From 515d2acf32802a8af458ca0947f658f8fd58c271 Mon Sep 17 00:00:00 2001 From: IanCa Date: Thu, 20 Jun 2024 18:52:28 -0500 Subject: [PATCH 01/11] Move settings to toml --- .codespellrc | 3 --- pyproject.toml | 66 +++++++++++++++++++++++++++++++++++++++++++++++++- setup.cfg | 61 ---------------------------------------------- 3 files changed, 65 insertions(+), 65 deletions(-) delete mode 100644 .codespellrc delete mode 100644 setup.cfg diff --git a/.codespellrc b/.codespellrc deleted file mode 100644 index 70e4ccb1..00000000 --- a/.codespellrc +++ /dev/null @@ -1,3 +0,0 @@ -[codespell] -skip = .git,*.pdf,*.svg,deprecated,*.xml,*.mediawiki,*.omn,*.toml,./hedweb/static/css/* -ignore-words-list = covert,hed,assertIn diff --git a/pyproject.toml b/pyproject.toml index 45050779..0eb68b87 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,6 +2,70 @@ requires = ["setuptools>=42", "versioneer[toml]"] build-backend = "setuptools.build_meta" +[project] +name = "hedweb" +dynamic = ["version"] +description = "Web interface, REST services, and Docker deployment for HED tools." +readme = "README.md" +authors = [ + { name = "VisLab" }, + { name = "Ian Callanan" }, + { name = "Jeremy Cockfield" }, + { name = "Kay Robbins", email = "Kay.Robbins@utsa.edu" } +] +license = { text = "MIT License" } +requires-python = ">=3.9" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent" +] + +dependencies = [ + "click", + "coverage", + "defusedxml", + "et-xmlfile", + "Flask", + "Flask-WTF", + "inflect", + "itsdangerous", + "jdcal", + "Jinja2", + "MarkupSafe", + "numpy", + "openpyxl", + "pandas", + "portalocker", + "python-dateutil", + "pytz", + "requests", + "semantic-version", + "six", + "Sphinx", + "SphinxExtensions", + "sphinx_rtd_theme", + "Werkzeug", + "xlrd", + "attrs" +] + +[project.urls] +"Homepage" = "https://github.com/hed-standard/hed-web/" +"Bug Tracker" = "https://github.com/hed-standard/hed-web/issues" + +[tool.setuptools.packages.find] +namespaces = true +include = ["hed*"] + +[tool.versioneer] +VCS = "git" +style = "pep440" +versionfile_source = "hedweb/_version.py" +versionfile_build = "hedweb/_version.py" +tag_prefix = "" +parentdir_prefix = "hedweb-" + [tool.codespell] skip = '*.git,*.pdf,*.xml,*.mediawiki,*.svg,versioneer.py,venv*,*.tsv,*.yaml,*.yml,*.json,*.rdf,*.jsonld,spec_tests,*.css,*.css.map' -ignore-words-list = 'te,parms,cACE' +ignore-words-list = 'te,parms,cACE,assertIn' \ No newline at end of file diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index ae7c12ef..00000000 --- a/setup.cfg +++ /dev/null @@ -1,61 +0,0 @@ -[metadata] -name = hedweb -author = VisLab, Ian Callanan, Jeremy Cockfield, Kay Robbins -author_email = Kay.Robbins@utsa.edu -description = "Web interface, REST services, and Docker deployment for HED tools.", -long_description = file: README.md -long_description_content_type = text/markdown -url = https://github.com/hed-standard/hed-web/ -# project_urls = -bug tracker = https://github.com/hed-standard/hed-web/issues -classifiers = - Programming Language :: Python :: 3 - License :: OSI Approved :: MIT License - Operating System :: OS Independent - - - -[options] -package_dir = - = . -packages = find_namespace: -python_requires = >=3.9 -install_requires = - click - coverage - defusedxml - et-xmlfile - Flask - Flask-WTF - inflect - itsdangerous - jdcal - Jinja2 - MarkupSafe - numpy - openpyxl - pandas - portalocker - python-dateutil - pytz - requests - semantic-version - six - Sphinx - SphinxExtensions - sphinx_rtd_theme - Werkzeug - xlrd - attrs - - -[options.packages.find] -include = hed* - -[versioneer] -VCS = git -style = pep440 -versionfile_source = hedweb/_version.py -versionfile_build = hedweb/_version.py -tag_prefix = -parentdir_prefix = hedweb- From df7b3ae5e6a27a047c6adeb169ec45ad1747dfc8 Mon Sep 17 00:00:00 2001 From: IanCa Date: Fri, 21 Jun 2024 11:39:10 -0500 Subject: [PATCH 02/11] Pin to 3.8 requirements, pare down other requirements --- docs/requirements.txt | 58 ++++++++++++++++++++++--------------------- pyproject.toml | 22 +--------------- requirements.txt | 5 ++-- 3 files changed, 33 insertions(+), 52 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 458b6d22..97888199 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,29 +1,31 @@ -attrs>=21.4.0 -click>=8.1.3 -coverage>=6.3.2 -defusedxml>=0.7.1 -et-xmlfile>=1.1.0 -Flask>=3.0.3 -Flask-WTF>=1.2.1 -inflect>=5.5.2 -itsdangerous>=2.2.0 -jdcal>=1.4.1 -Jinja2>=3.1.2 +alabaster==0.7.13 +Babel==2.15.0 +certifi==2024.6.2 +charset-normalizer==3.3.2 +docutils==0.20.1 +idna==3.7 +imagesize==1.4.1 +importlib-metadata==7.2.0 +jinja2==3.1.4 +markdown-it-py==3.0.0 MarkupSafe==2.1.5 -myst-parser>=0.17.0 -numpy>=1.20.3 -numpydoc>=1.3.1 -openpyxl>=3.0.9 -pandas>=1.3.5 -portalocker>=2.8.2 -Pygments>=2.12.0 -python-dateutil>=2.8.2 -pytz>=2022.1 -semantic_version>=2.9.0 -six==1.16.0 -Sphinx>=4,<8 -SphinxExtensions>=0.2.0 -sphinx_rtd_theme>=1.0.0 -Werkzeug>=2.1.2 -WTForms>=3.0.1 -xlrd>=2.0.1 +mdit-py-plugins==0.4.1 +mdurl==0.1.2 +myst-parser==3.0.1 +packaging==24.1 +pygments==2.18.0 +pytz==2024.1 +PyYAML==6.0.1 +requests==2.32.3 +snowballstemmer==2.2.0 +sphinx==7.1.2 +sphinx-rtd-theme==2.0.0 +sphinxcontrib-applehelp==1.0.4 +sphinxcontrib-devhelp==1.0.2 +sphinxcontrib-htmlhelp==2.0.1 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.3 +sphinxcontrib-serializinghtml==1.1.5 +urllib3==2.2.2 +zipp==3.19.2 diff --git a/pyproject.toml b/pyproject.toml index 0eb68b87..12e7ffa6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -22,32 +22,12 @@ classifiers = [ ] dependencies = [ - "click", - "coverage", - "defusedxml", - "et-xmlfile", "Flask", "Flask-WTF", - "inflect", - "itsdangerous", - "jdcal", - "Jinja2", - "MarkupSafe", - "numpy", "openpyxl", "pandas", - "portalocker", - "python-dateutil", - "pytz", - "requests", - "semantic-version", - "six", - "Sphinx", - "SphinxExtensions", - "sphinx_rtd_theme", "Werkzeug", - "xlrd", - "attrs" + "requests" ] [project.urls] diff --git a/requirements.txt b/requirements.txt index 9344fdf7..fe69f4fc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,6 +1,5 @@ -flask>=3.0.3 -flask-wtf>=1.2.1 -config>=0.5.1 +Flask>=3.0.3 +Flask-WTF>=1.2.1 openpyxl>=3.1.2 pandas>=2.2.0 Werkzeug>=3.0.1 From 90e7c89a39d273696d873a3cf4e4c7afe0ba4740 Mon Sep 17 00:00:00 2001 From: IanCa Date: Fri, 21 Jun 2024 11:48:29 -0500 Subject: [PATCH 03/11] bump to 3.10 for docs --- docs/requirements.txt | 22 ++++++++++------------ readthedocs.yml | 2 +- 2 files changed, 11 insertions(+), 13 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 97888199..fa5697c6 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,31 +1,29 @@ -alabaster==0.7.13 +alabaster==0.7.16 Babel==2.15.0 certifi==2024.6.2 charset-normalizer==3.3.2 docutils==0.20.1 idna==3.7 imagesize==1.4.1 -importlib-metadata==7.2.0 -jinja2==3.1.4 +Jinja2==3.1.4 markdown-it-py==3.0.0 MarkupSafe==2.1.5 mdit-py-plugins==0.4.1 mdurl==0.1.2 myst-parser==3.0.1 packaging==24.1 -pygments==2.18.0 -pytz==2024.1 +Pygments==2.18.0 PyYAML==6.0.1 requests==2.32.3 snowballstemmer==2.2.0 -sphinx==7.1.2 +Sphinx==7.3.7 sphinx-rtd-theme==2.0.0 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 +sphinxcontrib-applehelp==1.0.8 +sphinxcontrib-devhelp==1.0.6 +sphinxcontrib-htmlhelp==2.0.5 sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.5 +sphinxcontrib-qthelp==1.0.7 +sphinxcontrib-serializinghtml==1.1.10 +tomli==2.0.1 urllib3==2.2.2 -zipp==3.19.2 diff --git a/readthedocs.yml b/readthedocs.yml index 6d56af39..9df6286b 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -7,7 +7,7 @@ formats: build: os: ubuntu-22.04 tools: - python: '3.8' + python: '3.10' # Build documentation in the docs/ directory with Sphinx sphinx: From 31d0430bca22a835f6236e7f0d0a2479e0b52d7f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 8 Jul 2024 20:04:23 +0000 Subject: [PATCH 04/11] Bump certifi from 2024.6.2 to 2024.7.4 Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.6.2 to 2024.7.4. - [Commits](https://github.com/certifi/python-certifi/compare/2024.06.02...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index fa5697c6..58d4a96e 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,6 +1,6 @@ alabaster==0.7.16 Babel==2.15.0 -certifi==2024.6.2 +certifi==2024.7.4 charset-normalizer==3.3.2 docutils==0.20.1 idna==3.7 From 8240ee2be62d7a4b341eb42b5d757583b48bf2c1 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Mon, 22 Jul 2024 11:01:46 -0500 Subject: [PATCH 05/11] Updated a broken link on home page --- .github/workflows/links.yaml | 24 ++++++++++++++++++++++++ .lycheeignore | 3 +++ hedweb/templates/hed-tools-home.html | 8 ++++---- 3 files changed, 31 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/links.yaml create mode 100644 .lycheeignore diff --git a/.github/workflows/links.yaml b/.github/workflows/links.yaml new file mode 100644 index 00000000..b1e98916 --- /dev/null +++ b/.github/workflows/links.yaml @@ -0,0 +1,24 @@ +--- +name: Lychee link checker + +on: + workflow_dispatch: + +permissions: + contents: read + +jobs: + codespell: + name: Lychee link checker + runs-on: ubuntu-latest + + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Link Checker + id: lychee + uses: lycheeverse/lychee-action@v1 + with: + # Check all markdown, html and reStructuredText files in repo (default) + args: --base . --verbose --no-progress './**/*.md' './**/*.html' './**/*.rst' \ No newline at end of file diff --git a/.lycheeignore b/.lycheeignore new file mode 100644 index 00000000..2ed7bd0e --- /dev/null +++ b/.lycheeignore @@ -0,0 +1,3 @@ + +(_anchor|-anchor) + diff --git a/hedweb/templates/hed-tools-home.html b/hedweb/templates/hed-tools-home.html index 0ffe1f31..b2ae77e8 100644 --- a/hedweb/templates/hed-tools-home.html +++ b/hedweb/templates/hed-tools-home.html @@ -112,8 +112,8 @@

HED online tools summary

are used by schema developers creating the HED vocabularies and are not of interest to annotators or analysts.

- More detailed help on using these online tools is available at: - HED online tools + More detailed help on using these online tools is available in the + HED online tools documentation.

HED REST services

@@ -121,8 +121,8 @@

HED REST services

The HED online tools are also available as callable web services. More detailed help on calling these services is available at: HED RESTful services - Downloadable examples of calling these services from a MATLAB program can be found at: - + Downloadable examples of calling these services from a MATLAB program can be found in the + GitHub MATLAB web service examples.

From ec7c6e39ff699924db386d8659ab14f87906d0ce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jul 2024 20:05:34 +0000 Subject: [PATCH 06/11] Bump sphinxcontrib-qthelp from 1.0.7 to 1.0.8 Bumps [sphinxcontrib-qthelp](https://github.com/sphinx-doc/sphinxcontrib-qthelp) from 1.0.7 to 1.0.8. - [Release notes](https://github.com/sphinx-doc/sphinxcontrib-qthelp/releases) - [Changelog](https://github.com/sphinx-doc/sphinxcontrib-qthelp/blob/master/CHANGES) - [Commits](https://github.com/sphinx-doc/sphinxcontrib-qthelp/compare/1.0.7...1.0.8) --- updated-dependencies: - dependency-name: sphinxcontrib-qthelp dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 58d4a96e..21bb7b4c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -23,7 +23,7 @@ sphinxcontrib-devhelp==1.0.6 sphinxcontrib-htmlhelp==2.0.5 sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.7 +sphinxcontrib-qthelp==1.0.8 sphinxcontrib-serializinghtml==1.1.10 tomli==2.0.1 urllib3==2.2.2 From f610bd9c90a00811766f0b973f3254d89532cffc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 Jul 2024 20:05:38 +0000 Subject: [PATCH 07/11] Bump sphinxcontrib-htmlhelp from 2.0.5 to 2.0.6 Bumps [sphinxcontrib-htmlhelp](https://github.com/sphinx-doc/sphinxcontrib-htmlhelp) from 2.0.5 to 2.0.6. - [Release notes](https://github.com/sphinx-doc/sphinxcontrib-htmlhelp/releases) - [Changelog](https://github.com/sphinx-doc/sphinxcontrib-htmlhelp/blob/master/CHANGES) - [Commits](https://github.com/sphinx-doc/sphinxcontrib-htmlhelp/compare/2.0.5...2.0.6) --- updated-dependencies: - dependency-name: sphinxcontrib-htmlhelp dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 58d4a96e..bb732eaf 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -20,7 +20,7 @@ Sphinx==7.3.7 sphinx-rtd-theme==2.0.0 sphinxcontrib-applehelp==1.0.8 sphinxcontrib-devhelp==1.0.6 -sphinxcontrib-htmlhelp==2.0.5 +sphinxcontrib-htmlhelp==2.0.6 sphinxcontrib-jquery==4.1 sphinxcontrib-jsmath==1.0.1 sphinxcontrib-qthelp==1.0.7 From ffb30d51b995fb57be6da4928586e00d38faf8b4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 23 Jul 2024 13:15:30 +0000 Subject: [PATCH 08/11] Bump sphinx from 7.3.7 to 7.4.7 Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.3.7 to 7.4.7. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.3.7...v7.4.7) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index ce0b1575..d22b259c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -16,7 +16,7 @@ Pygments==2.18.0 PyYAML==6.0.1 requests==2.32.3 snowballstemmer==2.2.0 -Sphinx==7.3.7 +Sphinx==7.4.7 sphinx-rtd-theme==2.0.0 sphinxcontrib-applehelp==1.0.8 sphinxcontrib-devhelp==1.0.6 From 45aac6934a077485cb86fb4576b52d30bce9ef03 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Tue, 23 Jul 2024 11:26:52 -0500 Subject: [PATCH 09/11] Fixed schema list ordering issue #199 --- hedweb/templates/hed-tools-home.html | 5 +++-- hedweb/templates/layout.html | 1 + hedweb/web_util.py | 7 +++---- tests/test_web_util.py | 17 +++++++++++++++-- 4 files changed, 22 insertions(+), 8 deletions(-) diff --git a/hedweb/templates/hed-tools-home.html b/hedweb/templates/hed-tools-home.html index b2ae77e8..b5a35446 100644 --- a/hedweb/templates/hed-tools-home.html +++ b/hedweb/templates/hed-tools-home.html @@ -18,13 +18,14 @@

HED online tools summary

The following table summarizes the available online tools. The tools are organized around the types of data that the tools handle. The Actions refer to the types of actions that can be performed on the data through the online tools. Each action is linked to its corresponding documentation to provide additional - information.

+ information. NEW: an experimental CTagger + online annotation tool is now available.

- + diff --git a/hedweb/templates/layout.html b/hedweb/templates/layout.html index 01fc004e..1223dbc7 100644 --- a/hedweb/templates/layout.html +++ b/hedweb/templates/layout.html @@ -63,6 +63,7 @@ aria-haspopup="true" aria-expanded="false">Quick links
HED schema browser + CTagger interactive annotation HED homepage HED on GitHub HED on YouTube diff --git a/hedweb/web_util.py b/hedweb/web_util.py index 28ed47d5..15bbc957 100644 --- a/hedweb/web_util.py +++ b/hedweb/web_util.py @@ -18,12 +18,11 @@ def convert_hed_versions(hed_info): hed_list = [] + standard_list = hed_info['schema_version_list'].get(None, []) for key, key_list in hed_info['schema_version_list'].items(): - if key is None: - hed_list = hed_list + key_list - else: + if key is not None: hed_list = hed_list + [key + '_' + element for element in key_list] - return {'schema_version_list': hed_list} + return {'schema_version_list': standard_list + hed_list} def file_extension_is_valid(filename, accepted_extensions=None): diff --git a/tests/test_web_util.py b/tests/test_web_util.py index 19292448..74b0ee82 100644 --- a/tests/test_web_util.py +++ b/tests/test_web_util.py @@ -9,6 +9,21 @@ class Test(TestWebBase): + def test_convert_hed_versions(self): + from hedweb.web_util import convert_hed_versions + no_none = {'schema_version_list': {'score': ['1.0.0', '2.0.0']}} + no_none_list = convert_hed_versions(no_none) + self.assertTrue(no_none_list['schema_version_list'] == ['score_1.0.0', 'score_2.0.0']) + just_none = {'schema_version_list': {None: ['8.0.0', '8.1.0']}} + just_none_list = convert_hed_versions(just_none) + self.assertTrue(just_none_list['schema_version_list'] == ['8.0.0', '8.1.0']) + just_blank = {'schema_version_list': {'': ['9.0.0', '9.1.0']}} + just_blank_list = convert_hed_versions(just_blank) + self.assertTrue(just_blank_list['schema_version_list'] == ['_9.0.0', '_9.1.0']) + alls = {'schema_version_list': {'score': ['1.0.0', '2.0.0'], None: ['8.0.0', '8.1.0']}} + alls_list = convert_hed_versions(alls) + self.assertTrue(alls_list['schema_version_list'] == ['8.0.0', '8.1.0', 'score_1.0.0', 'score_2.0.0']) + def test_form_has_file(self): from hedweb.web_util import form_has_file with self.app.test as _: @@ -241,7 +256,6 @@ def test_get_hed_schema_from_pull_down_empty(self): def test_get_hed_schema_from_pull_down_version(self): from hed.schema import HedSchema - from hedweb.constants import base_constants as bc from hedweb.web_util import get_hed_schema_from_pull_down with self.app.test: environ = create_environ(data={bc.SCHEMA_VERSION: '8.0.0'}) @@ -252,7 +266,6 @@ def test_get_hed_schema_from_pull_down_version(self): def test_get_hed_schema_from_pull_down_other(self): from hed.schema import HedSchema - from hedweb.constants import base_constants as bc from hedweb.web_util import get_hed_schema_from_pull_down with self.app.test: schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data/HED8.0.0.xml') From a20cdacb68ffd94c136651e760c6a0b5909cf22a Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Tue, 23 Jul 2024 11:51:41 -0500 Subject: [PATCH 10/11] Renamed test variable to make codespell happy --- tests/test_web_util.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/test_web_util.py b/tests/test_web_util.py index 74b0ee82..ecab70b2 100644 --- a/tests/test_web_util.py +++ b/tests/test_web_util.py @@ -20,9 +20,9 @@ def test_convert_hed_versions(self): just_blank = {'schema_version_list': {'': ['9.0.0', '9.1.0']}} just_blank_list = convert_hed_versions(just_blank) self.assertTrue(just_blank_list['schema_version_list'] == ['_9.0.0', '_9.1.0']) - alls = {'schema_version_list': {'score': ['1.0.0', '2.0.0'], None: ['8.0.0', '8.1.0']}} - alls_list = convert_hed_versions(alls) - self.assertTrue(alls_list['schema_version_list'] == ['8.0.0', '8.1.0', 'score_1.0.0', 'score_2.0.0']) + test_all = {'schema_version_list': {'score': ['1.0.0', '2.0.0'], None: ['8.0.0', '8.1.0']}} + test_all_list = convert_hed_versions(test_all) + self.assertTrue(test_all_list['schema_version_list'] == ['8.0.0', '8.1.0', 'score_1.0.0', 'score_2.0.0']) def test_form_has_file(self): from hedweb.web_util import form_has_file From 46f8ac16ad51d35423ae513a52cbc68c137b70e6 Mon Sep 17 00:00:00 2001 From: Kay Robbins <1189050+VisLab@users.noreply.github.com> Date: Wed, 24 Jul 2024 09:09:25 -0500 Subject: [PATCH 11/11] Fixed missing skip_columns in generate sidecars --- hedweb/event_operations.py | 24 +++++++++++++----------- hedweb/process_service.py | 1 + tests/test_events.py | 5 +++++ 3 files changed, 19 insertions(+), 11 deletions(-) diff --git a/hedweb/event_operations.py b/hedweb/event_operations.py index 98662a83..6989e6d5 100644 --- a/hedweb/event_operations.py +++ b/hedweb/event_operations.py @@ -123,17 +123,19 @@ def generate_sidecar(self): extension='.txt', append_datetime=True), bc.MSG_CATEGORY: 'warning', bc.MSG: f"Cannot generate sidecar because skipped and value column names overlap."} - - columns_info = TabularSummary.get_columns_info(self.events.dataframe) - hed_dict = {} - for column_name in columns_info: - if column_name in self.columns_skip: - continue - elif column_name in self.columns_value: - hed_dict[column_name] = generate_sidecar_entry(column_name) - else: - hed_dict[column_name] = generate_sidecar_entry(column_name, - column_values=list(columns_info[column_name].keys())) + tab_sum = TabularSummary(value_cols=self.columns_value, skip_cols=self.columns_skip) + tab_sum.update(self.events.dataframe) + hed_dict = tab_sum.extract_sidecar_template() + # columns_info = TabularSummary.get_columns_info(self.events.dataframe) + # hed_dict = {} + # for column_name in columns_info: + # if column_name in self.columns_skip: + # continue + # elif column_name in self.columns_value: + # hed_dict[column_name] = generate_sidecar_entry(column_name) + # else: + # hed_dict[column_name] = generate_sidecar_entry(column_name, + # column_values=list(columns_info[column_name].keys())) file_name = generate_filename(display_name, name_suffix='_generated', extension='.json', append_datetime=True) return {bc.COMMAND: bc.COMMAND_GENERATE_SIDECAR, bc.COMMAND_TARGET: 'events', diff --git a/hedweb/process_service.py b/hedweb/process_service.py index c7812205..5d764b3c 100644 --- a/hedweb/process_service.py +++ b/hedweb/process_service.py @@ -57,6 +57,7 @@ def set_parameters(arguments, params): arguments[bc.REQUEST_TYPE] = bc.FROM_SERVICE arguments[bc.COLUMNS_CATEGORICAL] = ProcessServices.get_list(bc.COLUMNS_CATEGORICAL, params) arguments[bc.COLUMNS_VALUE] = ProcessServices.get_list(bc.COLUMNS_VALUE, params) + arguments[bc.COLUMNS_SKIP] = ProcessServices.get_list(bc.COLUMNS_SKIP, params) arguments[bc.TAG_COLUMNS] = ProcessServices.get_list(bc.TAG_COLUMNS, params) arguments[bc.HAS_COLUMN_NAMES] = True diff --git a/tests/test_events.py b/tests/test_events.py index 3805aa1f..a6d69b8d 100644 --- a/tests/test_events.py +++ b/tests/test_events.py @@ -1,5 +1,6 @@ import os from io import StringIO +import json import pandas as pd import unittest from werkzeug.test import create_environ @@ -167,6 +168,10 @@ def test_generate_sidecar_valid(self): 'generate_sidecar results should have a data key when no errors') self.assertEqual('success', results['msg_category'], 'generate_sidecar msg_category should be success when no errors') + sidecar_template = json.loads(results['data']) + self.assertFalse('onset' in sidecar_template) + self.assertIsInstance(sidecar_template['event_type']['HED'], dict) + self.assertTrue(isinstance(sidecar_template['trial']['HED'], str)) def test_search_invalid(self): with self.app.app_context():
Data type
(linked to form>		Action
(linked to docs)		Description
Data type
(form link)		Action
(docs link)		Description
Events