diff --git a/docs/_build/doctrees/auth.doctree b/docs/_build/doctrees/auth.doctree index 2d070482..f27f0878 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 12830bb9..102a3062 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 2548928c..bd794497 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 3f4beb48..4d795d0b 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 f48407b8..3fb622e2 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 c32d7f08..7e2ece18 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 f38fe416..abb2e691 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 7ea6637f..c791cd27 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 be50afa8..b5695fff 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 887e3fb4..70bc7562 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 cc708b85..81b49913 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 0ed8107e..0a382eaf 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 3bb40a3c..92ce038a 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 3b662683..e085b89e 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 a8ee4213..95fd0aac 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 0d4fe35f..fe5cc45b 100644 --- a/docs/_build/html/.buildinfo +++ b/docs/_build/html/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 6e3a2fe708513a88258e49e3a60c949d +config: 5bae407aea2ae623a324546c20861315 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak index a55e85cb..0d4fe35f 100644 --- a/docs/_build/html/.buildinfo.bak +++ b/docs/_build/html/.buildinfo.bak @@ -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: 0743ca845f6724be988ecc05e5144ced +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 6e3a2fe708513a88258e49e3a60c949d tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_modules/gen3/auth.html b/docs/_build/html/_modules/gen3/auth.html index 36402a22..a6d77d0e 100644 --- a/docs/_build/html/_modules/gen3/auth.html +++ b/docs/_build/html/_modules/gen3/auth.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/file.html b/docs/_build/html/_modules/gen3/file.html index 0a8c1a5e..8bc4759c 100644 --- a/docs/_build/html/_modules/gen3/file.html +++ b/docs/_build/html/_modules/gen3/file.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/index.html b/docs/_build/html/_modules/gen3/index.html index e8ae5677..5ed710cc 100644 --- a/docs/_build/html/_modules/gen3/index.html +++ b/docs/_build/html/_modules/gen3/index.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/jobs.html b/docs/_build/html/_modules/gen3/jobs.html index 4fd10484..850554d3 100644 --- a/docs/_build/html/_modules/gen3/jobs.html +++ b/docs/_build/html/_modules/gen3/jobs.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/metadata.html b/docs/_build/html/_modules/gen3/metadata.html index b32a4d43..c5a2cff9 100644 --- a/docs/_build/html/_modules/gen3/metadata.html +++ b/docs/_build/html/_modules/gen3/metadata.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/object.html b/docs/_build/html/_modules/gen3/object.html index 0900851a..19cc6697 100644 --- a/docs/_build/html/_modules/gen3/object.html +++ b/docs/_build/html/_modules/gen3/object.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/query.html b/docs/_build/html/_modules/gen3/query.html index 42336600..af258709 100644 --- a/docs/_build/html/_modules/gen3/query.html +++ b/docs/_build/html/_modules/gen3/query.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/submission.html b/docs/_build/html/_modules/gen3/submission.html index 18c59636..1c274f61 100644 --- a/docs/_build/html/_modules/gen3/submission.html +++ b/docs/_build/html/_modules/gen3/submission.html @@ -9,8 +9,8 @@ - - + + 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 8cfa7615..e0432677 100644 --- a/docs/_build/html/_modules/gen3/tools/download/drs_download.html +++ b/docs/_build/html/_modules/gen3/tools/download/drs_download.html @@ -9,8 +9,8 @@ - - + + 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 c5ae2626..296f84d6 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/download_manifest.html @@ -9,8 +9,8 @@ - - + + 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 518cbc5d..9a6cab6f 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/index_manifest.html @@ -9,8 +9,8 @@ - - + + 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 41ef1ad0..69de9499 100644 --- a/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/indexing/verify_manifest.html @@ -9,8 +9,8 @@ - - + + 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 8573877f..a7575235 100644 --- a/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html +++ b/docs/_build/html/_modules/gen3/tools/metadata/ingest_manifest.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/gen3/wss.html b/docs/_build/html/_modules/gen3/wss.html index 6af2d1be..f828146d 100644 --- a/docs/_build/html/_modules/gen3/wss.html +++ b/docs/_build/html/_modules/gen3/wss.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html index 0d754483..31e298a3 100644 --- a/docs/_build/html/_modules/index.html +++ b/docs/_build/html/_modules/index.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/_static/base-stemmer.js b/docs/_build/html/_static/base-stemmer.js new file mode 100644 index 00000000..e6fa0c49 --- /dev/null +++ b/docs/_build/html/_static/base-stemmer.js @@ -0,0 +1,476 @@ +// @ts-check + +/**@constructor*/ +BaseStemmer = function() { + /** @protected */ + this.current = ''; + this.cursor = 0; + this.limit = 0; + this.limit_backward = 0; + this.bra = 0; + this.ket = 0; + + /** + * @param {string} value + */ + this.setCurrent = function(value) { + this.current = value; + this.cursor = 0; + this.limit = this.current.length; + this.limit_backward = 0; + this.bra = this.cursor; + this.ket = this.limit; + }; + + /** + * @return {string} + */ + this.getCurrent = function() { + return this.current; + }; + + /** + * @param {BaseStemmer} other + */ + this.copy_from = function(other) { + /** @protected */ + this.current = other.current; + this.cursor = other.cursor; + this.limit = other.limit; + this.limit_backward = other.limit_backward; + this.bra = other.bra; + this.ket = other.ket; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor++; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) + return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) + return true; + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.in_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return false; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return false; + this.cursor--; + return true; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_in_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) return true; + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) return true; + this.cursor--; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping = function(s, min, max) { + /** @protected */ + if (this.cursor >= this.limit) return false; + var ch = this.current.charCodeAt(this.cursor); + if (ch > max || ch < min) { + this.cursor++; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) == 0) { + this.cursor++; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping = function(s, min, max) { + /** @protected */ + while (this.cursor < this.limit) { + var ch = this.current.charCodeAt(this.cursor); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0X1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor++; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.out_grouping_b = function(s, min, max) { + /** @protected */ + if (this.cursor <= this.limit_backward) return false; + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch > max || ch < min) { + this.cursor--; + return true; + } + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) == 0) { + this.cursor--; + return true; + } + return false; + }; + + /** + * @param {number[]} s + * @param {number} min + * @param {number} max + * @return {boolean} + */ + this.go_out_grouping_b = function(s, min, max) { + /** @protected */ + while (this.cursor > this.limit_backward) { + var ch = this.current.charCodeAt(this.cursor - 1); + if (ch <= max && ch >= min) { + ch -= min; + if ((s[ch >>> 3] & (0x1 << (ch & 0x7))) != 0) { + return true; + } + } + this.cursor--; + } + return false; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s = function(s) + { + /** @protected */ + if (this.limit - this.cursor < s.length) return false; + if (this.current.slice(this.cursor, this.cursor + s.length) != s) + { + return false; + } + this.cursor += s.length; + return true; + }; + + /** + * @param {string} s + * @return {boolean} + */ + this.eq_s_b = function(s) + { + /** @protected */ + if (this.cursor - this.limit_backward < s.length) return false; + if (this.current.slice(this.cursor - s.length, this.cursor) != s) + { + return false; + } + this.cursor -= s.length; + return true; + }; + + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among = function(v) + { + /** @protected */ + var i = 0; + var j = v.length; + + var c = this.cursor; + var l = this.limit; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >>> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; // smaller + // w[0]: string, w[1]: substring_i, w[2]: result, w[3]: function (optional) + var w = v[k]; + var i2; + for (i2 = common; i2 < w[0].length; i2++) + { + if (c + common == l) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c + common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; // v->s has been inspected + if (j == i) break; // only one item in v + + // - but now we need to go round once more to get + // v->s inspected. This looks messy, but is actually + // the optimal approach. + + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c + w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c + w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + // find_among_b is for backwards processing. Same comments apply + /** + * @param {Among[]} v + * @return {number} + */ + this.find_among_b = function(v) + { + /** @protected */ + var i = 0; + var j = v.length + + var c = this.cursor; + var lb = this.limit_backward; + + var common_i = 0; + var common_j = 0; + + var first_key_inspected = false; + + while (true) + { + var k = i + ((j - i) >> 1); + var diff = 0; + var common = common_i < common_j ? common_i : common_j; + var w = v[k]; + var i2; + for (i2 = w[0].length - 1 - common; i2 >= 0; i2--) + { + if (c - common == lb) + { + diff = -1; + break; + } + diff = this.current.charCodeAt(c - 1 - common) - w[0].charCodeAt(i2); + if (diff != 0) break; + common++; + } + if (diff < 0) + { + j = k; + common_j = common; + } + else + { + i = k; + common_i = common; + } + if (j - i <= 1) + { + if (i > 0) break; + if (j == i) break; + if (first_key_inspected) break; + first_key_inspected = true; + } + } + do { + var w = v[i]; + if (common_i >= w[0].length) + { + this.cursor = c - w[0].length; + if (w.length < 4) return w[2]; + var res = w[3](this); + this.cursor = c - w[0].length; + if (res) return w[2]; + } + i = w[1]; + } while (i >= 0); + return 0; + }; + + /* to replace chars between c_bra and c_ket in this.current by the + * chars in s. + */ + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + * @return {number} + */ + this.replace_s = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = s.length - (c_ket - c_bra); + this.current = this.current.slice(0, c_bra) + s + this.current.slice(c_ket); + this.limit += adjustment; + if (this.cursor >= c_ket) this.cursor += adjustment; + else if (this.cursor > c_bra) this.cursor = c_bra; + return adjustment; + }; + + /** + * @return {boolean} + */ + this.slice_check = function() + { + /** @protected */ + if (this.bra < 0 || + this.bra > this.ket || + this.ket > this.limit || + this.limit > this.current.length) + { + return false; + } + return true; + }; + + /** + * @param {number} c_bra + * @return {boolean} + */ + this.slice_from = function(s) + { + /** @protected */ + var result = false; + if (this.slice_check()) + { + this.replace_s(this.bra, this.ket, s); + result = true; + } + return result; + }; + + /** + * @return {boolean} + */ + this.slice_del = function() + { + /** @protected */ + return this.slice_from(""); + }; + + /** + * @param {number} c_bra + * @param {number} c_ket + * @param {string} s + */ + this.insert = function(c_bra, c_ket, s) + { + /** @protected */ + var adjustment = this.replace_s(c_bra, c_ket, s); + if (c_bra <= this.bra) this.bra += adjustment; + if (c_bra <= this.ket) this.ket += adjustment; + }; + + /** + * @return {string} + */ + this.slice_to = function() + { + /** @protected */ + var result = ''; + if (this.slice_check()) + { + result = this.current.slice(this.bra, this.ket); + } + return result; + }; + + /** + * @return {string} + */ + this.assign_to = function() + { + /** @protected */ + return this.current.slice(0, this.limit); + }; +}; diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js index 0398ebb9..807cdb17 100644 --- a/docs/_build/html/_static/doctools.js +++ b/docs/_build/html/_static/doctools.js @@ -59,7 +59,7 @@ const Documentation = { Object.assign(Documentation.TRANSLATIONS, catalog.messages); Documentation.PLURAL_EXPR = new Function( "n", - `return (${catalog.plural_expr})` + `return (${catalog.plural_expr})`, ); Documentation.LOCALE = catalog.locale; }, @@ -89,7 +89,7 @@ const Documentation = { const togglerElements = document.querySelectorAll("img.toggler"); togglerElements.forEach((el) => - el.addEventListener("click", (event) => toggler(event.currentTarget)) + el.addEventListener("click", (event) => toggler(event.currentTarget)), ); togglerElements.forEach((el) => (el.style.display = "")); if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); @@ -98,14 +98,15 @@ const Documentation = { initOnKeyListeners: () => { // only install a listener if it is really needed if ( - !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && - !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS + && !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS ) return; document.addEventListener("keydown", (event) => { // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) + return; // bail with special keys if (event.altKey || event.ctrlKey || event.metaKey) return; diff --git a/docs/_build/html/_static/english-stemmer.js b/docs/_build/html/_static/english-stemmer.js new file mode 100644 index 00000000..056760ee --- /dev/null +++ b/docs/_build/html/_static/english-stemmer.js @@ -0,0 +1,1066 @@ +// Generated from english.sbl by Snowball 3.0.1 - https://snowballstem.org/ + +/**@constructor*/ +var EnglishStemmer = function() { + var base = new BaseStemmer(); + + /** @const */ var a_0 = [ + ["arsen", -1, -1], + ["commun", -1, -1], + ["emerg", -1, -1], + ["gener", -1, -1], + ["later", -1, -1], + ["organ", -1, -1], + ["past", -1, -1], + ["univers", -1, -1] + ]; + + /** @const */ var a_1 = [ + ["'", -1, 1], + ["'s'", 0, 1], + ["'s", -1, 1] + ]; + + /** @const */ var a_2 = [ + ["ied", -1, 2], + ["s", -1, 3], + ["ies", 1, 2], + ["sses", 1, 1], + ["ss", 1, -1], + ["us", 1, -1] + ]; + + /** @const */ var a_3 = [ + ["succ", -1, 1], + ["proc", -1, 1], + ["exc", -1, 1] + ]; + + /** @const */ var a_4 = [ + ["even", -1, 2], + ["cann", -1, 2], + ["inn", -1, 2], + ["earr", -1, 2], + ["herr", -1, 2], + ["out", -1, 2], + ["y", -1, 1] + ]; + + /** @const */ var a_5 = [ + ["", -1, -1], + ["ed", 0, 2], + ["eed", 1, 1], + ["ing", 0, 3], + ["edly", 0, 2], + ["eedly", 4, 1], + ["ingly", 0, 2] + ]; + + /** @const */ var a_6 = [ + ["", -1, 3], + ["bb", 0, 2], + ["dd", 0, 2], + ["ff", 0, 2], + ["gg", 0, 2], + ["bl", 0, 1], + ["mm", 0, 2], + ["nn", 0, 2], + ["pp", 0, 2], + ["rr", 0, 2], + ["at", 0, 1], + ["tt", 0, 2], + ["iz", 0, 1] + ]; + + /** @const */ var a_7 = [ + ["anci", -1, 3], + ["enci", -1, 2], + ["ogi", -1, 14], + ["li", -1, 16], + ["bli", 3, 12], + ["abli", 4, 4], + ["alli", 3, 8], + ["fulli", 3, 9], + ["lessli", 3, 15], + ["ousli", 3, 10], + ["entli", 3, 5], + ["aliti", -1, 8], + ["biliti", -1, 12], + ["iviti", -1, 11], + ["tional", -1, 1], + ["ational", 14, 7], + ["alism", -1, 8], + ["ation", -1, 7], + ["ization", 17, 6], + ["izer", -1, 6], + ["ator", -1, 7], + ["iveness", -1, 11], + ["fulness", -1, 9], + ["ousness", -1, 10], + ["ogist", -1, 13] + ]; + + /** @const */ var a_8 = [ + ["icate", -1, 4], + ["ative", -1, 6], + ["alize", -1, 3], + ["iciti", -1, 4], + ["ical", -1, 4], + ["tional", -1, 1], + ["ational", 5, 2], + ["ful", -1, 5], + ["ness", -1, 5] + ]; + + /** @const */ var a_9 = [ + ["ic", -1, 1], + ["ance", -1, 1], + ["ence", -1, 1], + ["able", -1, 1], + ["ible", -1, 1], + ["ate", -1, 1], + ["ive", -1, 1], + ["ize", -1, 1], + ["iti", -1, 1], + ["al", -1, 1], + ["ism", -1, 1], + ["ion", -1, 2], + ["er", -1, 1], + ["ous", -1, 1], + ["ant", -1, 1], + ["ent", -1, 1], + ["ment", 15, 1], + ["ement", 16, 1] + ]; + + /** @const */ var a_10 = [ + ["e", -1, 1], + ["l", -1, 2] + ]; + + /** @const */ var a_11 = [ + ["andes", -1, -1], + ["atlas", -1, -1], + ["bias", -1, -1], + ["cosmos", -1, -1], + ["early", -1, 5], + ["gently", -1, 3], + ["howe", -1, -1], + ["idly", -1, 2], + ["news", -1, -1], + ["only", -1, 6], + ["singly", -1, 7], + ["skies", -1, 1], + ["sky", -1, -1], + ["ugly", -1, 4] + ]; + + /** @const */ var /** Array */ g_aeo = [17, 64]; + + /** @const */ var /** Array */ g_v = [17, 65, 16, 1]; + + /** @const */ var /** Array */ g_v_WXY = [1, 17, 65, 208, 1]; + + /** @const */ var /** Array */ g_valid_LI = [55, 141, 2]; + + var /** boolean */ B_Y_found = false; + var /** number */ I_p2 = 0; + var /** number */ I_p1 = 0; + + + /** @return {boolean} */ + function r_prelude() { + B_Y_found = false; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + base.bra = base.cursor; + if (!(base.eq_s("'"))) + { + break lab0; + } + base.ket = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.cursor = v_1; + /** @const */ var /** number */ v_2 = base.cursor; + lab1: { + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab1; + } + base.ket = base.cursor; + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + } + base.cursor = v_2; + /** @const */ var /** number */ v_3 = base.cursor; + lab2: { + while(true) + { + /** @const */ var /** number */ v_4 = base.cursor; + lab3: { + golab4: while(true) + { + /** @const */ var /** number */ v_5 = base.cursor; + lab5: { + if (!(base.in_grouping(g_v, 97, 121))) + { + break lab5; + } + base.bra = base.cursor; + if (!(base.eq_s("y"))) + { + break lab5; + } + base.ket = base.cursor; + base.cursor = v_5; + break golab4; + } + base.cursor = v_5; + if (base.cursor >= base.limit) + { + break lab3; + } + base.cursor++; + } + if (!base.slice_from("Y")) + { + return false; + } + B_Y_found = true; + continue; + } + base.cursor = v_4; + break; + } + } + base.cursor = v_3; + return true; + }; + + /** @return {boolean} */ + function r_mark_regions() { + I_p1 = base.limit; + I_p2 = base.limit; + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + lab1: { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + if (base.find_among(a_0) == 0) + { + break lab2; + } + break lab1; + } + base.cursor = v_2; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + } + I_p1 = base.cursor; + if (!base.go_out_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + if (!base.go_in_grouping(g_v, 97, 121)) + { + break lab0; + } + base.cursor++; + I_p2 = base.cursor; + } + base.cursor = v_1; + return true; + }; + + /** @return {boolean} */ + function r_shortv() { + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.out_grouping_b(g_v_WXY, 89, 121))) + { + break lab1; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + lab2: { + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (!(base.in_grouping_b(g_v, 97, 121))) + { + break lab2; + } + if (base.cursor > base.limit_backward) + { + break lab2; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("past"))) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_R1() { + return I_p1 <= base.cursor; + }; + + /** @return {boolean} */ + function r_R2() { + return I_p2 <= base.cursor; + }; + + /** @return {boolean} */ + function r_Step_1a() { + var /** number */ among_var; + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab0: { + base.ket = base.cursor; + if (base.find_among_b(a_1) == 0) + { + base.cursor = base.limit - v_1; + break lab0; + } + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + base.ket = base.cursor; + among_var = base.find_among_b(a_2); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + if (!base.slice_from("ss")) + { + return false; + } + break; + case 2: + lab1: { + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + { + /** @const */ var /** number */ c1 = base.cursor - 2; + if (c1 < base.limit_backward) + { + break lab2; + } + base.cursor = c1; + } + if (!base.slice_from("i")) + { + return false; + } + break lab1; + } + base.cursor = base.limit - v_2; + if (!base.slice_from("ie")) + { + return false; + } + } + break; + case 3: + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1b() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_5); + base.bra = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + switch (among_var) { + case 1: + /** @const */ var /** number */ v_2 = base.limit - base.cursor; + lab2: { + lab3: { + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + lab4: { + if (base.find_among_b(a_3) == 0) + { + break lab4; + } + if (base.cursor > base.limit_backward) + { + break lab4; + } + break lab3; + } + base.cursor = base.limit - v_3; + if (!r_R1()) + { + break lab2; + } + if (!base.slice_from("ee")) + { + return false; + } + } + } + base.cursor = base.limit - v_2; + break; + case 2: + break lab1; + case 3: + among_var = base.find_among_b(a_4); + if (among_var == 0) + { + break lab1; + } + switch (among_var) { + case 1: + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + break lab1; + } + if (base.cursor > base.limit_backward) + { + break lab1; + } + base.cursor = base.limit - v_4; + base.bra = base.cursor; + if (!base.slice_from("ie")) + { + return false; + } + break; + case 2: + if (base.cursor > base.limit_backward) + { + break lab1; + } + break; + } + break; + } + break lab0; + } + base.cursor = base.limit - v_1; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + if (!base.go_out_grouping_b(g_v, 97, 121)) + { + return false; + } + base.cursor--; + base.cursor = base.limit - v_5; + if (!base.slice_del()) + { + return false; + } + base.ket = base.cursor; + base.bra = base.cursor; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + among_var = base.find_among_b(a_6); + switch (among_var) { + case 1: + if (!base.slice_from("e")) + { + return false; + } + return false; + case 2: + { + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + lab5: { + if (!(base.in_grouping_b(g_aeo, 97, 111))) + { + break lab5; + } + if (base.cursor > base.limit_backward) + { + break lab5; + } + return false; + } + base.cursor = base.limit - v_7; + } + break; + case 3: + if (base.cursor != I_p1) + { + return false; + } + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + if (!r_shortv()) + { + return false; + } + base.cursor = base.limit - v_8; + if (!base.slice_from("e")) + { + return false; + } + return false; + } + base.cursor = base.limit - v_6; + base.ket = base.cursor; + if (base.cursor <= base.limit_backward) + { + return false; + } + base.cursor--; + base.bra = base.cursor; + if (!base.slice_del()) + { + return false; + } + } + return true; + }; + + /** @return {boolean} */ + function r_Step_1c() { + base.ket = base.cursor; + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("y"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("Y"))) + { + return false; + } + } + base.bra = base.cursor; + if (!(base.out_grouping_b(g_v, 97, 121))) + { + return false; + } + lab2: { + if (base.cursor > base.limit_backward) + { + break lab2; + } + return false; + } + if (!base.slice_from("i")) + { + return false; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_2() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_7); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ence")) + { + return false; + } + break; + case 3: + if (!base.slice_from("ance")) + { + return false; + } + break; + case 4: + if (!base.slice_from("able")) + { + return false; + } + break; + case 5: + if (!base.slice_from("ent")) + { + return false; + } + break; + case 6: + if (!base.slice_from("ize")) + { + return false; + } + break; + case 7: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 8: + if (!base.slice_from("al")) + { + return false; + } + break; + case 9: + if (!base.slice_from("ful")) + { + return false; + } + break; + case 10: + if (!base.slice_from("ous")) + { + return false; + } + break; + case 11: + if (!base.slice_from("ive")) + { + return false; + } + break; + case 12: + if (!base.slice_from("ble")) + { + return false; + } + break; + case 13: + if (!base.slice_from("og")) + { + return false; + } + break; + case 14: + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_from("og")) + { + return false; + } + break; + case 15: + if (!base.slice_from("less")) + { + return false; + } + break; + case 16: + if (!(base.in_grouping_b(g_valid_LI, 99, 116))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_3() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_8); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R1()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("tion")) + { + return false; + } + break; + case 2: + if (!base.slice_from("ate")) + { + return false; + } + break; + case 3: + if (!base.slice_from("al")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ic")) + { + return false; + } + break; + case 5: + if (!base.slice_del()) + { + return false; + } + break; + case 6: + if (!r_R2()) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_4() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_9); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + if (!r_R2()) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_del()) + { + return false; + } + break; + case 2: + lab0: { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab1: { + if (!(base.eq_s_b("s"))) + { + break lab1; + } + break lab0; + } + base.cursor = base.limit - v_1; + if (!(base.eq_s_b("t"))) + { + return false; + } + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_Step_5() { + var /** number */ among_var; + base.ket = base.cursor; + among_var = base.find_among_b(a_10); + if (among_var == 0) + { + return false; + } + base.bra = base.cursor; + switch (among_var) { + case 1: + lab0: { + lab1: { + if (!r_R2()) + { + break lab1; + } + break lab0; + } + if (!r_R1()) + { + return false; + } + { + /** @const */ var /** number */ v_1 = base.limit - base.cursor; + lab2: { + if (!r_shortv()) + { + break lab2; + } + return false; + } + base.cursor = base.limit - v_1; + } + } + if (!base.slice_del()) + { + return false; + } + break; + case 2: + if (!r_R2()) + { + return false; + } + if (!(base.eq_s_b("l"))) + { + return false; + } + if (!base.slice_del()) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_exception1() { + var /** number */ among_var; + base.bra = base.cursor; + among_var = base.find_among(a_11); + if (among_var == 0) + { + return false; + } + base.ket = base.cursor; + if (base.cursor < base.limit) + { + return false; + } + switch (among_var) { + case 1: + if (!base.slice_from("sky")) + { + return false; + } + break; + case 2: + if (!base.slice_from("idl")) + { + return false; + } + break; + case 3: + if (!base.slice_from("gentl")) + { + return false; + } + break; + case 4: + if (!base.slice_from("ugli")) + { + return false; + } + break; + case 5: + if (!base.slice_from("earli")) + { + return false; + } + break; + case 6: + if (!base.slice_from("onli")) + { + return false; + } + break; + case 7: + if (!base.slice_from("singl")) + { + return false; + } + break; + } + return true; + }; + + /** @return {boolean} */ + function r_postlude() { + if (!B_Y_found) + { + return false; + } + while(true) + { + /** @const */ var /** number */ v_1 = base.cursor; + lab0: { + golab1: while(true) + { + /** @const */ var /** number */ v_2 = base.cursor; + lab2: { + base.bra = base.cursor; + if (!(base.eq_s("Y"))) + { + break lab2; + } + base.ket = base.cursor; + base.cursor = v_2; + break golab1; + } + base.cursor = v_2; + if (base.cursor >= base.limit) + { + break lab0; + } + base.cursor++; + } + if (!base.slice_from("y")) + { + return false; + } + continue; + } + base.cursor = v_1; + break; + } + return true; + }; + + this.stem = /** @return {boolean} */ function() { + lab0: { + /** @const */ var /** number */ v_1 = base.cursor; + lab1: { + if (!r_exception1()) + { + break lab1; + } + break lab0; + } + base.cursor = v_1; + lab2: { + { + /** @const */ var /** number */ v_2 = base.cursor; + lab3: { + { + /** @const */ var /** number */ c1 = base.cursor + 3; + if (c1 > base.limit) + { + break lab3; + } + base.cursor = c1; + } + break lab2; + } + base.cursor = v_2; + } + break lab0; + } + base.cursor = v_1; + r_prelude(); + r_mark_regions(); + base.limit_backward = base.cursor; base.cursor = base.limit; + /** @const */ var /** number */ v_3 = base.limit - base.cursor; + r_Step_1a(); + base.cursor = base.limit - v_3; + /** @const */ var /** number */ v_4 = base.limit - base.cursor; + r_Step_1b(); + base.cursor = base.limit - v_4; + /** @const */ var /** number */ v_5 = base.limit - base.cursor; + r_Step_1c(); + base.cursor = base.limit - v_5; + /** @const */ var /** number */ v_6 = base.limit - base.cursor; + r_Step_2(); + base.cursor = base.limit - v_6; + /** @const */ var /** number */ v_7 = base.limit - base.cursor; + r_Step_3(); + base.cursor = base.limit - v_7; + /** @const */ var /** number */ v_8 = base.limit - base.cursor; + r_Step_4(); + base.cursor = base.limit - v_8; + /** @const */ var /** number */ v_9 = base.limit - base.cursor; + r_Step_5(); + base.cursor = base.limit - v_9; + base.cursor = base.limit_backward; + /** @const */ var /** number */ v_10 = base.cursor; + r_postlude(); + base.cursor = v_10; + } + return true; + }; + + /**@return{string}*/ + this['stemWord'] = function(/**string*/word) { + base.setCurrent(word); + this.stem(); + return base.getCurrent(); + }; +}; diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js index c7fe6c6f..57767864 100644 --- a/docs/_build/html/_static/language_data.js +++ b/docs/_build/html/_static/language_data.js @@ -1,192 +1,13 @@ /* * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. + * namely the set of stopwords, stemmer, scorer and splitter. */ -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"]; +const stopwords = new Set(["a", "about", "above", "after", "again", "against", "all", "am", "an", "and", "any", "are", "aren't", "as", "at", "be", "because", "been", "before", "being", "below", "between", "both", "but", "by", "can't", "cannot", "could", "couldn't", "did", "didn't", "do", "does", "doesn't", "doing", "don't", "down", "during", "each", "few", "for", "from", "further", "had", "hadn't", "has", "hasn't", "have", "haven't", "having", "he", "he'd", "he'll", "he's", "her", "here", "here's", "hers", "herself", "him", "himself", "his", "how", "how's", "i", "i'd", "i'll", "i'm", "i've", "if", "in", "into", "is", "isn't", "it", "it's", "its", "itself", "let's", "me", "more", "most", "mustn't", "my", "myself", "no", "nor", "not", "of", "off", "on", "once", "only", "or", "other", "ought", "our", "ours", "ourselves", "out", "over", "own", "same", "shan't", "she", "she'd", "she'll", "she's", "should", "shouldn't", "so", "some", "such", "than", "that", "that's", "the", "their", "theirs", "them", "themselves", "then", "there", "there's", "these", "they", "they'd", "they'll", "they're", "they've", "this", "those", "through", "to", "too", "under", "until", "up", "very", "was", "wasn't", "we", "we'd", "we'll", "we're", "we've", "were", "weren't", "what", "what's", "when", "when's", "where", "where's", "which", "while", "who", "who's", "whom", "why", "why's", "with", "won't", "would", "wouldn't", "you", "you'd", "you'll", "you're", "you've", "your", "yours", "yourself", "yourselves"]); +window.stopwords = stopwords; // Export to global scope -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} - +/* Non-minified versions are copied as separate JavaScript files, if available */ +BaseStemmer=function(){this.current="",this.cursor=0,this.limit=0,this.limit_backward=0,this.bra=0,this.ket=0,this.setCurrent=function(t){this.current=t,this.cursor=0,this.limit=this.current.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},this.getCurrent=function(){return this.current},this.copy_from=function(t){this.current=t.current,this.cursor=t.cursor,this.limit=t.limit,this.limit_backward=t.limit_backward,this.bra=t.bra,this.ket=t.ket},this.in_grouping=function(t,r,i){return!(this.cursor>=this.limit||i<(i=this.current.charCodeAt(this.cursor))||i>>3]&1<<(7&i))||(this.cursor++,0))},this.go_in_grouping=function(t,r,i){for(;this.cursor>>3]&1<<(7&s)))return!0;this.cursor++}return!1},this.in_grouping_b=function(t,r,i){return!(this.cursor<=this.limit_backward||i<(i=this.current.charCodeAt(this.cursor-1))||i>>3]&1<<(7&i))||(this.cursor--,0))},this.go_in_grouping_b=function(t,r,i){for(;this.cursor>this.limit_backward;){var s=this.current.charCodeAt(this.cursor-1);if(i>>3]&1<<(7&s)))return!0;this.cursor--}return!1},this.out_grouping=function(t,r,i){return!(this.cursor>=this.limit)&&(i<(i=this.current.charCodeAt(this.cursor))||i>>3]&1<<(7&i)))&&(this.cursor++,!0)},this.go_out_grouping=function(t,r,i){for(;this.cursor>>3]&1<<(7&s)))return!0;this.cursor++}return!1},this.out_grouping_b=function(t,r,i){return!(this.cursor<=this.limit_backward)&&(i<(i=this.current.charCodeAt(this.cursor-1))||i>>3]&1<<(7&i)))&&(this.cursor--,!0)},this.go_out_grouping_b=function(t,r,i){for(;this.cursor>this.limit_backward;){var s=this.current.charCodeAt(this.cursor-1);if(s<=i&&r<=s&&0!=(t[(s-=r)>>>3]&1<<(7&s)))return!0;this.cursor--}return!1},this.eq_s=function(t){return!(this.limit-this.cursor>>1),o=0,a=e=(l=t[r])[0].length){if(this.cursor=s+l[0].length,l.length<4)return l[2];var g=l[3](this);if(this.cursor=s+l[0].length,g)return l[2]}}while(0<=(r=l[1]));return 0},this.find_among_b=function(t){for(var r=0,i=t.length,s=this.cursor,h=this.limit_backward,e=0,n=0,c=!1;;){for(var u,o=r+(i-r>>1),a=0,l=e=(u=t[r])[0].length){if(this.cursor=s-u[0].length,u.length<4)return u[2];var g=u[3](this);if(this.cursor=s-u[0].length,g)return u[2]}}while(0<=(r=u[1]));return 0},this.replace_s=function(t,r,i){var s=i.length-(r-t);return this.current=this.current.slice(0,t)+i+this.current.slice(r),this.limit+=s,this.cursor>=r?this.cursor+=s:this.cursor>t&&(this.cursor=t),s},this.slice_check=function(){return!(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>this.current.length)},this.slice_from=function(t){var r=!1;return this.slice_check()&&(this.replace_s(this.bra,this.ket,t),r=!0),r},this.slice_del=function(){return this.slice_from("")},this.insert=function(t,r,i){r=this.replace_s(t,r,i);t<=this.bra&&(this.bra+=r),t<=this.ket&&(this.ket+=r)},this.slice_to=function(){var t="";return t=this.slice_check()?this.current.slice(this.bra,this.ket):t},this.assign_to=function(){return this.current.slice(0,this.limit)}}; +var EnglishStemmer=function(){var a=new BaseStemmer,c=[["arsen",-1,-1],["commun",-1,-1],["emerg",-1,-1],["gener",-1,-1],["later",-1,-1],["organ",-1,-1],["past",-1,-1],["univers",-1,-1]],o=[["'",-1,1],["'s'",0,1],["'s",-1,1]],u=[["ied",-1,2],["s",-1,3],["ies",1,2],["sses",1,1],["ss",1,-1],["us",1,-1]],t=[["succ",-1,1],["proc",-1,1],["exc",-1,1]],l=[["even",-1,2],["cann",-1,2],["inn",-1,2],["earr",-1,2],["herr",-1,2],["out",-1,2],["y",-1,1]],n=[["",-1,-1],["ed",0,2],["eed",1,1],["ing",0,3],["edly",0,2],["eedly",4,1],["ingly",0,2]],f=[["",-1,3],["bb",0,2],["dd",0,2],["ff",0,2],["gg",0,2],["bl",0,1],["mm",0,2],["nn",0,2],["pp",0,2],["rr",0,2],["at",0,1],["tt",0,2],["iz",0,1]],_=[["anci",-1,3],["enci",-1,2],["ogi",-1,14],["li",-1,16],["bli",3,12],["abli",4,4],["alli",3,8],["fulli",3,9],["lessli",3,15],["ousli",3,10],["entli",3,5],["aliti",-1,8],["biliti",-1,12],["iviti",-1,11],["tional",-1,1],["ational",14,7],["alism",-1,8],["ation",-1,7],["ization",17,6],["izer",-1,6],["ator",-1,7],["iveness",-1,11],["fulness",-1,9],["ousness",-1,10],["ogist",-1,13]],m=[["icate",-1,4],["ative",-1,6],["alize",-1,3],["iciti",-1,4],["ical",-1,4],["tional",-1,1],["ational",5,2],["ful",-1,5],["ness",-1,5]],b=[["ic",-1,1],["ance",-1,1],["ence",-1,1],["able",-1,1],["ible",-1,1],["ate",-1,1],["ive",-1,1],["ize",-1,1],["iti",-1,1],["al",-1,1],["ism",-1,1],["ion",-1,2],["er",-1,1],["ous",-1,1],["ant",-1,1],["ent",-1,1],["ment",15,1],["ement",16,1]],k=[["e",-1,1],["l",-1,2]],g=[["andes",-1,-1],["atlas",-1,-1],["bias",-1,-1],["cosmos",-1,-1],["early",-1,5],["gently",-1,3],["howe",-1,-1],["idly",-1,2],["news",-1,-1],["only",-1,6],["singly",-1,7],["skies",-1,1],["sky",-1,-1],["ugly",-1,4]],d=[17,64],v=[17,65,16,1],i=[1,17,65,208,1],w=[55,141,2],p=!1,y=0,h=0;function q(){var r=a.limit-a.cursor;return!!(a.out_grouping_b(i,89,121)&&a.in_grouping_b(v,97,121)&&a.out_grouping_b(v,97,121)||(a.cursor=a.limit-r,a.out_grouping_b(v,97,121)&&a.in_grouping_b(v,97,121)&&!(a.cursor>a.limit_backward))||(a.cursor=a.limit-r,a.eq_s_b("past")))}function z(){return h<=a.cursor}function Y(){return y<=a.cursor}this.stem=function(){var r=a.cursor;if(!(()=>{var r;if(a.bra=a.cursor,0!=(r=a.find_among(g))&&(a.ket=a.cursor,!(a.cursora.limit)a.cursor=i;else{a.cursor=e,a.cursor=r,(()=>{p=!1;var r=a.cursor;if(a.bra=a.cursor,!a.eq_s("'")||(a.ket=a.cursor,a.slice_del())){a.cursor=r;r=a.cursor;if(a.bra=a.cursor,a.eq_s("y")){if(a.ket=a.cursor,!a.slice_from("Y"))return;p=!0}a.cursor=r;for(r=a.cursor;;){var i=a.cursor;r:{for(;;){var e=a.cursor;if(a.in_grouping(v,97,121)&&(a.bra=a.cursor,a.eq_s("y"))){a.ket=a.cursor,a.cursor=e;break}if(a.cursor=e,a.cursor>=a.limit)break r;a.cursor++}if(!a.slice_from("Y"))return;p=!0;continue}a.cursor=i;break}a.cursor=r}})(),h=a.limit,y=a.limit;i=a.cursor;r:{var s=a.cursor;if(0==a.find_among(c)){if(a.cursor=s,!a.go_out_grouping(v,97,121))break r;if(a.cursor++,!a.go_in_grouping(v,97,121))break r;a.cursor++}h=a.cursor,a.go_out_grouping(v,97,121)&&(a.cursor++,a.go_in_grouping(v,97,121))&&(a.cursor++,y=a.cursor)}a.cursor=i,a.limit_backward=a.cursor,a.cursor=a.limit;var e=a.limit-a.cursor,r=((()=>{var r=a.limit-a.cursor;if(a.ket=a.cursor,0==a.find_among_b(o))a.cursor=a.limit-r;else if(a.bra=a.cursor,!a.slice_del())return;if(a.ket=a.cursor,0!=(r=a.find_among_b(u)))switch(a.bra=a.cursor,r){case 1:if(a.slice_from("ss"))break;return;case 2:r:{var i=a.limit-a.cursor,e=a.cursor-2;if(!(e{a.ket=a.cursor,o=a.find_among_b(n),a.bra=a.cursor;r:{var r=a.limit-a.cursor;i:{switch(o){case 1:var i=a.limit-a.cursor;e:{var e=a.limit-a.cursor;if(0==a.find_among_b(t)||a.cursor>a.limit_backward){if(a.cursor=a.limit-e,!z())break e;if(!a.slice_from("ee"))return}}a.cursor=a.limit-i;break;case 2:break i;case 3:if(0==(o=a.find_among_b(l)))break i;switch(o){case 1:var s=a.limit-a.cursor;if(!a.out_grouping_b(v,97,121))break i;if(a.cursor>a.limit_backward)break i;if(a.cursor=a.limit-s,a.bra=a.cursor,a.slice_from("ie"))break;return;case 2:if(a.cursor>a.limit_backward)break i}}break r}a.cursor=a.limit-r;var c=a.limit-a.cursor;if(!a.go_out_grouping_b(v,97,121))return;if(a.cursor--,a.cursor=a.limit-c,!a.slice_del())return;a.ket=a.cursor,a.bra=a.cursor;var o,c=a.limit-a.cursor;switch(o=a.find_among_b(f)){case 1:return a.slice_from("e");case 2:var u=a.limit-a.cursor;if(a.in_grouping_b(d,97,111)&&!(a.cursor>a.limit_backward))return;a.cursor=a.limit-u;break;case 3:return a.cursor!=h||(u=a.limit-a.cursor,q()&&(a.cursor=a.limit-u,a.slice_from("e")))}if(a.cursor=a.limit-c,a.ket=a.cursor,a.cursor<=a.limit_backward)return;if(a.cursor--,a.bra=a.cursor,!a.slice_del())return}})(),a.cursor=a.limit-r,a.limit-a.cursor),r=(a.ket=a.cursor,e=a.limit-a.cursor,(a.eq_s_b("y")||(a.cursor=a.limit-e,a.eq_s_b("Y")))&&(a.bra=a.cursor,a.out_grouping_b(v,97,121))&&a.cursor>a.limit_backward&&a.slice_from("i"),a.cursor=a.limit-i,a.limit-a.cursor),e=((()=>{var r;if(a.ket=a.cursor,0!=(r=a.find_among_b(_))&&(a.bra=a.cursor,z()))switch(r){case 1:if(a.slice_from("tion"))break;return;case 2:if(a.slice_from("ence"))break;return;case 3:if(a.slice_from("ance"))break;return;case 4:if(a.slice_from("able"))break;return;case 5:if(a.slice_from("ent"))break;return;case 6:if(a.slice_from("ize"))break;return;case 7:if(a.slice_from("ate"))break;return;case 8:if(a.slice_from("al"))break;return;case 9:if(a.slice_from("ful"))break;return;case 10:if(a.slice_from("ous"))break;return;case 11:if(a.slice_from("ive"))break;return;case 12:if(a.slice_from("ble"))break;return;case 13:if(a.slice_from("og"))break;return;case 14:if(!a.eq_s_b("l"))return;if(a.slice_from("og"))break;return;case 15:if(a.slice_from("less"))break;return;case 16:if(!a.in_grouping_b(w,99,116))return;if(a.slice_del())break}})(),a.cursor=a.limit-r,a.limit-a.cursor),i=((()=>{var r;if(a.ket=a.cursor,0!=(r=a.find_among_b(m))&&(a.bra=a.cursor,z()))switch(r){case 1:if(a.slice_from("tion"))break;return;case 2:if(a.slice_from("ate"))break;return;case 3:if(a.slice_from("al"))break;return;case 4:if(a.slice_from("ic"))break;return;case 5:if(a.slice_del())break;return;case 6:if(!Y())return;if(a.slice_del())break}})(),a.cursor=a.limit-e,a.limit-a.cursor),r=((()=>{var r;if(a.ket=a.cursor,0!=(r=a.find_among_b(b))&&(a.bra=a.cursor,Y()))switch(r){case 1:if(a.slice_del())break;return;case 2:var i=a.limit-a.cursor;if(!a.eq_s_b("s")&&(a.cursor=a.limit-i,!a.eq_s_b("t")))return;if(a.slice_del())break}})(),a.cursor=a.limit-i,a.limit-a.cursor),e=((()=>{var r;if(a.ket=a.cursor,0!=(r=a.find_among_b(k)))switch(a.bra=a.cursor,r){case 1:if(!Y()){if(!z())return;var i=a.limit-a.cursor;if(q())return;a.cursor=a.limit-i}if(a.slice_del())break;return;case 2:if(!Y())return;if(!a.eq_s_b("l"))return;if(a.slice_del())break}})(),a.cursor=a.limit-r,a.cursor=a.limit_backward,a.cursor);(()=>{if(p)for(;;){var r=a.cursor;r:{for(;;){var i=a.cursor;if(a.bra=a.cursor,a.eq_s("Y")){a.ket=a.cursor,a.cursor=i;break}if(a.cursor=i,a.cursor>=a.limit)break r;a.cursor++}if(a.slice_from("y"))continue;return}a.cursor=r;break}})(),a.cursor=e}}return!0},this.stemWord=function(r){return a.setCurrent(r),this.stem(),a.getCurrent()}}; +window.Stemmer = EnglishStemmer; diff --git a/docs/_build/html/_static/searchtools.js b/docs/_build/html/_static/searchtools.js index 91f4be57..e29b1c75 100644 --- a/docs/_build/html/_static/searchtools.js +++ b/docs/_build/html/_static/searchtools.js @@ -41,11 +41,12 @@ if (typeof Scorer === "undefined") { } // Global search result kind enum, used by themes to style search results. +// prettier-ignore class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } } const _removeChildren = (element) => { @@ -58,6 +59,15 @@ const _removeChildren = (element) => { const _escapeRegExp = (string) => string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string +const _escapeHTML = (text) => { + return text + .replaceAll("&", "&") + .replaceAll("<", "<") + .replaceAll(">", ">") + .replaceAll('"', """) + .replaceAll("'", "'"); +}; + const _displayItem = (item, searchTerms, highlightTerms) => { const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; @@ -90,25 +100,30 @@ const _displayItem = (item, searchTerms, highlightTerms) => { let linkEl = listItem.appendChild(document.createElement("a")); linkEl.href = linkUrl + anchor; linkEl.dataset.score = score; - linkEl.innerHTML = title; + linkEl.innerHTML = _escapeHTML(title); if (descr) { listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; + ` (${_escapeHTML(descr)})`; // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) + if (SPHINX_HIGHLIGHT_ENABLED) + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + highlightTerms.forEach((term) => + _highlightText(listItem, term, "highlighted"), + ); + } else if (showSearchSummary) fetch(requestUrl) .then((responseData) => responseData.text()) .then((data) => { if (data) listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) + Search.makeSearchSummary(data, searchTerms, anchor), ); // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + if (SPHINX_HIGHLIGHT_ENABLED) + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + highlightTerms.forEach((term) => + _highlightText(listItem, term, "highlighted"), + ); }); Search.output.appendChild(listItem); }; @@ -117,14 +132,14 @@ const _finishSearch = (resultCount) => { Search.title.innerText = _("Search Results"); if (!resultCount) Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories.", ); else Search.status.innerText = Documentation.ngettext( "Search finished, found one page matching the search query.", "Search finished, found ${resultCount} pages matching the search query.", resultCount, - ).replace('${resultCount}', resultCount); + ).replace("${resultCount}", resultCount); }; const _displayNextItem = ( results, @@ -138,7 +153,7 @@ const _displayNextItem = ( _displayItem(results.pop(), searchTerms, highlightTerms); setTimeout( () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 + 5, ); } // search finished, update title and status message @@ -170,9 +185,10 @@ const _orderResultsByScoreThenName = (a, b) => { * This is the same as ``\W+`` in Python, preserving the surrogate pair area. */ if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query + var splitQuery = (query) => + query .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings + .filter((term) => term); // remove remaining empty strings } /** @@ -184,16 +200,23 @@ const Search = { _pulse_status: -1, htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + const htmlElement = new DOMParser().parseFromString( + htmlString, + "text/html", + ); for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + htmlElement.querySelectorAll(removalQuery).forEach((el) => { + el.remove(); + }); } if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${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.` + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`, ); } @@ -202,7 +225,7 @@ const Search = { if (docContent) return docContent.textContent; console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template.", ); return ""; }, @@ -287,12 +310,8 @@ const Search = { const queryTermLower = queryTerm.toLowerCase(); // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; + // stopwords set is from language_data.js + if (stopwords.has(queryTermLower) || queryTerm.match(/^\d+$/)) return; // stem the word let word = stemmer.stemWord(queryTermLower); @@ -304,8 +323,12 @@ const Search = { } }); - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + if (SPHINX_HIGHLIGHT_ENABLED) { + // SPHINX_HIGHLIGHT_ENABLED is set in sphinx_highlight.js + localStorage.setItem( + "sphinx_highlight_terms", + [...highlightTerms].join(" "), + ); } // console.debug("SEARCH: searching for:"); @@ -318,7 +341,13 @@ const Search = { /** * execute search (requires search index to be loaded) */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + _performSearch: ( + query, + searchTerms, + excludedTerms, + highlightTerms, + objectTerms, + ) => { const filenames = Search._index.filenames; const docNames = Search._index.docnames; const titles = Search._index.titles; @@ -334,10 +363,15 @@ const Search = { const queryLower = query.toLowerCase().trim(); for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + if ( + title.toLowerCase().trim().includes(queryLower) + && queryLower.length >= title.length / 2 + ) { for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + const score = Math.round( + (Scorer.title * queryLower.length) / title.length, + ); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, @@ -353,9 +387,9 @@ 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)) { + if (entry.includes(queryLower) && queryLower.length >= entry.length / 2) { for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); + const score = Math.round((100 * queryLower.length) / entry.length); const result = [ docNames[file], titles[file], @@ -376,11 +410,13 @@ const Search = { // lookup as object objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) + normalResults.push(...Search.performObjectSearch(term, objectTerms)), ); // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + normalResults.push( + ...Search.performTermsSearch(searchTerms, excludedTerms), + ); // let the scorer override scores with a custom scoring function if (Scorer.score) { @@ -401,7 +437,11 @@ const Search = { // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept let seen = new Set(); results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + let resultStr = result + .slice(0, 4) + .concat([result[5]]) + .map((v) => String(v)) + .join(","); if (!seen.has(resultStr)) { acc.push(result); seen.add(resultStr); @@ -413,8 +453,20 @@ const Search = { }, query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + 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 @@ -437,7 +489,7 @@ const Search = { const results = []; const objectSearchCallback = (prefix, match) => { - const name = match[4] + const name = match[4]; const fullname = (prefix ? prefix + "." : "") + name; const fullnameLower = fullname.toLowerCase(); if (fullnameLower.indexOf(object) < 0) return; @@ -489,9 +541,7 @@ const Search = { ]); }; Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) + objects[prefix].forEach((array) => objectSearchCallback(prefix, array)), ); return results; }, @@ -516,8 +566,14 @@ const Search = { // find documents, if any, containing the query word in their text/title term indices // use Object.hasOwnProperty to avoid mismatching against prototype properties const arr = [ - { files: terms.hasOwnProperty(word) ? terms[word] : undefined, score: Scorer.term }, - { files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, score: Scorer.title }, + { + files: terms.hasOwnProperty(word) ? terms[word] : undefined, + score: Scorer.term, + }, + { + files: titleTerms.hasOwnProperty(word) ? titleTerms[word] : undefined, + score: Scorer.title, + }, ]; // add support for partial matches if (word.length > 2) { @@ -558,7 +614,8 @@ const Search = { // create the mapping files.forEach((file) => { if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + else if (fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); }); }); @@ -569,11 +626,11 @@ const Search = { // as search terms with length < 3 are discarded const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 + (term) => term.length > 2, ).length; if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount + wordList.length !== searchTerms.size + && wordList.length !== filteredTermCount ) continue; @@ -581,10 +638,10 @@ const Search = { if ( [...excludedTerms].some( (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) + terms[term] === file + || titleTerms[term] === file + || (terms[term] || []).includes(file) + || (titleTerms[term] || []).includes(file), ) ) break; @@ -626,7 +683,8 @@ const Search = { let summary = document.createElement("p"); summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + summary.textContent = + top + text.substr(startWithContext, 240).trim() + tail; return summary; }, diff --git a/docs/_build/html/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js index 8a96c69a..a74e103a 100644 --- a/docs/_build/html/_static/sphinx_highlight.js +++ b/docs/_build/html/_static/sphinx_highlight.js @@ -1,7 +1,7 @@ /* Highlighting utilities for Sphinx HTML documentation. */ "use strict"; -const SPHINX_HIGHLIGHT_ENABLED = true +const SPHINX_HIGHLIGHT_ENABLED = true; /** * highlight a given string on a node by wrapping it in @@ -13,9 +13,9 @@ const _highlight = (node, addItems, text, className) => { const parent = node.parentNode; const pos = val.toLowerCase().indexOf(text); if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") + pos >= 0 + && !parent.classList.contains(className) + && !parent.classList.contains("nohighlight") ) { let span; @@ -30,13 +30,7 @@ const _highlight = (node, addItems, text, className) => { span.appendChild(document.createTextNode(val.substr(pos, text.length))); const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); + parent.insertBefore(span, parent.insertBefore(rest, node.nextSibling)); node.nodeValue = val.substr(0, pos); /* There may be more occurrences of search term in this node. So call this * function recursively on the remaining fragment. @@ -46,7 +40,7 @@ const _highlight = (node, addItems, text, className) => { if (isInSVG) { const rect = document.createElementNS( "http://www.w3.org/2000/svg", - "rect" + "rect", ); const bbox = parent.getBBox(); rect.x.baseVal.value = bbox.x; @@ -65,7 +59,7 @@ const _highlightText = (thisNode, text, className) => { let addItems = []; _highlight(thisNode, addItems, text, className); addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) + obj.parent.insertAdjacentElement("beforebegin", obj.target), ); }; @@ -73,25 +67,31 @@ const _highlightText = (thisNode, text, className) => { * Small JavaScript module for the documentation. */ const SphinxHighlight = { - /** * highlight the search words provided in localstorage in the text */ highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight // get and clear terms from localstorage const url = new URL(window.location); const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms"); + // Update history only if '?highlight' is present; otherwise it + // clears text fragments (not set in window.location by the browser) + if (url.searchParams.has("highlight")) { + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + } // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + const terms = highlight + .toLowerCase() + .split(/\s+/) + .filter((x) => x); if (terms.length === 0) return; // nothing to do // There should never be more than one element matching "div.body" @@ -107,11 +107,11 @@ const SphinxHighlight = { document .createRange() .createContextualFragment( - '" - ) + '", + ), ); }, @@ -125,7 +125,7 @@ const SphinxHighlight = { document .querySelectorAll("span.highlighted") .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") + localStorage.removeItem("sphinx_highlight_terms"); }, initEscapeListener: () => { @@ -134,10 +134,15 @@ const SphinxHighlight = { document.addEventListener("keydown", (event) => { // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) + return; // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) + return; + if ( + DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + && event.key === "Escape" + ) { SphinxHighlight.hideSearchWords(); event.preventDefault(); } diff --git a/docs/_build/html/auth.html b/docs/_build/html/auth.html index f50c53be..4c24f392 100644 --- a/docs/_build/html/auth.html +++ b/docs/_build/html/auth.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

Gen3 Auth Helper

-class gen3.auth.Gen3Auth(endpoint=None, refresh_file=None, refresh_token=None, idp=None, client_credentials=None, client_scopes=None, access_token=None)[source]
+class gen3.auth.Gen3Auth(endpoint=None, refresh_file=None, refresh_token=None, idp=None, client_credentials=None, client_scopes=None, access_token=None)[source]

Bases: AuthBase

Gen3 auth helper class for use with requests auth.

Implements requests.auth.AuthBase in order to support JWT authentication. diff --git a/docs/_build/html/file.html b/docs/_build/html/file.html index a24a91e0..cb970d07 100644 --- a/docs/_build/html/file.html +++ b/docs/_build/html/file.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

Gen3 File Class

-class gen3.file.Gen3File(endpoint=None, auth_provider=None)[source]
+class gen3.file.Gen3File(endpoint=None, auth_provider=None)[source]

Bases: object

For interacting with Gen3 file management features.

A class for interacting with the Gen3 file download services. diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index a1858dda..fc7b36ca 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html index 09d78df5..d329e8bc 100644 --- a/docs/_build/html/index.html +++ b/docs/_build/html/index.html @@ -10,8 +10,8 @@ - - + + diff --git a/docs/_build/html/indexing.html b/docs/_build/html/indexing.html index 39ab0cc2..4448e460 100644 --- a/docs/_build/html/indexing.html +++ b/docs/_build/html/indexing.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

Gen3 Index Class

-class gen3.index.Gen3Index(endpoint=None, auth_provider=None, service_location='index')[source]
+class gen3.index.Gen3Index(endpoint=None, auth_provider=None, service_location='index')[source]

Bases: object

A class for interacting with the Gen3 Index services.

@@ -57,7 +57,7 @@

Gen3 Index Class
-async async_create_record(hashes, size, did=None, urls=None, file_name=None, metadata=None, baseid=None, acl=None, urls_metadata=None, version=None, authz=None, _ssl=None, description=None, content_created_date=None, content_updated_date=None)[source]
+async async_create_record(hashes, size, did=None, urls=None, file_name=None, metadata=None, baseid=None, acl=None, urls_metadata=None, version=None, authz=None, _ssl=None, description=None, content_created_date=None, content_updated_date=None)[source]

Asynchronous function to create a record in indexd.

Parameters:
@@ -90,7 +90,7 @@

Gen3 Index Class
-async async_get_record(guid=None, _ssl=None)[source]
+async async_get_record(guid=None, _ssl=None)[source]

Asynchronous function to request a record from indexd.

Parameters:
@@ -107,7 +107,7 @@

Gen3 Index Class
-async async_get_records_from_checksum(checksum, checksum_type='md5', _ssl=None)[source]
+async async_get_records_from_checksum(checksum, checksum_type='md5', _ssl=None)[source]

Asynchronous function to request records from indexd matching checksum.

Parameters:
@@ -127,7 +127,7 @@

Gen3 Index Class
-async async_get_records_on_page(limit=None, page=None, _ssl=None)[source]
+async async_get_records_on_page(limit=None, page=None, _ssl=None)[source]

Asynchronous function to request a page from indexd.

Parameters:
@@ -144,7 +144,7 @@

Gen3 Index Class
-async async_get_with_params(params, _ssl=None)[source]
+async async_get_with_params(params, _ssl=None)[source]

Return a document object corresponding to the supplied parameter

  • need to include all the hashes in the request

  • @@ -168,7 +168,7 @@

    Gen3 Index Class
    -async async_query_urls(pattern, _ssl=None)[source]
    +async async_query_urls(pattern, _ssl=None)[source]

    Asynchronous function to query urls from indexd.

    Parameters:
    @@ -185,7 +185,7 @@

    Gen3 Index Class
    -async async_update_record(guid, file_name=None, urls=None, version=None, metadata=None, acl=None, authz=None, urls_metadata=None, _ssl=None, description=None, content_created_date=None, content_updated_date=None, **kwargs)[source]
    +async async_update_record(guid, file_name=None, urls=None, version=None, metadata=None, acl=None, authz=None, urls_metadata=None, _ssl=None, description=None, content_created_date=None, content_updated_date=None, **kwargs)[source]

    Asynchronous function to update a record in indexd.

    Parameters:
    diff --git a/docs/_build/html/jobs.html b/docs/_build/html/jobs.html index d62a26a7..ef4d7609 100644 --- a/docs/_build/html/jobs.html +++ b/docs/_build/html/jobs.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

    Gen3 Jobs Class

    -class gen3.jobs.Gen3Jobs(endpoint=None, auth_provider=None, service_location='job')[source]
    +class gen3.jobs.Gen3Jobs(endpoint=None, auth_provider=None, service_location='job')[source]

    Bases: object

    A class for interacting with the Gen3’s Job Dispatching Service(s).

    Examples

    @@ -49,7 +49,7 @@

    Gen3 Jobs Class
    -async async_run_job_and_wait(job_name, job_input, _ssl=None, **kwargs)[source]
    +async async_run_job_and_wait(job_name, job_input, _ssl=None, **kwargs)[source]

    Asynchronous function to create a job, wait for output, and return. Will sleep in a linear delay until the job is done, starting with 1 second.

    diff --git a/docs/_build/html/metadata.html b/docs/_build/html/metadata.html index cb4adeee..182b95cb 100644 --- a/docs/_build/html/metadata.html +++ b/docs/_build/html/metadata.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

    Gen3 Metadata Class

    -class gen3.metadata.Gen3Metadata(endpoint=None, auth_provider=None, service_location='mds', admin_endpoint_suffix='-admin')[source]
    +class gen3.metadata.Gen3Metadata(endpoint=None, auth_provider=None, service_location='mds', admin_endpoint_suffix='-admin')[source]

    Bases: object

    A class for interacting with the Gen3 Metadata services.

    Examples

    @@ -71,7 +71,7 @@

    Gen3 Metadata Class
    -async async_create(guid, metadata, aliases=None, overwrite=False, _ssl=None, **kwargs)[source]
    +async async_create(guid, metadata, aliases=None, overwrite=False, _ssl=None, **kwargs)[source]

    Asynchronous function to create metadata

    Parameters:
    @@ -88,7 +88,7 @@

    Gen3 Metadata Class
    -async async_create_aliases(guid, aliases, _ssl=None, **kwargs)[source]
    +async async_create_aliases(guid, aliases, _ssl=None, **kwargs)[source]

    Asyncronously create Aliases for the given guid

    Parameters:
    @@ -110,7 +110,7 @@

    Gen3 Metadata Class
    -async async_delete_alias(guid, alias, _ssl=None, **kwargs)[source]
    +async async_delete_alias(guid, alias, _ssl=None, **kwargs)[source]

    Asyncronously delete single Aliases for the given guid

    Parameters:
    @@ -132,7 +132,7 @@

    Gen3 Metadata Class
    -async async_delete_aliases(guid, _ssl=None, **kwargs)[source]
    +async async_delete_aliases(guid, _ssl=None, **kwargs)[source]

    Asyncronously delete all Aliases for the given guid

    Parameters:
    @@ -153,7 +153,7 @@

    Gen3 Metadata Class
    -async async_get(guid, _ssl=None, **kwargs)[source]
    +async async_get(guid, _ssl=None, **kwargs)[source]

    Asynchronous function to get metadata

    Parameters:
    @@ -173,7 +173,7 @@

    Gen3 Metadata Class
    -async async_get_aliases(guid, _ssl=None, **kwargs)[source]
    +async async_get_aliases(guid, _ssl=None, **kwargs)[source]

    Asyncronously get Aliases for the given guid

    Parameters:
    @@ -194,7 +194,7 @@

    Gen3 Metadata Class
    -async async_update(guid, metadata, aliases=None, merge=False, _ssl=None, **kwargs)[source]
    +async async_update(guid, metadata, aliases=None, merge=False, _ssl=None, **kwargs)[source]

    Asynchronous function to update metadata

    Parameters:
    @@ -214,7 +214,7 @@

    Gen3 Metadata Class
    -async async_update_aliases(guid, aliases, merge=False, _ssl=None, **kwargs)[source]
    +async async_update_aliases(guid, aliases, merge=False, _ssl=None, **kwargs)[source]

    Asyncronously update Aliases for the given guid

    Parameters:
    diff --git a/docs/_build/html/object.html b/docs/_build/html/object.html index 11762fee..cc648045 100644 --- a/docs/_build/html/object.html +++ b/docs/_build/html/object.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

    Gen3 Object Class

    -class gen3.object.Gen3Object(auth_provider=None)[source]
    +class gen3.object.Gen3Object(auth_provider=None)[source]

    Bases: object

    For interacting with Gen3 object level features.

    A class for interacting with the Gen3 object services. diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html index 8f136bce..d168bbc4 100644 --- a/docs/_build/html/py-modindex.html +++ b/docs/_build/html/py-modindex.html @@ -9,8 +9,8 @@ - - + + diff --git a/docs/_build/html/query.html b/docs/_build/html/query.html index afa93fc0..94d535d1 100644 --- a/docs/_build/html/query.html +++ b/docs/_build/html/query.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

    Gen3 Query Class

    -class gen3.query.Gen3Query(auth_provider)[source]
    +class gen3.query.Gen3Query(auth_provider)[source]

    Bases: object

    Query ElasticSearch data from a Gen3 system.

    diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html index 4633b6dc..12b2a7ce 100644 --- a/docs/_build/html/search.html +++ b/docs/_build/html/search.html @@ -10,8 +10,8 @@ - - + + diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 5e758f3c..fa7273f9 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles":{"DRS Download Tools":[[10,null]],"Download":[[11,"module-gen3.tools.indexing.download_manifest"]],"Gen3 Auth Helper":[[0,null]],"Gen3 File Class":[[1,null]],"Gen3 Index Class":[[3,null]],"Gen3 Jobs Class":[[4,null]],"Gen3 Metadata Class":[[5,null]],"Gen3 Object Class":[[6,null]],"Gen3 Query Class":[[7,null]],"Gen3 Submission Class":[[8,null]],"Gen3 Tools":[[9,null]],"Gen3 Workspace Storage":[[13,null]],"Index":[[11,"module-gen3.tools.indexing.index_manifest"]],"Indexing Tools":[[11,null]],"Indices and tables":[[2,"indices-and-tables"]],"Ingest":[[12,"module-gen3.tools.metadata.ingest_manifest"]],"Metadata Tools":[[12,null]],"Verify":[[11,"module-gen3.tools.indexing.verify_manifest"]],"Welcome to Gen3 SDK\u2019s documentation!":[[2,null]]},"docnames":["auth","file","index","indexing","jobs","metadata","object","query","submission","tools","tools/drs_pull","tools/indexing","tools/metadata","wss"],"envversion":{"sphinx":65,"sphinx.domains.c":3,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":9,"sphinx.domains.index":1,"sphinx.domains.javascript":3,"sphinx.domains.math":2,"sphinx.domains.python":4,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.viewcode":1},"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"],"indexentries":{"_manager (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable._manager",false]],"access_methods (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.access_methods",false]],"acls (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.ACLS",false]],"async_create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_create",false]],"async_create_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_create_aliases",false]],"async_create_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_create_record",false]],"async_delete_alias() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_delete_alias",false]],"async_delete_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_delete_aliases",false]],"async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.async_download_object_manifest",false]],"async_get() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_get",false]],"async_get_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_get_aliases",false]],"async_get_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_record",false]],"async_get_records_from_checksum() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_records_from_checksum",false]],"async_get_records_on_page() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_records_on_page",false]],"async_get_with_params() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_with_params",false]],"async_ingest_metadata_manifest() (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest",false]],"async_query_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_query_urls",false]],"async_query_urls_from_indexd() (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd",false]],"async_run_job_and_wait() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.async_run_job_and_wait",false]],"async_update() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_update",false]],"async_update_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_update_aliases",false]],"async_update_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_update_record",false]],"async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.async_verify_object_manifest",false]],"auth_provider (gen3.metadata.gen3metadata attribute)":[[5,"gen3.metadata.Gen3Metadata.auth_provider",false]],"authz (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.AUTHZ",false]],"batch_create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.batch_create",false]],"cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens",false]],"children (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.children",false]],"column_to_use_as_guid (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID",false]],"commons_url (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.commons_url",false]],"copy() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.copy",false]],"create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create",false]],"create_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create_aliases",false]],"create_blank() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_blank",false]],"create_index_key_path() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create_index_key_path",false]],"create_job() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.create_job",false]],"create_new_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_new_version",false]],"create_object_list() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.create_object_list",false]],"create_program() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.create_program",false]],"create_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.create_project",false]],"create_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_record",false]],"created_time (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.created_time",false]],"curl() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.curl",false]],"current_dir (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.CURRENT_DIR",false]],"current_dir (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.CURRENT_DIR",false]],"current_dir (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.CURRENT_DIR",false]],"delete() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete",false]],"delete_alias() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_alias",false]],"delete_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_aliases",false]],"delete_all_guids() (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.delete_all_guids",false]],"delete_file() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.delete_file",false]],"delete_file_locations() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.delete_file_locations",false]],"delete_index_key_path() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_index_key_path",false]],"delete_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_node",false]],"delete_nodes() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_nodes",false]],"delete_object() (gen3.object.gen3object method)":[[6,"gen3.object.Gen3Object.delete_object",false]],"delete_program() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_program",false]],"delete_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_project",false]],"delete_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.delete_record",false]],"delete_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_record",false]],"delete_records() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_records",false]],"download() (gen3.tools.download.drs_download.downloadable method)":[[10,"gen3.tools.download.drs_download.Downloadable.download",false]],"download() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.download",false]],"download() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.download",false]],"download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.download_files_in_drs_manifest",false]],"download_single() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.download_single",false]],"download_url() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.download_url",false]],"downloadable (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.Downloadable",false]],"downloadmanager (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.DownloadManager",false]],"downloadstatus (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.DownloadStatus",false]],"end_time (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.end_time",false]],"endpoint (gen3.metadata.gen3metadata attribute)":[[5,"gen3.metadata.Gen3Metadata.endpoint",false]],"export_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.export_node",false]],"export_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.export_record",false]],"file_name (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.file_name",false]],"file_name (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.file_name",false]],"file_size (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.file_size",false]],"file_size (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.file_size",false]],"gen3.tools":[[9,"module-gen3.tools",false]],"gen3.tools.download.drs_download":[[10,"module-gen3.tools.download.drs_download",false]],"gen3.tools.indexing.download_manifest":[[11,"module-gen3.tools.indexing.download_manifest",false]],"gen3.tools.indexing.index_manifest":[[11,"module-gen3.tools.indexing.index_manifest",false]],"gen3.tools.indexing.verify_manifest":[[11,"module-gen3.tools.indexing.verify_manifest",false]],"gen3.tools.metadata.ingest_manifest":[[12,"module-gen3.tools.metadata.ingest_manifest",false]],"gen3auth (class in gen3.auth)":[[0,"gen3.auth.Gen3Auth",false]],"gen3file (class in gen3.file)":[[1,"gen3.file.Gen3File",false]],"gen3index (class in gen3.index)":[[3,"gen3.index.Gen3Index",false]],"gen3jobs (class in gen3.jobs)":[[4,"gen3.jobs.Gen3Jobs",false]],"gen3metadata (class in gen3.metadata)":[[5,"gen3.metadata.Gen3Metadata",false]],"gen3object (class in gen3.object)":[[6,"gen3.object.Gen3Object",false]],"gen3query (class in gen3.query)":[[7,"gen3.query.Gen3Query",false]],"gen3submission (class in gen3.submission)":[[8,"gen3.submission.Gen3Submission",false]],"gen3wsstorage (class in gen3.wss)":[[13,"gen3.wss.Gen3WsStorage",false]],"get() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get",false]],"get() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get",false]],"get_access_token() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.get_access_token",false]],"get_access_token_from_wts() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.get_access_token_from_wts",false]],"get_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_aliases",false]],"get_all_records() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_all_records",false]],"get_dictionary_all() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_dictionary_all",false]],"get_dictionary_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_dictionary_node",false]],"get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.get_fresh_token",false]],"get_graphql_schema() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_graphql_schema",false]],"get_guids_prefix() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_guids_prefix",false]],"get_index_key_paths() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_index_key_paths",false]],"get_latest_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_latest_version",false]],"get_output() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_output",false]],"get_presigned_url() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.get_presigned_url",false]],"get_programs() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_programs",false]],"get_project_dictionary() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_project_dictionary",false]],"get_project_manifest() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_project_manifest",false]],"get_projects() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_projects",false]],"get_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_record",false]],"get_record_doc() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_record_doc",false]],"get_records() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_records",false]],"get_records_on_page() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_records_on_page",false]],"get_stats() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_stats",false]],"get_status() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_status",false]],"get_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_urls",false]],"get_valid_guids() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_valid_guids",false]],"get_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_version",false]],"get_version() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_version",false]],"get_version() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_version",false]],"get_versions() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_versions",false]],"get_with_params() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_with_params",false]],"graphql_query() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.graphql_query",false]],"guid (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.GUID",false]],"guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT",false]],"guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT",false]],"hostname (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.hostname",false]],"index_object_manifest() (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.index_object_manifest",false]],"indexd_record_page_size (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE",false]],"is_healthy() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.is_healthy",false]],"is_healthy() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.is_healthy",false]],"is_healthy() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.is_healthy",false]],"list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_access_in_drs_manifest",false]],"list_drs_object() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_drs_object",false]],"list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_files_in_drs_manifest",false]],"list_jobs() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.list_jobs",false]],"load() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.load",false]],"load_manifest() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.load_manifest",false]],"ls() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.ls",false]],"ls_path() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.ls_path",false]],"manifest (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.Manifest",false]],"max_concurrent_requests (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS",false]],"max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS",false]],"max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS",false]],"md5 (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.MD5",false]],"md5sum (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.md5sum",false]],"module":[[9,"module-gen3.tools",false],[10,"module-gen3.tools.download.drs_download",false],[11,"module-gen3.tools.indexing.download_manifest",false],[11,"module-gen3.tools.indexing.index_manifest",false],[11,"module-gen3.tools.indexing.verify_manifest",false],[12,"module-gen3.tools.metadata.ingest_manifest",false]],"object_id (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.object_id",false]],"object_id (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.object_id",false]],"object_type (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.object_type",false]],"open_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.open_project",false]],"pprint() (gen3.tools.download.drs_download.downloadable method)":[[10,"gen3.tools.download.drs_download.Downloadable.pprint",false]],"prev_guid (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.PREV_GUID",false]],"query() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.query",false]],"query() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.query",false]],"query() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.query",false]],"query_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.query_urls",false]],"raw_data_download() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.raw_data_download",false]],"refresh_access_token() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.refresh_access_token",false]],"resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.resolve_objects",false]],"rm() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.rm",false]],"rm_path() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.rm_path",false]],"size (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.SIZE",false]],"start_time (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.start_time",false]],"status (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.status",false]],"submit_file() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.submit_file",false]],"submit_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.submit_record",false]],"threadcontrol (class in gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.ThreadControl",false]],"tmp_folder (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.TMP_FOLDER",false]],"update() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.update",false]],"update_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.update_aliases",false]],"update_blank() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.update_blank",false]],"update_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.update_record",false]],"updated_time (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.updated_time",false]],"upload() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.upload",false]],"upload_file() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.upload_file",false]],"upload_file_to_guid() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.upload_file_to_guid",false]],"upload_url() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.upload_url",false]],"urls (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.URLS",false]],"user_access() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.user_access",false]]},"objects":{"gen3":[[9,3,0,"-","tools"]],"gen3.auth":[[0,0,1,"","Gen3Auth"]],"gen3.auth.Gen3Auth":[[0,1,1,"","curl"],[0,1,1,"","get_access_token"],[0,1,1,"","get_access_token_from_wts"],[0,1,1,"","refresh_access_token"]],"gen3.file":[[1,0,1,"","Gen3File"]],"gen3.file.Gen3File":[[1,1,1,"","delete_file"],[1,1,1,"","delete_file_locations"],[1,1,1,"","download_single"],[1,1,1,"","get_presigned_url"],[1,1,1,"","upload_file"],[1,1,1,"","upload_file_to_guid"]],"gen3.index":[[3,0,1,"","Gen3Index"]],"gen3.index.Gen3Index":[[3,1,1,"","async_create_record"],[3,1,1,"","async_get_record"],[3,1,1,"","async_get_records_from_checksum"],[3,1,1,"","async_get_records_on_page"],[3,1,1,"","async_get_with_params"],[3,1,1,"","async_query_urls"],[3,1,1,"","async_update_record"],[3,1,1,"","create_blank"],[3,1,1,"","create_new_version"],[3,1,1,"","create_record"],[3,1,1,"","delete_record"],[3,1,1,"","get"],[3,1,1,"","get_all_records"],[3,1,1,"","get_guids_prefix"],[3,1,1,"","get_latest_version"],[3,1,1,"","get_record"],[3,1,1,"","get_record_doc"],[3,1,1,"","get_records"],[3,1,1,"","get_records_on_page"],[3,1,1,"","get_stats"],[3,1,1,"","get_urls"],[3,1,1,"","get_valid_guids"],[3,1,1,"","get_version"],[3,1,1,"","get_versions"],[3,1,1,"","get_with_params"],[3,1,1,"","is_healthy"],[3,1,1,"","query_urls"],[3,1,1,"","update_blank"],[3,1,1,"","update_record"]],"gen3.jobs":[[4,0,1,"","Gen3Jobs"]],"gen3.jobs.Gen3Jobs":[[4,1,1,"","async_run_job_and_wait"],[4,1,1,"","create_job"],[4,1,1,"","get_output"],[4,1,1,"","get_status"],[4,1,1,"","get_version"],[4,1,1,"","is_healthy"],[4,1,1,"","list_jobs"]],"gen3.metadata":[[5,0,1,"","Gen3Metadata"]],"gen3.metadata.Gen3Metadata":[[5,1,1,"","async_create"],[5,1,1,"","async_create_aliases"],[5,1,1,"","async_delete_alias"],[5,1,1,"","async_delete_aliases"],[5,1,1,"","async_get"],[5,1,1,"","async_get_aliases"],[5,1,1,"","async_update"],[5,1,1,"","async_update_aliases"],[5,2,1,"","auth_provider"],[5,1,1,"","batch_create"],[5,1,1,"","create"],[5,1,1,"","create_aliases"],[5,1,1,"","create_index_key_path"],[5,1,1,"","delete"],[5,1,1,"","delete_alias"],[5,1,1,"","delete_aliases"],[5,1,1,"","delete_index_key_path"],[5,2,1,"","endpoint"],[5,1,1,"","get"],[5,1,1,"","get_aliases"],[5,1,1,"","get_index_key_paths"],[5,1,1,"","get_version"],[5,1,1,"","is_healthy"],[5,1,1,"","query"],[5,1,1,"","update"],[5,1,1,"","update_aliases"]],"gen3.object":[[6,0,1,"","Gen3Object"]],"gen3.object.Gen3Object":[[6,1,1,"","delete_object"]],"gen3.query":[[7,0,1,"","Gen3Query"]],"gen3.query.Gen3Query":[[7,1,1,"","graphql_query"],[7,1,1,"","query"],[7,1,1,"","raw_data_download"]],"gen3.submission":[[8,0,1,"","Gen3Submission"]],"gen3.submission.Gen3Submission":[[8,1,1,"","create_program"],[8,1,1,"","create_project"],[8,1,1,"","delete_node"],[8,1,1,"","delete_nodes"],[8,1,1,"","delete_program"],[8,1,1,"","delete_project"],[8,1,1,"","delete_record"],[8,1,1,"","delete_records"],[8,1,1,"","export_node"],[8,1,1,"","export_record"],[8,1,1,"","get_dictionary_all"],[8,1,1,"","get_dictionary_node"],[8,1,1,"","get_graphql_schema"],[8,1,1,"","get_programs"],[8,1,1,"","get_project_dictionary"],[8,1,1,"","get_project_manifest"],[8,1,1,"","get_projects"],[8,1,1,"","open_project"],[8,1,1,"","query"],[8,1,1,"","submit_file"],[8,1,1,"","submit_record"]],"gen3.tools.download":[[10,3,0,"-","drs_download"]],"gen3.tools.download.drs_download":[[10,0,1,"","DownloadManager"],[10,0,1,"","DownloadStatus"],[10,0,1,"","Downloadable"],[10,0,1,"","Manifest"],[10,4,1,"","download_files_in_drs_manifest"],[10,4,1,"","list_access_in_drs_manifest"],[10,4,1,"","list_drs_object"],[10,4,1,"","list_files_in_drs_manifest"]],"gen3.tools.download.drs_download.DownloadManager":[[10,1,1,"","cache_hosts_wts_tokens"],[10,1,1,"","download"],[10,1,1,"","get_fresh_token"],[10,1,1,"","resolve_objects"],[10,1,1,"","user_access"]],"gen3.tools.download.drs_download.DownloadStatus":[[10,2,1,"","end_time"],[10,2,1,"","start_time"],[10,2,1,"","status"]],"gen3.tools.download.drs_download.Downloadable":[[10,2,1,"","_manager"],[10,2,1,"","access_methods"],[10,2,1,"","children"],[10,2,1,"","created_time"],[10,1,1,"","download"],[10,2,1,"","file_name"],[10,2,1,"","file_size"],[10,2,1,"","hostname"],[10,2,1,"","object_id"],[10,2,1,"","object_type"],[10,1,1,"","pprint"],[10,2,1,"","updated_time"]],"gen3.tools.download.drs_download.Manifest":[[10,2,1,"","commons_url"],[10,1,1,"","create_object_list"],[10,2,1,"","file_name"],[10,2,1,"","file_size"],[10,1,1,"","load"],[10,1,1,"","load_manifest"],[10,2,1,"","md5sum"],[10,2,1,"","object_id"]],"gen3.tools.indexing":[[11,3,0,"-","download_manifest"],[11,3,0,"-","index_manifest"],[11,3,0,"-","verify_manifest"]],"gen3.tools.indexing.download_manifest":[[11,2,1,"","CURRENT_DIR"],[11,2,1,"","INDEXD_RECORD_PAGE_SIZE"],[11,2,1,"","MAX_CONCURRENT_REQUESTS"],[11,2,1,"","TMP_FOLDER"],[11,4,1,"","async_download_object_manifest"]],"gen3.tools.indexing.index_manifest":[[11,2,1,"","ACLS"],[11,2,1,"","AUTHZ"],[11,2,1,"","CURRENT_DIR"],[11,2,1,"","GUID"],[11,2,1,"","MD5"],[11,2,1,"","PREV_GUID"],[11,2,1,"","SIZE"],[11,0,1,"","ThreadControl"],[11,2,1,"","URLS"],[11,4,1,"","delete_all_guids"],[11,4,1,"","index_object_manifest"]],"gen3.tools.indexing.verify_manifest":[[11,2,1,"","CURRENT_DIR"],[11,2,1,"","MAX_CONCURRENT_REQUESTS"],[11,4,1,"","async_verify_object_manifest"]],"gen3.tools.metadata":[[12,3,0,"-","ingest_manifest"]],"gen3.tools.metadata.ingest_manifest":[[12,2,1,"","COLUMN_TO_USE_AS_GUID"],[12,2,1,"","GUID_TYPE_FOR_INDEXED_FILE_OBJECT"],[12,2,1,"","GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"],[12,2,1,"","MAX_CONCURRENT_REQUESTS"],[12,4,1,"","async_ingest_metadata_manifest"],[12,4,1,"","async_query_urls_from_indexd"]],"gen3.wss":[[13,0,1,"","Gen3WsStorage"]],"gen3.wss.Gen3WsStorage":[[13,1,1,"","copy"],[13,1,1,"","download"],[13,1,1,"","download_url"],[13,1,1,"","ls"],[13,1,1,"","ls_path"],[13,1,1,"","rm"],[13,1,1,"","rm_path"],[13,1,1,"","upload"],[13,1,1,"","upload_url"]]},"objnames":{"0":["py","class","Python class"],"1":["py","method","Python method"],"2":["py","attribute","Python attribute"],"3":["py","module","Python module"],"4":["py","function","Python function"]},"objtypes":{"0":"py:class","1":"py:method","2":"py:attribute","3":"py:module","4":"py:function"},"terms":{"":[1,4,8,10,11],"0":[5,7,8,11],"0a80fada010c":11,"0a80fada096c":11,"0a80fada097c":11,"0a80fada098c":11,"0a80fada099c":11,"1":[4,5,8,10,11],"10":[5,7,11],"100":[8,11],"11e9":11,"1756725":11,"1762549731":[],"1762550046":[11,12],"2":[5,11],"24":[11,12],"255e396f":11,"3":[5,11],"30":8,"33":5,"333":5,"343434344":11,"363455714":11,"390404":12,"4":[5,11],"450c":11,"4714":8,"473d83400bc1bc9dc635e334fadd433c":11,"473d83400bc1bc9dc635e334faddd33c":11,"473d83400bc1bc9dc635e334fadde33c":11,"473d83400bc1bc9dc635e334faddf33c":11,"5":[0,5],"50":7,"543434443":11,"6592991":[],"6f90":8,"7d3d8d2083b4":11,"8420":8,"8675854":[],"93d9af72":11,"9a07":11,"A":[1,3,4,5,6,7,8,10,11,13],"AND":5,"Be":1,"But":5,"By":11,"For":[1,5,6,7,8,9,11],"IF":11,"If":[0,1,7,11,12],"In":10,"It":10,"NOT":12,"OR":5,"One":7,"Such":9,"THE":11,"That":3,"The":[0,1,2,3,5,8,10,11],"There":11,"These":9,"To":11,"Will":[4,7,10],"_get_acl_from_row":11,"_get_authz_from_row":11,"_get_file_name_from_row":11,"_get_file_size_from_row":11,"_get_guid_for_row":12,"_get_guid_from_row":11,"_get_md5_from_row":11,"_get_urls_from_row":11,"_guid_typ":12,"_manag":[2,9,10],"_query_for_associated_indexd_record_guid":12,"_ssl":[3,4,5],"a5c6":11,"ab167e49d25b488939b1ede42752458b":3,"about":[2,3],"abov":11,"access":[0,1,3,7,10],"access_method":[2,9,10],"access_token":0,"accesstoken":0,"acl":[2,3,9,11],"across":11,"act":0,"action":[9,11],"actual":11,"ad":3,"add":[3,5],"addit":[3,5,10,11],"admin":[5,11],"admin_endpoint_suffix":5,"after":10,"against":[3,7,8,11,12],"algorithm":3,"alia":[3,5],"alias":5,"aliv":7,"all":[1,3,4,5,6,7,8,10,11,12],"allow":[0,6,8,10,11,12],"allowed_data_upload_bucket":1,"along":2,"alreadi":9,"also":1,"altern":[5,11],"alwai":5,"ammount":12,"amount":[1,9],"an":[0,3,6,8,10,11],"ani":[0,5,10,11],"anoth":5,"api":[0,5,8,11],"api_kei":11,"appli":7,"appropri":13,"ar":[5,7,8,9,10,11],"arbitrari":0,"argument":[0,13],"arrai":8,"asc":7,"assign":9,"assist":10,"associ":[3,5],"assum":11,"async":[3,4,5,9,11,12],"async_cr":[2,5],"async_create_alias":[2,5],"async_create_record":[2,3],"async_delete_alia":[2,5],"async_delete_alias":[2,5],"async_download_object_manifest":[2,9,11],"async_get":[2,5],"async_get_alias":[2,5],"async_get_record":[2,3],"async_get_records_from_checksum":[2,3],"async_get_records_on_pag":[2,3],"async_get_with_param":[2,3],"async_ingest_metadata_manifest":[2,9,12],"async_query_url":[2,3],"async_query_urls_from_indexd":[2,9,12],"async_run_job_and_wait":[2,4],"async_upd":[2,5],"async_update_alias":[2,5],"async_update_record":[2,3],"async_verify_object_manifest":[2,9,11],"asynchron":[3,4,5],"asyncio":[11,12],"asyncron":5,"attach":[3,5],"attempt":11,"attribut":[10,11],"auth":[1,2,3,4,5,6,7,8,10,11,12,13],"auth_provid":[1,2,3,4,5,6,7,8,13],"authbas":0,"authent":0,"author":1,"authz":[0,1,2,3,9,10,11],"auto":[0,2],"automat":0,"avail":[1,2,10,11],"az":1,"b":[5,11],"b0f1":11,"bar":10,"base":[0,1,3,4,5,6,7,8,9,11,13],"baseid":3,"basic":[3,11,12],"batch_creat":[2,5],"batch_siz":8,"behalf":0,"behavior":11,"being":3,"belong":8,"below":11,"blank":3,"blob":[5,7],"bodi":3,"bool":[4,5,8,10,11,12],"boolean":3,"bownload":10,"broad":9,"broken":9,"bucket":[1,6],"bundl":10,"byte":10,"c":[5,11],"cach":10,"cache_hosts_wts_token":[2,9,10],"call":[10,13],"can":[0,3,4,8,11,12],"capabl":9,"case":[0,10],"categori":9,"ccle":8,"ccle_one_record":8,"ccle_sample_nod":8,"cdi":7,"chang":[3,11],"checksum":[3,10],"checksum_typ":3,"child":10,"children":[2,9,10],"chunk_siz":8,"class":[0,2,10,11,13],"cli":10,"client":[0,3],"client_credenti":0,"client_id":0,"client_scop":0,"client_secret":0,"code":[2,8],"column":[11,12],"column_to_use_as_guid":[2,9,12],"columna":11,"columnb":11,"columnc":11,"com":7,"comma":11,"command":[10,11],"common":[0,1,3,4,5,6,7,8,9,10,11,12,13],"commons_url":[2,9,10,11,12],"complet":[4,11],"complex":7,"concat":11,"concurr":[11,12],"configur":1,"connect":12,"consist":3,"constructor":0,"contain":[0,2,5,8,9,10,11,12],"content":[3,13],"content_created_d":3,"content_updated_d":3,"continu":10,"control":3,"conveni":10,"copi":[2,13],"coroutin":11,"correspond":3,"count":3,"crdc":0,"creat":[2,3,4,5,6,8,10,11],"create_alias":[2,5],"create_blank":[2,3],"create_index_key_path":[2,5],"create_job":[2,4],"create_new_vers":[2,3],"create_object_list":[2,9,10],"create_program":[2,8],"create_project":[2,8],"create_record":[2,3],"created_tim":[2,9,10],"creation":[3,11],"cred":3,"credenti":[0,1,3,4,5,6,7,8,10,11,13],"csv":[8,11,12],"curl":[0,2],"current":[6,8,10],"current_dir":[2,9,11],"custom":11,"d":5,"d70b41b9":8,"data":[0,1,3,5,7,8,10,11],"data_spreadsheet":8,"data_typ":7,"data_upload_bucket":1,"dataa":11,"datab":11,"databas":5,"datacommon":0,"datafil":10,"datamanag":10,"date":3,"datetim":[1,3,10],"dbgap":12,"dcf":8,"def":11,"default":[0,1,3,7,8,11,12],"defin":[5,8,10],"delai":4,"delet":[0,1,2,3,5,6,8,10,11],"delete_alia":[2,5],"delete_alias":[2,5],"delete_all_guid":[2,9,11],"delete_fil":[1,2],"delete_file_loc":[1,2,6],"delete_index_key_path":[2,5],"delete_nod":[2,8],"delete_object":[2,6],"delete_program":[2,8],"delete_project":[2,8],"delete_record":[2,3,8],"delete_unpacked_packag":10,"delimet":[11,12],"delimit":11,"demograph":8,"deprec":1,"descript":[3,5],"desir":11,"dest_path":13,"dest_urlstr":13,"dest_w":13,"dest_wskei":13,"detail":[2,7,10],"determin":[10,11,12],"dev":11,"dict":[3,4,5,10,11,12],"dictionari":[3,4,5,7,8],"did":3,"differ":5,"direct":0,"directori":[10,11],"disabl":10,"discoveri":10,"disk":13,"dispatch":4,"dist_resolut":3,"distribut":3,"doc":[7,10],"docstr":2,"document":[1,3],"doe":[0,12],"domain":[11,12],"done":4,"download":[0,1,2,3,4,5,6,7,8,9,13],"download_files_in_drs_manifest":[2,9,10],"download_list":10,"download_manifest":11,"download_singl":[1,2],"download_url":[2,13],"downloadmanag":[2,9,10],"downloadstatu":[2,9,10],"dr":[2,9],"drs_download":10,"drs_hostnam":10,"drsdownload":10,"drsobjecttyp":10,"e":[5,10],"e043ab8b77b9":8,"each":[3,8,10,11],"effici":9,"eg":3,"either":8,"elasticsearch":7,"els":[0,12],"elsewher":12,"empti":[8,11],"enabl":11,"end":[5,10],"end_tim":[2,9,10],"endpoint":[0,1,2,3,4,5,7,8,13],"entir":8,"entri":[3,11],"env":0,"environ":0,"equal":7,"error":[10,11,12],"error_nam":11,"etc":8,"even":11,"everi":[9,11],"everyth":11,"ex":[0,11,12],"exampl":[0,1,3,4,5,6,7,8,10,11,13],"exclud":3,"execut":[7,8,11],"exist":[1,3,5,6,9,12],"expect":[5,9,11],"experi":8,"expir":[0,1],"expires_in":1,"export":[8,10],"export_nod":[2,8],"export_record":[2,8],"f1f8":11,"factori":10,"fail":[8,10],"fals":[3,5,6,10,11],"featur":[1,6],"fenc":[0,1],"fetch":0,"field":[3,5,7,11,12],"fieldnam":11,"file":[0,2,3,4,8,9,10,11,12,13],"file_nam":[1,2,3,9,10,11],"file_s":[2,9,10,11],"file_st":3,"fileformat":8,"filenam":[0,8,10,11,12],"files":10,"fill":12,"filter":[5,7],"filter_object":7,"first":[7,8],"flag":11,"folder":11,"follow":[0,11],"forc":11,"force_metadata_columns_even_if_empti":11,"form":13,"format":[3,5,8,11],"from":[0,1,2,3,4,5,6,7,8,9,10,11,12,13],"func_to_parse_row":[11,12],"function":[2,3,4,5,9,10,11,12],"g":10,"gen3":[10,11,12],"gen3_api_kei":0,"gen3_oidc_client_creds_secret":0,"gen3auth":[0,1,2,3,4,5,6,7,8,10,11,12,13],"gen3fil":[1,2],"gen3index":[2,3],"gen3job":[2,4,10],"gen3metadata":[2,5],"gen3object":[2,6],"gen3queri":[2,7],"gen3submiss":[2,8],"gen3wsstorag":[2,13],"gener":[0,1,2,3,4,5,6,7,8,10,13],"get":[0,1,2,3,4,5,8,10,11,12,13],"get_access_token":[0,2],"get_access_token_from_wt":[0,2],"get_alias":[2,5],"get_all_record":[2,3],"get_dictionary_al":[2,8],"get_dictionary_nod":[2,8],"get_fresh_token":[2,9,10],"get_graphql_schema":[2,8],"get_guid_from_fil":12,"get_guids_prefix":[2,3],"get_index_key_path":[2,5],"get_latest_vers":[2,3],"get_output":[2,4],"get_presigned_url":[1,2],"get_program":[2,8],"get_project":[2,8],"get_project_dictionari":[2,8],"get_project_manifest":[2,8],"get_record":[2,3],"get_record_doc":[2,3],"get_records_on_pag":[2,3],"get_stat":[2,3],"get_statu":[2,4],"get_url":[2,3],"get_valid_guid":[2,3],"get_vers":[2,3,4,5],"get_with_param":[2,3],"giangb":11,"github":[2,7],"give":1,"given":[0,3,4,5,8,10,12,13],"global":[4,5],"good":3,"grant":0,"graph":8,"graphql":[7,8],"graphql_queri":[2,7],"group":3,"guid":[1,2,3,5,6,9,11,12],"guid_exampl":11,"guid_for_row":12,"guid_from_fil":12,"guid_type_for_indexed_file_object":[2,9,12],"guid_type_for_non_indexed_file_object":[2,9,12],"guppi":7,"ha":[0,11],"handl":[3,10],"hardcod":0,"has_vers":3,"hash":[3,11],"hash_typ":3,"have":[5,11],"header":11,"healthi":[3,4,5],"help":11,"helper":2,"hit":11,"host":10,"hostnam":[2,9,10],"how":[8,11],"howto":10,"http":[0,7,11,12],"i":[0,1,2,3,4,5,8,10,11,12],"id":[0,1,3,5,10,11],"idea":3,"identifi":[3,5,9,11],"idp":0,"illustr":11,"immut":3,"implement":0,"implic":11,"import":11,"includ":[0,3],"indent":10,"index":[0,2,5,9],"index_manifest":11,"index_object_manifest":[2,9,11],"indexd":[1,3,6,10,11,12],"indexd_field":[11,12],"indexd_record_page_s":[2,9,11],"indexed_file_object_guid":12,"indic":[0,11],"infil":10,"info":[3,11],"inform":[2,3,10],"ingest":[2,9],"ingest_manifest":12,"initi":[0,10],"input":[4,10,11],"input_manifest":11,"instal":[0,2,11],"instanc":[1,3,6,7,8,9,10],"instead":[1,7,11],"int":[1,3,5,7,8,10,11,12],"integ":[1,3,8],"intend":0,"interact":[1,3,4,5,6,8,13],"interest":10,"interpret":0,"introspect":8,"involv":9,"is_healthi":[2,3,4,5],"is_indexed_file_object":12,"isn":1,"issu":0,"its":[1,3],"job":2,"job_id":4,"job_input":4,"job_nam":4,"json":[0,1,3,4,5,6,7,8,10,11,13],"just":[5,11,12],"jwt":0,"kei":[0,3,5,13],"know":11,"known":10,"kwarg":[3,4,5],"l":[2,13],"larg":9,"last":10,"latest":3,"least":3,"level":6,"librari":11,"like":[3,5,9,11,12],"limit":[1,3,5,12],"linear":4,"linux":10,"list":[0,1,3,4,5,7,8,10,11,13],"list_access_in_drs_manifest":[2,9,10],"list_drs_object":[2,9,10],"list_files_in_drs_manifest":[2,9,10],"list_job":[2,4],"live":[11,12],"load":[2,9,10],"load_manifest":[2,9,10],"local":[0,13],"locat":[1,6],"lock":12,"log":[8,10,11,12],"logic":[5,12],"loop":11,"ls_path":[2,13],"maco":11,"made":3,"mai":[0,9,11],"main":10,"make":[9,11],"manag":[1,5,10],"mani":[8,11],"manifest":[2,8,9,10,11,12],"manifest_1":10,"manifest_fil":[11,12],"manifest_file_delimit":[11,12],"manifest_row_pars":[11,12],"map":[0,11],"mark":8,"master":7,"match":[3,5,12],"max":5,"max_concurrent_request":[2,9,11,12],"max_presigned_url_ttl":1,"max_tri":8,"maximum":[11,12],"md":[5,7,10,12],"md5":[2,3,9,11],"md5_hash":11,"md5sum":[2,9,10],"mean":8,"mechan":3,"merg":5,"metadata":[2,3,6,9,11],"metadata_list":5,"metadata_sourc":12,"metadata_typ":12,"metdata":12,"method":[1,7,10],"minimum":10,"minut":0,"mode":7,"modul":[2,10,11],"more":[2,5,7,9,10],"most":9,"mostli":2,"multipl":[8,11],"must":[1,5],"my_common":10,"my_credenti":10,"my_field":7,"my_index":7,"my_program":7,"my_project":7,"name":[3,4,8,10,11,12,13],"namespac":[0,12],"necessari":[3,5],"need":[3,7,10,11],"nest":5,"net":11,"never":0,"new":[0,3],"node":8,"node_nam":8,"node_typ":8,"none":[0,1,3,4,5,6,7,8,10,11,12,13],"note":[0,3,11,12],"noth":[3,6],"now":[1,8],"num":5,"num_process":11,"num_total_fil":11,"number":[3,7,8,11,12],"o":0,"object":[1,2,3,4,5,7,8,9,10,11,13],"object_id":[1,2,9,10],"object_list":10,"object_typ":[2,9,10],"objectid":10,"obtain":[0,10],"occur":10,"off":5,"offset":[5,7],"oidc":0,"old":3,"one":[3,5,10,11],"onli":[3,5,7,8,10,11],"open":[8,10,11],"open_project":[2,8],"openid":0,"opt":0,"option":[0,1,3,4,5,6,7,8,10,11],"order":[0,8],"ordered_node_list":8,"org":10,"otherwis":10,"output":[4,5,11,12],"output_dir":10,"output_filenam":[11,12],"overrid":[0,11,12],"overwrit":5,"own":0,"packag":10,"page":[0,1,2,3,4,5,6,7,8,10,11,13],"pagin":3,"parallel":11,"param":[3,5,8,10],"paramet":[0,1,3,4,5,6,7,8,10,11,12,13],"pars":[10,11,12,13],"parser":[11,12],"particular":0,"pass":[0,7,8,10],"password":[11,12],"path":[0,1,5,10,11,13],"path_to_manifest":11,"pattern":[3,12],"pdcdatastor":11,"pend":10,"per":[11,12],"peregrin":8,"permiss":10,"persist":9,"phs0001":11,"phs0002":11,"pick":1,"pla":11,"place":11,"planx":11,"point":[0,1,3,4,5,6,7,8,10,13],"popul":[10,12],"posit":[1,7],"possibl":10,"post":[0,11],"pprint":[2,9,10],"prefix":3,"presign":1,"pretti":10,"prev_guid":[2,9,11],"previou":[3,11],"previous":4,"print":[8,10],"process":11,"processed_fil":11,"profil":[0,1,3,4,5,6,7,8,10,13],"program":[8,11],"progress":[8,10],"project":[8,11],"project_id":[7,8],"protocol":1,"provid":[0,1,3,5,7,8,12],"public":[3,5],"put":0,"py":11,"python":[2,9,11],"python3":11,"python_subprocess_command":11,"queri":[1,2,3,5,8,11,12],"query_str":7,"query_txt":[7,8],"query_url":[2,3],"quickstart":2,"rather":0,"raw":[7,11],"raw_data_download":[2,7],"rbac":3,"read":[3,5,11],"readm":2,"reason":10,"record":[1,3,5,7,8,11,12],"refresh":[0,10],"refresh_access_token":[0,2],"refresh_fil":[0,1,3,4,5,6,7,8,10,13],"refresh_token":0,"regist":8,"regular":7,"relat":9,"remov":[1,6,11,13],"replac":11,"replace_url":11,"repo":2,"repres":[3,5,10],"represent":[1,3],"request":[0,1,3,5,8,11,12],"requir":10,"resolv":10,"resolve_object":[2,9,10],"respect":7,"respons":[0,1,3,4,5],"result":[1,8,10,11],"retri":8,"retriev":[1,8,10,12],"return":[0,1,3,4,5,6,7,8,10,11],"return_full_metadata":5,"rev":3,"revers":8,"revis":3,"right":1,"rm":[2,13],"rm_path":[2,13],"root":[11,12],"row":[7,8,11,12],"row_offset":8,"rtype":3,"run":[8,11],"s3":[1,10,11],"safe":11,"same":[5,11,13],"sampl":[8,10],"sandbox":[0,1,3,4,5,6,7,8,10,13],"save":10,"save_directori":10,"schema":8,"scope":[0,1],"screen":8,"script":2,"search":[0,2,3],"second":[1,4],"secret":0,"see":[7,10,11],"self":10,"semaphon":12,"semaphor":12,"separ":[0,11],"server":10,"servic":[1,3,4,5,6,8,11,12,13],"service_loc":[3,4,5],"session":11,"set":[0,1,5,10],"setup":2,"sheepdog":8,"should":[0,8,11],"show":10,"show_progress":10,"shown":11,"sign":1,"signpost":3,"similar":10,"simpl":3,"simpli":11,"sinc":3,"singl":[1,5,8],"size":[2,3,9,10,11],"skip":8,"sleep":4,"so":11,"some":[0,2],"someth":11,"sort":7,"sort_field":7,"sort_object":7,"sourc":[0,1,2,3,4,5,6,7,8,10,11,12,13],"space":[0,11],"specif":[5,8,11,12],"specifi":[0,1,3,11,13],"spreadsheet":8,"src_path":13,"src_urlstr":13,"src_w":13,"src_wskei":13,"ssl":[3,4,5],"start":[4,7,8,10],"start_tim":[2,9,10],"static":10,"statu":[2,4,9,10],"storag":[1,2,6],"store":[1,3,10],"str":[0,1,3,4,5,7,8,10,11,12],"string":[0,3,5,11,13],"strip":11,"sub":8,"subject":[7,8],"submiss":2,"submit":[8,11],"submit_additional_metadata_column":11,"submit_fil":[2,8],"submit_record":[2,8],"submitter_id":7,"success":10,"successfulli":10,"suffici":3,"suppli":3,"support":[0,1,5,8,11],"sure":1,"synchron":11,"syntax":7,"system":[6,7,8,9],"t":[1,5,11],"tab":11,"task":9,"temporari":11,"test":11,"test1":11,"test2":11,"test3":11,"test4":11,"test5":11,"text":[1,7,8],"than":[0,5],"thei":[0,10],"them":[10,11],"thi":[0,1,2,3,4,5,6,7,8,10,11,12,13],"those":11,"thread":11,"thread_num":11,"threadcontrol":[2,9,11],"through":[8,11],"tier":7,"time":[1,3,8,10,11],"timestamp":10,"tmp_folder":[2,9,11],"token":[0,10],"tool":2,"total":11,"treat":[1,5],"tree":10,"true":[3,4,5,6,7,8,10,11,12],"try":0,"tsv":[8,11,12],"tupl":[0,3,11,12],"type":[1,3,4,5,7,8,10,11,12],"typic":10,"uc":7,"unaccess":7,"under":[0,8,13],"uniqu":[1,5],"unknown":10,"unpack":10,"unpack_packag":10,"until":[4,10],"up":[5,9],"updat":[2,3,5,10,11],"update_alias":[2,5],"update_blank":[2,3],"update_record":[2,3],"updated_tim":[2,9,10],"upload":[1,2,3,8,13],"upload_fil":[1,2],"upload_file_to_guid":[1,2],"upload_url":[2,13],"url":[1,2,3,9,10,11,12,13],"urls_metadata":3,"us":[0,1,3,4,5,6,7,8,10,11,12,13],"usag":11,"use_agg_md":5,"user":[0,10,12],"user_access":[2,9,10],"usual":12,"utcnow":1,"util":9,"uuid":[1,3,8],"uuid1":8,"uuid2":8,"valid":[3,7],"valu":[0,1,3,5,7,10,11],"value_from_indexd":11,"value_from_manifest":11,"variabl":[0,7,8],"variou":2,"verbos":[7,8],"verif":11,"verifi":[2,9],"verify_manifest":11,"verify_object_manifest":11,"version":[3,4,5],"vital_statu":7,"w":13,"wa":0,"wai":10,"wait":4,"want":[0,3,8],"warn":11,"we":[3,11],"web":0,"what":5,"when":[0,3,7,10,12],"where":[0,3,5,11,12],"whether":[3,4,5,8,11,12],"which":[8,10],"while":[0,1,3,4,5,6,7,8,10,13],"whose":5,"within":[0,2,9],"without":[3,5],"won":5,"work":[0,10],"workaround":11,"worksheet":8,"workspac":[0,2],"wrapper":10,"write":11,"ws_urlstr":13,"wskei":13,"wss":13,"wt":[0,10],"x":11,"xlsx":8,"you":[0,3,8,11],"your":0},"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"],"titleterms":{"":2,"auth":0,"class":[1,3,4,5,6,7,8],"document":2,"download":[10,11],"dr":10,"file":1,"gen3":[0,1,2,3,4,5,6,7,8,9,13],"helper":0,"index":[3,11],"indic":2,"ingest":12,"job":4,"metadata":[5,12],"object":6,"queri":7,"sdk":2,"storag":13,"submiss":8,"tabl":2,"tool":[9,10,11,12],"verifi":11,"welcom":2,"workspac":13}}) \ No newline at end of file +Search.setIndex({"alltitles":{"DRS Download Tools":[[10,null]],"Download":[[11,"module-gen3.tools.indexing.download_manifest"]],"Gen3 Auth Helper":[[0,null]],"Gen3 File Class":[[1,null]],"Gen3 Index Class":[[3,null]],"Gen3 Jobs Class":[[4,null]],"Gen3 Metadata Class":[[5,null]],"Gen3 Object Class":[[6,null]],"Gen3 Query Class":[[7,null]],"Gen3 Submission Class":[[8,null]],"Gen3 Tools":[[9,null]],"Gen3 Workspace Storage":[[13,null]],"Index":[[11,"module-gen3.tools.indexing.index_manifest"]],"Indexing Tools":[[11,null]],"Indices and tables":[[2,"indices-and-tables"]],"Ingest":[[12,"module-gen3.tools.metadata.ingest_manifest"]],"Metadata Tools":[[12,null]],"Verify":[[11,"module-gen3.tools.indexing.verify_manifest"]],"Welcome to Gen3 SDK\u2019s documentation!":[[2,null]]},"docnames":["auth","file","index","indexing","jobs","metadata","object","query","submission","tools","tools/drs_pull","tools/indexing","tools/metadata","wss"],"envversion":{"sphinx":66,"sphinx.domains.c":3,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":9,"sphinx.domains.index":1,"sphinx.domains.javascript":3,"sphinx.domains.math":2,"sphinx.domains.python":4,"sphinx.domains.rst":2,"sphinx.domains.std":2,"sphinx.ext.viewcode":1},"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"],"indexentries":{"_manager (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable._manager",false]],"access_methods (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.access_methods",false]],"acls (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.ACLS",false]],"async_create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_create",false]],"async_create_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_create_aliases",false]],"async_create_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_create_record",false]],"async_delete_alias() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_delete_alias",false]],"async_delete_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_delete_aliases",false]],"async_download_object_manifest() (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.async_download_object_manifest",false]],"async_get() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_get",false]],"async_get_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_get_aliases",false]],"async_get_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_record",false]],"async_get_records_from_checksum() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_records_from_checksum",false]],"async_get_records_on_page() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_records_on_page",false]],"async_get_with_params() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_get_with_params",false]],"async_ingest_metadata_manifest() (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.async_ingest_metadata_manifest",false]],"async_query_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_query_urls",false]],"async_query_urls_from_indexd() (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd",false]],"async_run_job_and_wait() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.async_run_job_and_wait",false]],"async_update() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_update",false]],"async_update_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.async_update_aliases",false]],"async_update_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.async_update_record",false]],"async_verify_object_manifest() (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.async_verify_object_manifest",false]],"auth_provider (gen3.metadata.gen3metadata attribute)":[[5,"gen3.metadata.Gen3Metadata.auth_provider",false]],"authz (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.AUTHZ",false]],"batch_create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.batch_create",false]],"cache_hosts_wts_tokens() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.cache_hosts_wts_tokens",false]],"children (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.children",false]],"column_to_use_as_guid (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.COLUMN_TO_USE_AS_GUID",false]],"commons_url (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.commons_url",false]],"copy() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.copy",false]],"create() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create",false]],"create_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create_aliases",false]],"create_blank() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_blank",false]],"create_index_key_path() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.create_index_key_path",false]],"create_job() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.create_job",false]],"create_new_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_new_version",false]],"create_object_list() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.create_object_list",false]],"create_program() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.create_program",false]],"create_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.create_project",false]],"create_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.create_record",false]],"created_time (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.created_time",false]],"curl() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.curl",false]],"current_dir (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.CURRENT_DIR",false]],"current_dir (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.CURRENT_DIR",false]],"current_dir (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.CURRENT_DIR",false]],"delete() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete",false]],"delete_alias() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_alias",false]],"delete_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_aliases",false]],"delete_all_guids() (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.delete_all_guids",false]],"delete_file() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.delete_file",false]],"delete_file_locations() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.delete_file_locations",false]],"delete_index_key_path() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.delete_index_key_path",false]],"delete_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_node",false]],"delete_nodes() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_nodes",false]],"delete_object() (gen3.object.gen3object method)":[[6,"gen3.object.Gen3Object.delete_object",false]],"delete_program() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_program",false]],"delete_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_project",false]],"delete_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.delete_record",false]],"delete_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_record",false]],"delete_records() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.delete_records",false]],"download() (gen3.tools.download.drs_download.downloadable method)":[[10,"gen3.tools.download.drs_download.Downloadable.download",false]],"download() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.download",false]],"download() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.download",false]],"download_files_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.download_files_in_drs_manifest",false]],"download_single() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.download_single",false]],"download_url() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.download_url",false]],"downloadable (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.Downloadable",false]],"downloadmanager (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.DownloadManager",false]],"downloadstatus (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.DownloadStatus",false]],"end_time (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.end_time",false]],"endpoint (gen3.metadata.gen3metadata attribute)":[[5,"gen3.metadata.Gen3Metadata.endpoint",false]],"export_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.export_node",false]],"export_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.export_record",false]],"file_name (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.file_name",false]],"file_name (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.file_name",false]],"file_size (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.file_size",false]],"file_size (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.file_size",false]],"gen3.tools":[[9,"module-gen3.tools",false]],"gen3.tools.download.drs_download":[[10,"module-gen3.tools.download.drs_download",false]],"gen3.tools.indexing.download_manifest":[[11,"module-gen3.tools.indexing.download_manifest",false]],"gen3.tools.indexing.index_manifest":[[11,"module-gen3.tools.indexing.index_manifest",false]],"gen3.tools.indexing.verify_manifest":[[11,"module-gen3.tools.indexing.verify_manifest",false]],"gen3.tools.metadata.ingest_manifest":[[12,"module-gen3.tools.metadata.ingest_manifest",false]],"gen3auth (class in gen3.auth)":[[0,"gen3.auth.Gen3Auth",false]],"gen3file (class in gen3.file)":[[1,"gen3.file.Gen3File",false]],"gen3index (class in gen3.index)":[[3,"gen3.index.Gen3Index",false]],"gen3jobs (class in gen3.jobs)":[[4,"gen3.jobs.Gen3Jobs",false]],"gen3metadata (class in gen3.metadata)":[[5,"gen3.metadata.Gen3Metadata",false]],"gen3object (class in gen3.object)":[[6,"gen3.object.Gen3Object",false]],"gen3query (class in gen3.query)":[[7,"gen3.query.Gen3Query",false]],"gen3submission (class in gen3.submission)":[[8,"gen3.submission.Gen3Submission",false]],"gen3wsstorage (class in gen3.wss)":[[13,"gen3.wss.Gen3WsStorage",false]],"get() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get",false]],"get() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get",false]],"get_access_token() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.get_access_token",false]],"get_access_token_from_wts() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.get_access_token_from_wts",false]],"get_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_aliases",false]],"get_all_records() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_all_records",false]],"get_dictionary_all() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_dictionary_all",false]],"get_dictionary_node() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_dictionary_node",false]],"get_fresh_token() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.get_fresh_token",false]],"get_graphql_schema() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_graphql_schema",false]],"get_guids_prefix() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_guids_prefix",false]],"get_index_key_paths() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_index_key_paths",false]],"get_latest_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_latest_version",false]],"get_output() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_output",false]],"get_presigned_url() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.get_presigned_url",false]],"get_programs() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_programs",false]],"get_project_dictionary() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_project_dictionary",false]],"get_project_manifest() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_project_manifest",false]],"get_projects() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.get_projects",false]],"get_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_record",false]],"get_record_doc() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_record_doc",false]],"get_records() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_records",false]],"get_records_on_page() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_records_on_page",false]],"get_stats() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_stats",false]],"get_status() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_status",false]],"get_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_urls",false]],"get_valid_guids() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_valid_guids",false]],"get_version() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_version",false]],"get_version() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.get_version",false]],"get_version() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.get_version",false]],"get_versions() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_versions",false]],"get_with_params() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.get_with_params",false]],"graphql_query() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.graphql_query",false]],"guid (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.GUID",false]],"guid_type_for_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_INDEXED_FILE_OBJECT",false]],"guid_type_for_non_indexed_file_object (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT",false]],"hostname (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.hostname",false]],"index_object_manifest() (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.index_object_manifest",false]],"indexd_record_page_size (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.INDEXD_RECORD_PAGE_SIZE",false]],"is_healthy() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.is_healthy",false]],"is_healthy() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.is_healthy",false]],"is_healthy() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.is_healthy",false]],"list_access_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_access_in_drs_manifest",false]],"list_drs_object() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_drs_object",false]],"list_files_in_drs_manifest() (in module gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.list_files_in_drs_manifest",false]],"list_jobs() (gen3.jobs.gen3jobs method)":[[4,"gen3.jobs.Gen3Jobs.list_jobs",false]],"load() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.load",false]],"load_manifest() (gen3.tools.download.drs_download.manifest static method)":[[10,"gen3.tools.download.drs_download.Manifest.load_manifest",false]],"ls() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.ls",false]],"ls_path() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.ls_path",false]],"manifest (class in gen3.tools.download.drs_download)":[[10,"gen3.tools.download.drs_download.Manifest",false]],"max_concurrent_requests (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.MAX_CONCURRENT_REQUESTS",false]],"max_concurrent_requests (in module gen3.tools.indexing.verify_manifest)":[[11,"gen3.tools.indexing.verify_manifest.MAX_CONCURRENT_REQUESTS",false]],"max_concurrent_requests (in module gen3.tools.metadata.ingest_manifest)":[[12,"gen3.tools.metadata.ingest_manifest.MAX_CONCURRENT_REQUESTS",false]],"md5 (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.MD5",false]],"md5sum (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.md5sum",false]],"module":[[9,"module-gen3.tools",false],[10,"module-gen3.tools.download.drs_download",false],[11,"module-gen3.tools.indexing.download_manifest",false],[11,"module-gen3.tools.indexing.index_manifest",false],[11,"module-gen3.tools.indexing.verify_manifest",false],[12,"module-gen3.tools.metadata.ingest_manifest",false]],"object_id (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.object_id",false]],"object_id (gen3.tools.download.drs_download.manifest attribute)":[[10,"gen3.tools.download.drs_download.Manifest.object_id",false]],"object_type (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.object_type",false]],"open_project() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.open_project",false]],"pprint() (gen3.tools.download.drs_download.downloadable method)":[[10,"gen3.tools.download.drs_download.Downloadable.pprint",false]],"prev_guid (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.PREV_GUID",false]],"query() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.query",false]],"query() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.query",false]],"query() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.query",false]],"query_urls() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.query_urls",false]],"raw_data_download() (gen3.query.gen3query method)":[[7,"gen3.query.Gen3Query.raw_data_download",false]],"refresh_access_token() (gen3.auth.gen3auth method)":[[0,"gen3.auth.Gen3Auth.refresh_access_token",false]],"resolve_objects() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.resolve_objects",false]],"rm() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.rm",false]],"rm_path() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.rm_path",false]],"size (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.SIZE",false]],"start_time (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.start_time",false]],"status (gen3.tools.download.drs_download.downloadstatus attribute)":[[10,"gen3.tools.download.drs_download.DownloadStatus.status",false]],"submit_file() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.submit_file",false]],"submit_record() (gen3.submission.gen3submission method)":[[8,"gen3.submission.Gen3Submission.submit_record",false]],"threadcontrol (class in gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.ThreadControl",false]],"tmp_folder (in module gen3.tools.indexing.download_manifest)":[[11,"gen3.tools.indexing.download_manifest.TMP_FOLDER",false]],"update() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.update",false]],"update_aliases() (gen3.metadata.gen3metadata method)":[[5,"gen3.metadata.Gen3Metadata.update_aliases",false]],"update_blank() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.update_blank",false]],"update_record() (gen3.index.gen3index method)":[[3,"gen3.index.Gen3Index.update_record",false]],"updated_time (gen3.tools.download.drs_download.downloadable attribute)":[[10,"gen3.tools.download.drs_download.Downloadable.updated_time",false]],"upload() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.upload",false]],"upload_file() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.upload_file",false]],"upload_file_to_guid() (gen3.file.gen3file method)":[[1,"gen3.file.Gen3File.upload_file_to_guid",false]],"upload_url() (gen3.wss.gen3wsstorage method)":[[13,"gen3.wss.Gen3WsStorage.upload_url",false]],"urls (in module gen3.tools.indexing.index_manifest)":[[11,"gen3.tools.indexing.index_manifest.URLS",false]],"user_access() (gen3.tools.download.drs_download.downloadmanager method)":[[10,"gen3.tools.download.drs_download.DownloadManager.user_access",false]]},"objects":{"gen3":[[9,3,0,"-","tools"]],"gen3.auth":[[0,0,1,"","Gen3Auth"]],"gen3.auth.Gen3Auth":[[0,1,1,"","curl"],[0,1,1,"","get_access_token"],[0,1,1,"","get_access_token_from_wts"],[0,1,1,"","refresh_access_token"]],"gen3.file":[[1,0,1,"","Gen3File"]],"gen3.file.Gen3File":[[1,1,1,"","delete_file"],[1,1,1,"","delete_file_locations"],[1,1,1,"","download_single"],[1,1,1,"","get_presigned_url"],[1,1,1,"","upload_file"],[1,1,1,"","upload_file_to_guid"]],"gen3.index":[[3,0,1,"","Gen3Index"]],"gen3.index.Gen3Index":[[3,1,1,"","async_create_record"],[3,1,1,"","async_get_record"],[3,1,1,"","async_get_records_from_checksum"],[3,1,1,"","async_get_records_on_page"],[3,1,1,"","async_get_with_params"],[3,1,1,"","async_query_urls"],[3,1,1,"","async_update_record"],[3,1,1,"","create_blank"],[3,1,1,"","create_new_version"],[3,1,1,"","create_record"],[3,1,1,"","delete_record"],[3,1,1,"","get"],[3,1,1,"","get_all_records"],[3,1,1,"","get_guids_prefix"],[3,1,1,"","get_latest_version"],[3,1,1,"","get_record"],[3,1,1,"","get_record_doc"],[3,1,1,"","get_records"],[3,1,1,"","get_records_on_page"],[3,1,1,"","get_stats"],[3,1,1,"","get_urls"],[3,1,1,"","get_valid_guids"],[3,1,1,"","get_version"],[3,1,1,"","get_versions"],[3,1,1,"","get_with_params"],[3,1,1,"","is_healthy"],[3,1,1,"","query_urls"],[3,1,1,"","update_blank"],[3,1,1,"","update_record"]],"gen3.jobs":[[4,0,1,"","Gen3Jobs"]],"gen3.jobs.Gen3Jobs":[[4,1,1,"","async_run_job_and_wait"],[4,1,1,"","create_job"],[4,1,1,"","get_output"],[4,1,1,"","get_status"],[4,1,1,"","get_version"],[4,1,1,"","is_healthy"],[4,1,1,"","list_jobs"]],"gen3.metadata":[[5,0,1,"","Gen3Metadata"]],"gen3.metadata.Gen3Metadata":[[5,1,1,"","async_create"],[5,1,1,"","async_create_aliases"],[5,1,1,"","async_delete_alias"],[5,1,1,"","async_delete_aliases"],[5,1,1,"","async_get"],[5,1,1,"","async_get_aliases"],[5,1,1,"","async_update"],[5,1,1,"","async_update_aliases"],[5,2,1,"","auth_provider"],[5,1,1,"","batch_create"],[5,1,1,"","create"],[5,1,1,"","create_aliases"],[5,1,1,"","create_index_key_path"],[5,1,1,"","delete"],[5,1,1,"","delete_alias"],[5,1,1,"","delete_aliases"],[5,1,1,"","delete_index_key_path"],[5,2,1,"","endpoint"],[5,1,1,"","get"],[5,1,1,"","get_aliases"],[5,1,1,"","get_index_key_paths"],[5,1,1,"","get_version"],[5,1,1,"","is_healthy"],[5,1,1,"","query"],[5,1,1,"","update"],[5,1,1,"","update_aliases"]],"gen3.object":[[6,0,1,"","Gen3Object"]],"gen3.object.Gen3Object":[[6,1,1,"","delete_object"]],"gen3.query":[[7,0,1,"","Gen3Query"]],"gen3.query.Gen3Query":[[7,1,1,"","graphql_query"],[7,1,1,"","query"],[7,1,1,"","raw_data_download"]],"gen3.submission":[[8,0,1,"","Gen3Submission"]],"gen3.submission.Gen3Submission":[[8,1,1,"","create_program"],[8,1,1,"","create_project"],[8,1,1,"","delete_node"],[8,1,1,"","delete_nodes"],[8,1,1,"","delete_program"],[8,1,1,"","delete_project"],[8,1,1,"","delete_record"],[8,1,1,"","delete_records"],[8,1,1,"","export_node"],[8,1,1,"","export_record"],[8,1,1,"","get_dictionary_all"],[8,1,1,"","get_dictionary_node"],[8,1,1,"","get_graphql_schema"],[8,1,1,"","get_programs"],[8,1,1,"","get_project_dictionary"],[8,1,1,"","get_project_manifest"],[8,1,1,"","get_projects"],[8,1,1,"","open_project"],[8,1,1,"","query"],[8,1,1,"","submit_file"],[8,1,1,"","submit_record"]],"gen3.tools.download":[[10,3,0,"-","drs_download"]],"gen3.tools.download.drs_download":[[10,0,1,"","DownloadManager"],[10,0,1,"","DownloadStatus"],[10,0,1,"","Downloadable"],[10,0,1,"","Manifest"],[10,4,1,"","download_files_in_drs_manifest"],[10,4,1,"","list_access_in_drs_manifest"],[10,4,1,"","list_drs_object"],[10,4,1,"","list_files_in_drs_manifest"]],"gen3.tools.download.drs_download.DownloadManager":[[10,1,1,"","cache_hosts_wts_tokens"],[10,1,1,"","download"],[10,1,1,"","get_fresh_token"],[10,1,1,"","resolve_objects"],[10,1,1,"","user_access"]],"gen3.tools.download.drs_download.DownloadStatus":[[10,2,1,"","end_time"],[10,2,1,"","start_time"],[10,2,1,"","status"]],"gen3.tools.download.drs_download.Downloadable":[[10,2,1,"","_manager"],[10,2,1,"","access_methods"],[10,2,1,"","children"],[10,2,1,"","created_time"],[10,1,1,"","download"],[10,2,1,"","file_name"],[10,2,1,"","file_size"],[10,2,1,"","hostname"],[10,2,1,"","object_id"],[10,2,1,"","object_type"],[10,1,1,"","pprint"],[10,2,1,"","updated_time"]],"gen3.tools.download.drs_download.Manifest":[[10,2,1,"","commons_url"],[10,1,1,"","create_object_list"],[10,2,1,"","file_name"],[10,2,1,"","file_size"],[10,1,1,"","load"],[10,1,1,"","load_manifest"],[10,2,1,"","md5sum"],[10,2,1,"","object_id"]],"gen3.tools.indexing":[[11,3,0,"-","download_manifest"],[11,3,0,"-","index_manifest"],[11,3,0,"-","verify_manifest"]],"gen3.tools.indexing.download_manifest":[[11,2,1,"","CURRENT_DIR"],[11,2,1,"","INDEXD_RECORD_PAGE_SIZE"],[11,2,1,"","MAX_CONCURRENT_REQUESTS"],[11,2,1,"","TMP_FOLDER"],[11,4,1,"","async_download_object_manifest"]],"gen3.tools.indexing.index_manifest":[[11,2,1,"","ACLS"],[11,2,1,"","AUTHZ"],[11,2,1,"","CURRENT_DIR"],[11,2,1,"","GUID"],[11,2,1,"","MD5"],[11,2,1,"","PREV_GUID"],[11,2,1,"","SIZE"],[11,0,1,"","ThreadControl"],[11,2,1,"","URLS"],[11,4,1,"","delete_all_guids"],[11,4,1,"","index_object_manifest"]],"gen3.tools.indexing.verify_manifest":[[11,2,1,"","CURRENT_DIR"],[11,2,1,"","MAX_CONCURRENT_REQUESTS"],[11,4,1,"","async_verify_object_manifest"]],"gen3.tools.metadata":[[12,3,0,"-","ingest_manifest"]],"gen3.tools.metadata.ingest_manifest":[[12,2,1,"","COLUMN_TO_USE_AS_GUID"],[12,2,1,"","GUID_TYPE_FOR_INDEXED_FILE_OBJECT"],[12,2,1,"","GUID_TYPE_FOR_NON_INDEXED_FILE_OBJECT"],[12,2,1,"","MAX_CONCURRENT_REQUESTS"],[12,4,1,"","async_ingest_metadata_manifest"],[12,4,1,"","async_query_urls_from_indexd"]],"gen3.wss":[[13,0,1,"","Gen3WsStorage"]],"gen3.wss.Gen3WsStorage":[[13,1,1,"","copy"],[13,1,1,"","download"],[13,1,1,"","download_url"],[13,1,1,"","ls"],[13,1,1,"","ls_path"],[13,1,1,"","rm"],[13,1,1,"","rm_path"],[13,1,1,"","upload"],[13,1,1,"","upload_url"]]},"objnames":{"0":["py","class","Python class"],"1":["py","method","Python method"],"2":["py","attribute","Python attribute"],"3":["py","module","Python module"],"4":["py","function","Python function"]},"objtypes":{"0":"py:class","1":"py:method","2":"py:attribute","3":"py:module","4":"py:function"},"terms":{"0a80fada010c":11,"0a80fada096c":11,"0a80fada097c":11,"0a80fada098c":11,"0a80fada099c":11,"11e9":11,"255e396f":11,"450c":11,"473d83400bc1bc9dc635e334fadd433c":11,"473d83400bc1bc9dc635e334faddd33c":11,"473d83400bc1bc9dc635e334fadde33c":11,"473d83400bc1bc9dc635e334faddf33c":11,"6f90":8,"7d3d8d2083b4":11,"93d9af72":11,"9a07":11,"A":[1,3,4,5,6,7,8,10,11,13],"ALL":7,"AND":5,"All":11,"Be":1,"But":5,"By":11,"For":[1,5,6,7,8,9,11],"IF":11,"If":[0,1,7,11,12],"In":10,"It":10,"Most":9,"NOT":12,"OR":5,"Same":13,"Such":9,"THE":11,"THIS":11,"That":3,"The":[0,1,2,3,5,8,10,11],"There":11,"These":9,"This":[0,1,2,3,4,5,6,7,8,10,11,13],"To":11,"We":11,"When":12,"YOU":11,"_get_acl_from_row":11,"_get_authz_from_row":11,"_get_file_name_from_row":11,"_get_file_size_from_row":11,"_get_guid_for_row":12,"_get_guid_from_row":11,"_get_md5_from_row":11,"_get_urls_from_row":11,"_guid_typ":12,"_manag":[2,9,10],"_query_for_associated_indexd_record_guid":12,"_ssl":[3,4,5],"a5c6":11,"ab167e49d25b488939b1ede42752458b":3,"abov":11,"access":[0,1,3,7,10],"access_method":[2,9,10],"access_token":0,"accesstoken":0,"acl":[2,3,9,11],"across":11,"act":0,"action":[9,11],"actual":11,"add":[3,5],"addit":[3,5,10,11],"admin":[5,11],"admin_endpoint_suffix":5,"algorithm":3,"alia":[3,5],"alias":5,"aliv":7,"allow":[0,6,8,10,11,12],"allowed_data_upload_bucket":1,"along":2,"alreadi":9,"also":1,"altern":[5,11],"alway":5,"ammount":12,"amount":[1,9],"ani":[0,5,10,11],"anoth":5,"api":[0,5,8,11],"api_key":11,"appli":7,"appropri":13,"arbitrari":0,"argument":[0,13],"array":8,"asc":7,"assign":9,"assist":10,"associ":[3,5],"assum":11,"async":[3,4,5,9,11,12],"async_cr":[2,5],"async_create_alias":[2,5],"async_create_record":[2,3],"async_delete_alia":[2,5],"async_delete_alias":[2,5],"async_download_object_manifest":[2,9,11],"async_get":[2,5],"async_get_alias":[2,5],"async_get_record":[2,3],"async_get_records_from_checksum":[2,3],"async_get_records_on_pag":[2,3],"async_get_with_param":[2,3],"async_ingest_metadata_manifest":[2,9,12],"async_query_url":[2,3],"async_query_urls_from_indexd":[2,9,12],"async_run_job_and_wait":[2,4],"async_upd":[2,5],"async_update_alias":[2,5],"async_update_record":[2,3],"async_verify_object_manifest":[2,9,11],"asynchron":[3,4,5],"asyncio":[11,12],"asyncron":5,"attach":[3,5],"attempt":11,"attribut":[10,11],"auth":[1,2,3,4,5,6,7,8,10,11,12,13],"auth_provid":[1,2,3,4,5,6,7,8,13],"authbas":0,"authent":0,"author":1,"authz":[0,1,2,3,9,10,11],"auto":[0,2],"automat":0,"avail":[1,2,10,11],"az":1,"b":[5,11],"b0f1":11,"bar":10,"base":[0,1,3,4,5,6,7,8,9,11,13],"baseid":3,"basic":[3,11,12],"batch_creat":[2,5],"batch_siz":8,"behalf":0,"behavior":11,"belong":8,"blank":3,"blob":[5,7],"bodi":3,"bool":[4,5,8,10,11,12],"boolean":3,"bownload":10,"broad":9,"broken":9,"bucket":[1,6],"bundl":10,"byte":10,"c":[5,11],"cach":10,"cache_hosts_wts_token":[2,9,10],"call":[10,13],"can":[0,3,4,8,11,12],"capabl":9,"case":[0,10],"categori":9,"ccle":8,"ccle_one_record":8,"ccle_sample_nod":8,"cdis":7,"chang":[3,11],"checksum":[3,10],"checksum_typ":3,"child":10,"children":[2,9,10],"chunk_siz":8,"class":[0,2,10,11,13],"cli":10,"client":[0,3],"client_credenti":0,"client_id":0,"client_scop":0,"client_secret":0,"code":[2,8],"column":[11,12],"column_to_use_as_guid":[2,9,12],"columna":11,"columnb":11,"columnc":11,"com":7,"comma":11,"command":[10,11],"common":[0,1,3,4,5,6,7,8,9,10,11,12,13],"commons_url":[2,9,10,11,12],"complet":[4,11],"complex":7,"concat":11,"concurr":[11,12],"configur":1,"connect":12,"consist":3,"constructor":0,"contain":[0,2,5,8,9,10,11,12],"content":[3,13],"content_created_d":3,"content_updated_d":3,"continu":10,"control":3,"conveni":10,"copi":[2,13],"coroutin":11,"correspond":3,"count":3,"crdc":0,"creat":[2,3,4,5,6,8,10,11],"create_alias":[2,5],"create_blank":[2,3],"create_index_key_path":[2,5],"create_job":[2,4],"create_new_vers":[2,3],"create_object_list":[2,9,10],"create_program":[2,8],"create_project":[2,8],"create_record":[2,3],"created_tim":[2,9,10],"creation":[3,11],"cred":3,"credenti":[0,1,3,4,5,6,7,8,10,11,13],"csv":[8,11,12],"curl":[0,2],"current":[6,8,10],"current_dir":[2,9,11],"custom":11,"d":5,"d70b41b9":8,"data":[0,1,3,5,7,8,10,11],"data_spreadsheet":8,"data_typ":7,"data_upload_bucket":1,"dataa":11,"datab":11,"databas":5,"datacommon":0,"datafil":10,"datamanag":10,"date":3,"datetim":[1,3,10],"dbgap":12,"dcf":8,"def":11,"default":[0,1,3,7,8,11,12],"defin":[5,8,10],"delay":4,"delet":[0,1,2,3,5,6,8,10,11],"delete_alia":[2,5],"delete_alias":[2,5],"delete_all_guid":[2,9,11],"delete_fil":[1,2],"delete_file_loc":[1,2,6],"delete_index_key_path":[2,5],"delete_nod":[2,8],"delete_object":[2,6],"delete_program":[2,8],"delete_project":[2,8],"delete_record":[2,3,8],"delete_unpacked_packag":10,"delimet":[11,12],"delimit":11,"demograph":8,"deprec":1,"descript":[3,5],"desir":11,"dest_path":13,"dest_urlstr":13,"dest_w":13,"dest_wskey":13,"detail":[2,7,10],"determin":[10,11,12],"dev":11,"dict":[3,4,5,10,11,12],"dictionari":[3,4,5,7,8],"dids":3,"differ":5,"direct":0,"directori":[10,11],"disabl":10,"discoveri":10,"disk":13,"dispatch":4,"dist_resolut":3,"distribut":3,"doc":[7,10],"docstr":2,"document":[1,3],"doe":[0,12],"domain":[11,12],"done":4,"download":[0,1,2,3,4,5,6,7,8,9,13],"download_files_in_drs_manifest":[2,9,10],"download_list":10,"download_manifest":11,"download_singl":[1,2],"download_url":[2,13],"downloadmanag":[2,9,10],"downloadstatus":[2,9,10],"drs":[2,9],"drs_download":10,"drs_hostnam":10,"drsdownload":10,"drsobjecttyp":10,"e":[5,10],"e043ab8b77b9":8,"effici":9,"eg":3,"either":8,"elasticsearch":7,"els":[0,12],"elsewher":12,"empti":[8,11],"enabl":11,"end":[5,10],"end_tim":[2,9,10],"endpoint":[0,1,2,3,4,5,7,8,13],"entir":8,"entri":[3,11],"env":0,"environ":0,"equal":7,"error":[10,11,12],"error_nam":11,"etc":8,"even":11,"everi":[9,11],"everyth":11,"ex":[0,11,12],"exampl":[0,1,3,4,5,6,7,8,10,11,13],"exclud":3,"execut":[7,8,11],"exist":[1,3,5,6,9,12],"expect":[5,9,11],"experi":8,"expir":[0,1],"expires_in":1,"export":[8,10],"export_nod":[2,8],"export_record":[2,8],"f1f8":11,"factori":10,"fail":[8,10],"fals":[3,5,6,10,11],"featur":[1,6],"fenc":[0,1],"fetch":0,"field":[3,5,7,11,12],"fieldnam":11,"file":[0,2,3,4,8,9,10,11,12,13],"file_nam":[1,2,3,9,10,11],"file_s":[2,9,10,11],"file_st":3,"fileformat":8,"filenam":[0,8,10,11,12],"files":10,"fill":12,"filter":[5,7],"filter_object":7,"first":[7,8],"flag":11,"folder":11,"follow":[0,11],"forc":11,"force_metadata_columns_even_if_empti":11,"form":13,"format":[3,5,8,11],"func_to_parse_row":[11,12],"function":[2,3,4,5,9,10,11,12],"g":10,"gen3":[10,11,12],"gen3_api_key":0,"gen3_oidc_client_creds_secret":0,"gen3auth":[0,1,2,3,4,5,6,7,8,10,11,12,13],"gen3fil":[1,2],"gen3index":[2,3],"gen3job":[2,4,10],"gen3metadata":[2,5],"gen3object":[2,6],"gen3queri":[2,7],"gen3submiss":[2,8],"gen3wsstorag":[2,13],"generat":[0,1,2,3,4,5,6,7,8,10,13],"get":[0,1,2,3,4,5,8,10,11,12,13],"get_access_token":[0,2],"get_access_token_from_wt":[0,2],"get_alias":[2,5],"get_all_record":[2,3],"get_dictionary_al":[2,8],"get_dictionary_nod":[2,8],"get_fresh_token":[2,9,10],"get_graphql_schema":[2,8],"get_guid_from_fil":12,"get_guids_prefix":[2,3],"get_index_key_path":[2,5],"get_latest_vers":[2,3],"get_output":[2,4],"get_presigned_url":[1,2],"get_program":[2,8],"get_project":[2,8],"get_project_dictionari":[2,8],"get_project_manifest":[2,8],"get_record":[2,3],"get_record_doc":[2,3],"get_records_on_pag":[2,3],"get_stat":[2,3],"get_status":[2,4],"get_url":[2,3],"get_valid_guid":[2,3],"get_vers":[2,3,4,5],"get_with_param":[2,3],"giangb":11,"github":[2,7],"give":1,"given":[0,3,4,5,8,10,12,13],"global":[4,5],"good":3,"grant":0,"graph":8,"graphql":[7,8],"graphql_queri":[2,7],"group":3,"guid":[1,2,3,5,6,9,11,12],"guid_exampl":11,"guid_for_row":12,"guid_from_fil":12,"guid_type_for_indexed_file_object":[2,9,12],"guid_type_for_non_indexed_file_object":[2,9,12],"guppi":7,"handl":[3,10],"hardcod":0,"has_vers":3,"hash":[3,11],"hash_typ":3,"header":11,"healthi":[3,4,5],"help":11,"helper":2,"hit":11,"host":10,"hostnam":[2,9,10],"howto":10,"http":12,"https":[0,7,11],"id":[0,1,3,5,10,11],"idea":3,"identifi":[3,5,9,11],"idp":0,"illustr":11,"immut":3,"implement":0,"implic":11,"import":11,"includ":[0,3],"indent":10,"index":[0,2,5,9],"index_manifest":11,"index_object_manifest":[2,9,11],"indexd":[1,3,6,10,11,12],"indexd_field":[11,12],"indexd_record_page_s":[2,9,11],"indexed_file_object_guid":12,"indic":[0,11],"infil":10,"info":[3,11],"inform":[2,3,10],"ingest":[2,9],"ingest_manifest":12,"initi":[0,10],"input":[4,10,11],"input_manifest":11,"instal":[0,2,11],"instanc":[1,3,6,7,8,9,10],"instead":[1,7,11],"int":[1,3,5,7,8,10,11,12],"integ":[1,3,8],"intend":0,"interact":[1,3,4,5,6,8,13],"interest":10,"interpret":0,"introspect":8,"involv":9,"is_healthi":[2,3,4,5],"is_indexed_file_object":12,"isn":1,"issu":0,"job":2,"job_id":4,"job_input":4,"job_nam":4,"json":[0,1,3,4,5,6,7,8,10,11,13],"just":[5,11,12],"jwt":0,"key":[0,3,5,13],"know":11,"known":10,"kwarg":[3,4,5],"larg":9,"last":10,"latest":3,"least":3,"level":6,"librari":11,"like":[3,5,9,11,12],"limit":[1,3,5,12],"linear":4,"linux":10,"list":[0,1,3,4,5,7,8,10,11,13],"list_access_in_drs_manifest":[2,9,10],"list_drs_object":[2,9,10],"list_files_in_drs_manifest":[2,9,10],"list_job":[2,4],"live":[11,12],"load":[2,9,10],"load_manifest":[2,9,10],"local":[0,13],"locat":[1,6],"lock":12,"log":[8,10,11,12],"logic":[5,12],"loop":11,"ls":[2,13],"ls_path":[2,13],"maco":11,"made":3,"main":10,"make":[9,11],"manag":[1,5,10],"mani":[8,11],"manifest":[2,8,9,10,11,12],"manifest_1":10,"manifest_fil":[11,12],"manifest_file_delimit":[11,12],"manifest_row_pars":[11,12],"map":[0,11],"mark":8,"master":7,"match":[3,5,12],"max":5,"max_concurrent_request":[2,9,11,12],"max_presigned_url_ttl":1,"max_tri":8,"maximum":[11,12],"may":[0,9,11],"md":[7,10],"md5":[2,3,9,11],"md5_hash":11,"md5sum":[2,9,10],"mds":[5,12],"mean":8,"mechan":3,"merg":5,"metadata":[2,3,6,9,11],"metadata_list":5,"metadata_sourc":12,"metadata_typ":12,"metdata":12,"method":[1,7,10],"minimum":10,"minut":0,"mode":7,"modul":[2,10,11],"mostly":2,"multipl":[8,11],"must":[1,5],"my_common":10,"my_credenti":10,"my_field":7,"my_index":7,"my_program":7,"my_project":7,"name":[3,4,8,10,11,12,13],"namespac":[0,12],"necessari":[3,5],"need":[3,7,10,11],"nest":5,"net":11,"never":0,"new":[0,3],"node":8,"node_nam":8,"node_typ":8,"none":[0,1,3,4,5,6,7,8,10,11,12,13],"note":[0,3,11,12],"noth":[3,6],"now":[1,8],"num":5,"num_process":11,"num_total_fil":11,"number":[3,7,8,11,12],"object":[1,2,3,4,5,7,8,9,10,11,13],"object_id":[1,2,9,10],"object_list":10,"object_typ":[2,9,10],"objectid":10,"obtain":[0,10],"occur":10,"offset":[5,7],"oidc":0,"old":3,"one":[3,5,7,10,11],"onli":[3,5,7,8,10,11],"open":[8,10,11],"open_project":[2,8],"openid":0,"opt":0,"option":[0,1,3,4,5,6,7,8,10,11],"order":[0,8],"ordered_node_list":8,"org":10,"os":0,"otherwis":10,"output":[4,5,11,12],"output_dir":10,"output_filenam":[11,12],"overrid":[0,11,12],"overwrit":5,"packag":10,"page":[0,1,2,3,4,5,6,7,8,10,11,13],"pagin":3,"parallel":11,"param":[3,5,8,10],"paramet":[0,1,3,4,5,6,7,8,10,11,12,13],"pars":[10,11,12,13],"parser":[11,12],"particular":0,"pass":[0,7,8,10],"password":[11,12],"path":[0,1,5,10,11,13],"path_to_manifest":11,"pattern":[3,12],"pdcdatastor":11,"pend":10,"per":[11,12],"peregrin":8,"permiss":10,"persist":9,"phs0001":11,"phs0002":11,"pick":1,"pla":11,"place":11,"planx":11,"point":[0,1,3,4,5,6,7,8,10,13],"popul":[10,12],"posit":[1,7],"possibl":10,"post":[0,11],"pprint":[2,9,10],"prefix":3,"presign":1,"pretti":10,"prev_guid":[2,9,11],"previous":[3,4,11],"print":[8,10],"process":11,"processed_fil":11,"profil":[0,1,3,4,5,6,7,8,10,13],"program":[8,11],"progress":[8,10],"project":[8,11],"project_id":[7,8],"protocol":1,"provid":[0,1,3,5,7,8,12],"public":[3,5],"put":0,"py":11,"python":[2,9,11],"python3":11,"python_subprocess_command":11,"queri":[1,2,3,5,8,11,12],"query_str":7,"query_txt":[7,8],"query_url":[2,3],"quickstart":2,"rather":0,"raw":[7,11],"raw_data_download":[2,7],"rbac":3,"read":[3,5,11],"readm":2,"reason":10,"record":[1,3,5,7,8,11,12],"refresh":[0,10],"refresh_access_token":[0,2],"refresh_fil":[0,1,3,4,5,6,7,8,10,13],"refresh_token":0,"regist":8,"regular":7,"relat":9,"remov":[1,6,11,13],"replac":11,"replace_url":11,"repo":2,"repres":[3,5,10],"represent":[1,3],"request":[0,1,3,5,8,11,12],"requir":10,"resolv":10,"resolve_object":[2,9,10],"respect":7,"respons":[0,1,3,4,5],"result":[1,8,10,11],"retri":8,"retriev":[1,8,10,12],"return":[0,1,3,4,5,6,7,8,10,11],"return_full_metadata":5,"rev":3,"revers":8,"revis":3,"right":1,"rm":[2,13],"rm_path":[2,13],"root":[11,12],"row":[7,8,11,12],"row_offset":8,"rtype":3,"run":[8,11],"s":[1,4,8,10,11],"s3":[1,10,11],"safe":11,"sampl":[8,10],"sandbox":[0,1,3,4,5,6,7,8,10,13],"save":10,"save_directori":10,"schema":8,"scope":[0,1],"screen":8,"script":2,"search":[0,2,3],"second":[1,4],"secret":0,"see":[7,10,11],"self":10,"semaphon":12,"semaphor":12,"separ":[0,11],"server":10,"servic":[1,3,4,5,6,8,11,12,13],"service_loc":[3,4,5],"session":11,"set":[0,1,5,10],"setup":2,"sheepdog":8,"show":10,"show_progress":10,"shown":11,"sign":1,"signpost":3,"similar":10,"simpl":3,"simpli":11,"sinc":3,"singl":[1,5,8],"size":[2,3,9,10,11],"skip":8,"sleep":4,"someth":11,"sort":7,"sort_field":7,"sort_object":7,"sourc":[0,1,2,3,4,5,6,7,8,10,11,12,13],"space":[0,11],"specif":[5,8,11,12],"specifi":[0,1,3,11,13],"spreadsheet":8,"src_path":13,"src_urlstr":13,"src_ws":13,"src_wskey":13,"ssl":[3,4,5],"start":[4,7,8,10],"start_tim":[2,9,10],"static":10,"status":[2,4,9,10],"storag":[1,2,6],"store":[1,3,10],"str":[0,1,3,4,5,7,8,10,11,12],"string":[0,3,5,11,13],"strip":11,"sub":8,"subject":[7,8],"submiss":2,"submit":[8,11],"submit_additional_metadata_column":11,"submit_fil":[2,8],"submit_record":[2,8],"submitter_id":7,"success":10,"suffici":3,"suppli":3,"support":[0,1,5,8,11],"sure":1,"synchron":11,"syntax":7,"system":[6,7,8,9],"t":[1,5,11],"tab":11,"task":9,"temporari":11,"test":11,"test1":11,"test2":11,"test3":11,"test4":11,"test5":11,"text":[1,7,8],"thread":11,"thread_num":11,"threadcontrol":[2,9,11],"tier":7,"time":[1,3,8,10,11],"timestamp":10,"tmp_folder":[2,9,11],"token":[0,10],"tool":2,"total":11,"treat":[1,5],"tree":10,"tri":0,"true":[3,4,5,6,7,8,10,11,12],"tsv":[8,11,12],"tupl":[0,3,11,12],"type":[1,3,4,5,7,8,10,11,12],"typic":10,"uc":7,"unaccess":7,"uniqu":[1,5],"unknown":10,"unpack":10,"unpack_packag":10,"updat":[2,3,5,10,11],"update_alias":[2,5],"update_blank":[2,3],"update_record":[2,3],"updated_tim":[2,9,10],"upload":[1,2,3,8,13],"upload_fil":[1,2],"upload_file_to_guid":[1,2],"upload_url":[2,13],"url":[1,2,3,9,10,11,12,13],"urls_metadata":3,"usag":11,"use":[0,1,3,4,5,6,7,8,10,11,12,13],"use_agg_md":5,"user":[0,10,12],"user_access":[2,9,10],"usual":12,"utcnow":1,"util":9,"uuid":[1,3,8],"uuid1":8,"uuid2":8,"valid":[3,7],"valu":[0,1,3,5,7,10,11],"value_from_indexd":11,"value_from_manifest":11,"variabl":[0,7,8],"various":2,"verbos":[7,8],"verif":11,"verifi":[2,9],"verify_manifest":11,"verify_object_manifest":11,"version":[3,4,5],"vital_status":7,"wait":4,"want":[0,3,8],"warn":11,"way":10,"web":0,"whether":[3,4,5,8,11,12],"whose":5,"will":[1,3,4,5,7,10,11,12],"within":[0,2,9],"without":[3,5],"won":5,"work":[0,10],"workaround":11,"worksheet":8,"workspac":[0,2],"wrapper":10,"write":11,"ws":13,"ws_urlstr":13,"wskey":13,"wss":13,"wts":[0,10],"x":11,"xlsx":8},"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"],"titleterms":{"auth":0,"class":[1,3,4,5,6,7,8],"document":2,"download":[10,11],"drs":10,"file":1,"gen3":[0,1,2,3,4,5,6,7,8,9,13],"helper":0,"index":[3,11],"indic":2,"ingest":12,"job":4,"metadata":[5,12],"object":6,"queri":7,"s":2,"sdk":2,"storag":13,"submiss":8,"tabl":2,"tool":[9,10,11,12],"verifi":11,"welcom":2,"workspac":13}}) \ No newline at end of file diff --git a/docs/_build/html/submission.html b/docs/_build/html/submission.html index 03e13ee3..b9c4f829 100644 --- a/docs/_build/html/submission.html +++ b/docs/_build/html/submission.html @@ -10,8 +10,8 @@ - - + + @@ -37,7 +37,7 @@

    Gen3 Submission Class

    -class gen3.submission.Gen3Submission(endpoint=None, auth_provider=None)[source]
    +class gen3.submission.Gen3Submission(endpoint=None, auth_provider=None)[source]

    Bases: object

    Submit/Export/Query data from a Gen3 Submission system.

    A class for interacting with the Gen3 submission services. diff --git a/docs/_build/html/tools.html b/docs/_build/html/tools.html index 1f285696..003b4a0e 100644 --- a/docs/_build/html/tools.html +++ b/docs/_build/html/tools.html @@ -10,8 +10,8 @@ - - + + diff --git a/docs/_build/html/tools/drs_pull.html b/docs/_build/html/tools/drs_pull.html index b80a139d..a3e74543 100644 --- a/docs/_build/html/tools/drs_pull.html +++ b/docs/_build/html/tools/drs_pull.html @@ -10,8 +10,8 @@ - - + + @@ -55,7 +55,7 @@

    -class gen3.tools.download.drs_download.DownloadManager(hostname: str, auth: Gen3Auth, download_list: List[Downloadable], show_progress: bool = False, commons_url: str = None)[source]
    +class gen3.tools.download.drs_download.DownloadManager(hostname: str, auth: Gen3Auth, download_list: List[Downloadable], show_progress: bool = False, commons_url: str = None)[source]

    Class to assist in downloading a list of Downloadable object which at a minimum is a json manifest of DRS object ids. The methods of interest are download and user_access.

    @@ -131,7 +131,7 @@
    -class gen3.tools.download.drs_download.DownloadStatus(filename: str, status: str = 'pending', start_time: datetime | None = None, end_time: datetime | None = None)[source]
    +class gen3.tools.download.drs_download.DownloadStatus(filename: str, status: str = 'pending', start_time: datetime | None = None, end_time: datetime | None = None)[source]

    Stores the download status of objectIDs.

    The DataManager will return a list of DownloadStatus as a result of calling the download method

    Status is “pending” until it is downloaded or an error occurs. @@ -181,7 +181,7 @@

    -class gen3.tools.download.drs_download.Downloadable(object_id: str, object_type: ~gen3.tools.download.drs_download.DRSObjectType | None = DRSObjectType.unknown, hostname: str | None = None, file_size: int | None = -1, file_name: str | None = None, updated_time: ~datetime.datetime | None = None, created_time: ~datetime.datetime | None = None, access_methods: ~typing.List[~typing.Dict[str, ~typing.Any]] = <factory>, children: ~typing.List[~gen3.tools.download.drs_download.Downloadable] = <factory>)[source]
    +class gen3.tools.download.drs_download.Downloadable(object_id: str, object_type: DRSObjectType | None = DRSObjectType.unknown, hostname: str | None = None, file_size: int | None = -1, file_name: str | None = None, updated_time: datetime | None = None, created_time: datetime | None = None, access_methods: Dict[str, ~typing.Any]]=<factory>, children: List[Downloadable] = <factory>)[source]

    Class handling the information for a DRS object. The information is populated from the manifest or by retrieving the information from a DRS server.

    @@ -311,7 +311,7 @@
    -class gen3.tools.download.drs_download.Manifest(object_id: str, file_size: int | None = -1, file_name: str | None = None, md5sum: str | None = None, commons_url: str | None = None)[source]
    +class gen3.tools.download.drs_download.Manifest(object_id: str, file_size: int | None = -1, file_name: str | None = None, md5sum: str | None = None, commons_url: str | None = None)[source]

    Data class representing a Gen3 JSON manifest typically exported from a Gen3 discovery page.

    The class is passed to the DownloadManager to download or list all of the files in the manifest. The Download manager will cache additional information (if available)

    @@ -372,7 +372,7 @@
    -static create_object_list(manifest) List[Downloadable][source]
    +static create_object_list(manifest) List[Downloadable][source]

    Create a list of Downloadable instances from the manifest

    Parameters:
    @@ -386,7 +386,7 @@
    -static load(filename: Path) List[Downloadable] | None[source]
    +static load(filename: Path) List[Downloadable] | None[source]

    Method to load a json manifest and return a list of Bownloadable object. This list is passed to the DownloadManager methods of download, and list

    @@ -401,7 +401,7 @@
    -static load_manifest(path: Path)[source]
    +static load_manifest(path: Path)[source]

    Loads a json manifest

    diff --git a/docs/_build/html/tools/indexing.html b/docs/_build/html/tools/indexing.html index f2aae699..2188b195 100644 --- a/docs/_build/html/tools/indexing.html +++ b/docs/_build/html/tools/indexing.html @@ -10,8 +10,8 @@ - - + + @@ -97,7 +97,7 @@

    Indexing Tools
    -async gen3.tools.indexing.download_manifest.async_download_object_manifest(commons_url, output_filename='object-manifest.csv', num_processes=4, max_concurrent_requests=24, input_manifest=None, python_subprocess_command='python')[source]
    +async gen3.tools.indexing.download_manifest.async_download_object_manifest(commons_url, output_filename='object-manifest.csv', num_processes=4, max_concurrent_requests=24, input_manifest=None, python_subprocess_command='python')[source]

    Download all file object records into a manifest csv

    Parameters:
    @@ -231,7 +231,7 @@

    Indexing Tools
    -class gen3.tools.indexing.index_manifest.ThreadControl(processed_files=0, num_total_files=0)[source]
    +class gen3.tools.indexing.index_manifest.ThreadControl(processed_files=0, num_total_files=0)[source]

    Bases: object

    Class for thread synchronization

    @@ -382,7 +382,7 @@

    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-1762550046.1756725.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-1767382301.9216049.log')[source]

    Verify all file object records into a manifest csv

    Parameters:
    diff --git a/docs/_build/html/tools/metadata.html b/docs/_build/html/tools/metadata.html index 3ceef482..db421ff6 100644 --- a/docs/_build/html/tools/metadata.html +++ b/docs/_build/html/tools/metadata.html @@ -10,8 +10,8 @@ - - + + @@ -103,7 +103,7 @@

    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-1762550046.390404.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-1767382302.1590407.log', get_guid_from_file=True, metadata_type=None)[source]

    Ingest all metadata records into a manifest csv

    Parameters:
    @@ -138,7 +138,7 @@

    Metadata Tools
    -async gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd(pattern, commons_url, lock)[source]
    +async gen3.tools.metadata.ingest_manifest.async_query_urls_from_indexd(pattern, commons_url, lock)[source]

    Gets a semaphore then requests a record for the given pattern

    Parameters:
    diff --git a/docs/_build/html/wss.html b/docs/_build/html/wss.html index c3b6b461..d373f5e2 100644 --- a/docs/_build/html/wss.html +++ b/docs/_build/html/wss.html @@ -10,8 +10,8 @@ - - + + @@ -36,7 +36,7 @@

    Gen3 Workspace Storage

    -class gen3.wss.Gen3WsStorage(auth_provider=None)[source]
    +class gen3.wss.Gen3WsStorage(auth_provider=None)[source]

    Bases: object

    A class for interacting with the Gen3 workspace storage service.

    Examples

    diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 00000000..1fda6cdc --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,2 @@ +def test_import_cli(): + import gen3.cli.__main__