diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml new file mode 100644 index 000000000..5c6080e5b --- /dev/null +++ b/.github/workflows/build.yaml @@ -0,0 +1,81 @@ +# push will run on every pushed commit to any branch (so this will rerun the tests +# once a branch gets merged to main in addition to any new commits on any branch) +on: push + +name: Build + +jobs: + pyinstaller: + runs-on: ${{ matrix.os }} + + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + + steps: + - name: Check out code + uses: actions/checkout@v3 + with: + persist-credentials: false + + - name: Set up python + uses: actions/setup-python@v4 + with: + python-version: '3.9' + + - name: Install PostgreSQL and dependencies on Ubuntu + if: matrix.os == 'ubuntu-latest' + run: | + sudo apt-get update + sudo apt-get install -y postgresql postgresql-contrib libpq-dev + + - name: Install PostgreSQL and dependencies on macOS + if: matrix.os == 'macos-latest' + run: | + brew update + brew install postgresql + + - name: Install PostgreSQL and dependencies on Windows + if: matrix.os == 'windows-latest' + run: | + choco install postgresql + + # https://pyinstaller.org/en/stable/when-things-go-wrong.html#helping-pyinstaller-find-modules + - name: Install poetry + run: | + pip install --upgrade pip + pip --version + # this isn't the recommended way to install b/c the poetry deps are now + # mixed with the service deps. However, getting the alternative to work + # on all OSes was getting difficult. This is a quick hack to move forward + pip install poetry + python -m poetry --version + python -m poetry self add poetry-pyinstaller-plugin + - name: Install dependencies and then build using pyinstaller + run: | + python -m poetry install -vv --all-extras --no-interaction --no-cache + python -m poetry show -vv + python -m poetry env info + python -m poetry build + # pip install pyinstaller==6.6.0 + # pyinstaller --paths=./gen3 --clean --name gen3 --hidden-import gen3users --onefile ./gen3/cli/__main__.py + # pyinstaller --log-level=DEBUG --debug=imports --clean --name gen3 --hidden-import gen3users --onefile ./gen3/cli/__main__.py + - name: Test build + run: | + ls ./dist/pyinstaller/*/gen3 + ls ./dist/pyinstaller/*/gen3/gen3 + cp ./dist/pyinstaller/*/gen3/gen3 ./gen3 + ls + ./gen3 --help + - name: Archive artifacts + uses: actions/upload-artifact@v4 + with: + name: dist-without-markdown + path: | + dist + !dist/**/*.md + + + + diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index abbc82607..254128d04 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,10 +1,6 @@ name: CI -on: - # run on pushed commits to master and on new commits on pull requests - push: - pull_request: - types: [opened, synchronize] +on: push jobs: Security: diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 645370329..077f1d396 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -5,6 +5,7 @@ on: push: branches-ignore: - 'master' + - 'main' paths-ignore: - 'docs/**' # Use push trigger since 'paths-ignore' are not respected as expected by 'on.pull_request.paths-ignore', see https://github.com/actions/runner/issues/2324 diff --git a/docs/_build/doctrees/auth.doctree b/docs/_build/doctrees/auth.doctree index 797c48e20..974418d02 100644 Binary files a/docs/_build/doctrees/auth.doctree and b/docs/_build/doctrees/auth.doctree differ diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 9f457f8fb..5e7923098 100644 Binary files a/docs/_build/doctrees/environment.pickle and b/docs/_build/doctrees/environment.pickle differ diff --git a/docs/_build/doctrees/file.doctree b/docs/_build/doctrees/file.doctree index 4c3eb53b5..94b5d49c3 100644 Binary files a/docs/_build/doctrees/file.doctree and b/docs/_build/doctrees/file.doctree differ diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree index 8179ccf0b..b97c09ddb 100644 Binary files a/docs/_build/doctrees/index.doctree and b/docs/_build/doctrees/index.doctree differ diff --git a/docs/_build/doctrees/indexing.doctree b/docs/_build/doctrees/indexing.doctree index 6e290dec7..33900f90a 100644 Binary files a/docs/_build/doctrees/indexing.doctree and b/docs/_build/doctrees/indexing.doctree differ diff --git a/docs/_build/doctrees/jobs.doctree b/docs/_build/doctrees/jobs.doctree index 050b3b31d..1c4d1a675 100644 Binary files a/docs/_build/doctrees/jobs.doctree and b/docs/_build/doctrees/jobs.doctree differ diff --git a/docs/_build/doctrees/metadata.doctree b/docs/_build/doctrees/metadata.doctree index 75b1f4694..17fa5e908 100644 Binary files a/docs/_build/doctrees/metadata.doctree and b/docs/_build/doctrees/metadata.doctree differ diff --git a/docs/_build/doctrees/object.doctree b/docs/_build/doctrees/object.doctree index 8b3d30b62..45456f19f 100644 Binary files a/docs/_build/doctrees/object.doctree and b/docs/_build/doctrees/object.doctree differ diff --git a/docs/_build/doctrees/query.doctree b/docs/_build/doctrees/query.doctree index 218c50e4c..a392973f7 100644 Binary files a/docs/_build/doctrees/query.doctree and b/docs/_build/doctrees/query.doctree differ diff --git a/docs/_build/doctrees/submission.doctree b/docs/_build/doctrees/submission.doctree index 8ed54272a..f8327aff0 100644 Binary files a/docs/_build/doctrees/submission.doctree and b/docs/_build/doctrees/submission.doctree differ diff --git a/docs/_build/doctrees/tools.doctree b/docs/_build/doctrees/tools.doctree index 2f3e2df38..97758bb31 100644 Binary files a/docs/_build/doctrees/tools.doctree and b/docs/_build/doctrees/tools.doctree differ diff --git a/docs/_build/doctrees/tools/drs_pull.doctree b/docs/_build/doctrees/tools/drs_pull.doctree index 6b3e2107f..5d16b18e7 100644 Binary files a/docs/_build/doctrees/tools/drs_pull.doctree and b/docs/_build/doctrees/tools/drs_pull.doctree differ diff --git a/docs/_build/doctrees/tools/indexing.doctree b/docs/_build/doctrees/tools/indexing.doctree index 2aededbb0..02d02e858 100644 Binary files a/docs/_build/doctrees/tools/indexing.doctree and b/docs/_build/doctrees/tools/indexing.doctree differ diff --git a/docs/_build/doctrees/tools/metadata.doctree b/docs/_build/doctrees/tools/metadata.doctree index 2aeec7339..2282ecf82 100644 Binary files a/docs/_build/doctrees/tools/metadata.doctree and b/docs/_build/doctrees/tools/metadata.doctree differ diff --git a/docs/_build/doctrees/wss.doctree b/docs/_build/doctrees/wss.doctree index 81babe9ab..4d973cdd2 100644 Binary files a/docs/_build/doctrees/wss.doctree and b/docs/_build/doctrees/wss.doctree differ diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo index c1d984323..16006a834 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 5f84980db6ce51f04ab25ae1f011fb32 +config: b941f35ac2dd283dbbba3d55c4f31d39 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/gen3/auth.html b/docs/_build/html/_modules/gen3/auth.html index 5460aa6d3..cbceed811 100644 --- a/docs/_build/html/_modules/gen3/auth.html +++ b/docs/_build/html/_modules/gen3/auth.html @@ -8,7 +8,7 @@ - + @@ -720,7 +720,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/file.html b/docs/_build/html/_modules/gen3/file.html index e7a6c5036..3a7945131 100644 --- a/docs/_build/html/_modules/gen3/file.html +++ b/docs/_build/html/_modules/gen3/file.html @@ -8,7 +8,7 @@ - + @@ -359,7 +359,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/index.html b/docs/_build/html/_modules/gen3/index.html index 2ac12ffd6..55c89c086 100644 --- a/docs/_build/html/_modules/gen3/index.html +++ b/docs/_build/html/_modules/gen3/index.html @@ -8,7 +8,7 @@ - + @@ -1100,7 +1100,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/jobs.html b/docs/_build/html/_modules/gen3/jobs.html index 4584edd42..b3f266ef7 100644 --- a/docs/_build/html/_modules/gen3/jobs.html +++ b/docs/_build/html/_modules/gen3/jobs.html @@ -8,7 +8,7 @@ - + @@ -331,7 +331,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/metadata.html b/docs/_build/html/_modules/gen3/metadata.html index 733e14789..0dc385551 100644 --- a/docs/_build/html/_modules/gen3/metadata.html +++ b/docs/_build/html/_modules/gen3/metadata.html @@ -8,7 +8,7 @@ - + @@ -1118,7 +1118,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/object.html b/docs/_build/html/_modules/gen3/object.html index a531e5a3d..ec15a5180 100644 --- a/docs/_build/html/_modules/gen3/object.html +++ b/docs/_build/html/_modules/gen3/object.html @@ -8,7 +8,7 @@ - + @@ -150,7 +150,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/query.html b/docs/_build/html/_modules/gen3/query.html index 45c3491f8..090d4c48f 100644 --- a/docs/_build/html/_modules/gen3/query.html +++ b/docs/_build/html/_modules/gen3/query.html @@ -8,7 +8,7 @@ - + @@ -306,7 +306,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/submission.html b/docs/_build/html/_modules/gen3/submission.html index 7f760de51..982c67c80 100644 --- a/docs/_build/html/_modules/gen3/submission.html +++ b/docs/_build/html/_modules/gen3/submission.html @@ -8,7 +8,7 @@ - + @@ -857,7 +857,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/tools/download/drs_download.html b/docs/_build/html/_modules/gen3/tools/download/drs_download.html index a38140eb2..7fe0f1c3a 100644 --- a/docs/_build/html/_modules/gen3/tools/download/drs_download.html +++ b/docs/_build/html/_modules/gen3/tools/download/drs_download.html @@ -8,7 +8,7 @@ - + @@ -1527,7 +1527,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html index 0804272be..5d84308c7 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html @@ -8,7 +8,7 @@ - + @@ -607,7 +607,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html index 95d5e273a..a43fad6bf 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html @@ -8,7 +8,7 @@ - + @@ -715,7 +715,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html index e18deccb3..04f9b5602 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html @@ -8,7 +8,7 @@ - + @@ -513,7 +513,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html b/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html index 4cf4e71d9..b4f1bc9fd 100644 --- a/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html @@ -8,7 +8,7 @@ - + @@ -617,7 +617,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/gen3/wss.html b/docs/_build/html/_modules/gen3/wss.html index deb8d058f..815b18805 100644 --- a/docs/_build/html/_modules/gen3/wss.html +++ b/docs/_build/html/_modules/gen3/wss.html @@ -8,7 +8,7 @@ - + @@ -289,7 +289,7 @@

Related Topics

- + diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html index 233fbb291..6ddccd2a7 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -8,7 +8,7 @@ - + @@ -89,7 +89,7 @@

Related Topics

- + diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css index 4157edf27..e5179b7a9 100644 --- a/docs/_build/html/_static/basic.css +++ b/docs/_build/html/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js index d06a71d75..4d67807d1 100644 --- a/docs/_build/html/_static/doctools.js +++ b/docs/_build/html/_static/doctools.js @@ -4,7 +4,7 @@ * * Base JavaScript utilities for all Sphinx HTML documentation. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js index 250f5665f..367b8ed81 100644 --- a/docs/_build/html/_static/language_data.js +++ b/docs/_build/html/_static/language_data.js @@ -5,7 +5,7 @@ * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -13,7 +13,7 @@ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; -/* Non-minified version is copied as a separate JS file, is available */ +/* Non-minified version is copied as a separate JS file, if available */ /** * Porter Stemmer diff --git a/docs/_build/html/_static/searchtools.js b/docs/_build/html/_static/searchtools.js index 7918c3fab..92da3f8b2 100644 --- a/docs/_build/html/_static/searchtools.js +++ b/docs/_build/html/_static/searchtools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for the full-text search. * - * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -99,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => { .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms) + Search.makeSearchSummary(data, searchTerms, anchor) ); // highlight search terms in the summary if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js @@ -116,8 +116,8 @@ const _finishSearch = (resultCount) => { ); else Search.status.innerText = _( - `Search finished, found ${resultCount} page(s) matching the search query.` - ); + "Search finished, found ${resultCount} page(s) matching the search query." + ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( results, @@ -137,6 +137,22 @@ const _displayNextItem = ( // search finished, update title and status message else _finishSearch(resultCount); }; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; /** * Default splitQuery function. Can be overridden in ``sphinx.search`` with a @@ -160,13 +176,26 @@ const Search = { _queued_query: null, _pulse_status: -1, - htmlToText: (htmlString) => { + htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + for (const removalQuery of [".headerlinks", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; + if (docContent) return docContent.textContent; + console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." ); return ""; }, @@ -239,16 +268,7 @@ const Search = { else Search.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - + _parseQuery: (query) => { // stem the search terms and add them to the correct list const stemmer = new Stemmer(); const searchTerms = new Set(); @@ -284,16 +304,32 @@ const Search = { // console.info("required: ", [...searchTerms]); // console.info("excluded: ", [...excludedTerms]); - // array of [docname, title, anchor, descr, score, filename] - let results = []; + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename]. + const normalResults = []; + const nonMainIndexResults = []; + _removeChildren(document.getElementById("search-progress")); - const queryLower = query.toLowerCase(); + const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { let score = Math.round(100 * queryLower.length / title.length) - results.push([ + normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", @@ -308,46 +344,47 @@ const Search = { // search for explicit entries in index directives for (const [entry, foundEntries] of Object.entries(indexEntries)) { if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ docNames[file], titles[file], id ? "#" + id : "", null, score, filenames[file], - ]); + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } } } } // lookup as object objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)) ); // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; // remove duplicate search results // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept @@ -361,7 +398,12 @@ const Search = { return acc; }, []); - results = results.reverse(); + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); // for debugging //Search.lastresults = results.slice(); // a copy @@ -466,14 +508,18 @@ const Search = { // add support for partial matches if (word.length > 2) { const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } } // no match but word was a required one @@ -496,9 +542,8 @@ const Search = { // create the mapping files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); }); }); @@ -549,8 +594,8 @@ const Search = { * search summary for a given text. keywords is a list * of stemmed words. */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); if (text === "") return null; const textLower = text.toLowerCase(); diff --git a/docs/_build/html/auth.html b/docs/_build/html/auth.html index 26971e2c5..a95a7d956 100644 --- a/docs/_build/html/auth.html +++ b/docs/_build/html/auth.html @@ -9,7 +9,7 @@ - + @@ -188,7 +188,7 @@

Related Topics

- + diff --git a/docs/_build/html/file.html b/docs/_build/html/file.html index f7927b4ae..98b162de3 100644 --- a/docs/_build/html/file.html +++ b/docs/_build/html/file.html @@ -9,7 +9,7 @@ - + @@ -237,7 +237,7 @@

Related Topics

- + diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 5b481505e..d7372298c 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -8,7 +8,7 @@ - + @@ -678,7 +678,7 @@

Related Topics

- + diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index 016cb7fc6..36787eb40 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -9,7 +9,7 @@ - + @@ -347,7 +347,7 @@

Related Topics

- + diff --git a/docs/_build/html/indexing.html b/docs/_build/html/indexing.html index 0db7bc49a..1df22043b 100644 --- a/docs/_build/html/indexing.html +++ b/docs/_build/html/indexing.html @@ -9,7 +9,7 @@ - + @@ -206,10 +206,10 @@

Gen3 Index Class
Parameters:
    -

  • format (json - json in the) –

    • +

  • format (json - json in the)

  • { – ‘uploader’: type(string) ‘file_name’: type(string) (optional*)

    • -

  • } –

    • +

  • }

@@ -307,7 +307,7 @@

Gen3 Index Class

Parameters:
    -

  • delete (guid -- GUID of the object to) –

    • -

  • True (delete_file_locations -- if) –

    • -

  • location (removes the object from existing bucket) –

    • +

  • delete (guid -- GUID of the object to)

    • +

  • True (delete_file_locations -- if)

    • +

  • location (removes the object from existing bucket)

Returns:
@@ -127,7 +127,7 @@

Related Topics

- + diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html index 78808627d..30c6e7322 100644 --- a/docs/_build/html/py-modindex.html +++ b/docs/_build/html/py-modindex.html @@ -8,7 +8,7 @@ - + @@ -125,7 +125,7 @@

Related Topics

- + diff --git a/docs/_build/html/query.html b/docs/_build/html/query.html index 2946ab0c5..9acf1a925 100644 --- a/docs/_build/html/query.html +++ b/docs/_build/html/query.html @@ -9,7 +9,7 @@ - + @@ -212,7 +212,7 @@

Related Topics

- + diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html index d78a97984..5b922a554 100644 --- a/docs/_build/html/search.html +++ b/docs/_build/html/search.html @@ -9,14 +9,15 @@ - + - - + + + @@ -60,10 +61,7 @@

Search

- -
- -
+
diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index e4b41225c..6ff6152ee 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["auth", "file", "index", "indexing", "jobs", "metadata", "object", "query", "submission", "tools", "tools/drs_pull", "tools/indexing", "tools/metadata", "wss"], "filenames": ["auth.rst", "file.rst", "index.rst", "indexing.rst", "jobs.rst", "metadata.rst", "object.rst", "query.rst", "submission.rst", "tools.rst", "tools/drs_pull.rst", "tools/indexing.rst", "tools/metadata.rst", "wss.rst"], "titles": ["Gen3 Auth Helper", "Gen3 File Class", "Welcome to Gen3 SDK\u2019s documentation!", "Gen3 Index Class", "Gen3 Jobs Class", "Gen3 Metadata Class", "Gen3 Object Class", "Gen3 Query Class", "Gen3 Submission Class", "Gen3 Tools", "DRS Download Tools", "Indexing Tools", "Metadata Tools", "Gen3 Workspace Storage"], "terms": {"class": [0, 2, 10, 11, 13], "gen3auth": [0, 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"Indexing Tools": [[11, "indexing-tools"]], "Download": [[11, "module-gen3.tools.indexing.download_manifest"]], "Index": [[11, "module-gen3.tools.indexing.index_manifest"]], "Verify": [[11, "module-gen3.tools.indexing.verify_manifest"]], "Metadata Tools": [[12, "metadata-tools"]], "Ingest": [[12, "module-gen3.tools.metadata.ingest_manifest"]], "Gen3 Workspace Storage": [[13, "gen3-workspace-storage"]]}, "indexentries": {"gen3auth (class in gen3.auth)": [[0, "gen3.auth.Gen3Auth"]], "curl() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.curl"]], "get_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token"]], "get_access_token_from_wts() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.get_access_token_from_wts"]], "refresh_access_token() (gen3.auth.gen3auth method)": [[0, "gen3.auth.Gen3Auth.refresh_access_token"]], "gen3file (class in gen3.file)": [[1, "gen3.file.Gen3File"]], "delete_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file"]], "delete_file_locations() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.delete_file_locations"]], "download_single() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.download_single"]], "get_presigned_url() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.get_presigned_url"]], "upload_file() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file"]], "upload_file_to_guid() (gen3.file.gen3file method)": [[1, "gen3.file.Gen3File.upload_file_to_guid"]], "gen3index (class in gen3.index)": [[3, "gen3.index.Gen3Index"]], "async_create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_create_record"]], "async_get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_record"]], "async_get_records_from_checksum() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_from_checksum"]], "async_get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_records_on_page"]], "async_get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_get_with_params"]], "async_query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_query_urls"]], "async_update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.async_update_record"]], "create_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_blank"]], "create_new_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_new_version"]], "create_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.create_record"]], "delete_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.delete_record"]], "get() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get"]], "get_all_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_all_records"]], "get_guids_prefix() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_guids_prefix"]], "get_latest_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_latest_version"]], "get_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record"]], "get_record_doc() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_record_doc"]], "get_records() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records"]], "get_records_on_page() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_records_on_page"]], "get_stats() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_stats"]], "get_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_urls"]], "get_valid_guids() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_valid_guids"]], "get_version() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_version"]], "get_versions() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_versions"]], "get_with_params() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.get_with_params"]], "is_healthy() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.is_healthy"]], "query_urls() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.query_urls"]], "update_blank() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_blank"]], "update_record() (gen3.index.gen3index method)": [[3, "gen3.index.Gen3Index.update_record"]], "gen3jobs (class in gen3.jobs)": [[4, "gen3.jobs.Gen3Jobs"]], "async_run_job_and_wait() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.async_run_job_and_wait"]], "create_job() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.create_job"]], "get_output() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_output"]], "get_status() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_status"]], "get_version() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.get_version"]], "is_healthy() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.is_healthy"]], "list_jobs() (gen3.jobs.gen3jobs method)": [[4, "gen3.jobs.Gen3Jobs.list_jobs"]], "gen3metadata (class in gen3.metadata)": [[5, "gen3.metadata.Gen3Metadata"]], "async_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create"]], "async_create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_create_aliases"]], "async_delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_alias"]], "async_delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_delete_aliases"]], "async_get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get"]], "async_get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_get_aliases"]], "async_update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update"]], "async_update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.async_update_aliases"]], "auth_provider (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.auth_provider"]], "batch_create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.batch_create"]], "create() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create"]], "create_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_aliases"]], "create_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.create_index_key_path"]], "delete() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete"]], "delete_alias() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_alias"]], "delete_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_aliases"]], "delete_index_key_path() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.delete_index_key_path"]], "endpoint (gen3.metadata.gen3metadata attribute)": [[5, "gen3.metadata.Gen3Metadata.endpoint"]], "get() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get"]], "get_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_aliases"]], "get_index_key_paths() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_index_key_paths"]], "get_version() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.get_version"]], "is_healthy() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.is_healthy"]], "query() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.query"]], "update() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update"]], "update_aliases() (gen3.metadata.gen3metadata method)": [[5, "gen3.metadata.Gen3Metadata.update_aliases"]], "gen3object (class in gen3.object)": [[6, "gen3.object.Gen3Object"]], "delete_object() (gen3.object.gen3object method)": [[6, "gen3.object.Gen3Object.delete_object"]], "gen3query (class in gen3.query)": [[7, "gen3.query.Gen3Query"]], "graphql_query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.graphql_query"]], "query() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.query"]], "raw_data_download() (gen3.query.gen3query method)": [[7, "gen3.query.Gen3Query.raw_data_download"]], "gen3submission (class in gen3.submission)": [[8, "gen3.submission.Gen3Submission"]], "create_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_program"]], "create_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.create_project"]], "delete_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_node"]], "delete_nodes() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_nodes"]], "delete_program() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_program"]], "delete_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_project"]], "delete_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_record"]], "delete_records() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.delete_records"]], "export_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_node"]], "export_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.export_record"]], "get_dictionary_all() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_all"]], "get_dictionary_node() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_dictionary_node"]], "get_graphql_schema() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_graphql_schema"]], "get_programs() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_programs"]], "get_project_dictionary() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_dictionary"]], "get_project_manifest() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_project_manifest"]], "get_projects() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.get_projects"]], "open_project() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.open_project"]], "query() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.query"]], "submit_file() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_file"]], "submit_record() (gen3.submission.gen3submission method)": [[8, "gen3.submission.Gen3Submission.submit_record"]], "gen3.tools": [[9, "module-gen3.tools"]], "module": [[9, "module-gen3.tools"], [10, "module-gen3.tools.download.drs_download"], [11, "module-gen3.tools.indexing.download_manifest"], [11, "module-gen3.tools.indexing.index_manifest"], [11, "module-gen3.tools.indexing.verify_manifest"], [12, "module-gen3.tools.metadata.ingest_manifest"]], "downloadmanager (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadManager"]], "downloadstatus (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.DownloadStatus"]], "downloadable (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Downloadable"]], "manifest (class in gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.Manifest"]], "_manager (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable._manager"]], "access_methods (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.access_methods"]], "cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens"]], "children (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.children"]], "commons_url (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.commons_url"]], "create_object_list() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.create_object_list"]], "created_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.created_time"]], "download() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.download"]], "download() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.download"]], "download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.download_files_in_drs_manifest"]], "end_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.end_time"]], "file_name (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_name"]], "file_name (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_name"]], "file_size (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.file_size"]], "file_size (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.file_size"]], "gen3.tools.download.drs_download": [[10, "module-gen3.tools.download.drs_download"]], "get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.get_fresh_token"]], "hostname (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.hostname"]], "list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_access_in_drs_manifest"]], "list_drs_object() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_drs_object"]], "list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)": [[10, "gen3.tools.download.drs_download.list_files_in_drs_manifest"]], "load() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load"]], "load_manifest() (gen3.tools.download.drs_download.manifest static method)": [[10, "gen3.tools.download.drs_download.Manifest.load_manifest"]], "md5sum (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.md5sum"]], "object_id (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_id"]], "object_id (gen3.tools.download.drs_download.manifest attribute)": [[10, "gen3.tools.download.drs_download.Manifest.object_id"]], "object_type (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.object_type"]], "pprint() (gen3.tools.download.drs_download.downloadable method)": [[10, "gen3.tools.download.drs_download.Downloadable.pprint"]], "resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.resolve_objects"]], "start_time (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.start_time"]], "status (gen3.tools.download.drs_download.downloadstatus attribute)": [[10, "gen3.tools.download.drs_download.DownloadStatus.status"]], "updated_time (gen3.tools.download.drs_download.downloadable attribute)": [[10, "gen3.tools.download.drs_download.Downloadable.updated_time"]], "user_access() (gen3.tools.download.drs_download.downloadmanager method)": [[10, "gen3.tools.download.drs_download.DownloadManager.user_access"]], "acls (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.ACLS"]], "authz (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.AUTHZ"]], "current_dir (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.CURRENT_DIR"]], "current_dir (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.CURRENT_DIR"]], "guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.GUID"]], "indexd_record_page_size (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE"]], "max_concurrent_requests (in module gen3.tools.indexing.download_manifest)": [[11, "gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS"]], "max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)": [[11, "gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS"]], "md5 (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.MD5"]], "prev_guid (in module gen3.tools.indexing.index_manifest)": [[11, "gen3.tools.indexing.index_manifest.PREV_GUID"]], "size (in module gen3.tools.indexing.index_manifest)": 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a/docs/_build/html/submission.html b/docs/_build/html/submission.html index edc7b38db..69a9f5e5d 100644 --- a/docs/_build/html/submission.html +++ b/docs/_build/html/submission.html @@ -9,7 +9,7 @@ - + @@ -514,7 +514,7 @@

Related Topics

- + diff --git a/docs/_build/html/tools.html b/docs/_build/html/tools.html index 49e7af7d0..0dddee8a4 100644 --- a/docs/_build/html/tools.html +++ b/docs/_build/html/tools.html @@ -9,7 +9,7 @@ - + @@ -185,7 +185,7 @@

Related Topics

- + diff --git a/docs/_build/html/tools/drs_pull.html b/docs/_build/html/tools/drs_pull.html index eb16ffd32..8148d1361 100644 --- a/docs/_build/html/tools/drs_pull.html +++ b/docs/_build/html/tools/drs_pull.html @@ -9,7 +9,7 @@ - + @@ -76,7 +76,7 @@
Parameters:
    -

  • object_list (List[Downloadable]) –

    • +

  • object_list (List[Downloadable])

  • save_directory (str) – directory to save to (will be created)

  • show_progress (bool) – show a download progress bar

  • unpack_packages (bool) – set to False to disable the unpacking of downloaded packages

    • @@ -573,7 +573,7 @@

    Related Topics

- + diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index 4647d50ac..980a2885d 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -9,7 +9,7 @@ - + @@ -381,7 +381,7 @@

Indexing Tools
-async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1711461363.0524344.log')[source]
+async gen3.tools.indexing.verify_manifest.async_verify_object_manifest(commons_url, manifest_file, max_concurrent_requests=24, manifest_row_parsers={'acl': <function _get_acl_from_row>, 'authz': <function _get_authz_from_row>, 'file_name': <function _get_file_name_from_row>, 'file_size': <function _get_file_size_from_row>, 'guid': <function _get_guid_from_row>, 'md5': <function _get_md5_from_row>, 'urls': <function _get_urls_from_row>}, manifest_file_delimiter=None, output_filename='verify-manifest-errors-1717185181.7131712.log')[source]

Verify all file object records into a manifest csv

Parameters:
@@ -483,7 +483,7 @@

Related Topics

- + diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 5d5f99763..af7a0c0e5 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -9,7 +9,7 @@ - + @@ -102,7 +102,7 @@

Metadata Tools
-async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1711461363.3879402.log', get_guid_from_file=True, metadata_type=None)[source]
+async gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest(commons_url, manifest_file, metadata_source, auth=None, max_concurrent_requests=24, manifest_row_parsers={'guid_for_row': <function _get_guid_for_row>, 'indexed_file_object_guid': <function _query_for_associated_indexd_record_guid>}, manifest_file_delimiter=None, output_filename='ingest-metadata-manifest-errors-1717185182.0089867.log', get_guid_from_file=True, metadata_type=None)[source]

Ingest all metadata records into a manifest csv

Parameters:
@@ -218,7 +218,7 @@

Related Topics

- + diff --git a/docs/_build/html/wss.html b/docs/_build/html/wss.html index e2d7abfc5..e3daccc57 100644 --- a/docs/_build/html/wss.html +++ b/docs/_build/html/wss.html @@ -9,7 +9,7 @@ - + @@ -215,7 +215,7 @@

Related Topics

- + diff --git a/poetry.lock b/poetry.lock index d2822a747..df73fda67 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "aiofiles" @@ -13,87 +13,87 @@ files = [ [[package]] name = "aiohttp" -version = "3.9.3" +version = "3.9.5" description = "Async http client/server framework (asyncio)" optional = false python-versions = ">=3.8" files = [ - {file = "aiohttp-3.9.3-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:939677b61f9d72a4fa2a042a5eee2a99a24001a67c13da113b2e30396567db54"}, - {file = "aiohttp-3.9.3-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:1f5cd333fcf7590a18334c90f8c9147c837a6ec8a178e88d90a9b96ea03194cc"}, - {file = "aiohttp-3.9.3-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:82e6aa28dd46374f72093eda8bcd142f7771ee1eb9d1e223ff0fa7177a96b4a5"}, - {file = "aiohttp-3.9.3-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f56455b0c2c7cc3b0c584815264461d07b177f903a04481dfc33e08a89f0c26b"}, - {file = "aiohttp-3.9.3-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = 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"werkzeug-3.0.3.tar.gz", hash = "sha256:097e5bfda9f0aba8da6b8545146def481d06aa7d3266e7448e2cccf67dd8bd18"}, ] [package.dependencies] @@ -2274,18 +2275,18 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.18.1" +version = "3.19.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, - {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, + {file = "zipp-3.19.0-py3-none-any.whl", hash = "sha256:96dc6ad62f1441bcaccef23b274ec471518daf4fbbc580341204936a5a3dddec"}, + {file = "zipp-3.19.0.tar.gz", hash = "sha256:952df858fb3164426c976d9338d3961e8e8b3758e2e059e0f754b8c4262625ee"}, ] [package.extras] docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] fhir = ["fhirclient"] @@ -2293,4 +2294,4 @@ fhir = ["fhirclient"] [metadata] lock-version = "2.0" python-versions = ">=3.9, <4" -content-hash = "f123fc10ee0d55ae9d502be7145a52ea0a864e4aee076f4f16c64c401a7d1831" +content-hash = "2abb0a0a475f434e858aa42b8fe8af0e69978cc970cc0a8035ac3f55188b1e79" diff --git a/pyproject.toml b/pyproject.toml index 364f17a9f..8a4891149 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,7 +39,7 @@ urllib3 = ">2.0.0" httpx = "*" xmltodict = "^0.13.0" pyyaml = ">=6.0.1" -gen3users = "*" +gen3users = { git = "https://github.com/uc-cdis/gen3users.git", branch = "feat/python" } # A list of all of the optional dependencies, some of which are included in the # below `extras`. They can be opted into by apps. @@ -70,3 +70,11 @@ addopts = "-vv" testpaths = [ "tests", ] + +# https://pypi.org/project/poetry-pyinstaller-plugin/ +[tool.poetry-pyinstaller-plugin.scripts] +gen3 = { source = "./gen3/cli/__main__.py", type = "onedir", bundle = false } + +[tool.poetry-pyinstaller-plugin.collect] +# Collect all submodules, data files & binaries for 'package_A' and 'package_B' +all = ['gen3', 'asyncio']