diff --git a/Cargo.lock b/Cargo.lock index 0f8a1d8..bf44def 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1133,7 +1133,7 @@ dependencies = [ [[package]] name = "genomeshader" -version = "0.1.26" +version = "0.1.28" dependencies = [ "anyhow", "backoff", diff --git a/playground.ipynb b/playground.ipynb index c37ea93..30b56a4 100644 --- a/playground.ipynb +++ b/playground.ipynb @@ -128,7 +128,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -137,537 +137,21 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "metadata": {}, "outputs": [ { "data": { - "application/javascript": [ - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = true;\n", - " var py_version = '3.1.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", - " var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n", - " var reloading = false;\n", - " var Bokeh = root.Bokeh;\n", - " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", - "\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", - " root._bokeh_timeout = Date.now() + 5000;\n", - " root._bokeh_failed_load = false;\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " try {\n", - " root._bokeh_onload_callbacks.forEach(function(callback) {\n", - " if (callback != null)\n", - " callback();\n", - " });\n", - " } finally {\n", - " delete root._bokeh_onload_callbacks;\n", - " }\n", - " console.debug(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n", - " if (css_urls == null) css_urls = [];\n", - " if (js_urls == null) js_urls = [];\n", - " if (js_modules == null) js_modules = [];\n", - " if (js_exports == null) js_exports = {};\n", - "\n", - " root._bokeh_onload_callbacks.push(callback);\n", - "\n", - " if (root._bokeh_is_loading > 0) {\n", - " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " if (!reloading) {\n", - " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " }\n", - "\n", - " function on_load() {\n", - " root._bokeh_is_loading--;\n", - " if (root._bokeh_is_loading === 0) {\n", - " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", - " run_callbacks()\n", - " }\n", - " }\n", - " window._bokeh_on_load = on_load\n", - "\n", - " function on_error() {\n", - " console.error(\"failed to load \" + url);\n", - " }\n", - "\n", - " var skip = [];\n", - " if (window.requirejs) {\n", - " window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n", - " require([\"jspanel\"], function(jsPanel) {\n", - "\twindow.jsPanel = jsPanel\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-modal\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-tooltip\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-hint\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-layout\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-contextmenu\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"jspanel-dock\"], function() {\n", - "\ton_load()\n", - " })\n", - " require([\"gridstack\"], function(GridStack) {\n", - "\twindow.GridStack = GridStack\n", - "\ton_load()\n", - " })\n", - " require([\"notyf\"], function() {\n", - "\ton_load()\n", - " })\n", - " root._bokeh_is_loading = css_urls.length + 9;\n", - " } else {\n", - " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n", - " }\n", - "\n", - " var existing_stylesheets = []\n", - " var links = document.getElementsByTagName('link')\n", - " for (var i = 0; i < links.length; i++) {\n", - " var link = links[i]\n", - " if (link.href != null) {\n", - "\texisting_stylesheets.push(link.href)\n", - " }\n", - " }\n", - " for (var i = 0; i < css_urls.length; i++) {\n", - " var url = css_urls[i];\n", - " if (existing_stylesheets.indexOf(url) !== -1) {\n", - "\ton_load()\n", - "\tcontinue;\n", - " }\n", - " const element = document.createElement(\"link\");\n", - " element.onload = on_load;\n", - " element.onerror = on_error;\n", - " element.rel = \"stylesheet\";\n", - " element.type = \"text/css\";\n", - " element.href = url;\n", - " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", - " document.body.appendChild(element);\n", - " } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n", - " var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n", - " for (var i = 0; i < urls.length; i++) {\n", - " skip.push(urls[i])\n", - " }\n", - " } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n", - " var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n", - " for (var i = 0; i < urls.length; i++) {\n", - " skip.push(urls[i])\n", - " }\n", - " } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n", - " var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n", - " for (var i = 0; i < urls.length; i++) {\n", - " skip.push(urls[i])\n", - " }\n", - " } var existing_scripts = []\n", - " var scripts = document.getElementsByTagName('script')\n", - " for (var i = 0; i < scripts.length; i++) {\n", - " var script = scripts[i]\n", - " if (script.src != null) {\n", - "\texisting_scripts.push(script.src)\n", - " }\n", - " }\n", - " for (var i = 0; i < js_urls.length; i++) {\n", - " var url = js_urls[i];\n", - " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", - "\tif (!window.requirejs) {\n", - "\t on_load();\n", - "\t}\n", - "\tcontinue;\n", - " }\n", - " var element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error;\n", - " element.async = false;\n", - " element.src = url;\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " for (var i = 0; i < js_modules.length; i++) {\n", - " var url = js_modules[i];\n", - " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", - "\tif (!window.requirejs) {\n", - "\t on_load();\n", - "\t}\n", - "\tcontinue;\n", - " }\n", - " var element = document.createElement('script');\n", - " element.onload = on_load;\n", - " element.onerror = on_error;\n", - " element.async = false;\n", - " element.src = url;\n", - " element.type = \"module\";\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.head.appendChild(element);\n", - " }\n", - " for (const name in js_exports) {\n", - " var url = js_exports[name];\n", - " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", - "\tif (!window.requirejs) {\n", - "\t on_load();\n", - "\t}\n", - "\tcontinue;\n", - " }\n", - " var element = document.createElement('script');\n", - " element.onerror = on_error;\n", - " element.async = false;\n", - " element.type = \"module\";\n", - " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " element.textContent = `\n", - " import ${name} from \"${url}\"\n", - " window.${name} = ${name}\n", - " window._bokeh_on_load()\n", - " `\n", - " document.head.appendChild(element);\n", - " }\n", - " if (!js_urls.length && !js_modules.length) {\n", - " on_load()\n", - " }\n", - " };\n", - "\n", - " function inject_raw_css(css) {\n", - " const element = document.createElement(\"style\");\n", - " element.appendChild(document.createTextNode(css));\n", - " document.body.appendChild(element);\n", - " }\n", - "\n", - " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.holoviz.org/panel/1.2.3/dist/panel.min.js\"];\n", - " var js_modules = [];\n", - " var js_exports = {};\n", - " var css_urls = [];\n", - " var inline_js = [ function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - "function(Bokeh) {} // ensure no trailing comma for IE\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " if ((root.Bokeh !== undefined) || (force === true)) {\n", - " for (var i = 0; i < inline_js.length; i++) {\n", - " inline_js[i].call(root, root.Bokeh);\n", - " }\n", - " // Cache old bokeh versions\n", - " if (Bokeh != undefined && !reloading) {\n", - "\tvar NewBokeh = root.Bokeh;\n", - "\tif (Bokeh.versions === undefined) {\n", - "\t Bokeh.versions = new Map();\n", - "\t}\n", - "\tif (NewBokeh.version !== Bokeh.version) {\n", - "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", - "\t}\n", - "\troot.Bokeh = Bokeh;\n", - " }} else if (Date.now() < root._bokeh_timeout) {\n", - " setTimeout(run_inline_js, 100);\n", - " } else if (!root._bokeh_failed_load) {\n", - " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", - " root._bokeh_failed_load = true;\n", - " }\n", - " root._bokeh_is_initializing = false\n", - " }\n", - "\n", - " function load_or_wait() {\n", - " // Implement a backoff loop that tries to ensure we do not load multiple\n", - " // versions of Bokeh and its dependencies at the same time.\n", - " // In recent versions we use the root._bokeh_is_initializing flag\n", - " // to determine whether there is an ongoing attempt to initialize\n", - " // bokeh, however for backward compatibility we also try to ensure\n", - " // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n", - " // before older versions are fully initialized.\n", - " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", - " root._bokeh_is_initializing = false;\n", - " root._bokeh_onload_callbacks = undefined;\n", - " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", - " load_or_wait();\n", - " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", - " setTimeout(load_or_wait, 100);\n", - " } else {\n", - " Bokeh = root.Bokeh;\n", - " bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", - " root._bokeh_is_initializing = true\n", - " root._bokeh_onload_callbacks = []\n", - " if (!reloading && (!bokeh_loaded || is_dev)) {\n", - "\troot.Bokeh = undefined;\n", - " }\n", - " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", - "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", - "\trun_inline_js();\n", - " });\n", - " }\n", - " }\n", - " // Give older versions of the autoload script a head-start to ensure\n", - " // they initialize before we start loading newer version.\n", - " setTimeout(load_or_wait, 100)\n", - "}(window));" - ], - "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.1.1'.replace('rc', '-rc.').replace('.dev', '-dev.');\n var is_dev = py_version.indexOf(\"+\") !== -1 || py_version.indexOf(\"-\") !== -1;\n var reloading = false;\n var Bokeh = root.Bokeh;\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n\n if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n }\n if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n run_callbacks();\n return null;\n }\n if (!reloading) {\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n\n function on_load() {\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock', 'gridstack': 'https://cdn.jsdelivr.net/npm/gridstack@7.2.3/dist/gridstack-all', 'notyf': 'https://cdn.jsdelivr.net/npm/notyf@3/notyf.min'}, 'shim': {'jspanel': {'exports': 'jsPanel'}, 'gridstack': {'exports': 'GridStack'}}});\n require([\"jspanel\"], function(jsPanel) {\n\twindow.jsPanel = jsPanel\n\ton_load()\n })\n require([\"jspanel-modal\"], function() {\n\ton_load()\n })\n require([\"jspanel-tooltip\"], function() {\n\ton_load()\n })\n require([\"jspanel-hint\"], function() {\n\ton_load()\n })\n require([\"jspanel-layout\"], function() {\n\ton_load()\n })\n require([\"jspanel-contextmenu\"], function() {\n\ton_load()\n })\n require([\"jspanel-dock\"], function() {\n\ton_load()\n })\n require([\"gridstack\"], function(GridStack) {\n\twindow.GridStack = GridStack\n\ton_load()\n })\n require([\"notyf\"], function() {\n\ton_load()\n })\n root._bokeh_is_loading = css_urls.length + 9;\n } else {\n root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n }\n\n var existing_stylesheets = []\n var links = document.getElementsByTagName('link')\n for (var i = 0; i < links.length; i++) {\n var link = links[i]\n if (link.href != null) {\n\texisting_stylesheets.push(link.href)\n }\n }\n for (var i = 0; i < css_urls.length; i++) {\n var url = css_urls[i];\n if (existing_stylesheets.indexOf(url) !== -1) {\n\ton_load()\n\tcontinue;\n }\n const element = document.createElement(\"link\");\n element.onload = on_load;\n element.onerror = on_error;\n element.rel = \"stylesheet\";\n element.type = \"text/css\";\n element.href = url;\n console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n document.body.appendChild(element);\n } if (((window['jsPanel'] !== undefined) && (!(window['jsPanel'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/jspanel.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu.js', 'https://cdn.holoviz.org/panel/1.2.3/dist/bundled/floatpanel/jspanel4@4.12.0/dist/extensions/dock/jspanel.dock.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['GridStack'] !== undefined) && (!(window['GridStack'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/gridstack/gridstack@7.2.3/dist/gridstack-all.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } if (((window['Notyf'] !== undefined) && (!(window['Notyf'] instanceof HTMLElement))) || window.requirejs) {\n var urls = ['https://cdn.holoviz.org/panel/1.2.3/dist/bundled/notificationarea/notyf@3/notyf.min.js'];\n for (var i = 0; i < urls.length; i++) {\n skip.push(urls[i])\n }\n } var existing_scripts = []\n var scripts = document.getElementsByTagName('script')\n for (var i = 0; i < scripts.length; i++) {\n var script = scripts[i]\n if (script.src != null) {\n\texisting_scripts.push(script.src)\n }\n }\n for (var i = 0; i < js_urls.length; i++) {\n var url = js_urls[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (var i = 0; i < js_modules.length; i++) {\n var url = js_modules[i];\n if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n var url = js_exports[name];\n if (skip.indexOf(url) >= 0 || root[name] != null) {\n\tif (!window.requirejs) {\n\t on_load();\n\t}\n\tcontinue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.1.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.1.1.min.js\", \"https://cdn.holoviz.org/panel/1.2.3/dist/panel.min.js\"];\n var js_modules = [];\n var js_exports = {};\n var css_urls = [];\n var inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (var i = 0; i < inline_js.length; i++) {\n inline_js[i].call(root, root.Bokeh);\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n\tvar NewBokeh = root.Bokeh;\n\tif (Bokeh.versions === undefined) {\n\t Bokeh.versions = new Map();\n\t}\n\tif (NewBokeh.version !== Bokeh.version) {\n\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n\t}\n\troot.Bokeh = Bokeh;\n }} else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n Bokeh = root.Bokeh;\n bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n if 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{\n root._bokeh_is_loading--;\n if (root._bokeh_is_loading === 0) {\n console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n run_callbacks()\n }\n }\n window._bokeh_on_load = on_load\n\n function on_error() {\n console.error(\"failed to load \" + url);\n }\n\n var skip = [];\n if (window.requirejs) {\n window.requirejs.config({'packages': {}, 'paths': {'jspanel': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/jspanel', 'jspanel-modal': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/modal/jspanel.modal', 'jspanel-tooltip': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/tooltip/jspanel.tooltip', 'jspanel-hint': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/hint/jspanel.hint', 'jspanel-layout': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/layout/jspanel.layout', 'jspanel-contextmenu': 'https://cdn.jsdelivr.net/npm/jspanel4@4.12.0/dist/extensions/contextmenu/jspanel.contextmenu', 'jspanel-dock': 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newScript.setAttribute(attr.name, attr.value) });\n", - " newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n", - " oldScript.parentNode.replaceChild(newScript, oldScript);\n", - " });\n", - " if (JS_MIME_TYPE in output.data) {\n", - " toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n", - " }\n", - " output_area._hv_plot_id = id;\n", - " if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n", - " window.PyViz.plot_index[id] = Bokeh.index[id];\n", - " } else {\n", - " window.PyViz.plot_index[id] = null;\n", - " }\n", - " } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", - " var bk_div = document.createElement(\"div\");\n", - " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", - " var script_attrs = bk_div.children[0].attributes;\n", - " for (var i = 0; i < script_attrs.length; i++) {\n", - " toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n", - " }\n", - " // store reference to server id on output_area\n", - " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", - " }\n", - "}\n", - "\n", - "/**\n", - " * Handle when an output is cleared or removed\n", - " */\n", - "function handle_clear_output(event, handle) {\n", - " var id = handle.cell.output_area._hv_plot_id;\n", - " var server_id = handle.cell.output_area._bokeh_server_id;\n", - " if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n", - " var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n", - " if (server_id !== null) {\n", - " comm.send({event_type: 'server_delete', 'id': server_id});\n", - " return;\n", - " } else if (comm !== null) {\n", - " comm.send({event_type: 'delete', 'id': id});\n", - " }\n", - " delete PyViz.plot_index[id];\n", - " if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n", - " var doc = window.Bokeh.index[id].model.document\n", - " doc.clear();\n", - " const i = window.Bokeh.documents.indexOf(doc);\n", - " if (i > -1) {\n", - " window.Bokeh.documents.splice(i, 1);\n", - " }\n", - " }\n", - "}\n", - "\n", - "/**\n", - " * Handle kernel restart event\n", - " */\n", - "function handle_kernel_cleanup(event, handle) {\n", - " delete PyViz.comms[\"hv-extension-comm\"];\n", - " window.PyViz.plot_index = {}\n", - "}\n", - "\n", - "/**\n", - " * Handle update_display_data messages\n", - " */\n", - "function handle_update_output(event, handle) {\n", - " handle_clear_output(event, {cell: {output_area: handle.output_area}})\n", - " handle_add_output(event, handle)\n", - "}\n", - "\n", - "function register_renderer(events, OutputArea) {\n", - " function append_mime(data, metadata, element) {\n", - " // create a DOM node to render to\n", - " var toinsert = this.create_output_subarea(\n", - " metadata,\n", - " CLASS_NAME,\n", - " EXEC_MIME_TYPE\n", - " );\n", - " this.keyboard_manager.register_events(toinsert);\n", - " // Render to node\n", - " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", - " render(props, toinsert[0]);\n", - " element.append(toinsert);\n", - " return toinsert\n", - " }\n", - "\n", - " events.on('output_added.OutputArea', handle_add_output);\n", - " events.on('output_updated.OutputArea', handle_update_output);\n", - " events.on('clear_output.CodeCell', handle_clear_output);\n", - " events.on('delete.Cell', handle_clear_output);\n", - " events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n", - "\n", - " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", - " safe: true,\n", - " index: 0\n", - " });\n", - "}\n", - "\n", - "if (window.Jupyter !== undefined) {\n", - " try {\n", - " var events = require('base/js/events');\n", - " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", - " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", - " register_renderer(events, OutputArea);\n", - " }\n", - " } catch(err) {\n", - " }\n", - "}\n" - ], - "application/vnd.holoviews_load.v0+json": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n function JupyterCommManager() {\n }\n\n JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n comm_manager.register_target(comm_id, function(comm) {\n comm.on_msg(msg_handler);\n });\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n comm.onMsg = msg_handler;\n });\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n console.log(message)\n var content = {data: message.data, comm_id};\n var buffers = []\n for (var buffer of message.buffers || []) {\n buffers.push(new DataView(buffer))\n }\n var metadata = message.metadata || {};\n var msg = {content, buffers, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n })\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n if (msg_handler) {\n comm.on_msg(msg_handler);\n }\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n comm.open();\n if (msg_handler) {\n comm.onMsg = msg_handler;\n }\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n var comm_promise = google.colab.kernel.comms.open(comm_id)\n comm_promise.then((comm) => {\n window.PyViz.comms[comm_id] = comm;\n if (msg_handler) {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n var content = {data: message.data};\n var metadata = message.metadata || {comm_id};\n var msg = {content, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n }\n }) \n var sendClosure = (data, metadata, buffers, disposeOnDone) => {\n return comm_promise.then((comm) => {\n comm.send(data, metadata, buffers, disposeOnDone);\n });\n };\n var comm = {\n send: sendClosure\n };\n }\n window.PyViz.comms[comm_id] = comm;\n return comm;\n }\n window.PyViz.comm_manager = new JupyterCommManager();\n \n\n\nvar JS_MIME_TYPE = 'application/javascript';\nvar HTML_MIME_TYPE = 'text/html';\nvar EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\nvar CLASS_NAME = 'output';\n\n/**\n * Render data to the DOM node\n */\nfunction render(props, node) {\n var div = document.createElement(\"div\");\n var script = document.createElement(\"script\");\n node.appendChild(div);\n node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n var output_area = handle.output_area;\n var output = handle.output;\n if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n return\n }\n var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n if (id !== undefined) {\n var nchildren = toinsert.length;\n var html_node = toinsert[nchildren-1].children[0];\n html_node.innerHTML = output.data[HTML_MIME_TYPE];\n var scripts = [];\n var nodelist = html_node.querySelectorAll(\"script\");\n for (var i in nodelist) {\n if (nodelist.hasOwnProperty(i)) {\n scripts.push(nodelist[i])\n }\n }\n\n scripts.forEach( function (oldScript) {\n var newScript = document.createElement(\"script\");\n var attrs = [];\n var nodemap = oldScript.attributes;\n for (var j in nodemap) {\n if (nodemap.hasOwnProperty(j)) {\n attrs.push(nodemap[j])\n }\n }\n attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n oldScript.parentNode.replaceChild(newScript, oldScript);\n });\n if (JS_MIME_TYPE in output.data) {\n toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n }\n output_area._hv_plot_id = id;\n if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n window.PyViz.plot_index[id] = Bokeh.index[id];\n } else {\n window.PyViz.plot_index[id] = null;\n }\n } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n var bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n var script_attrs = bk_div.children[0].attributes;\n for (var i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n var server_id = handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" + "application/javascript": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n function JupyterCommManager() {\n }\n\n JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n comm_manager.register_target(comm_id, function(comm) {\n comm.on_msg(msg_handler);\n });\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n comm.onMsg = msg_handler;\n });\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n console.log(message)\n var content = {data: message.data, comm_id};\n var buffers = []\n for (var buffer of message.buffers || []) {\n buffers.push(new DataView(buffer))\n }\n var metadata = message.metadata || {};\n var msg = {content, buffers, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n })\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n if (msg_handler) {\n comm.on_msg(msg_handler);\n }\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n comm.open();\n if (msg_handler) {\n comm.onMsg = msg_handler;\n }\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n var comm_promise = google.colab.kernel.comms.open(comm_id)\n comm_promise.then((comm) => {\n window.PyViz.comms[comm_id] = comm;\n if (msg_handler) {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n var content = {data: message.data};\n var metadata = message.metadata || {comm_id};\n var msg = {content, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n }\n }) \n var sendClosure = (data, metadata, buffers, disposeOnDone) => {\n return comm_promise.then((comm) => {\n comm.send(data, metadata, buffers, disposeOnDone);\n });\n };\n var comm = {\n send: sendClosure\n };\n }\n window.PyViz.comms[comm_id] = comm;\n return comm;\n }\n window.PyViz.comm_manager = new JupyterCommManager();\n \n\n\nvar JS_MIME_TYPE = 'application/javascript';\nvar HTML_MIME_TYPE = 'text/html';\nvar EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\nvar CLASS_NAME = 'output';\n\n/**\n * Render data to the DOM node\n */\nfunction render(props, node) {\n var div = document.createElement(\"div\");\n var script = document.createElement(\"script\");\n node.appendChild(div);\n node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n var output_area = handle.output_area;\n var output = handle.output;\n if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n return\n }\n var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n if (id !== undefined) {\n var nchildren = toinsert.length;\n var html_node = toinsert[nchildren-1].children[0];\n html_node.innerHTML = output.data[HTML_MIME_TYPE];\n var scripts = [];\n var nodelist = html_node.querySelectorAll(\"script\");\n for (var i in nodelist) {\n if (nodelist.hasOwnProperty(i)) {\n scripts.push(nodelist[i])\n }\n }\n\n scripts.forEach( function (oldScript) {\n var newScript = document.createElement(\"script\");\n var attrs = [];\n var nodemap = oldScript.attributes;\n for (var j in nodemap) {\n if (nodemap.hasOwnProperty(j)) {\n attrs.push(nodemap[j])\n }\n }\n attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n oldScript.parentNode.replaceChild(newScript, oldScript);\n });\n if (JS_MIME_TYPE in output.data) {\n toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n }\n output_area._hv_plot_id = id;\n if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n window.PyViz.plot_index[id] = Bokeh.index[id];\n } else {\n window.PyViz.plot_index[id] = null;\n }\n } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n var bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n var script_attrs = bk_div.children[0].attributes;\n for (var i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n var server_id = handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n", + "application/vnd.holoviews_load.v0+json": "" }, "metadata": {}, "output_type": "display_data" @@ -793,16 +277,16 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "'0.1.18'" + "'0.1.28'" ] }, - "execution_count": 2, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -820,7 +304,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -836,7 +320,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -925,16 +409,27 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "bams = [\n", + " 'gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam',\n", + "]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "79" + "1" ] }, - "execution_count": 5, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -945,38 +440,11 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [], - "source": [ - "#s.attach_reads(bams[0:5], 'cohort-1')" - ] - }, - { - "cell_type": "code", - "execution_count": 11, - "metadata": {}, - "outputs": [], - "source": [ - "s.reset()" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [], - "source": [ - "bams = ['gs://fc-secure-f7d80b48-be60-426f-aa6b-f037a1bf7f34/outputs/GRCh38/PBCCSWholeGenome/1000513/variants/small/1000513.MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam']" - ] - }, - { - "cell_type": "code", - "execution_count": 5, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ - "s.attach_reads(bams, 'aou-lr-phase1')" + "s.attach_reads(bams, 'cohort-1')" ] }, { @@ -988,7 +456,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -996,7 +464,7 @@ "output_type": "stream", "text": [ "Reads:\n", - " - gs://fc-secure-f7d80b48-be60-426f-aa6b-f037a1bf7f34/outputs/GRCh38/PBCCSWholeGenome/1000513/variants/small/1000513.MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam (aou-lr-phase1)\n", + " - gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam (cohort-1)\n", "Loci:\n", "Staging:\n" ] @@ -1015,7 +483,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -1024,7 +492,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -1032,7 +500,7 @@ "output_type": "stream", "text": [ "Reads:\n", - " - gs://fc-secure-f7d80b48-be60-426f-aa6b-f037a1bf7f34/outputs/GRCh38/PBCCSWholeGenome/1000513/variants/small/1000513.MARGIN_PHASED.PEPPER_SNP_MARGIN.haplotagged.bam (aou-lr-phase1)\n", + " - gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam (cohort-1)\n", "Loci:\n", " - (\"chr15\", 23960193, 23963918)\n", "Staging:\n" @@ -1059,100 +527,7 @@ }, { "cell_type": "code", - "execution_count": 9, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Updated property [core/account].\n" - ] - } - ], - "source": [ - "!gcloud config set account 'kiran.garimella@pmi-ops.org'" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ya29.a0AfB_byAXLUjS87OomVAoo1D2S96HGVoIurLjc3uokleOaDcHfzOQkpWq06PZm7uBwcU_HfmHjNS3xrcTtB5Bioyp_ZGCl86KBwzy_08kkEfp3gN39wRkDoPrA8GCYIdODd3Q_bSBimP5RXa71EG2mNL_85gHfrfq2AFF4QaCgYKAWcSARASFQHGX2MitTQ_xbciSGJQE-9f6Cdo5A0173\n" - ] - } - ], - "source": [ - "!export gcloud auth application-default print-access-token" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "env: GCS_OAUTH_TOKEN=ya29.a0AfB_byDmme871_sPbcY1qT3aSmfhT3SG70bG8YkyP3NmdnxFfzxNQ972oIGhWx0sLGhVq1lduqFUXNzok-uQyRIS_WUoWYqbBZ_zdwKPm_Q7VSrknfiBhwONKh_RKMm1TC1ibIbrsYGSW2sB5HuWVGi0Bx-9H4XFAbcRUAaCgYKAU0SARASFQHGX2Mi1654raP34lkc52n1Qvftgg0173\n" - ] - } - ], - "source": [ - "token=!gcloud auth application-default print-access-token\n", - "%env GCS_OAUTH_TOKEN={token[0]}" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ya29.a0AfB_byDmme871_sPbcY1qT3aSmfhT3SG70bG8YkyP3NmdnxFfzxNQ972oIGhWx0sLGhVq1lduqFUXNzok-uQyRIS_WUoWYqbBZ_zdwKPm_Q7VSrknfiBhwONKh_RKMm1TC1ibIbrsYGSW2sB5HuWVGi0Bx-9H4XFAbcRUAaCgYKAU0SARASFQHGX2Mi1654raP34lkc52n1Qvftgg0173\n" - ] - } - ], - "source": [ - "print(os.environ['GCS_OAUTH_TOKEN'])" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Your browser has been opened to visit:\n", - "\n", - " https://accounts.google.com/o/oauth2/auth?response_type=code&client_id=32555940559.apps.googleusercontent.com&redirect_uri=http%3A%2F%2Flocalhost%3A8085%2F&scope=openid+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fuserinfo.email+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fcloud-platform+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fappengine.admin+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fcompute+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Faccounts.reauth&state=RbMmyt66i1Ivn8tJ8DrJ66qJuFZLDE&access_type=offline&code_challenge=q2GRVT5QB62dnZ_2OrBC8jtpyniwP4Nom1eH0WsUzgs&code_challenge_method=S256\n", - "\n", - "\n", - "You are now logged in as [kiran.garimella@pmi-ops.org].\n", - "Your current project is [broad-dsp-lrma]. You can change this setting by running:\n", - " $ gcloud config set project PROJECT_ID\n" - ] - } - ], - "source": [ - "!gcloud auth login" - ] - }, - { - "cell_type": "code", - "execution_count": 27, + "execution_count": null, "metadata": {}, "outputs": [ { @@ -1292,9 +667,6 @@ "source": [ "%%time\n", "\n", - "!gcloud auth list\n", - "!echo $GCS_OAUTH_TOKEN\n", - "\n", "s.stage(use_cache=False)" ] }, diff --git a/src/stage.rs b/src/stage.rs index f5efc5c..29d2d7c 100644 --- a/src/stage.rs +++ b/src/stage.rs @@ -1,7 +1,7 @@ use std::collections::{HashSet, HashMap}; use std::env; +use std::error::Error; use std::path::PathBuf; -use std::sync::Mutex; use url::Url; use backoff::ExponentialBackoff; @@ -12,39 +12,30 @@ use rust_htslib::bam::IndexedReader; use crate::alignment::extract_reads; use crate::env::{gcs_authorize_data_access, local_guess_curl_ca_bundle}; -fn open_bam(reads_url: &Url, cache_path: &PathBuf) -> IndexedReader { +fn open_bam(reads_url: &Url, cache_path: &PathBuf) -> Result> { env::set_current_dir(cache_path).unwrap(); - println!("1 GCS_OAUTH_TOKEN: {:?}", std::env::var("GCS_OAUTH_TOKEN")); - println!("1 CURL_CA_BUNDLE: {:?}", std::env::var("CURL_CA_BUNDLE")); - let bam = match IndexedReader::from_url(reads_url) { Ok(bam) => bam, Err(_) => { gcs_authorize_data_access(); - println!("2 GCS_OAUTH_TOKEN: {:?}", std::env::var("GCS_OAUTH_TOKEN")); - println!("2 CURL_CA_BUNDLE: {:?}", std::env::var("CURL_CA_BUNDLE")); - match IndexedReader::from_url(reads_url) { Ok(bam) => bam, Err(_) => { local_guess_curl_ca_bundle(); - println!("3 GCS_OAUTH_TOKEN: {:?}", std::env::var("GCS_OAUTH_TOKEN")); - println!("3 CURL_CA_BUNDLE: {:?}", std::env::var("CURL_CA_BUNDLE")); - - IndexedReader::from_url(reads_url).unwrap() + IndexedReader::from_url(reads_url)? } } } }; - bam + Ok(bam) } -fn stage_data_from_one_file(reads_url: &Url, cohort: &String, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result> { - let mut bam = open_bam(reads_url, cache_path); +fn stage_data_from_one_file(reads_url: &Url, cohort: &String, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result> { + let mut bam = open_bam(reads_url, cache_path)?; let mut outer_df = DataFrame::default(); for (chr, start, stop) in loci.iter() { @@ -57,37 +48,39 @@ fn stage_data_from_one_file(reads_url: &Url, cohort: &String, loci: &HashSet<(St Ok(outer_df) } -fn stage_data_from_all_files(reads_cohort: &HashSet<(Url, String)>, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result>, Box> { - let dfs = Mutex::new(Vec::new()); - - reads_cohort +fn stage_data_from_all_files(reads_cohort: &HashSet<(Url, String)>, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result, Box> { + let dfs: Vec<_> = reads_cohort .par_iter() - .for_each(|(reads, cohort)| { + .map(|(reads, cohort)| { let op = || { let df = stage_data_from_one_file(reads, cohort, loci, cache_path, use_cache)?; Ok(df) }; match backoff::retry(ExponentialBackoff::default(), op) { - Ok(df) => { dfs.lock().unwrap().push(df); }, - Err(e) => { eprintln!("Error: {}", e); } + Ok(df) => { + df + }, + Err(e) => { + panic!("Error: {}", e); + } } - } - ); + }) + .collect(); Ok(dfs) } -fn write_to_disk(dfs: Mutex>, cache_path: &PathBuf) -> Result, Box> { +fn write_to_disk(dfs: Vec, cache_path: &PathBuf) -> Result, Box> { let mut outer_df = DataFrame::default(); - for df in dfs.lock().unwrap().iter() { + for df in dfs { outer_df.vstack_mut(&df).unwrap(); } let mut locus_to_file = HashMap::new(); let groups = outer_df.group_by(["chunk"]).unwrap(); - while let Ok(mut group) = groups.groups() { + for mut group in groups.groups() { let l_fmt = group.column("chunk").unwrap().str().unwrap().get(0).unwrap().to_string(); let parts: Vec<&str> = l_fmt.split(|c| c == ':' || c == '-').collect(); @@ -136,9 +129,57 @@ fn locus_should_be_fetched(chr: &String, start: &u64, stop: &u64, reads_paths: & false } -pub fn stage_data(reads_cohort: &HashSet<(Url, String)>, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result, Box> { +pub fn stage_data(reads_cohort: &HashSet<(Url, String)>, loci: &HashSet<(String, u64, u64)>, cache_path: &PathBuf, use_cache: bool) -> Result, Box> { let dfs = stage_data_from_all_files(reads_cohort, loci, cache_path, use_cache)?; let locus_to_file = write_to_disk(dfs, cache_path)?; Ok(locus_to_file) +} + +#[cfg(test)] +mod tests { + use super::*; + use url::Url; + use std::collections::HashSet; + + #[test] + fn test_open_bam() { + let reads_url = Url::parse("gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam").unwrap(); + let cache_path = std::env::temp_dir(); + + let bam = open_bam(&reads_url, &cache_path); + + assert!(bam.is_ok(), "Failed to open bam file"); + } + + #[test] + fn test_stage_data_from_one_file() { + let reads_url = Url::parse("gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam").unwrap(); + let cohort = String::from("test_cohort"); + let loci = HashSet::from([("chr15".to_string(), 23960193, 23963918)]); + let cache_path = std::env::temp_dir(); + let use_cache = false; + + let result = stage_data_from_one_file(&reads_url, &cohort, &loci, &cache_path, use_cache); + + assert!(result.is_ok(), "Failed to stage data from one file"); + + println!("{:?}", result.unwrap()); + } + + #[test] + fn test_stage_data() { + let reads_url = Url::parse("gs://fc-8c3900db-633f-477f-96b3-fb31ae265c44/results/PBFlowcell/m84060_230907_210011_s2/reads/ccs/aligned/m84060_230907_210011_s2.bam").unwrap(); + let cohort = String::from("test_cohort_1"); + let loci = HashSet::from([("chr15".to_string(), 23960193, 23963918)]); + let cache_path = std::env::temp_dir(); + let use_cache = false; + let reads_cohort = HashSet::from([(reads_url, cohort)]); + + let result = stage_data(&reads_cohort, &loci, &cache_path, use_cache); + + assert!(result.is_ok(), "Failed to stage data from all files"); + + println!("{:?}", result.unwrap()); + } } \ No newline at end of file