 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 3e4b276d1..792755185 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 3cdc2ba5f..6efb6e514 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 bb3a270e4..93957ba72 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 c52ec3825..3acbff138 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 f28ee1bd8..2e977c539 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 b131f4159..bec03e27d 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 f2e79a614..422eeeb5c 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 669e72ad4..2ba222e5a 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 3d220d155..d517a74e9 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 54682fc74..52f051570 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 72a3f4aab..5a5e982e2 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 d3f3f9c1b..a45f7d957 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 eb0616a3b..edd36dd8a 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/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/consent/management/commands/make_ethics_pack.py b/crate_anon/crateweb/consent/management/commands/make_ethics_pack.py index db4f7a450..9dba0f42e 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 ab5e5e62b..78dcc7091 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 818a25b23..d45245826 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 4d24737ec..293c508c9 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 25657f79f..5eba2fdcc 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 b0a5017c3..003027bcf 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 ea7e477fe..e2d7bc69a 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 6f48be608..1612c364f 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 d110b08d5..50a601445 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 ba5f45773..ade27267c 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 367af2f2a..abd7897a9 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 0f0386543..d384848ac 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 5e9dcb3bb..27c76983e 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 62a9af7f7..1fe67a3ef 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 0d21a98e2..2fbe4bb11 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 6067b4c11..772b7feaa 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 8d2645917..77b7f0d94 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 3e8ed182a..cb5d92f19 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 086a7a77a..7da8c2615 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 4ac2cc651..43bacc70a 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 3a9e3a7bd..b160b814a 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 808985602..e4cc09cb1 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 8befd3b0a..07b67fd9a 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 670a870a2..a95fc68a1 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 f10bb678c..69828dc65 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 76486610c..67f75578d 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 87faed633..7c319bf77 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 4069ab625..ead2a113b 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 71d1ee0b5..ddce0f6d4 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 be90fc698..00aee864f 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 3f2398f9d..1c71b39a7 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 80d38e83f..c1696402b 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 69321ead9..a7de753c1 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/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/core/middleware.py b/crate_anon/crateweb/core/middleware.py index c109cf2ee..bea2abede 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 72c072116..234854398 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 ca9da2617..ba74c799e 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 019981e85..ccba06ba1 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 4a7142527..0663ca0e1 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 4ca1ac2e4..0c56162c4 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 eba43e535..81eabe4c2 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/manage.py b/crate_anon/crateweb/manage.py old mode 100644 new mode 100755 diff --git a/crate_anon/crateweb/research/__init__.py b/crate_anon/crateweb/research/__init__.py index e36db3ff6..2d5e6e32b 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 cb6afa0d1..a7ec49169 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 c748403e6..9f2f09dbb 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 e2b2ce40c..1cc88fbce 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 5af5f86e2..d865b9bc8 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 338ad074f..a6a80bce5 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 ab57c4960..24c6b0ad2 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 091583fa6..00769f4dc 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 8e9d1dceb..4079cac32 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 c8f60ce20..9b22d361e 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 c8535102c..4a55bf89e 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 2b1b39954..ff6613008 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 47d787856..7c24c0a50 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 04a968f43..2de287e4e 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 4bd7ab570..caaa0039b 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 4608f24a3..61ab8bcef 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 1cad8ed71..08ae4b0eb 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 991985210..269fb65d7 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 11cda6452..bedb4b901 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 70a8e15fb..85b0062cc 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 470f90995..6ba3d9503 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 e0944ced8..29c5966a5 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 ab84f4b7c..c48d12002 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 fb62cdc39..79fb17597 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 84a555f3b..153e95086 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 044f39e03..a6fa0e0b2 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 f787f368d..55001c37f 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 5c8105761..cfd0ce8fe 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 b66170485..fbb44d83d 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 57fa4f18e..8e58e024f 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 e027c4886..ab57ed9a0 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 5203744a1..1d4126259 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 d230f2d5a..1663228fb 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 20ee9b3d6..eb8bbcf06 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 e4202976c..695aea7e8 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 762a477c5..db1641416 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 0cf2f8770..bc982e3ae 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 2f0b352b6..a68f761a9 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 9229d348b..a47636ca5 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 bda023889..6249720ce 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 12d040c6e..e15be3ee7 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 ea12f8c0d..adb122888 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 f14d19783..a54074c5a 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/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/__init__.py b/crate_anon/nlp_manager/__init__.py index b1b7a2a15..a77df6a22 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 87685280e..9ac84628a 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 c5422a72b..ac56a4a8d 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/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/cloud_config.py b/crate_anon/nlp_manager/cloud_config.py index 587a2cc13..854bd16e3 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 bd3f92e31..670fbab2b 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 f085f1a95..0926c1244 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 3032be604..8a0b7107e 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 019b96784..f936e7477 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 0f3a2dfc1..50ff1436c 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 25c0f1ff0..a01b440b4 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/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/models.py b/crate_anon/nlp_manager/models.py index 84df1bda1..0cff20369 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 a3acf5c0b..8a932866c 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/nlp_manager.py b/crate_anon/nlp_manager/nlp_manager.py old mode 100644 new mode 100755 diff --git a/crate_anon/nlp_manager/number.py b/crate_anon/nlp_manager/number.py index 267be8290..62bdab285 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 7b81e17aa..8b2766fa9 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 176ff5dba..ebf19088e 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 f4250090b..af931e797 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 c69a5aea0..8f11cc4b3 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 5fdcfc392..7e887f77d 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 26235390c..5468823c0 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 91b5cbe3e..128105ab4 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 4b6408782..abb244655 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/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_manager/regex_func.py b/crate_anon/nlp_manager/regex_func.py index 69fdd8d18..f4f0bdd04 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 b16b0d00d..e6232f936 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 9c5d40c4b..9cb862867 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 e8b04822f..1d34d1e3d 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 5254225ed..79ac3ff73 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 7a610dfbf..50f14e616 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 dabf8740d..679d19373 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 57c5d2c63..8142ec4b6 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 68a71373e..48fdfe82a 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 79349d464..e8fd18897 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 10e8050dc..cd012dcf6 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 56eead2aa..481e19e51 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 2cc18fb60..e9238ce4d 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 ce801eeed..a08f902f7 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 e76fc77d4..056fab537 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 324bc275f..9808e5a6a 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 c53bb7943..80fad9f0f 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 04440ffae..2f4d1684d 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 54519a596..d263e0275 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 2ab76c88e..6aef96ada 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 b08cd8ed8..f126eba5d 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/manage_users.py b/crate_anon/nlp_webserver/manage_users.py old mode 100644 new mode 100755 index 121e3f5b0..605067f86 --- 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/models.py b/crate_anon/nlp_webserver/models.py index aec8f62a9..b75aea721 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/print_demos.py b/crate_anon/nlp_webserver/print_demos.py old mode 100644 new mode 100755 index d5bd594fc..2b561262e --- 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() diff --git a/crate_anon/nlp_webserver/procs.py b/crate_anon/nlp_webserver/procs.py index f53f1a7ca..77cb837d7 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 36c34b2f4..5277eebf2 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/server_processor.py b/crate_anon/nlp_webserver/server_processor.py index be3176109..c2e92af43 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/crate_anon/nlp_webserver/settings.py b/crate_anon/nlp_webserver/settings.py index 7709bc0d7..3c76de377 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 523207d0d..cc1157e99 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 8bccec9ee..064e71461 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 73bc62be8..9fe896699 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 6a89e36ef..7042e43cb 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 b08830eb3..f0a46b302 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 bdf47818a..6c297c98d 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 +23,6 @@ =============================================================================== -crate_anon/nlp_manager/__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 3738e6d5c..199ace8cb 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 2512ff14e..4c32f804f 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 d96c0a5a1..192b4129b 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/nlprp_test_client.py b/crate_anon/nlprp/nlprp_test_client.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/nlprp/version.py b/crate_anon/nlprp/version.py index 41839a8a8..f1570d0ae 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 f4c7777b8..fd8d14b45 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 9e78812cc..887d42c4d 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 ae76fe491..eb25d0311 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/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/preprocess/rio_constants.py b/crate_anon/preprocess/rio_constants.py index 806644565..0dd642ca2 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 9520e8745..7b1d1e9f6 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 13bd2540e..1eb566463 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 2b9f06363..2ee47858b 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 620936117..f5ea47aa2 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 11439e6ee..4daf61e9d 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 949e31e50..80d7f361c 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 9c313c0ba..19a9cb3cb 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 ea4f31929..4f8aa250b 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/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/crate_anon/version.py b/crate_anon/version.py index 42e230b97..31b02f93a 100644 --- a/crate_anon/version.py +++ b/crate_anon/version.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ crate_anon/version.py 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 index 72329e899..a5faffe95 --- a/docs/__init__.py +++ b/docs/__init__.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ docs/__init__.py diff --git a/docs/recreate_inclusion_files.py b/docs/recreate_inclusion_files.py index b07cba477..17403f02a 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/conf.py b/docs/source/conf.py old mode 100644 new mode 100755 index 63c5fd41a..744ebdc99 --- 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/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/nlp/_nlprp_test_client.py b/docs/source/nlp/_nlprp_test_client.py old mode 100644 new mode 100755 diff --git a/docs/source/nlp/_nlprp_test_server.py b/docs/source/nlp/_nlprp_test_server.py 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 index edf17a7c9..9a1ad0adb --- a/setup.py +++ b/setup.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python - """ setup.py @@ -128,7 +126,7 @@ # Packages for cloud NLP: # ------------------------------------------------------------------------- "bcrypt==3.1.7", # bcrypt encryption - "cryptography==41.0.6", # 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 @@ -143,9 +141,9 @@ # ------------------------------------------------------------------------- # 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 @@ -155,6 +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 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