From b47dbdea37f70c40788ade79de0dca4d01bbaebc Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 29 Oct 2024 12:06:07 +0000 Subject: [PATCH 01/18] put in the outline for the joss publication --- docs/joss-publication/paper.md | 1 + docs/joss-publication/references.bib | 0 2 files changed, 1 insertion(+) create mode 100644 docs/joss-publication/paper.md create mode 100644 docs/joss-publication/references.bib diff --git a/docs/joss-publication/paper.md b/docs/joss-publication/paper.md new file mode 100644 index 000000000..c6c0206c8 --- /dev/null +++ b/docs/joss-publication/paper.md @@ -0,0 +1 @@ +This is the file where the paper must be written \ No newline at end of file diff --git a/docs/joss-publication/references.bib b/docs/joss-publication/references.bib new file mode 100644 index 000000000..e69de29bb From ba6d0c075b93d347fe9fdcdb71502b1971c88034 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 29 Oct 2024 15:05:03 +0000 Subject: [PATCH 02/18] bib file should also be called paper --- docs/joss-publication/{references.bib => paper.bib} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/joss-publication/{references.bib => paper.bib} (100%) diff --git a/docs/joss-publication/references.bib b/docs/joss-publication/paper.bib similarity index 100% rename from docs/joss-publication/references.bib rename to docs/joss-publication/paper.bib From c8b64831d47e55bf0fbbf933dfc1cc78424794a3 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Mon, 11 Nov 2024 14:29:40 +0000 Subject: [PATCH 03/18] typo --- test/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/README.md b/test/README.md index 2a3723cca..c27c70748 100644 --- a/test/README.md +++ b/test/README.md @@ -10,7 +10,7 @@ consumers started. **Then** the DICOM study exists in the "anon" PIXL Orthanc instance. -After setting up your [.secrets.env](../README.md#project-secrets)), you can run the system test with: +After setting up your [.secrets.env](../README.md#project-secrets), you can run the system test with: ```bash ./run-system-test.sh From a5b490865cf61ea33eb28c6a7e03204895c03187 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Fri, 15 Nov 2024 15:04:41 +0000 Subject: [PATCH 04/18] added either a readme or toc with a list of the directories files present --- .github/ISSUE_TEMPLATE/README.md | 10 +++ .github/README.md | 12 ++++ .github/workflows/README.md | 6 ++ bin/README.md | 6 ++ bin/linters/README.md | 6 ++ cli/src/README.md | 6 ++ cli/src/pixl_cli/README.md | 18 +++++ cli/tests/toc.md | 22 ++++++ cli/toc.md | 14 ++++ docker/README.md | 22 ++++++ docker/export-api/README.md | 6 ++ docker/hasher-api/README.md | 6 ++ docker/imaging-api/README.md | 6 ++ docker/orthanc-anon/README.md | 6 ++ docker/orthanc-raw/README.md | 6 ++ docker/postgres/README.md | 6 ++ docs/README.md | 14 ++++ docs/design/README.md | 10 +++ docs/design/diagrams/README.md | 8 +++ docs/file_types/README.md | 6 ++ docs/joss-publication/README.md | 12 ++++ docs/joss-publication/figures/README.md | 2 + docs/services/README.md | 8 +++ docs/setup/README.md | 10 +++ hasher/src/README.md | 6 ++ hasher/src/hasher/README.md | 12 ++++ hasher/tests/README.md | 12 ++++ hasher/toc.md | 14 ++++ orthanc/assets/README.md | 10 +++ orthanc/orthanc-anon/config/README.md | 8 +++ orthanc/orthanc-anon/docs/README.md | 10 +++ orthanc/orthanc-anon/docs/assets/README.md | 6 ++ orthanc/orthanc-anon/plugin/README.md | 8 +++ orthanc/orthanc-anon/toc.md | 14 ++++ orthanc/orthanc-raw/config/README.md | 10 +++ orthanc/orthanc-raw/plugin/README.md | 6 ++ orthanc/orthanc-raw/toc.md | 12 ++++ orthanc/toc.md | 14 ++++ pixl_core/src/README.md | 6 ++ pixl_core/src/core/README.md | 26 +++++++ pixl_core/src/core/db/README.md | 10 +++ pixl_core/src/core/patient_queue/README.md | 14 ++++ pixl_core/src/core/project_config/README.md | 12 ++++ pixl_core/src/core/rest_api/README.md | 8 +++ pixl_core/src/core/token_buffer/README.md | 10 +++ pixl_core/src/core/uploader/README.md | 16 +++++ pixl_core/tests/README.md | 22 ++++++ pixl_core/tests/data/README.md | 10 +++ pixl_core/tests/patient_queue/README.md | 10 +++ pixl_core/tests/project_config/README.md | 8 +++ pixl_core/tests/token_buffer/README.md | 6 ++ pixl_core/tests/uploader/README.md | 12 ++++ pixl_core/toc.md | 14 ++++ pixl_dcmd/src/README.md | 6 ++ pixl_dcmd/src/pixl_dcmd/README.md | 22 ++++++ pixl_dcmd/src/pixl_dcmd/resources/README.md | 6 ++ pixl_dcmd/tests/README.md | 16 +++++ pixl_dcmd/toc.md | 14 ++++ pixl_export/src/README.md | 6 ++ pixl_export/src/pixl_export/README.md | 12 ++++ pixl_export/tests/README.md | 10 +++ pixl_export/toc.md | 14 ++++ pixl_imaging/alembic/toc.md | 20 ++++++ pixl_imaging/alembic/versions/README.md | 12 ++++ pixl_imaging/scripts/README.md | 6 ++ pixl_imaging/src/README.md | 6 ++ pixl_imaging/src/pixl_imaging/README.md | 12 ++++ pixl_imaging/tests/README.md | 14 ++++ .../tests/orthanc_raw_config/README.md | 8 +++ pixl_imaging/toc.md | 18 +++++ postgres/toc.md | 10 +++ projects/README.md | 8 +++ projects/configs/README.md | 22 ++++++ projects/configs/tag-operations/README.md | 24 +++++++ .../manufacturer-overrides/README.md | 8 +++ pytest-pixl/scripts/README.md | 6 ++ pytest-pixl/src/README.md | 8 +++ pytest-pixl/src/pytest_pixl/README.md | 18 +++++ pytest-pixl/src/pytest_pixl/data/README.md | 12 ++++ .../pytest_pixl/data/omop-resources/README.md | 18 +++++ .../data/omop-resources/omop/README.md | 12 ++++ .../omop-resources/omop/private/README.md | 8 +++ .../data/omop-resources/omop/public/README.md | 6 ++ pytest-pixl/src/resources/README.md | 6 ++ pytest-pixl/src/resources/ssl/README.md | 8 +++ pytest-pixl/tests/README.md | 12 ++++ .../tests/samples_for_fixture_tests/README.md | 6 ++ .../test_ftpserver_fixture/README.md | 6 ++ pytest-pixl/toc.md | 16 +++++ schemas/README.md | 6 ++ scripts/README.md | 12 ++++ test/dicomweb_config/README.md | 10 +++ test/resources/README.md | 14 ++++ test/resources/omop-dicomweb/README.md | 12 ++++ .../resources/omop-dicomweb/private/README.md | 8 +++ test/resources/omop-dicomweb/public/README.md | 6 ++ test/resources/omop/README.md | 12 ++++ test/resources/omop/private/README.md | 8 +++ test/resources/omop/public/README.md | 6 ++ test/toc.md | 30 ++++++++ test/vna_config/README.md | 8 +++ toc.md | 72 +++++++++++++++++++ 102 files changed, 1174 insertions(+) create mode 100644 .github/ISSUE_TEMPLATE/README.md create mode 100644 .github/README.md create mode 100644 .github/workflows/README.md create mode 100644 bin/README.md create mode 100644 bin/linters/README.md create mode 100644 cli/src/README.md create mode 100644 cli/src/pixl_cli/README.md create mode 100644 cli/tests/toc.md create mode 100644 cli/toc.md create mode 100644 docker/README.md create mode 100644 docker/export-api/README.md create mode 100644 docker/hasher-api/README.md create mode 100644 docker/imaging-api/README.md create mode 100644 docker/orthanc-anon/README.md create mode 100644 docker/orthanc-raw/README.md create mode 100644 docker/postgres/README.md create mode 100644 docs/README.md create mode 100644 docs/design/README.md create mode 100644 docs/design/diagrams/README.md create mode 100644 docs/file_types/README.md create mode 100644 docs/joss-publication/README.md create mode 100644 docs/joss-publication/figures/README.md create mode 100644 docs/services/README.md create mode 100644 docs/setup/README.md create mode 100644 hasher/src/README.md create mode 100644 hasher/src/hasher/README.md create mode 100644 hasher/tests/README.md create mode 100644 hasher/toc.md create mode 100644 orthanc/assets/README.md create mode 100644 orthanc/orthanc-anon/config/README.md create mode 100644 orthanc/orthanc-anon/docs/README.md create mode 100644 orthanc/orthanc-anon/docs/assets/README.md create mode 100644 orthanc/orthanc-anon/plugin/README.md create mode 100644 orthanc/orthanc-anon/toc.md create mode 100644 orthanc/orthanc-raw/config/README.md create mode 100644 orthanc/orthanc-raw/plugin/README.md create mode 100644 orthanc/orthanc-raw/toc.md create mode 100644 orthanc/toc.md create mode 100644 pixl_core/src/README.md create mode 100644 pixl_core/src/core/README.md create mode 100644 pixl_core/src/core/db/README.md create mode 100644 pixl_core/src/core/patient_queue/README.md create mode 100644 pixl_core/src/core/project_config/README.md create mode 100644 pixl_core/src/core/rest_api/README.md create mode 100644 pixl_core/src/core/token_buffer/README.md create mode 100644 pixl_core/src/core/uploader/README.md create mode 100644 pixl_core/tests/README.md create mode 100644 pixl_core/tests/data/README.md create mode 100644 pixl_core/tests/patient_queue/README.md create mode 100644 pixl_core/tests/project_config/README.md create mode 100644 pixl_core/tests/token_buffer/README.md create mode 100644 pixl_core/tests/uploader/README.md create mode 100644 pixl_core/toc.md create mode 100644 pixl_dcmd/src/README.md create mode 100644 pixl_dcmd/src/pixl_dcmd/README.md create mode 100644 pixl_dcmd/src/pixl_dcmd/resources/README.md create mode 100644 pixl_dcmd/tests/README.md create mode 100644 pixl_dcmd/toc.md create mode 100644 pixl_export/src/README.md create mode 100644 pixl_export/src/pixl_export/README.md create mode 100644 pixl_export/tests/README.md create mode 100644 pixl_export/toc.md create mode 100644 pixl_imaging/alembic/toc.md create mode 100644 pixl_imaging/alembic/versions/README.md create mode 100644 pixl_imaging/scripts/README.md create mode 100644 pixl_imaging/src/README.md create mode 100644 pixl_imaging/src/pixl_imaging/README.md create mode 100644 pixl_imaging/tests/README.md create mode 100644 pixl_imaging/tests/orthanc_raw_config/README.md create mode 100644 pixl_imaging/toc.md create mode 100644 postgres/toc.md create mode 100644 projects/README.md create mode 100644 projects/configs/README.md create mode 100644 projects/configs/tag-operations/README.md create mode 100644 projects/configs/tag-operations/manufacturer-overrides/README.md create mode 100644 pytest-pixl/scripts/README.md create mode 100644 pytest-pixl/src/README.md create mode 100644 pytest-pixl/src/pytest_pixl/README.md create mode 100644 pytest-pixl/src/pytest_pixl/data/README.md create mode 100644 pytest-pixl/src/pytest_pixl/data/omop-resources/README.md create mode 100644 pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md create mode 100644 pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md create mode 100644 pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md create mode 100644 pytest-pixl/src/resources/README.md create mode 100644 pytest-pixl/src/resources/ssl/README.md create mode 100644 pytest-pixl/tests/README.md create mode 100644 pytest-pixl/tests/samples_for_fixture_tests/README.md create mode 100644 pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md create mode 100644 pytest-pixl/toc.md create mode 100644 schemas/README.md create mode 100644 scripts/README.md create mode 100644 test/dicomweb_config/README.md create mode 100644 test/resources/README.md create mode 100644 test/resources/omop-dicomweb/README.md create mode 100644 test/resources/omop-dicomweb/private/README.md create mode 100644 test/resources/omop-dicomweb/public/README.md create mode 100644 test/resources/omop/README.md create mode 100644 test/resources/omop/private/README.md create mode 100644 test/resources/omop/public/README.md create mode 100644 test/toc.md create mode 100644 test/vna_config/README.md create mode 100644 toc.md diff --git a/.github/ISSUE_TEMPLATE/README.md b/.github/ISSUE_TEMPLATE/README.md new file mode 100644 index 000000000..0ae02773e --- /dev/null +++ b/.github/ISSUE_TEMPLATE/README.md @@ -0,0 +1,10 @@ +## 'ISSUE_TEMPLATE' Directory Contents + +### Files + +bug_report.yml + +feature_request.yaml + +voxl.yml + diff --git a/.github/README.md b/.github/README.md new file mode 100644 index 000000000..a69bc55f0 --- /dev/null +++ b/.github/README.md @@ -0,0 +1,12 @@ +## '.github' Directory Contents + +### Subdirectories + +[ISSUE_TEMPLATE](./ISSUE_TEMPLATE/README.md) + +[workflows](./workflows/README.md) + +### Files + +pull_request_template.md + diff --git a/.github/workflows/README.md b/.github/workflows/README.md new file mode 100644 index 000000000..7a4b38642 --- /dev/null +++ b/.github/workflows/README.md @@ -0,0 +1,6 @@ +## 'workflows' Directory Contents + +### Files + +main.yml + diff --git a/bin/README.md b/bin/README.md new file mode 100644 index 000000000..bd9e79b7f --- /dev/null +++ b/bin/README.md @@ -0,0 +1,6 @@ +## 'bin' Directory Contents + +### Subdirectories + +[linters](./linters/README.md) + diff --git a/bin/linters/README.md b/bin/linters/README.md new file mode 100644 index 000000000..a6c131b8e --- /dev/null +++ b/bin/linters/README.md @@ -0,0 +1,6 @@ +## 'linters' Directory Contents + +### Files + +check_headers_exist.sh + diff --git a/cli/src/README.md b/cli/src/README.md new file mode 100644 index 000000000..23f0b3564 --- /dev/null +++ b/cli/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[pixl_cli](./pixl_cli/README.md) + diff --git a/cli/src/pixl_cli/README.md b/cli/src/pixl_cli/README.md new file mode 100644 index 000000000..b52bef0d3 --- /dev/null +++ b/cli/src/pixl_cli/README.md @@ -0,0 +1,18 @@ +## 'pixl_cli' Directory Contents + +### Files + +main.py + +_config.py + +_database.py + +_docker_commands.py + +_io.py + +_message_processing.py + +__init__.py + diff --git a/cli/tests/toc.md b/cli/tests/toc.md new file mode 100644 index 000000000..1f58ca89f --- /dev/null +++ b/cli/tests/toc.md @@ -0,0 +1,22 @@ +## 'tests' Directory Contents + +### Files + +conftest.py + +README.md + +test_check_env.py + +test_database.py + +test_docker_commands.py + +test_io.py + +test_messages_from_files.py + +test_message_processing.py + +test_populate.py + diff --git a/cli/toc.md b/cli/toc.md new file mode 100644 index 000000000..200731dff --- /dev/null +++ b/cli/toc.md @@ -0,0 +1,14 @@ +## 'cli' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 000000000..c1e61f136 --- /dev/null +++ b/docker/README.md @@ -0,0 +1,22 @@ +## 'docker' Directory Contents + +### Subdirectories + +[export-api](./export-api/README.md) + +[hasher-api](./hasher-api/README.md) + +[imaging-api](./imaging-api/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +[postgres](./postgres/README.md) + +### Files + +.dockerignore + +common.env + diff --git a/docker/export-api/README.md b/docker/export-api/README.md new file mode 100644 index 000000000..8496615e5 --- /dev/null +++ b/docker/export-api/README.md @@ -0,0 +1,6 @@ +## 'export-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/hasher-api/README.md b/docker/hasher-api/README.md new file mode 100644 index 000000000..ad524fbed --- /dev/null +++ b/docker/hasher-api/README.md @@ -0,0 +1,6 @@ +## 'hasher-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/imaging-api/README.md b/docker/imaging-api/README.md new file mode 100644 index 000000000..72eee7467 --- /dev/null +++ b/docker/imaging-api/README.md @@ -0,0 +1,6 @@ +## 'imaging-api' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/orthanc-anon/README.md b/docker/orthanc-anon/README.md new file mode 100644 index 000000000..eb8fdea56 --- /dev/null +++ b/docker/orthanc-anon/README.md @@ -0,0 +1,6 @@ +## 'orthanc-anon' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/orthanc-raw/README.md b/docker/orthanc-raw/README.md new file mode 100644 index 000000000..7529e53e8 --- /dev/null +++ b/docker/orthanc-raw/README.md @@ -0,0 +1,6 @@ +## 'orthanc-raw' Directory Contents + +### Files + +Dockerfile + diff --git a/docker/postgres/README.md b/docker/postgres/README.md new file mode 100644 index 000000000..81fd8a9fb --- /dev/null +++ b/docker/postgres/README.md @@ -0,0 +1,6 @@ +## 'postgres' Directory Contents + +### Files + +Dockerfile + diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..e16f21e9e --- /dev/null +++ b/docs/README.md @@ -0,0 +1,14 @@ +## 'docs' Directory Contents + +### Subdirectories + +[design](./design/README.md) + +[file_types](./file_types/README.md) + +[joss-publication](./joss-publication/README.md) + +[services](./services/README.md) + +[setup](./setup/README.md) + diff --git a/docs/design/README.md b/docs/design/README.md new file mode 100644 index 000000000..d8321a79d --- /dev/null +++ b/docs/design/README.md @@ -0,0 +1,10 @@ +## 'design' Directory Contents + +### Subdirectories + +[diagrams](./diagrams/README.md) + +### Files + +bigger_picture.md + diff --git a/docs/design/diagrams/README.md b/docs/design/diagrams/README.md new file mode 100644 index 000000000..84a5f3b77 --- /dev/null +++ b/docs/design/diagrams/README.md @@ -0,0 +1,8 @@ +## 'diagrams' Directory Contents + +### Files + +pixl-multi-project-config.drawio + +pixl-multi-project-config.png + diff --git a/docs/file_types/README.md b/docs/file_types/README.md new file mode 100644 index 000000000..76f1f0b56 --- /dev/null +++ b/docs/file_types/README.md @@ -0,0 +1,6 @@ +## 'file_types' Directory Contents + +### Files + +parquet_files.md + diff --git a/docs/joss-publication/README.md b/docs/joss-publication/README.md new file mode 100644 index 000000000..3e5436d6d --- /dev/null +++ b/docs/joss-publication/README.md @@ -0,0 +1,12 @@ +## 'joss-publication' Directory Contents + +### Subdirectories + +[figures](./figures/README.md) + +### Files + +paper.bib + +paper.md + diff --git a/docs/joss-publication/figures/README.md b/docs/joss-publication/figures/README.md new file mode 100644 index 000000000..5d3d5f51f --- /dev/null +++ b/docs/joss-publication/figures/README.md @@ -0,0 +1,2 @@ +## 'figures' Directory Contents + diff --git a/docs/services/README.md b/docs/services/README.md new file mode 100644 index 000000000..3656b9659 --- /dev/null +++ b/docs/services/README.md @@ -0,0 +1,8 @@ +## 'services' Directory Contents + +### Files + +ftp-server.md + +pixl_database.md + diff --git a/docs/setup/README.md b/docs/setup/README.md new file mode 100644 index 000000000..163a60cee --- /dev/null +++ b/docs/setup/README.md @@ -0,0 +1,10 @@ +## 'setup' Directory Contents + +### Files + +azure-keyvault.md + +developer.md + +uclh-infrastructure-setup.md + diff --git a/hasher/src/README.md b/hasher/src/README.md new file mode 100644 index 000000000..1926fa1ef --- /dev/null +++ b/hasher/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[hasher](./hasher/README.md) + diff --git a/hasher/src/hasher/README.md b/hasher/src/hasher/README.md new file mode 100644 index 000000000..2e54f6cd5 --- /dev/null +++ b/hasher/src/hasher/README.md @@ -0,0 +1,12 @@ +## 'hasher' Directory Contents + +### Files + +endpoints.py + +hashing.py + +main.py + +__init__.py + diff --git a/hasher/tests/README.md b/hasher/tests/README.md new file mode 100644 index 000000000..16ed31500 --- /dev/null +++ b/hasher/tests/README.md @@ -0,0 +1,12 @@ +## 'tests' Directory Contents + +### Files + +conftest.py + +test_endpoints.py + +test_hashing.py + +__init__.py + diff --git a/hasher/toc.md b/hasher/toc.md new file mode 100644 index 000000000..5a9e64b99 --- /dev/null +++ b/hasher/toc.md @@ -0,0 +1,14 @@ +## 'hasher' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/orthanc/assets/README.md b/orthanc/assets/README.md new file mode 100644 index 000000000..009759a47 --- /dev/null +++ b/orthanc/assets/README.md @@ -0,0 +1,10 @@ +## 'assets' Directory Contents + +### Files + +orthanc-anon-az-dicom.png + +orthanc-anon-web.png + +orthanc-raw-web.png + diff --git a/orthanc/orthanc-anon/config/README.md b/orthanc/orthanc-anon/config/README.md new file mode 100644 index 000000000..d92c56561 --- /dev/null +++ b/orthanc/orthanc-anon/config/README.md @@ -0,0 +1,8 @@ +## 'config' Directory Contents + +### Files + +dicom.json + +orthanc.json + diff --git a/orthanc/orthanc-anon/docs/README.md b/orthanc/orthanc-anon/docs/README.md new file mode 100644 index 000000000..1159c4424 --- /dev/null +++ b/orthanc/orthanc-anon/docs/README.md @@ -0,0 +1,10 @@ +## 'docs' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +### Files + +DicomServiceViaAAD.md + diff --git a/orthanc/orthanc-anon/docs/assets/README.md b/orthanc/orthanc-anon/docs/assets/README.md new file mode 100644 index 000000000..74938b342 --- /dev/null +++ b/orthanc/orthanc-anon/docs/assets/README.md @@ -0,0 +1,6 @@ +## 'assets' Directory Contents + +### Files + +DicomServiceAuthority.png + diff --git a/orthanc/orthanc-anon/plugin/README.md b/orthanc/orthanc-anon/plugin/README.md new file mode 100644 index 000000000..a39e61831 --- /dev/null +++ b/orthanc/orthanc-anon/plugin/README.md @@ -0,0 +1,8 @@ +## 'plugin' Directory Contents + +### Files + +download_dicom_spec.py + +pixl.py + diff --git a/orthanc/orthanc-anon/toc.md b/orthanc/orthanc-anon/toc.md new file mode 100644 index 000000000..4f4278757 --- /dev/null +++ b/orthanc/orthanc-anon/toc.md @@ -0,0 +1,14 @@ +## 'orthanc-anon' Directory Contents + +### Subdirectories + +[config](./config/README.md) + +[docs](./docs/README.md) + +[plugin](./plugin/README.md) + +### Files + +README.md + diff --git a/orthanc/orthanc-raw/config/README.md b/orthanc/orthanc-raw/config/README.md new file mode 100644 index 000000000..b384c23c7 --- /dev/null +++ b/orthanc/orthanc-raw/config/README.md @@ -0,0 +1,10 @@ +## 'config' Directory Contents + +### Files + +dicom.json + +orthanc.json + +postgres.json + diff --git a/orthanc/orthanc-raw/plugin/README.md b/orthanc/orthanc-raw/plugin/README.md new file mode 100644 index 000000000..26e9667d2 --- /dev/null +++ b/orthanc/orthanc-raw/plugin/README.md @@ -0,0 +1,6 @@ +## 'plugin' Directory Contents + +### Files + +pixl.py + diff --git a/orthanc/orthanc-raw/toc.md b/orthanc/orthanc-raw/toc.md new file mode 100644 index 000000000..fdceef2fa --- /dev/null +++ b/orthanc/orthanc-raw/toc.md @@ -0,0 +1,12 @@ +## 'orthanc-raw' Directory Contents + +### Subdirectories + +[config](./config/README.md) + +[plugin](./plugin/README.md) + +### Files + +README.md + diff --git a/orthanc/toc.md b/orthanc/toc.md new file mode 100644 index 000000000..217f0294e --- /dev/null +++ b/orthanc/toc.md @@ -0,0 +1,14 @@ +## 'orthanc' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +### Files + +README.md + diff --git a/pixl_core/src/README.md b/pixl_core/src/README.md new file mode 100644 index 000000000..fc88e8f53 --- /dev/null +++ b/pixl_core/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[core](./core/README.md) + diff --git a/pixl_core/src/core/README.md b/pixl_core/src/core/README.md new file mode 100644 index 000000000..c23e4c11a --- /dev/null +++ b/pixl_core/src/core/README.md @@ -0,0 +1,26 @@ +## 'core' Directory Contents + +### Subdirectories + +[db](./db/README.md) + +[patient_queue](./patient_queue/README.md) + +[project_config](./project_config/README.md) + +[rest_api](./rest_api/README.md) + +[token_buffer](./token_buffer/README.md) + +[uploader](./uploader/README.md) + +### Files + +dicom_tags.py + +exceptions.py + +exports.py + +__init__.py + diff --git a/pixl_core/src/core/db/README.md b/pixl_core/src/core/db/README.md new file mode 100644 index 000000000..ddb128131 --- /dev/null +++ b/pixl_core/src/core/db/README.md @@ -0,0 +1,10 @@ +## 'db' Directory Contents + +### Files + +models.py + +queries.py + +__init__.py + diff --git a/pixl_core/src/core/patient_queue/README.md b/pixl_core/src/core/patient_queue/README.md new file mode 100644 index 000000000..25457ba5c --- /dev/null +++ b/pixl_core/src/core/patient_queue/README.md @@ -0,0 +1,14 @@ +## 'patient_queue' Directory Contents + +### Files + +message.py + +producer.py + +subscriber.py + +_base.py + +__init__.py + diff --git a/pixl_core/src/core/project_config/README.md b/pixl_core/src/core/project_config/README.md new file mode 100644 index 000000000..ecd68cfc5 --- /dev/null +++ b/pixl_core/src/core/project_config/README.md @@ -0,0 +1,12 @@ +## 'project_config' Directory Contents + +### Files + +pixl_config_model.py + +secrets.py + +tag_operations.py + +__init__.py + diff --git a/pixl_core/src/core/rest_api/README.md b/pixl_core/src/core/rest_api/README.md new file mode 100644 index 000000000..2f2158655 --- /dev/null +++ b/pixl_core/src/core/rest_api/README.md @@ -0,0 +1,8 @@ +## 'rest_api' Directory Contents + +### Files + +router.py + +__init__.py + diff --git a/pixl_core/src/core/token_buffer/README.md b/pixl_core/src/core/token_buffer/README.md new file mode 100644 index 000000000..59006b80a --- /dev/null +++ b/pixl_core/src/core/token_buffer/README.md @@ -0,0 +1,10 @@ +## 'token_buffer' Directory Contents + +### Files + +models.py + +tokens.py + +__init__.py + diff --git a/pixl_core/src/core/uploader/README.md b/pixl_core/src/core/uploader/README.md new file mode 100644 index 000000000..fd0c364be --- /dev/null +++ b/pixl_core/src/core/uploader/README.md @@ -0,0 +1,16 @@ +## 'uploader' Directory Contents + +### Files + +base.py + +_dicomweb.py + +_ftps.py + +_orthanc.py + +_xnat.py + +__init__.py + diff --git a/pixl_core/tests/README.md b/pixl_core/tests/README.md new file mode 100644 index 000000000..60978a4c5 --- /dev/null +++ b/pixl_core/tests/README.md @@ -0,0 +1,22 @@ +## 'tests' Directory Contents + +### Subdirectories + +[data](./data/README.md) + +[patient_queue](./patient_queue/README.md) + +[project_config](./project_config/README.md) + +[token_buffer](./token_buffer/README.md) + +[uploader](./uploader/README.md) + +### Files + +conftest.py + +docker-compose.yml + +test_exports.py + diff --git a/pixl_core/tests/data/README.md b/pixl_core/tests/data/README.md new file mode 100644 index 000000000..16da4c31e --- /dev/null +++ b/pixl_core/tests/data/README.md @@ -0,0 +1,10 @@ +## 'data' Directory Contents + +### Files + +dicom_series.zip + +public.zip + +xnat_project.xml + diff --git a/pixl_core/tests/patient_queue/README.md b/pixl_core/tests/patient_queue/README.md new file mode 100644 index 000000000..0d64a43fc --- /dev/null +++ b/pixl_core/tests/patient_queue/README.md @@ -0,0 +1,10 @@ +## 'patient_queue' Directory Contents + +### Files + +test_message.py + +test_producer.py + +test_subscriber.py + diff --git a/pixl_core/tests/project_config/README.md b/pixl_core/tests/project_config/README.md new file mode 100644 index 000000000..6e5df5eab --- /dev/null +++ b/pixl_core/tests/project_config/README.md @@ -0,0 +1,8 @@ +## 'project_config' Directory Contents + +### Files + +test_project_config.py + +test_secrets.py + diff --git a/pixl_core/tests/token_buffer/README.md b/pixl_core/tests/token_buffer/README.md new file mode 100644 index 000000000..9027983ab --- /dev/null +++ b/pixl_core/tests/token_buffer/README.md @@ -0,0 +1,6 @@ +## 'token_buffer' Directory Contents + +### Files + +test_tokens.py + diff --git a/pixl_core/tests/uploader/README.md b/pixl_core/tests/uploader/README.md new file mode 100644 index 000000000..4ff10f374 --- /dev/null +++ b/pixl_core/tests/uploader/README.md @@ -0,0 +1,12 @@ +## 'uploader' Directory Contents + +### Files + +test_base.py + +test_dicomweb.py + +test_ftps.py + +test_xnat.py + diff --git a/pixl_core/toc.md b/pixl_core/toc.md new file mode 100644 index 000000000..7844ef0ad --- /dev/null +++ b/pixl_core/toc.md @@ -0,0 +1,14 @@ +## 'pixl_core' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_dcmd/src/README.md b/pixl_dcmd/src/README.md new file mode 100644 index 000000000..e41c2e20f --- /dev/null +++ b/pixl_dcmd/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[pixl_dcmd](./pixl_dcmd/README.md) + diff --git a/pixl_dcmd/src/pixl_dcmd/README.md b/pixl_dcmd/src/pixl_dcmd/README.md new file mode 100644 index 000000000..db8089521 --- /dev/null +++ b/pixl_dcmd/src/pixl_dcmd/README.md @@ -0,0 +1,22 @@ +## 'pixl_dcmd' Directory Contents + +### Subdirectories + +[resources](./resources/README.md) + +### Files + +main.py + +tagrecording.py + +_database.py + +_dicom_helpers.py + +_tag_schemes.py + +_version.py + +__init__.py + diff --git a/pixl_dcmd/src/pixl_dcmd/resources/README.md b/pixl_dcmd/src/pixl_dcmd/resources/README.md new file mode 100644 index 000000000..60b1932f2 --- /dev/null +++ b/pixl_dcmd/src/pixl_dcmd/resources/README.md @@ -0,0 +1,6 @@ +## 'resources' Directory Contents + +### Files + +recorded-headers.yml + diff --git a/pixl_dcmd/tests/README.md b/pixl_dcmd/tests/README.md new file mode 100644 index 000000000..c1fd46fa3 --- /dev/null +++ b/pixl_dcmd/tests/README.md @@ -0,0 +1,16 @@ +## 'tests' Directory Contents + +### Files + +conftest.py + +test_database.py + +test_dicom_validator.py + +test_main.py + +test_tagrecording.py + +test_tag_schemes.py + diff --git a/pixl_dcmd/toc.md b/pixl_dcmd/toc.md new file mode 100644 index 000000000..e52595be5 --- /dev/null +++ b/pixl_dcmd/toc.md @@ -0,0 +1,14 @@ +## 'pixl_dcmd' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_export/src/README.md b/pixl_export/src/README.md new file mode 100644 index 000000000..b501220d1 --- /dev/null +++ b/pixl_export/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[pixl_export](./pixl_export/README.md) + diff --git a/pixl_export/src/pixl_export/README.md b/pixl_export/src/pixl_export/README.md new file mode 100644 index 000000000..285f38516 --- /dev/null +++ b/pixl_export/src/pixl_export/README.md @@ -0,0 +1,12 @@ +## 'pixl_export' Directory Contents + +### Files + +main.py + +_databases.py + +_queries.py + +__init__.py + diff --git a/pixl_export/tests/README.md b/pixl_export/tests/README.md new file mode 100644 index 000000000..c80cd9e4e --- /dev/null +++ b/pixl_export/tests/README.md @@ -0,0 +1,10 @@ +## 'tests' Directory Contents + +### Files + +conftest.py + +docker-compose.yml + +test_app.py + diff --git a/pixl_export/toc.md b/pixl_export/toc.md new file mode 100644 index 000000000..71a39a35d --- /dev/null +++ b/pixl_export/toc.md @@ -0,0 +1,14 @@ +## 'pixl_export' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_imaging/alembic/toc.md b/pixl_imaging/alembic/toc.md new file mode 100644 index 000000000..812d7f9ca --- /dev/null +++ b/pixl_imaging/alembic/toc.md @@ -0,0 +1,20 @@ +## 'alembic' Directory Contents + +### Subdirectories + +[versions](./versions/README.md) + +### Files + +alembic.ini + +autogenerate-migration.sh + +env.py + +migrations.env + +README.md + +script.py.mako + diff --git a/pixl_imaging/alembic/versions/README.md b/pixl_imaging/alembic/versions/README.md new file mode 100644 index 000000000..0a2a9f02a --- /dev/null +++ b/pixl_imaging/alembic/versions/README.md @@ -0,0 +1,12 @@ +## 'versions' Directory Contents + +### Files + +83dcb3812628_add_study_uid_column_to_image_table.py + +bcaef54e2bfe_create_extract_and_image_tables.py + +cb5ee12a6e20_replace_hashed_id_with_pseudo_study_uid.py + +d947cc715eb1_add_pseudo_patient_id_column_to_image_table.py + diff --git a/pixl_imaging/scripts/README.md b/pixl_imaging/scripts/README.md new file mode 100644 index 000000000..ca833da88 --- /dev/null +++ b/pixl_imaging/scripts/README.md @@ -0,0 +1,6 @@ +## 'scripts' Directory Contents + +### Files + +migrate_and_run.sh + diff --git a/pixl_imaging/src/README.md b/pixl_imaging/src/README.md new file mode 100644 index 000000000..adb442a5f --- /dev/null +++ b/pixl_imaging/src/README.md @@ -0,0 +1,6 @@ +## 'src' Directory Contents + +### Subdirectories + +[pixl_imaging](./pixl_imaging/README.md) + diff --git a/pixl_imaging/src/pixl_imaging/README.md b/pixl_imaging/src/pixl_imaging/README.md new file mode 100644 index 000000000..bc6dd139e --- /dev/null +++ b/pixl_imaging/src/pixl_imaging/README.md @@ -0,0 +1,12 @@ +## 'pixl_imaging' Directory Contents + +### Files + +main.py + +_orthanc.py + +_processing.py + +__init__.py + diff --git a/pixl_imaging/tests/README.md b/pixl_imaging/tests/README.md new file mode 100644 index 000000000..d3f574bd9 --- /dev/null +++ b/pixl_imaging/tests/README.md @@ -0,0 +1,14 @@ +## 'tests' Directory Contents + +### Subdirectories + +[orthanc_raw_config](./orthanc_raw_config/README.md) + +### Files + +conftest.py + +docker-compose.yml + +test_imaging_processing.py + diff --git a/pixl_imaging/tests/orthanc_raw_config/README.md b/pixl_imaging/tests/orthanc_raw_config/README.md new file mode 100644 index 000000000..b8d893380 --- /dev/null +++ b/pixl_imaging/tests/orthanc_raw_config/README.md @@ -0,0 +1,8 @@ +## 'orthanc_raw_config' Directory Contents + +### Files + +dicom.json + +orthanc.json + diff --git a/pixl_imaging/toc.md b/pixl_imaging/toc.md new file mode 100644 index 000000000..5d0eb87e0 --- /dev/null +++ b/pixl_imaging/toc.md @@ -0,0 +1,18 @@ +## 'pixl_imaging' Directory Contents + +### Subdirectories + +[alembic](./alembic/README.md) + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/postgres/toc.md b/postgres/toc.md new file mode 100644 index 000000000..f5aa398e9 --- /dev/null +++ b/postgres/toc.md @@ -0,0 +1,10 @@ +## 'postgres' Directory Contents + +### Files + +pixl-db_init.sh + +postgres.conf + +README.md + diff --git a/projects/README.md b/projects/README.md new file mode 100644 index 000000000..258b199f7 --- /dev/null +++ b/projects/README.md @@ -0,0 +1,8 @@ +## 'projects' Directory Contents + +### Subdirectories + +[configs](./configs/README.md) + +[exports](./exports/README.md) + diff --git a/projects/configs/README.md b/projects/configs/README.md new file mode 100644 index 000000000..97778a273 --- /dev/null +++ b/projects/configs/README.md @@ -0,0 +1,22 @@ +## 'configs' Directory Contents + +### Subdirectories + +[tag-operations](./tag-operations/README.md) + +### Files + +ms-pinpoint.yaml + +test-external-user.yaml + +test-extract-uclh-omop-cdm-dicomweb.yaml + +test-extract-uclh-omop-cdm-xnat.yaml + +test-extract-uclh-omop-cdm.yaml + +uclh-nasogastric-tube-project-ngt-only-full-dataset.yaml + +uclh-prostate-mri-external-dataset.yaml + diff --git a/projects/configs/tag-operations/README.md b/projects/configs/tag-operations/README.md new file mode 100644 index 000000000..bc2e06419 --- /dev/null +++ b/projects/configs/tag-operations/README.md @@ -0,0 +1,24 @@ +## 'tag-operations' Directory Contents + +### Subdirectories + +[manufacturer-overrides](./manufacturer-overrides/README.md) + +### Files + +base.yaml + +diffusion-weighted-mri.yaml + +mri.yaml + +ms-pinpoint.yaml + +test-external-user.yaml + +test-extract-uclh-omop-cdm.yaml + +uclh-nasogastric-tube-project-ngt-only-full-dataset.yaml + +xray.yaml + diff --git a/projects/configs/tag-operations/manufacturer-overrides/README.md b/projects/configs/tag-operations/manufacturer-overrides/README.md new file mode 100644 index 000000000..b77c531e3 --- /dev/null +++ b/projects/configs/tag-operations/manufacturer-overrides/README.md @@ -0,0 +1,8 @@ +## 'manufacturer-overrides' Directory Contents + +### Files + +mri-diffusion.yaml + +mri.yaml + diff --git a/pytest-pixl/scripts/README.md b/pytest-pixl/scripts/README.md new file mode 100644 index 000000000..6dfa6cf99 --- /dev/null +++ b/pytest-pixl/scripts/README.md @@ -0,0 +1,6 @@ +## 'scripts' Directory Contents + +### Files + +create_default_dicom_tags_json.py + diff --git a/pytest-pixl/src/README.md b/pytest-pixl/src/README.md new file mode 100644 index 000000000..aa0b1d86b --- /dev/null +++ b/pytest-pixl/src/README.md @@ -0,0 +1,8 @@ +## 'src' Directory Contents + +### Subdirectories + +[pytest_pixl](./pytest_pixl/README.md) + +[resources](./resources/README.md) + diff --git a/pytest-pixl/src/pytest_pixl/README.md b/pytest-pixl/src/pytest_pixl/README.md new file mode 100644 index 000000000..1a7997f1a --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/README.md @@ -0,0 +1,18 @@ +## 'pytest_pixl' Directory Contents + +### Subdirectories + +[data](./data/README.md) + +### Files + +dicom.py + +ftpserver.py + +helpers.py + +plugin.py + +__init__.py + diff --git a/pytest-pixl/src/pytest_pixl/data/README.md b/pytest-pixl/src/pytest_pixl/data/README.md new file mode 100644 index 000000000..067cc9833 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/README.md @@ -0,0 +1,12 @@ +## 'data' Directory Contents + +### Subdirectories + +[omop-resources](./omop-resources/README.md) + +### Files + +default_dicom_tags.json + +volume_dicom_variables.json + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md new file mode 100644 index 000000000..7a457c566 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/README.md @@ -0,0 +1,18 @@ +## 'omop-resources' Directory Contents + +### Subdirectories + +[omop](./omop/README.md) + +### Files + +batch_input.csv + +duplicate_input.csv + +multiple_projects.csv + +participant_id.csv + +test.csv + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md new file mode 100644 index 000000000..e5d45c492 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/README.md @@ -0,0 +1,12 @@ +## 'omop' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md new file mode 100644 index 000000000..2e47873ed --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/private/README.md @@ -0,0 +1,8 @@ +## 'private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md new file mode 100644 index 000000000..d35e10141 --- /dev/null +++ b/pytest-pixl/src/pytest_pixl/data/omop-resources/omop/public/README.md @@ -0,0 +1,6 @@ +## 'public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/pytest-pixl/src/resources/README.md b/pytest-pixl/src/resources/README.md new file mode 100644 index 000000000..2191a688c --- /dev/null +++ b/pytest-pixl/src/resources/README.md @@ -0,0 +1,6 @@ +## 'resources' Directory Contents + +### Subdirectories + +[ssl](./ssl/README.md) + diff --git a/pytest-pixl/src/resources/ssl/README.md b/pytest-pixl/src/resources/ssl/README.md new file mode 100644 index 000000000..4b01d4bd4 --- /dev/null +++ b/pytest-pixl/src/resources/ssl/README.md @@ -0,0 +1,8 @@ +## 'ssl' Directory Contents + +### Files + +localhost.crt + +localhost.key + diff --git a/pytest-pixl/tests/README.md b/pytest-pixl/tests/README.md new file mode 100644 index 000000000..3254ed84f --- /dev/null +++ b/pytest-pixl/tests/README.md @@ -0,0 +1,12 @@ +## 'tests' Directory Contents + +### Subdirectories + +[samples_for_fixture_tests](./samples_for_fixture_tests/README.md) + +### Files + +conftest.py + +test_ftpserver_fixture.py + diff --git a/pytest-pixl/tests/samples_for_fixture_tests/README.md b/pytest-pixl/tests/samples_for_fixture_tests/README.md new file mode 100644 index 000000000..bef9031dd --- /dev/null +++ b/pytest-pixl/tests/samples_for_fixture_tests/README.md @@ -0,0 +1,6 @@ +## 'samples_for_fixture_tests' Directory Contents + +### Subdirectories + +[test_ftpserver_fixture](./test_ftpserver_fixture/README.md) + diff --git a/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md new file mode 100644 index 000000000..86072e2d4 --- /dev/null +++ b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md @@ -0,0 +1,6 @@ +## 'test_ftpserver_fixture' Directory Contents + +### Files + +test_ftpserver_login.py + diff --git a/pytest-pixl/toc.md b/pytest-pixl/toc.md new file mode 100644 index 000000000..819de9cf4 --- /dev/null +++ b/pytest-pixl/toc.md @@ -0,0 +1,16 @@ +## 'pytest-pixl' Directory Contents + +### Subdirectories + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/schemas/README.md b/schemas/README.md new file mode 100644 index 000000000..db3679245 --- /dev/null +++ b/schemas/README.md @@ -0,0 +1,6 @@ +## 'schemas' Directory Contents + +### Files + +github-issue-forms.json + diff --git a/scripts/README.md b/scripts/README.md new file mode 100644 index 000000000..508753508 --- /dev/null +++ b/scripts/README.md @@ -0,0 +1,12 @@ +## 'scripts' Directory Contents + +### Files + +cmove_all_studies.py + +delete_oldest_n_studies.py + +filter_cohort_for_those_present_in_raw.py + +list_newest_n_studies.py + diff --git a/test/dicomweb_config/README.md b/test/dicomweb_config/README.md new file mode 100644 index 000000000..6ce0b6905 --- /dev/null +++ b/test/dicomweb_config/README.md @@ -0,0 +1,10 @@ +## 'dicomweb_config' Directory Contents + +### Files + +.env + +dicom.json + +orthanc.json + diff --git a/test/resources/README.md b/test/resources/README.md new file mode 100644 index 000000000..2f49e5556 --- /dev/null +++ b/test/resources/README.md @@ -0,0 +1,14 @@ +## 'resources' Directory Contents + +### Subdirectories + +[omop](./omop/README.md) + +[omop-dicomweb](./omop-dicomweb/README.md) + +### Files + +Dicom1.dcm + +Dicom2.dcm + diff --git a/test/resources/omop-dicomweb/README.md b/test/resources/omop-dicomweb/README.md new file mode 100644 index 000000000..0847fb646 --- /dev/null +++ b/test/resources/omop-dicomweb/README.md @@ -0,0 +1,12 @@ +## 'omop-dicomweb' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/test/resources/omop-dicomweb/private/README.md b/test/resources/omop-dicomweb/private/README.md new file mode 100644 index 000000000..2e47873ed --- /dev/null +++ b/test/resources/omop-dicomweb/private/README.md @@ -0,0 +1,8 @@ +## 'private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/test/resources/omop-dicomweb/public/README.md b/test/resources/omop-dicomweb/public/README.md new file mode 100644 index 000000000..d35e10141 --- /dev/null +++ b/test/resources/omop-dicomweb/public/README.md @@ -0,0 +1,6 @@ +## 'public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/test/resources/omop/README.md b/test/resources/omop/README.md new file mode 100644 index 000000000..e5d45c492 --- /dev/null +++ b/test/resources/omop/README.md @@ -0,0 +1,12 @@ +## 'omop' Directory Contents + +### Subdirectories + +[private](./private/README.md) + +[public](./public/README.md) + +### Files + +extract_summary.json + diff --git a/test/resources/omop/private/README.md b/test/resources/omop/private/README.md new file mode 100644 index 000000000..2e47873ed --- /dev/null +++ b/test/resources/omop/private/README.md @@ -0,0 +1,8 @@ +## 'private' Directory Contents + +### Files + +PERSON_LINKS.parquet + +PROCEDURE_OCCURRENCE_LINKS.parquet + diff --git a/test/resources/omop/public/README.md b/test/resources/omop/public/README.md new file mode 100644 index 000000000..d35e10141 --- /dev/null +++ b/test/resources/omop/public/README.md @@ -0,0 +1,6 @@ +## 'public' Directory Contents + +### Files + +PROCEDURE_OCCURRENCE.parquet + diff --git a/test/toc.md b/test/toc.md new file mode 100644 index 000000000..a60d7990a --- /dev/null +++ b/test/toc.md @@ -0,0 +1,30 @@ +## 'test' Directory Contents + +### Subdirectories + +[dicomweb_config](./dicomweb_config/README.md) + +[resources](./resources/README.md) + +[vna_config](./vna_config/README.md) + +### Files + +.env + +.secrets.env.sample + +conftest.py + +docker-compose.yml + +README.md + +run-system-test.sh + +system_test.py + +test_parquet_exports.py + +utils.py + diff --git a/test/vna_config/README.md b/test/vna_config/README.md new file mode 100644 index 000000000..d34408991 --- /dev/null +++ b/test/vna_config/README.md @@ -0,0 +1,8 @@ +## 'vna_config' Directory Contents + +### Files + +dicom.json + +orthanc.json + diff --git a/toc.md b/toc.md new file mode 100644 index 000000000..bfe3f4a34 --- /dev/null +++ b/toc.md @@ -0,0 +1,72 @@ +## 'PIXL' Directory Contents + +### Subdirectories + +[.git](./.git/README.md) + +[.github](./.github/README.md) + +[bin](./bin/README.md) + +[cli](./cli/README.md) + +[docker](./docker/README.md) + +[docs](./docs/README.md) + +[hasher](./hasher/README.md) + +[orthanc](./orthanc/README.md) + +[pixl_core](./pixl_core/README.md) + +[pixl_dcmd](./pixl_dcmd/README.md) + +[pixl_export](./pixl_export/README.md) + +[pixl_imaging](./pixl_imaging/README.md) + +[postgres](./postgres/README.md) + +[projects](./projects/README.md) + +[pytest-pixl](./pytest-pixl/README.md) + +[schemas](./schemas/README.md) + +[scripts](./scripts/README.md) + +[test](./test/README.md) + +### Files + +.env.sample + +.gitignore + +.pre-commit-config.yaml + +.renovaterc.json5 + +codecov.yml + +CODE_OF_CONDUCT.md + +CONTRIBUTING.md + +docker-compose.yml + +LICENSE + +mypy.ini + +NOTICE + +pytest.ini + +README.md + +ruff.toml + +template_config.yaml + From 0fbf6962c04d2715691b7ca4c99b062eab12d8f7 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 19 Nov 2024 11:36:55 +0000 Subject: [PATCH 05/18] making read me and table of contents consistent --- README.md | 72 +++++++++++++++++++++++++++++++++++ bin/README.md | 2 +- bin/linters/README.md | 2 +- cli/README.md | 15 ++++++++ cli/src/README.md | 2 +- cli/src/pixl_cli/README.md | 2 +- cli/tests/README.md | 22 +++++++++++ cli/tests/toc.md | 22 ----------- cli/toc.md | 14 ------- docker/README.md | 2 +- docker/export-api/README.md | 2 +- docker/hasher-api/README.md | 2 +- docker/imaging-api/README.md | 2 +- docker/orthanc-anon/README.md | 2 +- docker/orthanc-raw/README.md | 2 +- docker/postgres/README.md | 2 +- toc.md | 72 ----------------------------------- 17 files changed, 120 insertions(+), 119 deletions(-) delete mode 100644 cli/tests/toc.md delete mode 100644 cli/toc.md delete mode 100644 toc.md diff --git a/README.md b/README.md index e9a30860d..b5040e4a6 100644 --- a/README.md +++ b/README.md @@ -317,3 +317,75 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet git clone git@github.com:SAFEHR-data/PIXL.git ``` +## 'PIXL' Directory Contents + +### Subdirectories + +[.git](./.git/README.md) + +[.github](./.github/README.md) + +[bin](./bin/README.md) + +[cli](./cli/README.md) + +[docker](./docker/README.md) + +[docs](./docs/README.md) + +[hasher](./hasher/README.md) + +[orthanc](./orthanc/README.md) + +[pixl_core](./pixl_core/README.md) + +[pixl_dcmd](./pixl_dcmd/README.md) + +[pixl_export](./pixl_export/README.md) + +[pixl_imaging](./pixl_imaging/README.md) + +[postgres](./postgres/README.md) + +[projects](./projects/README.md) + +[pytest-pixl](./pytest-pixl/README.md) + +[schemas](./schemas/README.md) + +[scripts](./scripts/README.md) + +[test](./test/README.md) + +### Files + +.env.sample + +.gitignore + +.pre-commit-config.yaml + +.renovaterc.json5 + +codecov.yml + +CODE_OF_CONDUCT.md + +CONTRIBUTING.md + +docker-compose.yml + +LICENSE + +mypy.ini + +NOTICE + +pytest.ini + +README.md + +ruff.toml + +template_config.yaml + diff --git a/bin/README.md b/bin/README.md index bd9e79b7f..eedf89797 100644 --- a/bin/README.md +++ b/bin/README.md @@ -1,4 +1,4 @@ -## 'bin' Directory Contents +## 'PIXL/bin' Directory Contents ### Subdirectories diff --git a/bin/linters/README.md b/bin/linters/README.md index a6c131b8e..a03874a75 100644 --- a/bin/linters/README.md +++ b/bin/linters/README.md @@ -1,4 +1,4 @@ -## 'linters' Directory Contents +## 'PIXL/bin/linters' Directory Contents ### Files diff --git a/cli/README.md b/cli/README.md index 374c358bd..bbbddeef6 100644 --- a/cli/README.md +++ b/cli/README.md @@ -142,3 +142,18 @@ The CLI tests require a running instance of the `rabbitmq` service, for which we pytest -vs tests #for all tests pytest -vs tests/test_docker_commands.py #e.g., for particular tests ``` + +## 'PIXL/cli' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/cli/src/README.md b/cli/src/README.md index 23f0b3564..807a572b5 100644 --- a/cli/src/README.md +++ b/cli/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/cli/src' Directory Contents ### Subdirectories diff --git a/cli/src/pixl_cli/README.md b/cli/src/pixl_cli/README.md index b52bef0d3..11f286869 100644 --- a/cli/src/pixl_cli/README.md +++ b/cli/src/pixl_cli/README.md @@ -1,4 +1,4 @@ -## 'pixl_cli' Directory Contents +## 'PIXL/cli/src/pixl_cli' Directory Contents ### Files diff --git a/cli/tests/README.md b/cli/tests/README.md index 280d3bf6b..85977d651 100644 --- a/cli/tests/README.md +++ b/cli/tests/README.md @@ -5,3 +5,25 @@ Remove the db container and associated data docker container rm pixl-test-db -v -f ``` +## 'PIXL/cli/tests' Directory Contents + +### Files + +conftest.py + +README.md + +test_check_env.py + +test_database.py + +test_docker_commands.py + +test_io.py + +test_messages_from_files.py + +test_message_processing.py + +test_populate.py + diff --git a/cli/tests/toc.md b/cli/tests/toc.md deleted file mode 100644 index 1f58ca89f..000000000 --- a/cli/tests/toc.md +++ /dev/null @@ -1,22 +0,0 @@ -## 'tests' Directory Contents - -### Files - -conftest.py - -README.md - -test_check_env.py - -test_database.py - -test_docker_commands.py - -test_io.py - -test_messages_from_files.py - -test_message_processing.py - -test_populate.py - diff --git a/cli/toc.md b/cli/toc.md deleted file mode 100644 index 200731dff..000000000 --- a/cli/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'cli' Directory Contents - -### Subdirectories - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/docker/README.md b/docker/README.md index c1e61f136..d423d8cb6 100644 --- a/docker/README.md +++ b/docker/README.md @@ -1,4 +1,4 @@ -## 'docker' Directory Contents +## 'PIXL/docker' Directory Contents ### Subdirectories diff --git a/docker/export-api/README.md b/docker/export-api/README.md index 8496615e5..f12d22846 100644 --- a/docker/export-api/README.md +++ b/docker/export-api/README.md @@ -1,4 +1,4 @@ -## 'export-api' Directory Contents +## 'PIXL/docker/export-api' Directory Contents ### Files diff --git a/docker/hasher-api/README.md b/docker/hasher-api/README.md index ad524fbed..f54e14972 100644 --- a/docker/hasher-api/README.md +++ b/docker/hasher-api/README.md @@ -1,4 +1,4 @@ -## 'hasher-api' Directory Contents +## 'PIXL/docker/hasher-api' Directory Contents ### Files diff --git a/docker/imaging-api/README.md b/docker/imaging-api/README.md index 72eee7467..400bee965 100644 --- a/docker/imaging-api/README.md +++ b/docker/imaging-api/README.md @@ -1,4 +1,4 @@ -## 'imaging-api' Directory Contents +## 'PIXL/docker/imaging-api' Directory Contents ### Files diff --git a/docker/orthanc-anon/README.md b/docker/orthanc-anon/README.md index eb8fdea56..b1f2a60bc 100644 --- a/docker/orthanc-anon/README.md +++ b/docker/orthanc-anon/README.md @@ -1,4 +1,4 @@ -## 'orthanc-anon' Directory Contents +## 'PIXL/docker/orthanc-anon' Directory Contents ### Files diff --git a/docker/orthanc-raw/README.md b/docker/orthanc-raw/README.md index 7529e53e8..a137fb98a 100644 --- a/docker/orthanc-raw/README.md +++ b/docker/orthanc-raw/README.md @@ -1,4 +1,4 @@ -## 'orthanc-raw' Directory Contents +## 'PIXL/docker/orthanc-raw' Directory Contents ### Files diff --git a/docker/postgres/README.md b/docker/postgres/README.md index 81fd8a9fb..f43084e01 100644 --- a/docker/postgres/README.md +++ b/docker/postgres/README.md @@ -1,4 +1,4 @@ -## 'postgres' Directory Contents +## 'PIXL/docker/postgres' Directory Contents ### Files diff --git a/toc.md b/toc.md deleted file mode 100644 index bfe3f4a34..000000000 --- a/toc.md +++ /dev/null @@ -1,72 +0,0 @@ -## 'PIXL' Directory Contents - -### Subdirectories - -[.git](./.git/README.md) - -[.github](./.github/README.md) - -[bin](./bin/README.md) - -[cli](./cli/README.md) - -[docker](./docker/README.md) - -[docs](./docs/README.md) - -[hasher](./hasher/README.md) - -[orthanc](./orthanc/README.md) - -[pixl_core](./pixl_core/README.md) - -[pixl_dcmd](./pixl_dcmd/README.md) - -[pixl_export](./pixl_export/README.md) - -[pixl_imaging](./pixl_imaging/README.md) - -[postgres](./postgres/README.md) - -[projects](./projects/README.md) - -[pytest-pixl](./pytest-pixl/README.md) - -[schemas](./schemas/README.md) - -[scripts](./scripts/README.md) - -[test](./test/README.md) - -### Files - -.env.sample - -.gitignore - -.pre-commit-config.yaml - -.renovaterc.json5 - -codecov.yml - -CODE_OF_CONDUCT.md - -CONTRIBUTING.md - -docker-compose.yml - -LICENSE - -mypy.ini - -NOTICE - -pytest.ini - -README.md - -ruff.toml - -template_config.yaml - From acdda77f3f0ad884611ef4789c52886f29b6cabd Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 19 Nov 2024 14:57:58 +0000 Subject: [PATCH 06/18] making readme and table of contents consistent --- docs/README.md | 2 +- docs/design/README.md | 2 +- docs/design/diagrams/README.md | 2 +- docs/file_types/README.md | 2 +- docs/joss-publication/README.md | 2 +- docs/joss-publication/figures/README.md | 2 +- docs/services/README.md | 2 +- docs/setup/README.md | 2 +- hasher/README.md | 15 +++++++++++++++ hasher/src/README.md | 2 +- hasher/src/hasher/README.md | 2 +- hasher/tests/README.md | 2 +- hasher/toc.md | 14 -------------- orthanc/README.md | 15 +++++++++++++++ orthanc/assets/README.md | 2 +- orthanc/orthanc-anon/README.md | 15 +++++++++++++++ orthanc/orthanc-anon/config/README.md | 2 +- orthanc/orthanc-anon/docs/README.md | 2 +- orthanc/orthanc-anon/docs/assets/README.md | 2 +- orthanc/orthanc-anon/plugin/README.md | 2 +- orthanc/orthanc-anon/toc.md | 14 -------------- orthanc/orthanc-raw/README.md | 13 +++++++++++++ orthanc/orthanc-raw/config/README.md | 2 +- orthanc/orthanc-raw/plugin/README.md | 2 +- orthanc/orthanc-raw/toc.md | 12 ------------ orthanc/toc.md | 14 -------------- 26 files changed, 76 insertions(+), 72 deletions(-) delete mode 100644 hasher/toc.md delete mode 100644 orthanc/orthanc-anon/toc.md delete mode 100644 orthanc/orthanc-raw/toc.md delete mode 100644 orthanc/toc.md diff --git a/docs/README.md b/docs/README.md index e16f21e9e..26ff7826b 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,4 +1,4 @@ -## 'docs' Directory Contents +## 'PIXL/docs' Directory Contents ### Subdirectories diff --git a/docs/design/README.md b/docs/design/README.md index d8321a79d..f2b57d6bd 100644 --- a/docs/design/README.md +++ b/docs/design/README.md @@ -1,4 +1,4 @@ -## 'design' Directory Contents +## 'PIXL/docs/design' Directory Contents ### Subdirectories diff --git a/docs/design/diagrams/README.md b/docs/design/diagrams/README.md index 84a5f3b77..7da298bcc 100644 --- a/docs/design/diagrams/README.md +++ b/docs/design/diagrams/README.md @@ -1,4 +1,4 @@ -## 'diagrams' Directory Contents +## 'PIXL/docs/design/diagrams' Directory Contents ### Files diff --git a/docs/file_types/README.md b/docs/file_types/README.md index 76f1f0b56..a24a35216 100644 --- a/docs/file_types/README.md +++ b/docs/file_types/README.md @@ -1,4 +1,4 @@ -## 'file_types' Directory Contents +## 'PIXL/docs/file_types' Directory Contents ### Files diff --git a/docs/joss-publication/README.md b/docs/joss-publication/README.md index 3e5436d6d..83800df8e 100644 --- a/docs/joss-publication/README.md +++ b/docs/joss-publication/README.md @@ -1,4 +1,4 @@ -## 'joss-publication' Directory Contents +## 'PIXL/docs/joss-publication' Directory Contents ### Subdirectories diff --git a/docs/joss-publication/figures/README.md b/docs/joss-publication/figures/README.md index 5d3d5f51f..c6147e300 100644 --- a/docs/joss-publication/figures/README.md +++ b/docs/joss-publication/figures/README.md @@ -1,2 +1,2 @@ -## 'figures' Directory Contents +## 'PIXL/docs/joss-publication/figures' Directory Contents diff --git a/docs/services/README.md b/docs/services/README.md index 3656b9659..f0337901a 100644 --- a/docs/services/README.md +++ b/docs/services/README.md @@ -1,4 +1,4 @@ -## 'services' Directory Contents +## 'PIXL/docs/services' Directory Contents ### Files diff --git a/docs/setup/README.md b/docs/setup/README.md index 163a60cee..fd9845552 100644 --- a/docs/setup/README.md +++ b/docs/setup/README.md @@ -1,4 +1,4 @@ -## 'setup' Directory Contents +## 'PIXL/docs/setup' Directory Contents ### Files diff --git a/hasher/README.md b/hasher/README.md index 3119a298f..b9055be2c 100644 --- a/hasher/README.md +++ b/hasher/README.md @@ -67,3 +67,18 @@ HASHER_API_AZ_CLIENT_PASSWORD= HASHER_API_AZ_TENANT_ID= HASHER_API_AZ_KEY_VAULT_NAME= ``` + +## 'PIXL/hasher' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/hasher/src/README.md b/hasher/src/README.md index 1926fa1ef..99a56a701 100644 --- a/hasher/src/README.md +++ b/hasher/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/hasher/src' Directory Contents ### Subdirectories diff --git a/hasher/src/hasher/README.md b/hasher/src/hasher/README.md index 2e54f6cd5..40b064a8d 100644 --- a/hasher/src/hasher/README.md +++ b/hasher/src/hasher/README.md @@ -1,4 +1,4 @@ -## 'hasher' Directory Contents +## 'PIXL/hasher/src/hasher' Directory Contents ### Files diff --git a/hasher/tests/README.md b/hasher/tests/README.md index 16ed31500..1a161940e 100644 --- a/hasher/tests/README.md +++ b/hasher/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/hasher/tests' Directory Contents ### Files diff --git a/hasher/toc.md b/hasher/toc.md deleted file mode 100644 index 5a9e64b99..000000000 --- a/hasher/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'hasher' Directory Contents - -### Subdirectories - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/orthanc/README.md b/orthanc/README.md index 1683a2e5d..674d7d272 100644 --- a/orthanc/README.md +++ b/orthanc/README.md @@ -9,3 +9,18 @@ PIXL defines 2 types of ORTHANC instances: For both instances we define a plugin in `orthanc-*/plugin/pixl.py` that implements the custom functionality . + +## 'PIXL/orthanc' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +### Files + +README.md + diff --git a/orthanc/assets/README.md b/orthanc/assets/README.md index 009759a47..e6468fad6 100644 --- a/orthanc/assets/README.md +++ b/orthanc/assets/README.md @@ -1,4 +1,4 @@ -## 'assets' Directory Contents +## 'PIXL/orthanc/assets' Directory Contents ### Files diff --git a/orthanc/orthanc-anon/README.md b/orthanc/orthanc-anon/README.md index bef1b3f58..29417db44 100644 --- a/orthanc/orthanc-anon/README.md +++ b/orthanc/orthanc-anon/README.md @@ -105,3 +105,18 @@ start. ## References - [Cheat sheet of the REST API](https://book.orthanc-server.com/users/rest-cheatsheet.html) + +## 'orthanc' Directory Contents + +### Subdirectories + +[assets](./assets/README.md) + +[orthanc-anon](./orthanc-anon/README.md) + +[orthanc-raw](./orthanc-raw/README.md) + +### Files + +README.md + diff --git a/orthanc/orthanc-anon/config/README.md b/orthanc/orthanc-anon/config/README.md index d92c56561..ef5de4dce 100644 --- a/orthanc/orthanc-anon/config/README.md +++ b/orthanc/orthanc-anon/config/README.md @@ -1,4 +1,4 @@ -## 'config' Directory Contents +## 'PIXL/orthanc/orthanc-anon/config' Directory Contents ### Files diff --git a/orthanc/orthanc-anon/docs/README.md b/orthanc/orthanc-anon/docs/README.md index 1159c4424..8a6fa25bf 100644 --- a/orthanc/orthanc-anon/docs/README.md +++ b/orthanc/orthanc-anon/docs/README.md @@ -1,4 +1,4 @@ -## 'docs' Directory Contents +## 'PIXL/orthanc/orthanc-anon/docs' Directory Contents ### Subdirectories diff --git a/orthanc/orthanc-anon/docs/assets/README.md b/orthanc/orthanc-anon/docs/assets/README.md index 74938b342..484b4f3e3 100644 --- a/orthanc/orthanc-anon/docs/assets/README.md +++ b/orthanc/orthanc-anon/docs/assets/README.md @@ -1,4 +1,4 @@ -## 'assets' Directory Contents +## 'PIXL/orthanc/orthanc-anon/docs/assets' Directory Contents ### Files diff --git a/orthanc/orthanc-anon/plugin/README.md b/orthanc/orthanc-anon/plugin/README.md index a39e61831..6f5c0eba0 100644 --- a/orthanc/orthanc-anon/plugin/README.md +++ b/orthanc/orthanc-anon/plugin/README.md @@ -1,4 +1,4 @@ -## 'plugin' Directory Contents +## 'PIXL/orthanc/orthanc-anon/plugin' Directory Contents ### Files diff --git a/orthanc/orthanc-anon/toc.md b/orthanc/orthanc-anon/toc.md deleted file mode 100644 index 4f4278757..000000000 --- a/orthanc/orthanc-anon/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'orthanc-anon' Directory Contents - -### Subdirectories - -[config](./config/README.md) - -[docs](./docs/README.md) - -[plugin](./plugin/README.md) - -### Files - -README.md - diff --git a/orthanc/orthanc-raw/README.md b/orthanc/orthanc-raw/README.md index eec29a5a0..2e695cc3a 100644 --- a/orthanc/orthanc-raw/README.md +++ b/orthanc/orthanc-raw/README.md @@ -110,3 +110,16 @@ team. ## References - [Cheat sheet of the REST API](https://book.orthanc-server.com/users/rest-cheatsheet.html) + +## 'PIXL/orthanc/orthanc-raw' Directory Contents + +### Subdirectories + +[config](./config/README.md) + +[plugin](./plugin/README.md) + +### Files + +README.md + diff --git a/orthanc/orthanc-raw/config/README.md b/orthanc/orthanc-raw/config/README.md index b384c23c7..6d345e63e 100644 --- a/orthanc/orthanc-raw/config/README.md +++ b/orthanc/orthanc-raw/config/README.md @@ -1,4 +1,4 @@ -## 'config' Directory Contents +## 'PIXL/orthanc/orthanc-raw/config' Directory Contents ### Files diff --git a/orthanc/orthanc-raw/plugin/README.md b/orthanc/orthanc-raw/plugin/README.md index 26e9667d2..bfebf0781 100644 --- a/orthanc/orthanc-raw/plugin/README.md +++ b/orthanc/orthanc-raw/plugin/README.md @@ -1,4 +1,4 @@ -## 'plugin' Directory Contents +## 'PIXL/orthanc/orthanc-raw/plugin' Directory Contents ### Files diff --git a/orthanc/orthanc-raw/toc.md b/orthanc/orthanc-raw/toc.md deleted file mode 100644 index fdceef2fa..000000000 --- a/orthanc/orthanc-raw/toc.md +++ /dev/null @@ -1,12 +0,0 @@ -## 'orthanc-raw' Directory Contents - -### Subdirectories - -[config](./config/README.md) - -[plugin](./plugin/README.md) - -### Files - -README.md - diff --git a/orthanc/toc.md b/orthanc/toc.md deleted file mode 100644 index 217f0294e..000000000 --- a/orthanc/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'orthanc' Directory Contents - -### Subdirectories - -[assets](./assets/README.md) - -[orthanc-anon](./orthanc-anon/README.md) - -[orthanc-raw](./orthanc-raw/README.md) - -### Files - -README.md - From d60c426720709b8a362578c6e28add03bbaea191 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 19 Nov 2024 15:10:08 +0000 Subject: [PATCH 07/18] making readme and table of contents consistent --- pixl_core/README.md | 15 +++++++++++++++ pixl_core/src/README.md | 2 +- pixl_core/src/core/README.md | 2 +- pixl_core/src/core/db/README.md | 2 +- pixl_core/src/core/patient_queue/README.md | 2 +- pixl_core/src/core/project_config/README.md | 2 +- pixl_core/src/core/rest_api/README.md | 2 +- pixl_core/src/core/token_buffer/README.md | 2 +- pixl_core/src/core/uploader/README.md | 2 +- pixl_core/tests/README.md | 2 +- pixl_core/tests/data/README.md | 2 +- pixl_core/tests/patient_queue/README.md | 2 +- pixl_core/tests/project_config/README.md | 2 +- pixl_core/tests/token_buffer/README.md | 2 +- pixl_core/tests/uploader/README.md | 2 +- pixl_core/toc.md | 14 -------------- 16 files changed, 29 insertions(+), 28 deletions(-) delete mode 100644 pixl_core/toc.md diff --git a/pixl_core/README.md b/pixl_core/README.md index 8116ba49e..5b9f784fb 100644 --- a/pixl_core/README.md +++ b/pixl_core/README.md @@ -234,3 +234,18 @@ Note, it can take several minutes for the server to start up. Once the server has started, you can log in by visiting `http://localhost:8080` with the username and password set in the `XNAT_USER_NAME` and `XNAT_PASSWORD` environment variables. + +## 'PIXL/pixl_core' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_core/src/README.md b/pixl_core/src/README.md index fc88e8f53..56763ccf2 100644 --- a/pixl_core/src/README.md +++ b/pixl_core/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/pixl_core/src' Directory Contents ### Subdirectories diff --git a/pixl_core/src/core/README.md b/pixl_core/src/core/README.md index c23e4c11a..c450b32c7 100644 --- a/pixl_core/src/core/README.md +++ b/pixl_core/src/core/README.md @@ -1,4 +1,4 @@ -## 'core' Directory Contents +## 'PIXL/pixl_core/src/core' Directory Contents ### Subdirectories diff --git a/pixl_core/src/core/db/README.md b/pixl_core/src/core/db/README.md index ddb128131..2b3e187dd 100644 --- a/pixl_core/src/core/db/README.md +++ b/pixl_core/src/core/db/README.md @@ -1,4 +1,4 @@ -## 'db' Directory Contents +## 'PIXL/pixl_core/src/core/db' Directory Contents ### Files diff --git a/pixl_core/src/core/patient_queue/README.md b/pixl_core/src/core/patient_queue/README.md index 25457ba5c..f53cead1f 100644 --- a/pixl_core/src/core/patient_queue/README.md +++ b/pixl_core/src/core/patient_queue/README.md @@ -1,4 +1,4 @@ -## 'patient_queue' Directory Contents +## 'PIXL/pixl_core/src/core/patient_queue' Directory Contents ### Files diff --git a/pixl_core/src/core/project_config/README.md b/pixl_core/src/core/project_config/README.md index ecd68cfc5..4a8232810 100644 --- a/pixl_core/src/core/project_config/README.md +++ b/pixl_core/src/core/project_config/README.md @@ -1,4 +1,4 @@ -## 'project_config' Directory Contents +## 'PIXL/pixl_core/src/core/project_config' Directory Contents ### Files diff --git a/pixl_core/src/core/rest_api/README.md b/pixl_core/src/core/rest_api/README.md index 2f2158655..2d481757b 100644 --- a/pixl_core/src/core/rest_api/README.md +++ b/pixl_core/src/core/rest_api/README.md @@ -1,4 +1,4 @@ -## 'rest_api' Directory Contents +## 'PIXL/pixl_core/src/core/rest_api' Directory Contents ### Files diff --git a/pixl_core/src/core/token_buffer/README.md b/pixl_core/src/core/token_buffer/README.md index 59006b80a..d25fd7b64 100644 --- a/pixl_core/src/core/token_buffer/README.md +++ b/pixl_core/src/core/token_buffer/README.md @@ -1,4 +1,4 @@ -## 'token_buffer' Directory Contents +## 'PIXL/pixl_core/src/core/token_buffer' Directory Contents ### Files diff --git a/pixl_core/src/core/uploader/README.md b/pixl_core/src/core/uploader/README.md index fd0c364be..1a0e6a444 100644 --- a/pixl_core/src/core/uploader/README.md +++ b/pixl_core/src/core/uploader/README.md @@ -1,4 +1,4 @@ -## 'uploader' Directory Contents +## 'PIXL/pixl_core/src/core/uploader' Directory Contents ### Files diff --git a/pixl_core/tests/README.md b/pixl_core/tests/README.md index 60978a4c5..621d1b3c7 100644 --- a/pixl_core/tests/README.md +++ b/pixl_core/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/pixl_core/tests' Directory Contents ### Subdirectories diff --git a/pixl_core/tests/data/README.md b/pixl_core/tests/data/README.md index 16da4c31e..065c917e7 100644 --- a/pixl_core/tests/data/README.md +++ b/pixl_core/tests/data/README.md @@ -1,4 +1,4 @@ -## 'data' Directory Contents +## 'PIXL/pixl_core/tests/data' Directory Contents ### Files diff --git a/pixl_core/tests/patient_queue/README.md b/pixl_core/tests/patient_queue/README.md index 0d64a43fc..895a4d9fc 100644 --- a/pixl_core/tests/patient_queue/README.md +++ b/pixl_core/tests/patient_queue/README.md @@ -1,4 +1,4 @@ -## 'patient_queue' Directory Contents +## 'PIXL/pixl_core/tests/patient_queue' Directory Contents ### Files diff --git a/pixl_core/tests/project_config/README.md b/pixl_core/tests/project_config/README.md index 6e5df5eab..eb889f4e8 100644 --- a/pixl_core/tests/project_config/README.md +++ b/pixl_core/tests/project_config/README.md @@ -1,4 +1,4 @@ -## 'project_config' Directory Contents +## 'PIXL/pixl_core/tests/project_config' Directory Contents ### Files diff --git a/pixl_core/tests/token_buffer/README.md b/pixl_core/tests/token_buffer/README.md index 9027983ab..259ef6888 100644 --- a/pixl_core/tests/token_buffer/README.md +++ b/pixl_core/tests/token_buffer/README.md @@ -1,4 +1,4 @@ -## 'token_buffer' Directory Contents +## 'PIXL/pixl_core/tests/token_buffer' Directory Contents ### Files diff --git a/pixl_core/tests/uploader/README.md b/pixl_core/tests/uploader/README.md index 4ff10f374..e960568d5 100644 --- a/pixl_core/tests/uploader/README.md +++ b/pixl_core/tests/uploader/README.md @@ -1,4 +1,4 @@ -## 'uploader' Directory Contents +## 'PIXL/pixl_core/tests/uploader' Directory Contents ### Files diff --git a/pixl_core/toc.md b/pixl_core/toc.md deleted file mode 100644 index 7844ef0ad..000000000 --- a/pixl_core/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'pixl_core' Directory Contents - -### Subdirectories - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - From 2cf4837db194240192cd49a7ad2c46f7d0bf81c9 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 19 Nov 2024 15:50:38 +0000 Subject: [PATCH 08/18] making read me and table of contents consistent --- pixl_dcmd/README.md | 15 +++++++++ pixl_dcmd/src/README.md | 2 +- pixl_dcmd/src/pixl_dcmd/README.md | 2 +- pixl_dcmd/src/pixl_dcmd/resources/README.md | 2 +- pixl_dcmd/tests/README.md | 2 +- pixl_dcmd/toc.md | 14 --------- pixl_export/README.md | 15 +++++++++ pixl_export/src/README.md | 2 +- pixl_export/src/pixl_export/README.md | 2 +- pixl_export/tests/README.md | 2 +- pixl_export/toc.md | 14 --------- pixl_imaging/README.md | 19 ++++++++++++ pixl_imaging/alembic/README.md | 21 +++++++++++++ pixl_imaging/alembic/toc.md | 20 ------------ pixl_imaging/alembic/versions/README.md | 2 +- pixl_imaging/scripts/README.md | 2 +- pixl_imaging/src/README.md | 2 +- pixl_imaging/src/pixl_imaging/README.md | 2 +- pixl_imaging/tests/README.md | 2 +- .../tests/orthanc_raw_config/README.md | 2 +- pixl_imaging/toc.md | 18 ----------- postgres/README.md | 11 +++++++ postgres/toc.md | 10 ------ projects/README.md | 2 +- projects/configs/README.md | 2 +- projects/configs/tag-operations/README.md | 2 +- pytest-pixl/README.md | 16 ++++++++++ pytest-pixl/scripts/README.md | 2 +- pytest-pixl/src/README.md | 2 +- pytest-pixl/src/pytest_pixl/README.md | 2 +- pytest-pixl/src/pytest_pixl/data/README.md | 2 +- pytest-pixl/src/resources/README.md | 2 +- pytest-pixl/src/resources/ssl/README.md | 2 +- pytest-pixl/tests/README.md | 2 +- .../tests/samples_for_fixture_tests/README.md | 2 +- .../test_ftpserver_fixture/README.md | 2 +- pytest-pixl/toc.md | 16 ---------- schemas/README.md | 2 +- scripts/README.md | 2 +- test/README.md | 31 +++++++++++++++++++ test/dicomweb_config/README.md | 2 +- test/resources/README.md | 2 +- test/resources/omop/README.md | 2 +- test/resources/omop/private/README.md | 2 +- test/resources/omop/public/README.md | 2 +- test/toc.md | 30 ------------------ test/vna_config/README.md | 2 +- 47 files changed, 161 insertions(+), 155 deletions(-) delete mode 100644 pixl_dcmd/toc.md delete mode 100644 pixl_export/toc.md delete mode 100644 pixl_imaging/alembic/toc.md delete mode 100644 pixl_imaging/toc.md delete mode 100644 postgres/toc.md delete mode 100644 pytest-pixl/toc.md delete mode 100644 test/toc.md diff --git a/pixl_dcmd/README.md b/pixl_dcmd/README.md index daa9d8ec3..a614e865d 100644 --- a/pixl_dcmd/README.md +++ b/pixl_dcmd/README.md @@ -58,3 +58,18 @@ and optionally a `manufacturer_overrides`. If a `manufacturer_overrides` is defined, it will be used to override the `base` tags, if the manufacturer of the DICOM file matches the manufacturer in the `manufacturer_overrides`. Any tags in the `manufacturer_overrides` that are not in the `base` will be added to the scheme as well. + +## 'PIXL/pixl_dcmd' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_dcmd/src/README.md b/pixl_dcmd/src/README.md index e41c2e20f..2ba0cd0e1 100644 --- a/pixl_dcmd/src/README.md +++ b/pixl_dcmd/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/pixl_dcmd/src' Directory Contents ### Subdirectories diff --git a/pixl_dcmd/src/pixl_dcmd/README.md b/pixl_dcmd/src/pixl_dcmd/README.md index db8089521..e94fbfd07 100644 --- a/pixl_dcmd/src/pixl_dcmd/README.md +++ b/pixl_dcmd/src/pixl_dcmd/README.md @@ -1,4 +1,4 @@ -## 'pixl_dcmd' Directory Contents +## 'PIXL/pixl_dcmd/src/pixl_dcmd' Directory Contents ### Subdirectories diff --git a/pixl_dcmd/src/pixl_dcmd/resources/README.md b/pixl_dcmd/src/pixl_dcmd/resources/README.md index 60b1932f2..b6d19ecc6 100644 --- a/pixl_dcmd/src/pixl_dcmd/resources/README.md +++ b/pixl_dcmd/src/pixl_dcmd/resources/README.md @@ -1,4 +1,4 @@ -## 'resources' Directory Contents +## 'PIXL/pixl_dcmd/src/pixl_dcmd/resources' Directory Contents ### Files diff --git a/pixl_dcmd/tests/README.md b/pixl_dcmd/tests/README.md index c1fd46fa3..9f05da066 100644 --- a/pixl_dcmd/tests/README.md +++ b/pixl_dcmd/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/pixl_dcmd/tests' Directory Contents ### Files diff --git a/pixl_dcmd/toc.md b/pixl_dcmd/toc.md deleted file mode 100644 index e52595be5..000000000 --- a/pixl_dcmd/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'pixl_dcmd' Directory Contents - -### Subdirectories - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/pixl_export/README.md b/pixl_export/README.md index 9e34f283e..89481df38 100644 --- a/pixl_export/README.md +++ b/pixl_export/README.md @@ -43,3 +43,18 @@ Usage should be from the CLI driver, which calls the HTTP endpoints. ## Notes - The height/weight/GCS value is extracted only within a 24 h time window + +## 'PIXL/pixl_export' Directory Contents + +### Subdirectories + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_export/src/README.md b/pixl_export/src/README.md index b501220d1..06ab4efea 100644 --- a/pixl_export/src/README.md +++ b/pixl_export/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/pixl_export/src' Directory Contents ### Subdirectories diff --git a/pixl_export/src/pixl_export/README.md b/pixl_export/src/pixl_export/README.md index 285f38516..c21da40db 100644 --- a/pixl_export/src/pixl_export/README.md +++ b/pixl_export/src/pixl_export/README.md @@ -1,4 +1,4 @@ -## 'pixl_export' Directory Contents +## 'PIXL/pixl_export/src/pixl_export' Directory Contents ### Files diff --git a/pixl_export/tests/README.md b/pixl_export/tests/README.md index c80cd9e4e..607a81078 100644 --- a/pixl_export/tests/README.md +++ b/pixl_export/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/pixl_export/tests' Directory Contents ### Files diff --git a/pixl_export/toc.md b/pixl_export/toc.md deleted file mode 100644 index 71a39a35d..000000000 --- a/pixl_export/toc.md +++ /dev/null @@ -1,14 +0,0 @@ -## 'pixl_export' Directory Contents - -### Subdirectories - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/pixl_imaging/README.md b/pixl_imaging/README.md index 9f3419db8..26463b37c 100644 --- a/pixl_imaging/README.md +++ b/pixl_imaging/README.md @@ -60,3 +60,22 @@ The `SKIP_ALEMBIC` environmental variable is used to control whether migrations - `SKIP_ALEMBIC` is set to true for tests that do not use the database (e.g. `SKIP_ALEMBIC=true`). Otherwise you probably want to run this. - If you wanted to test out new migrations from a test/dev deployment on the GAE with data in, then you can redeploy just the `imaging-api` container while keeping the `postgres` container up. + +## 'PIXL/pixl_imaging' Directory Contents + +### Subdirectories + +[alembic](./alembic/README.md) + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pixl_imaging/alembic/README.md b/pixl_imaging/alembic/README.md index fa1a34d83..d7054661f 100644 --- a/pixl_imaging/alembic/README.md +++ b/pixl_imaging/alembic/README.md @@ -29,3 +29,24 @@ There's a couple of manual steps: - Check the changes autogenerated and update to match your intention - Commit the changes and review in a pull request as normal + +## 'PIXL/pixl_imaging/alembic' Directory Contents + +### Subdirectories + +[versions](./versions/README.md) + +### Files + +alembic.ini + +autogenerate-migration.sh + +env.py + +migrations.env + +README.md + +script.py.mako + diff --git a/pixl_imaging/alembic/toc.md b/pixl_imaging/alembic/toc.md deleted file mode 100644 index 812d7f9ca..000000000 --- a/pixl_imaging/alembic/toc.md +++ /dev/null @@ -1,20 +0,0 @@ -## 'alembic' Directory Contents - -### Subdirectories - -[versions](./versions/README.md) - -### Files - -alembic.ini - -autogenerate-migration.sh - -env.py - -migrations.env - -README.md - -script.py.mako - diff --git a/pixl_imaging/alembic/versions/README.md b/pixl_imaging/alembic/versions/README.md index 0a2a9f02a..ea043622a 100644 --- a/pixl_imaging/alembic/versions/README.md +++ b/pixl_imaging/alembic/versions/README.md @@ -1,4 +1,4 @@ -## 'versions' Directory Contents +## 'PIXL/pixl_imaging/alembic/versions' Directory Contents ### Files diff --git a/pixl_imaging/scripts/README.md b/pixl_imaging/scripts/README.md index ca833da88..afd8a5659 100644 --- a/pixl_imaging/scripts/README.md +++ b/pixl_imaging/scripts/README.md @@ -1,4 +1,4 @@ -## 'scripts' Directory Contents +## 'PIXL/pixl_imaging/scripts' Directory Contents ### Files diff --git a/pixl_imaging/src/README.md b/pixl_imaging/src/README.md index adb442a5f..a8f1b4ac5 100644 --- a/pixl_imaging/src/README.md +++ b/pixl_imaging/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/pixl_imaging/src' Directory Contents ### Subdirectories diff --git a/pixl_imaging/src/pixl_imaging/README.md b/pixl_imaging/src/pixl_imaging/README.md index bc6dd139e..8250982db 100644 --- a/pixl_imaging/src/pixl_imaging/README.md +++ b/pixl_imaging/src/pixl_imaging/README.md @@ -1,4 +1,4 @@ -## 'pixl_imaging' Directory Contents +## 'PIXL/pixl_imaging/src/pixl_imaging' Directory Contents ### Files diff --git a/pixl_imaging/tests/README.md b/pixl_imaging/tests/README.md index d3f574bd9..8903dd81c 100644 --- a/pixl_imaging/tests/README.md +++ b/pixl_imaging/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/pixl_imaging/tests' Directory Contents ### Subdirectories diff --git a/pixl_imaging/tests/orthanc_raw_config/README.md b/pixl_imaging/tests/orthanc_raw_config/README.md index b8d893380..3b95d29ca 100644 --- a/pixl_imaging/tests/orthanc_raw_config/README.md +++ b/pixl_imaging/tests/orthanc_raw_config/README.md @@ -1,4 +1,4 @@ -## 'orthanc_raw_config' Directory Contents +## 'PIXL/pixl_imaging/tests/orthanc_raw_config' Directory Contents ### Files diff --git a/pixl_imaging/toc.md b/pixl_imaging/toc.md deleted file mode 100644 index 5d0eb87e0..000000000 --- a/pixl_imaging/toc.md +++ /dev/null @@ -1,18 +0,0 @@ -## 'pixl_imaging' Directory Contents - -### Subdirectories - -[alembic](./alembic/README.md) - -[scripts](./scripts/README.md) - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/postgres/README.md b/postgres/README.md index b161ebf78..e532b9469 100644 --- a/postgres/README.md +++ b/postgres/README.md @@ -5,3 +5,14 @@ container and the pixl_imaging api uses [alembic](https://alembic.sqlalchemy.org This allows a reproducible way to update (or rollback) alterations to the PIXL pipeline's database schema. See [/pixl_imaging/alembic](../pixl_imaging/alembic) for how these are defined and how to create new migrations. + +## 'PIXL/postgres' Directory Contents + +### Files + +pixl-db_init.sh + +postgres.conf + +README.md + diff --git a/postgres/toc.md b/postgres/toc.md deleted file mode 100644 index f5aa398e9..000000000 --- a/postgres/toc.md +++ /dev/null @@ -1,10 +0,0 @@ -## 'postgres' Directory Contents - -### Files - -pixl-db_init.sh - -postgres.conf - -README.md - diff --git a/projects/README.md b/projects/README.md index 258b199f7..dcfdcd654 100644 --- a/projects/README.md +++ b/projects/README.md @@ -1,4 +1,4 @@ -## 'projects' Directory Contents +## 'PIXL/projects' Directory Contents ### Subdirectories diff --git a/projects/configs/README.md b/projects/configs/README.md index 97778a273..351680b9b 100644 --- a/projects/configs/README.md +++ b/projects/configs/README.md @@ -1,4 +1,4 @@ -## 'configs' Directory Contents +## 'PIXL/projects/configs' Directory Contents ### Subdirectories diff --git a/projects/configs/tag-operations/README.md b/projects/configs/tag-operations/README.md index bc2e06419..83c53c681 100644 --- a/projects/configs/tag-operations/README.md +++ b/projects/configs/tag-operations/README.md @@ -1,4 +1,4 @@ -## 'tag-operations' Directory Contents +## 'PIXL/projects/configs/tag-operations' Directory Contents ### Subdirectories diff --git a/pytest-pixl/README.md b/pytest-pixl/README.md index 4c4e9666e..30c8c4c21 100644 --- a/pytest-pixl/README.md +++ b/pytest-pixl/README.md @@ -102,3 +102,19 @@ default DICOM tag values used to generate fake DICOM data in `generate_dicom_dat The JSON file was created by running [`scripts/create_default_dicom_tags_json.py`](./scripts/create_default_dicom_tags_json.py), with the details implemented in [`pytest_pixl.dicom._create_default_json`](./src/pytest_pixl/dicom.py). +## 'PIXL/pytest-pixl' Directory Contents + +### Subdirectories + +[scripts](./scripts/README.md) + +[src](./src/README.md) + +[tests](./tests/README.md) + +### Files + +pyproject.toml + +README.md + diff --git a/pytest-pixl/scripts/README.md b/pytest-pixl/scripts/README.md index 6dfa6cf99..65085443d 100644 --- a/pytest-pixl/scripts/README.md +++ b/pytest-pixl/scripts/README.md @@ -1,4 +1,4 @@ -## 'scripts' Directory Contents +## 'PIXL/pytest-pixl/scripts' Directory Contents ### Files diff --git a/pytest-pixl/src/README.md b/pytest-pixl/src/README.md index aa0b1d86b..138dffa26 100644 --- a/pytest-pixl/src/README.md +++ b/pytest-pixl/src/README.md @@ -1,4 +1,4 @@ -## 'src' Directory Contents +## 'PIXL/pytest-pixl/src' Directory Contents ### Subdirectories diff --git a/pytest-pixl/src/pytest_pixl/README.md b/pytest-pixl/src/pytest_pixl/README.md index 1a7997f1a..98744d18c 100644 --- a/pytest-pixl/src/pytest_pixl/README.md +++ b/pytest-pixl/src/pytest_pixl/README.md @@ -1,4 +1,4 @@ -## 'pytest_pixl' Directory Contents +## 'PIXL/pytest-pixl/src/pytest_pixl' Directory Contents ### Subdirectories diff --git a/pytest-pixl/src/pytest_pixl/data/README.md b/pytest-pixl/src/pytest_pixl/data/README.md index 067cc9833..cfa58b0bb 100644 --- a/pytest-pixl/src/pytest_pixl/data/README.md +++ b/pytest-pixl/src/pytest_pixl/data/README.md @@ -1,4 +1,4 @@ -## 'data' Directory Contents +## 'PIXL/pytest-pixl/src/pytest_pixl/data' Directory Contents ### Subdirectories diff --git a/pytest-pixl/src/resources/README.md b/pytest-pixl/src/resources/README.md index 2191a688c..8c118dc40 100644 --- a/pytest-pixl/src/resources/README.md +++ b/pytest-pixl/src/resources/README.md @@ -1,4 +1,4 @@ -## 'resources' Directory Contents +## 'PIXL/pytest-pixl/src/resources' Directory Contents ### Subdirectories diff --git a/pytest-pixl/src/resources/ssl/README.md b/pytest-pixl/src/resources/ssl/README.md index 4b01d4bd4..20c619682 100644 --- a/pytest-pixl/src/resources/ssl/README.md +++ b/pytest-pixl/src/resources/ssl/README.md @@ -1,4 +1,4 @@ -## 'ssl' Directory Contents +## 'PIXL/pytest-pixl/src/resources/ssl' Directory Contents ### Files diff --git a/pytest-pixl/tests/README.md b/pytest-pixl/tests/README.md index 3254ed84f..d7c2900b2 100644 --- a/pytest-pixl/tests/README.md +++ b/pytest-pixl/tests/README.md @@ -1,4 +1,4 @@ -## 'tests' Directory Contents +## 'PIXL/pytest-pixl/tests' Directory Contents ### Subdirectories diff --git a/pytest-pixl/tests/samples_for_fixture_tests/README.md b/pytest-pixl/tests/samples_for_fixture_tests/README.md index bef9031dd..ee9d21902 100644 --- a/pytest-pixl/tests/samples_for_fixture_tests/README.md +++ b/pytest-pixl/tests/samples_for_fixture_tests/README.md @@ -1,4 +1,4 @@ -## 'samples_for_fixture_tests' Directory Contents +## 'PIXL/pytest-pixl/tests/samples_for_fixture_tests' Directory Contents ### Subdirectories diff --git a/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md index 86072e2d4..06effc923 100644 --- a/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md +++ b/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture/README.md @@ -1,4 +1,4 @@ -## 'test_ftpserver_fixture' Directory Contents +## 'PIXL/pytest-pixl/tests/samples_for_fixture_tests/test_ftpserver_fixture' Directory Contents ### Files diff --git a/pytest-pixl/toc.md b/pytest-pixl/toc.md deleted file mode 100644 index 819de9cf4..000000000 --- a/pytest-pixl/toc.md +++ /dev/null @@ -1,16 +0,0 @@ -## 'pytest-pixl' Directory Contents - -### Subdirectories - -[scripts](./scripts/README.md) - -[src](./src/README.md) - -[tests](./tests/README.md) - -### Files - -pyproject.toml - -README.md - diff --git a/schemas/README.md b/schemas/README.md index db3679245..432a9cc7b 100644 --- a/schemas/README.md +++ b/schemas/README.md @@ -1,4 +1,4 @@ -## 'schemas' Directory Contents +## 'PIXL/schemas' Directory Contents ### Files diff --git a/scripts/README.md b/scripts/README.md index 508753508..26ff995a3 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -1,4 +1,4 @@ -## 'scripts' Directory Contents +## 'PIXL/scripts' Directory Contents ### Files diff --git a/test/README.md b/test/README.md index c27c70748..b1c25278f 100644 --- a/test/README.md +++ b/test/README.md @@ -69,3 +69,34 @@ but configured to upload to a [DICOMweb server](#dicomweb-config) ### DICOMWeb config `./dicomweb_config/` contains the Orthanc configuration files for the mock [DICOMweb server](../docs/services/dicomweb-server.md). + +## 'PIXL/test' Directory Contents + +### Subdirectories + +[dicomweb_config](./dicomweb_config/README.md) + +[resources](./resources/README.md) + +[vna_config](./vna_config/README.md) + +### Files + +.env + +.secrets.env.sample + +conftest.py + +docker-compose.yml + +README.md + +run-system-test.sh + +system_test.py + +test_parquet_exports.py + +utils.py + diff --git a/test/dicomweb_config/README.md b/test/dicomweb_config/README.md index 6ce0b6905..41729879a 100644 --- a/test/dicomweb_config/README.md +++ b/test/dicomweb_config/README.md @@ -1,4 +1,4 @@ -## 'dicomweb_config' Directory Contents +## 'PIXL/test/dicomweb_config' Directory Contents ### Files diff --git a/test/resources/README.md b/test/resources/README.md index 2f49e5556..132dcb141 100644 --- a/test/resources/README.md +++ b/test/resources/README.md @@ -1,4 +1,4 @@ -## 'resources' Directory Contents +## 'PIXL/test/resources' Directory Contents ### Subdirectories diff --git a/test/resources/omop/README.md b/test/resources/omop/README.md index e5d45c492..f8f0010b4 100644 --- a/test/resources/omop/README.md +++ b/test/resources/omop/README.md @@ -1,4 +1,4 @@ -## 'omop' Directory Contents +## 'PIXL/test/resources/omop' Directory Contents ### Subdirectories diff --git a/test/resources/omop/private/README.md b/test/resources/omop/private/README.md index 2e47873ed..d0082ec64 100644 --- a/test/resources/omop/private/README.md +++ b/test/resources/omop/private/README.md @@ -1,4 +1,4 @@ -## 'private' Directory Contents +## 'PIXL/test/resources/omop/private' Directory Contents ### Files diff --git a/test/resources/omop/public/README.md b/test/resources/omop/public/README.md index d35e10141..be9075cd4 100644 --- a/test/resources/omop/public/README.md +++ b/test/resources/omop/public/README.md @@ -1,4 +1,4 @@ -## 'public' Directory Contents +## 'PIXL/test/resources/omop/public' Directory Contents ### Files diff --git a/test/toc.md b/test/toc.md deleted file mode 100644 index a60d7990a..000000000 --- a/test/toc.md +++ /dev/null @@ -1,30 +0,0 @@ -## 'test' Directory Contents - -### Subdirectories - -[dicomweb_config](./dicomweb_config/README.md) - -[resources](./resources/README.md) - -[vna_config](./vna_config/README.md) - -### Files - -.env - -.secrets.env.sample - -conftest.py - -docker-compose.yml - -README.md - -run-system-test.sh - -system_test.py - -test_parquet_exports.py - -utils.py - diff --git a/test/vna_config/README.md b/test/vna_config/README.md index d34408991..ee4cd9d44 100644 --- a/test/vna_config/README.md +++ b/test/vna_config/README.md @@ -1,4 +1,4 @@ -## 'vna_config' Directory Contents +## 'PIXL/test/vna_config' Directory Contents ### Files From 0e779997daaed77143d5e59bd5ce38ca651362c0 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 10:19:59 +0000 Subject: [PATCH 09/18] deleting this as it becomes the default --- .github/README.md | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 .github/README.md diff --git a/.github/README.md b/.github/README.md deleted file mode 100644 index a69bc55f0..000000000 --- a/.github/README.md +++ /dev/null @@ -1,12 +0,0 @@ -## '.github' Directory Contents - -### Subdirectories - -[ISSUE_TEMPLATE](./ISSUE_TEMPLATE/README.md) - -[workflows](./workflows/README.md) - -### Files - -pull_request_template.md - From 1e033e1000091921aad007fe31a9c6e9590001c0 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 10:28:39 +0000 Subject: [PATCH 10/18] a public repo cannot access a private repo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b5040e4a6..bc4841f8e 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. -Please see the [rolling-skeleton]([https://github.com/SAFEHR-data/the-rolling-skeleton=](https://github.com/SAFEHR-data/the-rolling-skeleton/blob/main/docs/design/100-day-design.md)) for more details. + PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). From 8d93e28339e89d6d25b2c0ed872faaaccb74f2b7 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 10:56:29 +0000 Subject: [PATCH 11/18] highlight UCLH specific instructions --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index bc4841f8e..eb4f5771d 100644 --- a/README.md +++ b/README.md @@ -7,11 +7,11 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. - -PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises +>[!UCLH SPECIFIC] +>PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). -To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). +>To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). ## Installation From b020ac8d587a876f1d8801087b474ae7bbb09752 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 10:58:54 +0000 Subject: [PATCH 12/18] trying to highlight specific --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index eb4f5771d..119c70698 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. ->[!UCLH SPECIFIC] +>[!NOTE] >PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). From 90363abf37ae0b40e95fb82674b760a9b22ce49e Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 13:21:05 +0000 Subject: [PATCH 13/18] still trying to highlight UCLH specific information --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 119c70698..2130af99c 100644 --- a/README.md +++ b/README.md @@ -8,10 +8,10 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. >[!NOTE] ->PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises +>UCLH SPECIFIC +PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). - ->To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). +To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). ## Installation From 8ca4e90d5b6522a91f213b1649bd2ae3f4475c19 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 15:40:20 +0000 Subject: [PATCH 14/18] make the read me not specific to UCLH --- README.md | 31 ++++++++++++++++++++----------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 2130af99c..db9c03c5b 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,18 @@ PIXL Image eXtraction Laboratory `PIXL` is a system for extracting, linking and de-identifying DICOM imaging data, structured EHR data and free-text data from radiology reports at UCLH. ->[!NOTE] ->UCLH SPECIFIC -PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s and comprises -several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). +It comprises several services orchestrated by [Docker Compose](https://docs.docker.com/compose/). + +
UCLH SPECIFIC + +PIXL is intended run on one of the [GAE (General Application Environments)](https://github.com/SAFEHR-data/Book-of-FlowEHR/blob/main/glossary.md#gaes)s. + To get access to the GAE, [see the documentation on Slab](https://uclh.slab.com/posts/gae-access-7hkddxap). -Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). + +Please request access to Slab and add further details in a [new blank issue](https://github.com/SAFEHR-data/PIXL/issues/new). + +
+ ## Installation @@ -67,7 +73,7 @@ destination. Provides helper functions for de-identifying DICOM data -### PostgreSQL +### [PostgreSQL](.postgres/README.md) RDBMS which stores DICOM metadata, application data and anonymised patient record data. @@ -79,7 +85,7 @@ HTTP API to export files (parquet and DICOM) from UCLH to endpoints. HTTP API to process messages from the `imaging` queue and populate the raw orthanc instance with images from PACS/VNA. -## Setup `PIXL` in GAE +## Setup `PIXL`
Click here to expand steps and configurations @@ -202,7 +208,7 @@ These variables can be set in the `.env` file. For testing, they can be set in the `test/.secrets.env` file. For dev purposes find the `pixl-dev-secrets.env` note on LastPass for the necessary values. -If an Azure Keyvault hasn't been set up yet, follow [these instructions](./docs/setup/azure-keyvault.md). +At UCLH if an Azure Keyvault hasn't been set up yet, follow [these instructions](./docs/setup/azure-keyvault.md). A second Azure Keyvault is used to store hashing keys and salts for the `hasher` service. This kevyault is configured with the following environment variables: @@ -218,7 +224,7 @@ See the [hasher documentation](./hasher/README.md) for more information.
-## Run `PIXL` in GAE +## Run `PIXL`
Click here to view detailed steps @@ -278,6 +284,9 @@ test/resources/omop/public /*.parquet ### OMOP ES extract dir (input to PIXL) +>[!NOTE] +> OMOP ES is the tool used to extract Electronic Health Records that may be linked to images. + EXTRACT_DIR is the directory passed to `pixl populate` as the input `PARQUET_PATH` argument. ``` @@ -288,8 +297,8 @@ EXTRACT_DIR/public /*.parquet ### PIXL Export dir (PIXL intermediate) -The directory where PIXL will copy the public OMOP extract files (which now contain -the radiology reports) to. +The directory where PIXL will copy the public OMOP extract files and the radiology reports. + These files will subsequently be uploaded to the `parquet` destination specified in the [project config](#3-configure-a-new-project). From 7fa6df17b80984b8a40167cab97aa34ff1f7bbb4 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 15:46:17 +0000 Subject: [PATCH 15/18] I don't think this is relevant --- README.md | 7 ------- 1 file changed, 7 deletions(-) diff --git a/README.md b/README.md index db9c03c5b..c4b54296b 100644 --- a/README.md +++ b/README.md @@ -319,13 +319,6 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet ..............................................omop/public/*.parquet ``` -## :octocat: Cloning repository -* Generate your SSH keys as suggested [here](https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) -* Clone the repository by typing (or copying) the following lines in a terminal -``` -git clone git@github.com:SAFEHR-data/PIXL.git -``` - ## 'PIXL' Directory Contents ### Subdirectories From b6232741e1e0bdbdbcf0e58672af3b62826a01e1 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Tue, 26 Nov 2024 16:15:14 +0000 Subject: [PATCH 16/18] testing a theory ifthe syntax works --- README.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c4b54296b..e13f32624 100644 --- a/README.md +++ b/README.md @@ -321,11 +321,13 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet ## 'PIXL' Directory Contents -### Subdirectories +
+ + +

Subdirectories with links to the relevant README

-[.git](./.git/README.md) + -[.github](./.github/README.md) [bin](./bin/README.md) @@ -358,7 +360,7 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet [scripts](./scripts/README.md) [test](./test/README.md) - +
### Files .env.sample From 6b6ff98f78c5dc04490906b431b9994dbc70f5ff Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Wed, 27 Nov 2024 15:26:02 +0000 Subject: [PATCH 17/18] make files a neat list --- README.md | 44 +++++++++++++++----------------------------- 1 file changed, 15 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index e13f32624..ade5b6ca9 100644 --- a/README.md +++ b/README.md @@ -361,35 +361,21 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet [test](./test/README.md)
-### Files - -.env.sample - -.gitignore - -.pre-commit-config.yaml - -.renovaterc.json5 - -codecov.yml - -CODE_OF_CONDUCT.md - -CONTRIBUTING.md - -docker-compose.yml - -LICENSE - -mypy.ini - -NOTICE - -pytest.ini - -README.md +
+ -ruff.toml +### Files -template_config.yaml + +| Configuration | User docs | Housekeeping | +| :--- | :--- | :--- | +| .env.sample | CODE_OF_CONDUCT.md | .renovaterc.json5 | +| .pre-commit-config.yaml | CONTRIBUTING.md | codecov.yml | +| docker-compose.yml | LICENSE | | +| mypy.ini | NOTICE | | +| pytest.ini | README.md | | +| ruff.toml | | | +| template_config.yaml | | | + +
\ No newline at end of file From e4f3fcc369c8c6645091c3f3a6ff0fec1472c0a4 Mon Sep 17 00:00:00 2001 From: Sarah Keating Date: Wed, 27 Nov 2024 15:45:16 +0000 Subject: [PATCH 18/18] make the headers bold --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ade5b6ca9..bf779e8d8 100644 --- a/README.md +++ b/README.md @@ -368,7 +368,7 @@ FTPROOT/PROJECT_SLUG/EXTRACT_DATETIME/parquet/radiology/radiology.parquet -| Configuration | User docs | Housekeeping | +| **Configuration** | **User docs** | **Housekeeping** | | :--- | :--- | :--- | | .env.sample | CODE_OF_CONDUCT.md | .renovaterc.json5 | | .pre-commit-config.yaml | CONTRIBUTING.md | codecov.yml |