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/.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/docs/requirements.txt b/docs/requirements.txt index 458b6d22..d22b259c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,29 +1,29 @@ -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==0.7.16 +Babel==2.15.0 +certifi==2024.7.4 +charset-normalizer==3.3.2 +docutils==0.20.1 +idna==3.7 +imagesize==1.4.1 +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 +PyYAML==6.0.1 +requests==2.32.3 +snowballstemmer==2.2.0 +Sphinx==7.4.7 +sphinx-rtd-theme==2.0.0 +sphinxcontrib-applehelp==1.0.8 +sphinxcontrib-devhelp==1.0.6 +sphinxcontrib-htmlhelp==2.0.6 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.8 +sphinxcontrib-serializinghtml==1.1.10 +tomli==2.0.1 +urllib3==2.2.2 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/hedweb/templates/hed-tools-home.html b/hedweb/templates/hed-tools-home.html index 0ffe1f31..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.

- + @@ -112,8 +113,8 @@

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 +122,8 @@

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.

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/pyproject.toml b/pyproject.toml index 45050779..12e7ffa6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -2,6 +2,50 @@ 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 = [ + "Flask", + "Flask-WTF", + "openpyxl", + "pandas", + "Werkzeug", + "requests" +] + +[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/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: 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 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- 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(): diff --git a/tests/test_web_util.py b/tests/test_web_util.py index 19292448..ecab70b2 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']) + 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 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')
Data type
(linked to form>		Action
(linked to docs)		Description
Data type
(form link)		Action
(docs link)		Description
Events