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An instantiated Terminal is the human/machine DSI interface. The person setting up a Core Terminal only needs to know how they want to ask questions, and what metadata they want to ask questions about. If they don’t see an option to ask questions the way they like, or they don’t see the metadata they want to ask questions about, then they should ask a Driver Contributor or a Plugin Contributor, respectively. + +A Core Terminal is a home for Plugins, and an interface for Drivers. A Core Terminal is instantiated with a set of default Plugins and Drivers, but they must be loaded before a user query is attempted. Here's an example of how you might work with DSI using an interactive Python interpreter for your data science workflows:: + +>>> from dsi.core import Terminal +>>> a=Terminal() +>>> a.list_available_modules('plugin') +>>> # ['Bueno', 'Hostname', 'SystemKernel'] +>>> a.load_module('plugin','Bueno','consumer',filename='./data/bueno.data') +>>> # Bueno plugin consumer loaded successfully. +>>> a.load_module('plugin','Hostname','producer') +>>> # Hostname plugin producer loaded successfully. +>>> a.list_loaded_modules() +>>> # {'producer': [], +>>> # 'consumer': [], +>>> # 'front-end': [], +>>> # 'back-end': []} + + +At this point, you might decide that you are ready to collect data for inspection. It is possible to utilize DSI Drivers to load additional metadata to supplement your Plugin metadata, but you can also sample Plugin data and search it directly. + + +The process of transforming a set of Plugin producers and consumers into a querable format is called transloading. A DSI Core Terminal has a ``transload()`` method which may be called to execute all Plugins at once:: + +>>> a.transload() +>>> a.active_metadata +>>> # OrderedDict([('uid', [1000]), ('effective_gid', [1000]), ('moniker', ['qwofford'])... + +Once a Core Terminal has been transloaded, no further Plugins may be added. However, the transload method can be used to samples of each plugin as many times as you like:: + +>>> a.transload() +>>> a.transload() +>>> a.transload() +>>> a.active_metadata +>>> # OrderedDict([('uid', [1000, 1000, 1000, 1000]), ('effective_gid', [1000, 1000, 1000... + +If you perform data science tasks using Python, it is not necessary to create a DSI Core Terminal front-end because the data is already in a Python data structure. If your data science tasks can be completed in one session, it is not required to interact with DSI Drivers. However, if you do want to save your work, you can load a DSI Driver with a back-end function:: + +>>> a.list_available_modules('driver') +>>> # ['Gufi', 'Sqlite', 'Parquet'] +>>> a.load_module('driver','Parquet','back-end',filename='parquet.data') +>>> # Parquet driver back-end loaded successfully. +>>> a.list_loaded_modules() +>>> # {'producer': [], +>>> # 'consumer': [], +>>> # 'front-end': [], +>>> # 'back-end': []} +>>> a.artifact_handler(interaction_type='put') + +The contents of the active DSI Core Terminal metadata storage will be saved to a Parquet object at the path you provided at module loading time. + +It is possible that you prefer to perform data science tasks using a higher level abstraction than Python itself. This is the purpose of the DSI Driver front-end functionality. Unlike Plugins, Drivers can be added after the initial ``transload()`` operation has been performed:: + +>>> a.load_module('driver','Parquet','front-end',filename='parquet.data') +>>> # Parquet driver front-end loaded successfully. +>>> a.list_loaded_modules() +>>> # {'producer': [], +>>> # 'consumer': [], +>>> # 'front-end': [], +>>> # 'back-end': []} + +Any front-end may be used, but in this case the Parquet driver has a front-end implementation which builds a jupyter notebook from scratch that loads your metadata collection into a Pandas Dataframe. The Parquet front-end will then launch the Jupyter Notebook to support an interactive data science workflow:: + +>>> a.artifact_handler(interaction_type='inspect') +>>> # Writing Jupyter notebook... +>>> # Opening Jupyter notebook... + +.. image:: jupyter_frontend.png + :scale: 33% + +You can then close your Jupyter notebook, ``transload()`` additionally to increase your sample size, and use the interface to explore more data. + +Although this demonstration only used one Plugin per Plugin functionality, any number of plugins can be added to collect an arbitrary amount of queriable metadata:: + +>>> a.load_module('plugin','SystemKernel','producer') +>>> # SystemKernel plugin producer loaded successfully +>>> a.list_loaded_modules() +>>> # {'producer': [, ], +>>> # 'consumer': [], +>>> # 'front-end': [], +>>> # 'back-end': []} + +.. automodule:: dsi.core + :members: diff --git a/_sources/drivers.rst.txt b/_sources/drivers.rst.txt new file mode 100644 index 00000000..d59d0f42 --- /dev/null +++ b/_sources/drivers.rst.txt @@ -0,0 +1,21 @@ +Drivers +======================== + +Drivers have front-end and back-end functions. Drivers connect users to DSI Core middleware (front-end), and Drivers allow DSI Middleware data structures to read and write to persistent external storage (back-end). Drivers are modular to support user contribution. Driver contributors are encouraged to offer custom Driver abstract classes and Driver implementations. A contributed Driver abstract class may extend another Driver to inherit the properties of the parent. In order to be compatible with DSI Core middleware, Drivers should create an interface to Python built-in data structures or data structures from the Python ``collections`` library. Driver extensions will be accepted conditional to the extention of ``drivers/tests`` to demonstrate new Driver capability. We can not accept pull requests that are not tested. + + +.. image:: DriverClassHierarchy.png + +.. automodule:: dsi.drivers.filesystem + :members: + +.. automodule:: dsi.drivers.sqlite + :members: + +.. automodule:: dsi.drivers.gufi + :members: + +.. automodule:: dsi.drivers.parquet + :members: + + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 00000000..ed68746f --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,26 @@ +.. DSI documentation master file, created by + sphinx-quickstart on Fri Apr 14 14:04:07 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +============================================= +The Data Science Infrastructure Project (DSI) +============================================= + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + introduction + installation + core + plugins + drivers + permissions + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt new file mode 100644 index 00000000..487ca750 --- /dev/null +++ b/_sources/installation.rst.txt @@ -0,0 +1,19 @@ +Installation +=================== + +1. Create or activate a DSI virtual environment. +2. ``cd`` into the project space root +3. ``python -m pip install .`` +4. [Optional] If you are running DSI Unit tests ``python -m pip install pytest gitpython coverage-badge pytest-cov``. +5. [Optional] If you are HTML documentation ``python -m pip install sphinx sphinx_rtd_theme`` + +How to create and activate a virtual environment +-------------------------------------------------- +We recommend Miniconda for virtual environment management (`https://docs.conda.io/en/latest/miniconda.html`). To create and activate a Miniconda virtual environment: + +1. Download and install the appropriate Miniconda installer for your platform. +2. If this is the first time creating a DSI virtual environment: ``conda create -n 'dsi' python=3.11``. The ``-n`` name argument can be anything you like. +3. Once the virtual environment is created, activate it with ``conda activate dsi``, or whatever name you picked in the preceding step. +4. Proceed with Step 2 in the "Installation" section. +5. When you've completed work, deativate the conda environment with ``conda deactivate``. + diff --git a/_sources/introduction.rst.txt b/_sources/introduction.rst.txt new file mode 100644 index 00000000..568bca55 --- /dev/null +++ b/_sources/introduction.rst.txt @@ -0,0 +1,39 @@ +============ +Introduction +============ + +The goal of the Data Science Infrastructure Project (DSI) is to provide a flexible, AI-ready metadata query capability which returns data subject to strict, POSIX-enforced file security. The data lifecycle for AI/ML requires seamless transitions from data-intensive/AI/ML research activity to long-term archiving and share data repositories. DSI enables flexible, data-intensive scientific workflows that meet researcher needs. + +.. image:: data_lifecycle.png + :scale: 50% + +DSI system design is driven by experiences which satisfy User Stories. DSI uses Object Oriented design principles to encourage modularity and to support contributions by the user community. + + +Implementation +============== +The DSI system is composed of three fundamental parts: + +.. image:: three_easy_pieces.png + :scale: 33% + +DSI Core Middleware +------------------- +DSI's core middleware is focused on delivering user-queries on unified metadata which are distributed across many files and security domains. DSI currently supports Linux, and is tested on RedHat- and Debian-based distributions. The DSI Core middleware is a home for DSI Plugins and an interface for DSI Drivers. + +Plugin Abstract Classes +----------------------- +Plugins transform an arbitrary data source into a format that is compatible with our middleware. We call the parsed and queriable attributes "metadata" (data about the data). Metadata share the same security profile as the source data. + +Plugins can operate as data consumers or data producers. A simple data consumer might parse an application's output file and place it into a middleware compatible data structure: Python built-ins and members of the popular Python ``collection`` module. A simple data producer might execute an application to supplement existing data and queriable metadata. + +Plugins are defined by a base abstract class, and support child abstract classes which inherit the properties of their ancestors. + +.. image:: PluginClassHierarchy.png + +Driver Abstract Classes +----------------------- +Drivers are an interface between the User and the Core, or an interface between the Core and a storage medium. Drivers can operate as Front-ends or Back-ends, and a Driver contributor can choose to implement one or both. Driver front-ends are built to deliver an experience which is compatible with a User Story. A simple supporting User Story is a need to query metadata by SQL query. Because the set of queriable metadata are spread across filesystems and security domains, a supporting Driver Back-end is required to assemble query results and present them to the DSI core middleware for transformation and return, creating an experience which is compatible with the User Story. + +.. image:: user_story.png + :scale: 50% diff --git a/_sources/permissions.rst.txt b/_sources/permissions.rst.txt new file mode 100644 index 00000000..5a2cbfbf --- /dev/null +++ b/_sources/permissions.rst.txt @@ -0,0 +1,55 @@ +Permissions +=================== +DSI is capable of consuming information from files, environments, and in-situ processes which may or may not have the same permissions authority. To track this information for the purposes of returning user queries into DSI storage, we utilize a permissions handler. The permissions handler bundles the authority by which information is read and adds this to each column data structure. Most relational database systems require that types are enforced by column, and DSI extends this idea to require that permissions are enforced by column. By tracking the permissions associated with each column, DSI can save files using the same POSIX permissions authority that initially granted access to the information, therefore preserving POSIX permssions as files are saved. + +By default, DSI will stop users from saving any metadata if the length of the union of the set of column permissions is greater than one. This prevents users from saving files that might have complex security implications. If a user enables the ``allow_multiple_permissions`` parameter of the ``PermissionsManager``, then the number of files that will be saved is equal to the length of the union of the set of column permissions in the middleware data structures being written (an example of this behavior follows). There will be one file for each set of columns read by the same permissions authority. + +By default, DSI will always respect the POSIX permissions authority by which information was read. If the user wishes to override this behavior and write all of their metadata to the same file with a unified UID and GID, they can enable the ``squash_permissions`` parameter of the ``PermissionsManager``. The user should be very certain that the information they are writing is protected appropriately in this case. + +An example helps illustrate these scenarios: + ++----------+----------+----------+ +| Col A | Col B | Col C | ++----------+----------+----------+ +| *Perm D* | *Perm D* | *Perm F* | ++----------+----------+----------+ +| Row A1 | Row B1 | Row C1 | ++----------+----------+----------+ +| Row A2 | Row B2 | Row C2 | ++----------+----------+----------+ + +By default, DSI will refuse to write this data structure to disk because ``len(union({D,D,F})) > 1`` + +If a user enables the ``allow_multiple_permissions`` parameter, two files will be saved: + +>>> $ cat file1 +>>> | Col A | Col B | +>>> =================== +>>> | Perm D | Perm D | +>>> | Row A1 | Row B1 | +>>> | Row A2 | Row B2 | +>>> $ get_perms(file1) +>>> Perm D +>>> $ cat file2 +>>> | Col C | +>>> ========== +>>> | Perm F | +>>> | Row C1 | +>>> | Row C2 | +>>> $ get_perms(file2) +>>> Perm F + +If a user enables ``allow_multiple_permissions`` and ``squash_permissions``, then a single file will be written with the user's UID and effective GID and 660 access: + +>>> $ cat file +>>> | Col A | Col B | Col C | +>>> ============================ +>>> | Perm D | Perm D | Perm F | +>>> | Row A1 | Row B1 | Row C1 | +>>> | Row A2 | Row B2 | Row C2 | +>>> $ get_perms(file) +>>> My UID and Effective GID, with 660 access controls. + + +.. automodule:: dsi.permissions.permissions + :members: diff --git a/_sources/plugins.rst.txt b/_sources/plugins.rst.txt new file mode 100644 index 00000000..172b838c --- /dev/null +++ b/_sources/plugins.rst.txt @@ -0,0 +1,12 @@ +Plugins +=================== +Plugins connect data-producing applications to DSI middleware. Plugins have "producer" or "consumer" functions. A Plugin consumer function deals with existing data files or input streams. A Plugin producer deals with generating new data. Plugins are modular to support user contribution. Plugin contributors are encouraged to offer custom Plugin abstract classes and Plugin implementations. A contributed Plugin abstract class may extend another plugin to inherit the properties of the parent. In order to be compatible with DSI middleware, Plugins should produce data in Python built-in data structures or data structures sourced from the Python ``collections`` library. Plugin extensions will be accepted conditional to the extention of ``plugins/tests`` to demonstrate the new Plugin capability. We can not accept pull requests that are not tested. + +.. image:: PluginClassHierarchy.png + +.. automodule:: dsi.plugins.metadata + :members: + +.. automodule:: dsi.plugins.env + :members: + diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 00000000..81415803 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. Multiple values per key are supported, + * it will always return arrays of strings for the value parts. + */ +jQuery.getQueryParameters = function(s) { + if (typeof s === 'undefined') + s = document.location.search; + var parts = s.substr(s.indexOf('?') + 1).split('&'); + var result = {}; + for (var i = 0; i < parts.length; i++) { + var tmp = parts[i].split('=', 2); + var key = jQuery.urldecode(tmp[0]); + var value = jQuery.urldecode(tmp[1]); + if (key in result) + result[key].push(value); + else + result[key] = [value]; + } + return result; +}; + +/** + * highlight a given string on a jquery object by wrapping it in + * span elements with the given class name. + */ +jQuery.fn.highlightText = function(text, className) { + function highlight(node, addItems) { + if (node.nodeType === 3) { + var val = node.nodeValue; + var pos = val.toLowerCase().indexOf(text); + if (pos >= 0 && + !jQuery(node.parentNode).hasClass(className) && + !jQuery(node.parentNode).hasClass("nohighlight")) { + var span; + var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.className = className; + } + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + node.parentNode.insertBefore(span, node.parentNode.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling)); + node.nodeValue = val.substr(0, pos); + if (isInSVG) { + var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute('class', className); + addItems.push({ + "parent": node.parentNode, + "target": rect}); + } + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this, addItems); + }); + } + } + var addItems = []; + var result = this.each(function() { + highlight(this, addItems); + }); + for (var i = 0; i < addItems.length; ++i) { + jQuery(addItems[i].parent).before(addItems[i].target); + } + return result; +}; + +/* + * backward compatibility for jQuery.browser + * This will be supported until firefox bug is fixed. + */ +if (!jQuery.browser) { + jQuery.uaMatch = function(ua) { + ua = ua.toLowerCase(); + + var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || + /(webkit)[ \/]([\w.]+)/.exec(ua) || + /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || + /(msie) ([\w.]+)/.exec(ua) || + ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || + []; + + return { + browser: match[ 1 ] || "", + version: match[ 2 ] || "0" + }; + }; + jQuery.browser = {}; + jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; +} diff --git a/_static/basic.css b/_static/basic.css new file mode 100644 index 00000000..7577acb1 --- /dev/null +++ b/_static/basic.css @@ -0,0 +1,903 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +div.section::after { + display: block; + content: ''; + clear: left; +} + +/* -- relbar ---------------------------------------------------------------- */ + +div.related { + width: 100%; + font-size: 90%; +} + +div.related h3 { + display: none; +} + +div.related ul { + margin: 0; + padding: 0 0 0 10px; + list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 230px; + margin-left: -100%; + font-size: 90%; + word-wrap: break-word; + overflow-wrap : break-word; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox form.search { + overflow: hidden; +} + +div.sphinxsidebar #searchbox input[type="text"] { + float: left; + width: 80%; + padding: 0.25em; + box-sizing: border-box; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + float: left; + width: 20%; + border-left: none; + padding: 0.25em; + box-sizing: border-box; +} + + +img { + border: 0; + max-width: 100%; +} + +/* -- search page 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top; +} + +table.indextable ul { + margin-top: 0; + margin-bottom: 0; + list-style-type: none; +} + +table.indextable > tbody > tr > td > ul { + padding-left: 0em; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- domain module index --------------------------------------------------- */ + +table.modindextable td { + padding: 2px; + border-collapse: collapse; +} + +/* -- general body styles --------------------------------------------------- */ + +div.body { + min-width: 360px; + max-width: 800px; +} + +div.body p, div.body dd, div.body li, div.body 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+ 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; + } +} + diff --git a/_static/minus.png b/_static/minus.png new file mode 100644 index 00000000..d96755fd Binary files /dev/null and b/_static/minus.png differ diff --git a/_static/plus.png b/_static/plus.png new file mode 100644 index 00000000..7107cec9 Binary files /dev/null and b/_static/plus.png differ diff --git a/_static/pygments.css b/_static/pygments.css new file mode 100644 index 00000000..08bec689 --- /dev/null +++ b/_static/pygments.css @@ -0,0 +1,74 @@ +pre { line-height: 125%; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + + const [docName, title, anchor, descr, score, _filename] = item; + + let listItem = document.createElement("li"); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = docUrlRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = docUrlRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms) + ); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + 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." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query: (query) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + // array of [docname, title, anchor, descr, score, filename] + let results = []; + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + let score = Math.round(100 * queryLower.length / title.length) + results.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id] of foundEntries) { + let score = Math.round(100 * queryLower.length / entry.length) + results.push([ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + ]); + } + } + } + + // lookup as object + objectTerms.forEach((term) => + results.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort((a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; + }); + + // remove duplicate search results + // 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(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + results = results.reverse(); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord) && !terms[word]) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord) && !titleTerms[word]) + arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); + }); + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) + fileMap.get(file).push(word); + else fileMap.set(file, [word]); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords) => { + const text = Search.htmlToText(htmlText); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 00000000..aae669d7 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,144 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + parent.insertBefore( + span, + parent.insertBefore( + document.createTextNode(val.substr(pos + text.length)), + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * 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 + + // 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); + + // get individual terms from highlight string + 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" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + 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")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(SphinxHighlight.highlightSearchWords); +_ready(SphinxHighlight.initEscapeListener); diff --git a/core.html b/core.html new file mode 100644 index 00000000..9dd99403 --- /dev/null +++ b/core.html @@ -0,0 +1,293 @@ + + + + + + + Core — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Core

+

The DSI Core middleware defines the Terminal concept. An instantiated Terminal is the human/machine DSI interface. The person setting up a Core Terminal only needs to know how they want to ask questions, and what metadata they want to ask questions about. If they don’t see an option to ask questions the way they like, or they don’t see the metadata they want to ask questions about, then they should ask a Driver Contributor or a Plugin Contributor, respectively.

+

A Core Terminal is a home for Plugins, and an interface for Drivers. A Core Terminal is instantiated with a set of default Plugins and Drivers, but they must be loaded before a user query is attempted. Here’s an example of how you might work with DSI using an interactive Python interpreter for your data science workflows:

+
>>> from dsi.core import Terminal
+>>> a=Terminal()
+>>> a.list_available_modules('plugin')
+>>> # ['Bueno', 'Hostname', 'SystemKernel']
+>>> a.load_module('plugin','Bueno','consumer',filename='./data/bueno.data')
+>>> # Bueno plugin consumer loaded successfully.
+>>> a.load_module('plugin','Hostname','producer')
+>>> # Hostname plugin producer loaded successfully.
+>>> a.list_loaded_modules()
+>>> # {'producer': [<dsi.plugins.env.Hostname object at 0x7f21232474d0>],
+>>> #  'consumer': [<dsi.plugins.env.Bueno object at 0x7f2123247410>],
+>>> #  'front-end': [],
+>>> #   'back-end': []}
+
+
+

At this point, you might decide that you are ready to collect data for inspection. It is possible to utilize DSI Drivers to load additional metadata to supplement your Plugin metadata, but you can also sample Plugin data and search it directly.

+

The process of transforming a set of Plugin producers and consumers into a querable format is called transloading. A DSI Core Terminal has a transload() method which may be called to execute all Plugins at once:

+
>>> a.transload()
+>>> a.active_metadata
+>>> # OrderedDict([('uid', [1000]), ('effective_gid', [1000]), ('moniker', ['qwofford'])...
+
+
+

Once a Core Terminal has been transloaded, no further Plugins may be added. However, the transload method can be used to samples of each plugin as many times as you like:

+
>>> a.transload()
+>>> a.transload()
+>>> a.transload()
+>>> a.active_metadata
+>>> # OrderedDict([('uid', [1000, 1000, 1000, 1000]), ('effective_gid', [1000, 1000, 1000...
+
+
+

If you perform data science tasks using Python, it is not necessary to create a DSI Core Terminal front-end because the data is already in a Python data structure. If your data science tasks can be completed in one session, it is not required to interact with DSI Drivers. However, if you do want to save your work, you can load a DSI Driver with a back-end function:

+
>>> a.list_available_modules('driver')
+>>> # ['Gufi', 'Sqlite', 'Parquet']
+>>> a.load_module('driver','Parquet','back-end',filename='parquet.data')
+>>> # Parquet driver back-end loaded successfully.
+>>> a.list_loaded_modules()
+>>> # {'producer': [<dsi.plugins.env.Hostname object at 0x7f21232474d0>],
+>>> #  'consumer': [<dsi.plugins.env.Bueno object at 0x7f2123247410>],
+>>> #  'front-end': [],
+>>> #   'back-end': [<dsi.drivers.parquet.Parquet object at 0x7f212325a110>]}
+>>> a.artifact_handler(interaction_type='put')
+
+
+

The contents of the active DSI Core Terminal metadata storage will be saved to a Parquet object at the path you provided at module loading time.

+

It is possible that you prefer to perform data science tasks using a higher level abstraction than Python itself. This is the purpose of the DSI Driver front-end functionality. Unlike Plugins, Drivers can be added after the initial transload() operation has been performed:

+
>>> a.load_module('driver','Parquet','front-end',filename='parquet.data')
+>>> # Parquet driver front-end loaded successfully.
+>>> a.list_loaded_modules()
+>>> # {'producer': [<dsi.plugins.env.Hostname object at 0x7fce3c612b50>],
+>>> # 'consumer': [<dsi.plugins.env.Bueno object at 0x7fce3c622110>],
+>>> # 'front-end': [<dsi.drivers.parquet.Parquet object at 0x7fce3c622290>],
+>>> # 'back-end': [<dsi.drivers.parquet.Parquet object at 0x7fce3c622650>]}
+
+
+

Any front-end may be used, but in this case the Parquet driver has a front-end implementation which builds a jupyter notebook from scratch that loads your metadata collection into a Pandas Dataframe. The Parquet front-end will then launch the Jupyter Notebook to support an interactive data science workflow:

+
>>> a.artifact_handler(interaction_type='inspect')
+>>> # Writing Jupyter notebook...
+>>> # Opening Jupyter notebook...
+
+
+_images/jupyter_frontend.png +

You can then close your Jupyter notebook, transload() additionally to increase your sample size, and use the interface to explore more data.

+

Although this demonstration only used one Plugin per Plugin functionality, any number of plugins can be added to collect an arbitrary amount of queriable metadata:

+
>>> a.load_module('plugin','SystemKernel','producer')
+>>> # SystemKernel plugin producer loaded successfully
+>>> a.list_loaded_modules()
+>>> # {'producer': [<dsi.plugins.env.Hostname object at 0x7fce3c612b50>, <dsi.plugins.env.SystemKernel object at 0x7fce68519250>],
+>>> # 'consumer': [<dsi.plugins.env.Bueno object at 0x7fce3c622110>],
+>>> # 'front-end': [<dsi.drivers.parquet.Parquet object at 0x7fce3c622290>],
+>>> # 'back-end': [<dsi.drivers.parquet.Parquet object at 0x7fce3c622650>]}
+
+
+
+
+class dsi.core.Terminal(allow_multiple_permissions=False, squash_permissions=False)
+

An instantiated Terminal is the DSI human/machine interface.

+

Terminals are a home for Plugins and an interface for Drivers. Drivers may be +front-ends or back-ends. Plugins may be producers or consumers. See documentation +for more information.

+
+
+add_external_python_module(mod_type, mod_name, mod_path)
+

Adds a given external, meaning not from the DSI repo, Python module to the module_collection

+

Afterwards, load_module can be used to load a DSI module from the added Python module. +Note: mod_type is needed because each Python module should only implement plugins or drivers

+

For example,

+

term = Terminal() +term.add_external_python_module(‘plugin’, ‘my_python_file’,

+
+

‘/the/path/to/my_python_file.py’)

+
+

term.load_module(‘plugin’, ‘MyPlugin’, ‘consumer’)

+

term.list_loaded_modules() # includes MyPlugin

+
+ +
+
+artifact_handler(interaction_type, **kwargs) → bool
+

Store or retrieve using all loaded DSI Drivers with back-end functionality.

+

A DSI Core Terminal may load zero or more Drivers with back-end storage functionality. +Calling artifact_handler will execute all back-end functionality currently loaded, given +the provided interaction_type.

+

Returns whether the interaction was successful or not.

+
+ +
+
+handle_permissions_interactions() → bool
+

Presents the user with information on how permissions are being handled +and recieves consent to the operations through input. +Returns whether or not the user wants the operation to be carried out.

+
+ +
+
+list_available_modules(mod_type)
+

List available DSI modules of an arbitrary module type.

+

This method is useful for Core Terminal setup. Plugin and Driver type DSI modules +are supported, but this getter can be extended to support any new DSI module +types which are added. Note: self.VALID_MODULES refers to _DSI_ Modules +however, DSI Modules are classes, hence the naming idiosynchrocies below.

+
+ +
+
+list_loaded_modules()
+

List DSI modules which have already been loaded.

+

These Plugins and Drivers are active or ready to execute a post-processing task.

+
+ +
+
+load_module(mod_type, mod_name, mod_function, **kwargs)
+

Load a DSI module from the available Plugin and Drive module collection.

+

DSI modules may be loaded which are not explicitly listed by the list_available_modules. +This flexibility ensures that advanced users can access higher level abstractions. +We expect most users will work with module implementations rather than templates, but +but all high level class abstractions are accessible with this method.

+
+ +
+
+put_report() → str
+

Generates a report of which columns are registered to which permissions +ex. col1: 444-444-0o660

+
+ +
+
+transload(**kwargs)
+

Transloading signals to the DSI Core Terminal that Plugin set up is complete.

+

A DSI Core Terminal must be transloaded before queries, metadata collection, or metadata +storage is possible. Transloading is the process of merging Plugin metadata from many +data sources to a single DSI Core Middleware data structure.

+
+ +
+
+unload_module(mod_type, mod_name, mod_function)
+

Unloads a DSI module from the active_modules collection

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/drivers.html b/drivers.html new file mode 100644 index 00000000..a2857bcb --- /dev/null +++ b/drivers.html @@ -0,0 +1,305 @@ + + + + + + + Drivers — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Drivers

+

Drivers have front-end and back-end functions. Drivers connect users to DSI Core middleware (front-end), and Drivers allow DSI Middleware data structures to read and write to persistent external storage (back-end). Drivers are modular to support user contribution. Driver contributors are encouraged to offer custom Driver abstract classes and Driver implementations. A contributed Driver abstract class may extend another Driver to inherit the properties of the parent. In order to be compatible with DSI Core middleware, Drivers should create an interface to Python built-in data structures or data structures from the Python collections library. Driver extensions will be accepted conditional to the extention of drivers/tests to demonstrate new Driver capability. We can not accept pull requests that are not tested.

+_images/DriverClassHierarchy.png +
+
+class dsi.drivers.sqlite.Artifact
+

Primary Artifact class that holds database schema in memory. +An Artifact is a generic construct that defines the schema for metadata that +defines the tables inside of SQL

+
+ +
+
+class dsi.drivers.sqlite.Sqlite(filename, **kwargs)
+

Primary storage class, inherits sql class

+
+
+check_type(text)
+

Tests input text and returns a predicted compatible SQL Type +text: text string +return: string description of a SQL data type

+
+ +
+
+export_csv(query, fname, isVerbose=False)
+

Function that outputs a csv file of a return query, given an initial query.

+

query: raw SQL query to be executed on current table

+

fname: target filename (including path) that will output the return query as a csv file

+

return: none

+
+ +
+
+get_artifact_list(isVerbose=False)
+

Function that returns a list of all of the Artifact names (represented as sql tables)

+

return: list of Artifact names

+
+ +
+
+put_artifact_type(types, isVerbose=False)
+

Primary class for defining metadata Artifact schema.

+
+
types: DataType derived class that defines the string name, properties

(named SQL type), and units for each column in the schema.

+
+
+

return: none

+
+ +
+
+put_artifacts(artifacts, isVerbose=False)
+

Primary class for insertion of Artifact metadata into a defined schema

+
+
Artifacts: DataType derived class that has a regular structure of a defined schema,

filled with rows to insert.

+
+
+

return: none

+
+ +
+
+put_artifacts_csv(fname, tname, isVerbose=False)
+

Function for insertion of Artifact metadata into a defined schema by using a CSV file, +where the first row of the CSV contains the column names of the schema. Any rows +thereafter contain data to be inserted. Data types are automatically assigned based on +typecasting and default to a string type if none can be found.

+

fname: filepath to the .csv file to be read and inserted into the database

+

tname: String name of the table to be inserted

+

return: none

+
+ +
+
+query_fctime(operator, ctime, isVerbose=False)
+

Function that queries file creation times within the filesystem metadata store

+

operator: operator input GT, LT, EQ as a modifier for a creation time search

+

ctime: creation time in POSIX format, see the utils dateToPosix conversion function

+

return: query list of filenames matching the creation time criteria with modifiers

+
+ +
+
+query_fname(name, isVerbose=False)
+

Function that queries filenames within the filesystem metadata store

+

name: string name of a subsection of a filename to be searched

+

return: query list of filenames matching name string

+
+ +
+
+query_fsize(operator, size, isVerbose=False)
+

Function that queries ranges of file sizes within the filesystem metadata store

+

operator: operator input GT, LT, EQ as a modifier for a filesize search

+

size: size in bytes

+

return: query list of filenames matching filesize criteria with modifiers

+
+ +
+
+sqlquery(query, isVerbose=False)
+

Function that provides a direct sql query passthrough to the database.

+

query: raw SQL query to be executed on current table

+

return: raw sql query list that contains result of the original query

+
+ +
+ +
+
+class dsi.drivers.gufi.Gufi(prefix, index, dbfile, table, column, verbose=False, **kwargs)
+

GUFI Datastore

+
+
+get_artifacts(query)
+

Retrieves GUFI’s metadata joined with a dsi database +query: an sql query into the dsi_entries table

+
+ +
+
+isVerbose = False
+

prefix: prefix to GUFI commands +index: directory with GUFI indexes +dbfile: sqlite db file from DSI +table: table name from the DSI db we want to join on +column: column name from the DSI db to join on

+
+ +
+ +
+
+class dsi.drivers.parquet.Parquet(filename, **kwargs)
+

Support for a Parquet back-end Driver.

+

Parquet is a convenient format when metadata are larger than SQLite supports.

+
+
+get_artifacts()
+

Get Parquet data from filename.

+
+ +
+
+static get_cmd_output(cmd: list) → str
+

Runs a given command and returns the stdout if successful.

+

If stderr is not empty, an exception is raised with the stderr text.

+
+ +
+
+inspect_artifacts(collection)
+

Populate a Jupyter notebook with tools required to look at Parquet data.

+
+ +
+
+put_artifacts(collection)
+

Put artifacts into file at filename path.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 00000000..dfdc2a24 --- /dev/null +++ b/genindex.html @@ -0,0 +1,462 @@ + + + + + + Index — DSI 0.0.0 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | C + | D + | E + | G + | H + | I + | L + | M + | P + | Q + | R + | S + | T + | U + +
+

A

+ + + +
+ +

C

+ + + +
+ +

D

+ + + +
    +
  • + dsi.core + +
    • +
  • + dsi.drivers.filesystem + +
    • +
  • + dsi.drivers.gufi + +
    • +
  • + dsi.drivers.parquet + +
    • +
    +
  • + dsi.drivers.sqlite + +
    • +
  • + dsi.permissions.permissions + +
    • +
  • + dsi.plugins.env + +
    • +
  • + dsi.plugins.metadata + +
    • +
+ +

E

+ + + +
+ +

G

+ + + +
+ +

H

+ + + +
+ +

I

+ + + +
+ +

L

+ + + +
+ +

M

+ + +
+ +

P

+ + + +
+ +

Q

+ + + +
+ +

R

+ + + +
+ +

S

+ + + +
+ +

T

+ + + +
+ +

U

+ + +
+ + + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/htmlcov/.gitignore b/htmlcov/.gitignore new file mode 100644 index 00000000..ccccf142 --- /dev/null +++ b/htmlcov/.gitignore @@ -0,0 +1,2 @@ +# Created by coverage.py +* diff --git a/htmlcov/coverage_html.js b/htmlcov/coverage_html.js new file mode 100644 index 00000000..4c321182 --- /dev/null +++ b/htmlcov/coverage_html.js @@ -0,0 +1,624 @@ +// Licensed under the Apache License: http://www.apache.org/licenses/LICENSE-2.0 +// For details: https://github.com/nedbat/coveragepy/blob/master/NOTICE.txt + +// Coverage.py HTML report browser code. +/*jslint browser: true, sloppy: true, vars: true, plusplus: true, maxerr: 50, indent: 4 */ +/*global coverage: true, document, window, $ */ + +coverage = {}; + +// General helpers +function debounce(callback, wait) { + let timeoutId = null; + return function(...args) { + clearTimeout(timeoutId); + timeoutId = setTimeout(() => { + callback.apply(this, args); + }, wait); + }; +}; + +function checkVisible(element) { + const rect = element.getBoundingClientRect(); + const viewBottom = Math.max(document.documentElement.clientHeight, window.innerHeight); + const viewTop = 30; + return !(rect.bottom < viewTop || rect.top >= viewBottom); +} + +function on_click(sel, fn) { + const elt = document.querySelector(sel); + if (elt) { + elt.addEventListener("click", fn); + } +} + +// Helpers for table sorting +function getCellValue(row, column = 0) { + const cell = row.cells[column] + if (cell.childElementCount == 1) { + const child = cell.firstElementChild + if (child instanceof HTMLTimeElement && child.dateTime) { + return child.dateTime + } else if (child instanceof HTMLDataElement && child.value) { + return child.value + } + } + return cell.innerText || cell.textContent; +} + +function rowComparator(rowA, rowB, column = 0) { + let valueA = getCellValue(rowA, column); + let valueB = getCellValue(rowB, column); + if (!isNaN(valueA) && !isNaN(valueB)) { + return valueA - valueB + } + return valueA.localeCompare(valueB, undefined, {numeric: true}); +} + +function sortColumn(th) { + // Get the current sorting direction of the selected header, + // clear state on other headers and then set the new sorting direction + const currentSortOrder = th.getAttribute("aria-sort"); + [...th.parentElement.cells].forEach(header => header.setAttribute("aria-sort", "none")); + if (currentSortOrder === "none") { + th.setAttribute("aria-sort", th.dataset.defaultSortOrder || "ascending"); + } else { + th.setAttribute("aria-sort", currentSortOrder === "ascending" ? "descending" : "ascending"); + } + + const column = [...th.parentElement.cells].indexOf(th) + + // Sort all rows and afterwards append them in order to move them in the DOM + Array.from(th.closest("table").querySelectorAll("tbody tr")) + .sort((rowA, rowB) => rowComparator(rowA, rowB, column) * (th.getAttribute("aria-sort") === "ascending" ? 1 : -1)) + .forEach(tr => tr.parentElement.appendChild(tr) ); +} + +// Find all the elements with data-shortcut attribute, and use them to assign a shortcut key. +coverage.assign_shortkeys = function () { + document.querySelectorAll("[data-shortcut]").forEach(element => { + document.addEventListener("keypress", event => { + if (event.target.tagName.toLowerCase() === "input") { + return; // ignore keypress from search filter + } + if (event.key === element.dataset.shortcut) { + element.click(); + } + }); + }); +}; + +// Create the events for the filter box. +coverage.wire_up_filter = function () { + // Cache elements. + const table = document.querySelector("table.index"); + const table_body_rows = table.querySelectorAll("tbody tr"); + const no_rows = document.getElementById("no_rows"); + + // Observe filter keyevents. + document.getElementById("filter").addEventListener("input", debounce(event => { + // Keep running total of each metric, first index contains number of shown rows + const totals = new Array(table.rows[0].cells.length).fill(0); + // Accumulate the percentage as fraction + totals[totals.length - 1] = { "numer": 0, "denom": 0 }; + + // Hide / show elements. + table_body_rows.forEach(row => { + if (!row.cells[0].textContent.includes(event.target.value)) { + // hide + row.classList.add("hidden"); + return; + } + + // show + row.classList.remove("hidden"); + totals[0]++; + + for (let column = 1; column < totals.length; column++) { + // Accumulate dynamic totals + cell = row.cells[column] + if (column === totals.length - 1) { + // Last column contains percentage + const [numer, denom] = cell.dataset.ratio.split(" "); + totals[column]["numer"] += parseInt(numer, 10); + totals[column]["denom"] += parseInt(denom, 10); + } else { + totals[column] += parseInt(cell.textContent, 10); + } + } + }); + + // Show placeholder if no rows will be displayed. + if (!totals[0]) { + // Show placeholder, hide table. + no_rows.style.display = "block"; + table.style.display = "none"; + return; + } + + // Hide placeholder, show table. + no_rows.style.display = null; + table.style.display = null; + + const footer = table.tFoot.rows[0]; + // Calculate new dynamic sum values based on visible rows. + for (let column = 1; column < totals.length; column++) { + // Get footer cell element. + const cell = footer.cells[column]; + + // Set value into dynamic footer cell element. + if (column === totals.length - 1) { + // Percentage column uses the numerator and denominator, + // and adapts to the number of decimal places. + const match = /\.([0-9]+)/.exec(cell.textContent); + const places = match ? match[1].length : 0; + const { numer, denom } = totals[column]; + cell.dataset.ratio = `${numer} ${denom}`; + // Check denom to prevent NaN if filtered files contain no statements + cell.textContent = denom + ? `${(numer * 100 / denom).toFixed(places)}%` + : `${(100).toFixed(places)}%`; + } else { + cell.textContent = totals[column]; + } + } + })); + + // Trigger change event on setup, to force filter on page refresh + // (filter value may still be present). + document.getElementById("filter").dispatchEvent(new Event("input")); +}; + +coverage.INDEX_SORT_STORAGE = "COVERAGE_INDEX_SORT_2"; + +// Loaded on index.html +coverage.index_ready = function () { + coverage.assign_shortkeys(); + coverage.wire_up_filter(); + document.querySelectorAll("[data-sortable] th[aria-sort]").forEach( + th => th.addEventListener("click", e => sortColumn(e.target)) + ); + + // Look for a localStorage item containing previous sort settings: + const stored_list = localStorage.getItem(coverage.INDEX_SORT_STORAGE); + + if (stored_list) { + const {column, direction} = JSON.parse(stored_list); + const th = document.querySelector("[data-sortable]").tHead.rows[0].cells[column]; + th.setAttribute("aria-sort", direction === "ascending" ? "descending" : "ascending"); + th.click() + } + + // Watch for page unload events so we can save the final sort settings: + window.addEventListener("unload", function () { + const th = document.querySelector('[data-sortable] th[aria-sort="ascending"], [data-sortable] [aria-sort="descending"]'); + if (!th) { + return; + } + localStorage.setItem(coverage.INDEX_SORT_STORAGE, JSON.stringify({ + column: [...th.parentElement.cells].indexOf(th), + direction: th.getAttribute("aria-sort"), + })); + }); + + on_click(".button_prev_file", coverage.to_prev_file); + on_click(".button_next_file", coverage.to_next_file); + + on_click(".button_show_hide_help", coverage.show_hide_help); +}; + +// -- pyfile stuff -- + +coverage.LINE_FILTERS_STORAGE = "COVERAGE_LINE_FILTERS"; + +coverage.pyfile_ready = function () { + // If we're directed to a particular line number, highlight the line. + var frag = location.hash; + if (frag.length > 2 && frag[1] === "t") { + document.querySelector(frag).closest(".n").classList.add("highlight"); + coverage.set_sel(parseInt(frag.substr(2), 10)); + } else { + coverage.set_sel(0); + } + + on_click(".button_toggle_run", coverage.toggle_lines); + on_click(".button_toggle_mis", coverage.toggle_lines); + on_click(".button_toggle_exc", coverage.toggle_lines); + on_click(".button_toggle_par", coverage.toggle_lines); + + on_click(".button_next_chunk", coverage.to_next_chunk_nicely); + on_click(".button_prev_chunk", coverage.to_prev_chunk_nicely); + on_click(".button_top_of_page", coverage.to_top); + on_click(".button_first_chunk", coverage.to_first_chunk); + + on_click(".button_prev_file", coverage.to_prev_file); + on_click(".button_next_file", coverage.to_next_file); + on_click(".button_to_index", coverage.to_index); + + on_click(".button_show_hide_help", coverage.show_hide_help); + + coverage.filters = undefined; + try { + coverage.filters = localStorage.getItem(coverage.LINE_FILTERS_STORAGE); + } catch(err) {} + + if (coverage.filters) { + coverage.filters = JSON.parse(coverage.filters); + } + else { + coverage.filters = {run: false, exc: true, mis: true, par: true}; + } + + for (cls in coverage.filters) { + coverage.set_line_visibilty(cls, coverage.filters[cls]); + } + + coverage.assign_shortkeys(); + coverage.init_scroll_markers(); + coverage.wire_up_sticky_header(); + + document.querySelectorAll("[id^=ctxs]").forEach( + cbox => cbox.addEventListener("click", coverage.expand_contexts) + ); + + // Rebuild scroll markers when the window height changes. + window.addEventListener("resize", coverage.build_scroll_markers); +}; + +coverage.toggle_lines = function (event) { + const btn = event.target.closest("button"); + const category = btn.value + const show = !btn.classList.contains("show_" + category); + coverage.set_line_visibilty(category, show); + coverage.build_scroll_markers(); + coverage.filters[category] = show; + try { + localStorage.setItem(coverage.LINE_FILTERS_STORAGE, JSON.stringify(coverage.filters)); + } catch(err) {} +}; + +coverage.set_line_visibilty = function (category, should_show) { + const cls = "show_" + category; + const btn = document.querySelector(".button_toggle_" + category); + if (btn) { + if (should_show) { + document.querySelectorAll("#source ." + category).forEach(e => e.classList.add(cls)); + btn.classList.add(cls); + } + else { + document.querySelectorAll("#source ." + category).forEach(e => e.classList.remove(cls)); + btn.classList.remove(cls); + } + } +}; + +// Return the nth line div. +coverage.line_elt = function (n) { + return document.getElementById("t" + n)?.closest("p"); +}; + +// Set the selection. b and e are line numbers. +coverage.set_sel = function (b, e) { + // The first line selected. + coverage.sel_begin = b; + // The next line not selected. + coverage.sel_end = (e === undefined) ? b+1 : e; +}; + +coverage.to_top = function () { + coverage.set_sel(0, 1); + coverage.scroll_window(0); +}; + +coverage.to_first_chunk = function () { + coverage.set_sel(0, 1); + coverage.to_next_chunk(); +}; + +coverage.to_prev_file = function () { + window.location = document.getElementById("prevFileLink").href; +} + +coverage.to_next_file = function () { + window.location = document.getElementById("nextFileLink").href; +} + +coverage.to_index = function () { + location.href = document.getElementById("indexLink").href; +} + +coverage.show_hide_help = function () { + const helpCheck = document.getElementById("help_panel_state") + helpCheck.checked = !helpCheck.checked; +} + +// Return a string indicating what kind of chunk this line belongs to, +// or null if not a chunk. +coverage.chunk_indicator = function (line_elt) { + const classes = line_elt?.className; + if (!classes) { + return null; + } + const match = classes.match(/\bshow_\w+\b/); + if (!match) { + return null; + } + return match[0]; +}; + +coverage.to_next_chunk = function () { + const c = coverage; + + // Find the start of the next colored chunk. + var probe = c.sel_end; + var chunk_indicator, probe_line; + while (true) { + probe_line = c.line_elt(probe); + if (!probe_line) { + return; + } + chunk_indicator = c.chunk_indicator(probe_line); + if (chunk_indicator) { + break; + } + probe++; + } + + // There's a next chunk, `probe` points to it. + var begin = probe; + + // Find the end of this chunk. + var next_indicator = chunk_indicator; + while (next_indicator === chunk_indicator) { + probe++; + probe_line = c.line_elt(probe); + next_indicator = c.chunk_indicator(probe_line); + } + c.set_sel(begin, probe); + c.show_selection(); +}; + +coverage.to_prev_chunk = function () { + const c = coverage; + + // Find the end of the prev colored chunk. + var probe = c.sel_begin-1; + var probe_line = c.line_elt(probe); + if (!probe_line) { + return; + } + var chunk_indicator = c.chunk_indicator(probe_line); + while (probe > 1 && !chunk_indicator) { + probe--; + probe_line = c.line_elt(probe); + if (!probe_line) { + return; + } + chunk_indicator = c.chunk_indicator(probe_line); + } + + // There's a prev chunk, `probe` points to its last line. + var end = probe+1; + + // Find the beginning of this chunk. + var prev_indicator = chunk_indicator; + while (prev_indicator === chunk_indicator) { + probe--; + if (probe <= 0) { + return; + } + probe_line = c.line_elt(probe); + prev_indicator = c.chunk_indicator(probe_line); + } + c.set_sel(probe+1, end); + c.show_selection(); +}; + +// Returns 0, 1, or 2: how many of the two ends of the selection are on +// the screen right now? +coverage.selection_ends_on_screen = function () { + if (coverage.sel_begin === 0) { + return 0; + } + + const begin = coverage.line_elt(coverage.sel_begin); + const end = coverage.line_elt(coverage.sel_end-1); + + return ( + (checkVisible(begin) ? 1 : 0) + + (checkVisible(end) ? 1 : 0) + ); +}; + +coverage.to_next_chunk_nicely = function () { + if (coverage.selection_ends_on_screen() === 0) { + // The selection is entirely off the screen: + // Set the top line on the screen as selection. + + // This will select the top-left of the viewport + // As this is most likely the span with the line number we take the parent + const line = document.elementFromPoint(0, 0).parentElement; + if (line.parentElement !== document.getElementById("source")) { + // The element is not a source line but the header or similar + coverage.select_line_or_chunk(1); + } else { + // We extract the line number from the id + coverage.select_line_or_chunk(parseInt(line.id.substring(1), 10)); + } + } + coverage.to_next_chunk(); +}; + +coverage.to_prev_chunk_nicely = function () { + if (coverage.selection_ends_on_screen() === 0) { + // The selection is entirely off the screen: + // Set the lowest line on the screen as selection. + + // This will select the bottom-left of the viewport + // As this is most likely the span with the line number we take the parent + const line = document.elementFromPoint(document.documentElement.clientHeight-1, 0).parentElement; + if (line.parentElement !== document.getElementById("source")) { + // The element is not a source line but the header or similar + coverage.select_line_or_chunk(coverage.lines_len); + } else { + // We extract the line number from the id + coverage.select_line_or_chunk(parseInt(line.id.substring(1), 10)); + } + } + coverage.to_prev_chunk(); +}; + +// Select line number lineno, or if it is in a colored chunk, select the +// entire chunk +coverage.select_line_or_chunk = function (lineno) { + var c = coverage; + var probe_line = c.line_elt(lineno); + if (!probe_line) { + return; + } + var the_indicator = c.chunk_indicator(probe_line); + if (the_indicator) { + // The line is in a highlighted chunk. + // Search backward for the first line. + var probe = lineno; + var indicator = the_indicator; + while (probe > 0 && indicator === the_indicator) { + probe--; + probe_line = c.line_elt(probe); + if (!probe_line) { + break; + } + indicator = c.chunk_indicator(probe_line); + } + var begin = probe + 1; + + // Search forward for the last line. + probe = lineno; + indicator = the_indicator; + while (indicator === the_indicator) { + probe++; + probe_line = c.line_elt(probe); + indicator = c.chunk_indicator(probe_line); + } + + coverage.set_sel(begin, probe); + } + else { + coverage.set_sel(lineno); + } +}; + +coverage.show_selection = function () { + // Highlight the lines in the chunk + document.querySelectorAll("#source .highlight").forEach(e => e.classList.remove("highlight")); + for (let probe = coverage.sel_begin; probe < coverage.sel_end; probe++) { + coverage.line_elt(probe).querySelector(".n").classList.add("highlight"); + } + + coverage.scroll_to_selection(); +}; + +coverage.scroll_to_selection = function () { + // Scroll the page if the chunk isn't fully visible. + if (coverage.selection_ends_on_screen() < 2) { + const element = coverage.line_elt(coverage.sel_begin); + coverage.scroll_window(element.offsetTop - 60); + } +}; + +coverage.scroll_window = function (to_pos) { + window.scroll({top: to_pos, behavior: "smooth"}); +}; + +coverage.init_scroll_markers = function () { + // Init some variables + coverage.lines_len = document.querySelectorAll("#source > p").length; + + // Build html + coverage.build_scroll_markers(); +}; + +coverage.build_scroll_markers = function () { + const temp_scroll_marker = document.getElementById("scroll_marker") + if (temp_scroll_marker) temp_scroll_marker.remove(); + // Don't build markers if the window has no scroll bar. + if (document.body.scrollHeight <= window.innerHeight) { + return; + } + + const marker_scale = window.innerHeight / document.body.scrollHeight; + const line_height = Math.min(Math.max(3, window.innerHeight / coverage.lines_len), 10); + + let previous_line = -99, last_mark, last_top; + + const scroll_marker = document.createElement("div"); + scroll_marker.id = "scroll_marker"; + document.getElementById("source").querySelectorAll( + "p.show_run, p.show_mis, p.show_exc, p.show_exc, p.show_par" + ).forEach(element => { + const line_top = Math.floor(element.offsetTop * marker_scale); + const line_number = parseInt(element.querySelector(".n a").id.substr(1)); + + if (line_number === previous_line + 1) { + // If this solid missed block just make previous mark higher. + last_mark.style.height = `${line_top + line_height - last_top}px`; + } else { + // Add colored line in scroll_marker block. + last_mark = document.createElement("div"); + last_mark.id = `m${line_number}`; + last_mark.classList.add("marker"); + last_mark.style.height = `${line_height}px`; + last_mark.style.top = `${line_top}px`; + scroll_marker.append(last_mark); + last_top = line_top; + } + + previous_line = line_number; + }); + + // Append last to prevent layout calculation + document.body.append(scroll_marker); +}; + +coverage.wire_up_sticky_header = function () { + const header = document.querySelector("header"); + const header_bottom = ( + header.querySelector(".content h2").getBoundingClientRect().top - + header.getBoundingClientRect().top + ); + + function updateHeader() { + if (window.scrollY > header_bottom) { + header.classList.add("sticky"); + } else { + header.classList.remove("sticky"); + } + } + + window.addEventListener("scroll", updateHeader); + updateHeader(); +}; + +coverage.expand_contexts = function (e) { + var ctxs = e.target.parentNode.querySelector(".ctxs"); + + if (!ctxs.classList.contains("expanded")) { + var ctxs_text = ctxs.textContent; + var width = Number(ctxs_text[0]); + ctxs.textContent = ""; + for (var i = 1; i < ctxs_text.length; i += width) { + key = ctxs_text.substring(i, i + width).trim(); + ctxs.appendChild(document.createTextNode(contexts[key])); + ctxs.appendChild(document.createElement("br")); + } + ctxs.classList.add("expanded"); + } +}; + +document.addEventListener("DOMContentLoaded", () => { + if (document.body.classList.contains("indexfile")) { + coverage.index_ready(); + } else { + coverage.pyfile_ready(); + } +}); diff --git a/htmlcov/d_54b267feee0cd80c_test_env_py.html b/htmlcov/d_54b267feee0cd80c_test_env_py.html new file mode 100644 index 00000000..7dc9c5e9 --- /dev/null +++ b/htmlcov/d_54b267feee0cd80c_test_env_py.html @@ -0,0 +1,203 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_env.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_env.py: + 100% +

+ +

+ 73 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1import collections 

+

2 

+

3from dsi.plugins.env import Hostname, SystemKernel, GitInfo 

+

4from dsi.permissions.permissions import PermissionsManager 

+

5import git 

+

6from json import loads 

+

7 

+

8 

+

9def get_git_root(path): 

+

10 git_repo = git.Repo(path, search_parent_directories=True) 

+

11 git_root = git_repo.git.rev_parse("--show-toplevel") 

+

12 return git_root 

+

13 

+

14 

+

15def test_hostname_plugin_type(): 

+

16 mock_pm = PermissionsManager() 

+

17 a = Hostname(perms_manager=mock_pm) 

+

18 a.add_rows() 

+

19 a.add_rows() 

+

20 assert type(a.output_collector) == collections.OrderedDict 

+

21 

+

22 

+

23def test_hostname_plugin_col_shape(): 

+

24 mock_pm = PermissionsManager() 

+

25 a = Hostname(perms_manager=mock_pm) 

+

26 a.add_rows() 

+

27 a.add_rows() 

+

28 assert len(a.output_collector.keys()) == len(a.output_collector.values()) 

+

29 

+

30 

+

31def test_hostname_plugin_row_shape(): 

+

32 for row_cnt in range(1, 10): 

+

33 mock_pm = PermissionsManager() 

+

34 a = Hostname(perms_manager=mock_pm) 

+

35 for _ in range(row_cnt): 

+

36 a.add_rows() 

+

37 column_values = list(a.output_collector.values()) 

+

38 row_shape = len(column_values[0]) 

+

39 for col in column_values[1:]: 

+

40 assert len(col) == row_shape == row_cnt 

+

41 

+

42 

+

43def test_envprov_plugin_type(): 

+

44 mock_pm = PermissionsManager() 

+

45 plug = SystemKernel(perms_manager=mock_pm) 

+

46 assert type(plug.output_collector) == collections.OrderedDict 

+

47 

+

48 

+

49def test_envprov_plugin_adds_rows(): 

+

50 mock_pm = PermissionsManager() 

+

51 plug = SystemKernel(perms_manager=mock_pm) 

+

52 plug.add_rows() 

+

53 plug.add_rows() 

+

54 

+

55 for key, val in plug.output_collector.items(): 

+

56 assert len(val) == 2 

+

57 

+

58 # 1 SystemKernel column + 4 inherited Env cols 

+

59 assert len(plug.output_collector.keys()) == 5 

+

60 

+

61 

+

62def test_systemkernel_plugin_blob_is_big(): 

+

63 mock_pm = PermissionsManager() 

+

64 plug = SystemKernel(perms_manager=mock_pm) 

+

65 plug.add_rows() 

+

66 

+

67 blob = plug.output_collector["kernel_info"][0] 

+

68 info_dict = loads(blob) 

+

69 

+

70 # 1 systemkernel col + 4 inherited Env cols 

+

71 assert len(plug.output_collector.keys()) == 5 

+

72 

+

73 # dict should have more than 1000 (~7000) keys 

+

74 assert len(info_dict.keys()) > 1000 

+

75 

+

76 

+

77def test_git_plugin_type(): 

+

78 mock_pm = PermissionsManager() 

+

79 root = get_git_root(".") 

+

80 plug = GitInfo(git_repo_path=root, perms_manager=mock_pm) 

+

81 plug.add_rows() 

+

82 assert type(plug.output_collector) == collections.OrderedDict 

+

83 

+

84 

+

85def test_git_plugin_adds_rows(): 

+

86 mock_pm = PermissionsManager() 

+

87 root = get_git_root(".") 

+

88 plug = GitInfo(git_repo_path=root, perms_manager=mock_pm) 

+

89 plug.add_rows() 

+

90 plug.add_rows() 

+

91 

+

92 for key, val in plug.output_collector.items(): 

+

93 assert len(val) == 2 

+

94 

+

95 # 2 Git cols + 4 inherited Env cols 

+

96 assert len(plug.output_collector.keys()) == 6 

+

97 

+

98 

+

99def test_git_plugin_infos_are_str(): 

+

100 mock_pm = PermissionsManager() 

+

101 root = get_git_root(".") 

+

102 plug = GitInfo(git_repo_path=root, perms_manager=mock_pm) 

+

103 plug.add_rows() 

+

104 

+

105 assert type(plug.output_collector["git_remote"][0]) == str 

+

106 assert type(plug.output_collector["git_commit"][0]) == str 

+
+ + + diff --git a/htmlcov/d_54b267feee0cd80c_test_file_consumer_py.html b/htmlcov/d_54b267feee0cd80c_test_file_consumer_py.html new file mode 100644 index 00000000..d6abf5d2 --- /dev/null +++ b/htmlcov/d_54b267feee0cd80c_test_file_consumer_py.html @@ -0,0 +1,193 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_file_consumer.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_file_consumer.py: + 100% +

+ +

+ 65 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1from dsi.core import Terminal 

+

2from collections import OrderedDict 

+

3import git 

+

4 

+

5from dsi.plugins.file_consumer import Bueno, Csv 

+

6from dsi.permissions.permissions import PermissionsManager 

+

7 

+

8 

+

9def get_git_root(path): 

+

10 git_repo = git.Repo(path, search_parent_directories=True) 

+

11 git_root = git_repo.git.rev_parse("--show-toplevel") 

+

12 return git_root 

+

13 

+

14 

+

15def test_bueno_plugin_type(): 

+

16 mock_pm = PermissionsManager() 

+

17 path = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

18 plug = Bueno(filenames=path, perms_manager=mock_pm) 

+

19 plug.add_rows() 

+

20 assert type(plug.output_collector) == OrderedDict 

+

21 

+

22 

+

23def test_bueno_plugin_adds_rows(): 

+

24 mock_pm = PermissionsManager() 

+

25 path1 = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

26 path2 = "/".join([get_git_root("."), "dsi/data", "bueno2.data"]) 

+

27 plug = Bueno(filenames=[path1, path2], perms_manager=mock_pm) 

+

28 plug.add_rows() 

+

29 plug.add_rows() 

+

30 

+

31 for key, val in plug.output_collector.items(): 

+

32 assert len(val) == 4 # two lists of length 4 

+

33 

+

34 # 4 Bueno cols 

+

35 assert len(plug.output_collector.keys()) == 4 

+

36 

+

37 

+

38def test_csv_plugin_type(): 

+

39 mock_pm = PermissionsManager() 

+

40 path = "/".join([get_git_root("."), "dsi/data", "wildfiredata.csv"]) 

+

41 plug = Csv(filenames=path, perms_manager=mock_pm) 

+

42 plug.add_rows() 

+

43 assert type(plug.output_collector) == OrderedDict 

+

44 

+

45 

+

46def test_csv_plugin_adds_rows(): 

+

47 mock_pm = PermissionsManager() 

+

48 path = "/".join([get_git_root("."), "dsi/data", "wildfiredata.csv"]) 

+

49 plug = Csv(filenames=path, perms_manager=mock_pm) 

+

50 plug.add_rows() 

+

51 

+

52 for key, val in plug.output_collector.items(): 

+

53 assert len(val) == 4 

+

54 

+

55 # 11 Csv cols + 1 inherited FileConsumer cols 

+

56 assert len(plug.output_collector.keys()) == 12 

+

57 

+

58 

+

59def test_csv_plugin_adds_rows_multiple_files(): 

+

60 mock_pm = PermissionsManager() 

+

61 path1 = "/".join([get_git_root("."), "dsi/data", "wildfiredata.csv"]) 

+

62 path2 = "/".join([get_git_root("."), "dsi/data", "yosemite5.csv"]) 

+

63 

+

64 plug = Csv(filenames=[path1, path2], perms_manager=mock_pm) 

+

65 plug.add_rows() 

+

66 

+

67 for key, val in plug.output_collector.items(): 

+

68 assert len(val) == 8 

+

69 

+

70 # 13 Csv cols + 2 inherited FileConsumer cols 

+

71 assert len(plug.output_collector.keys()) == 15 

+

72 

+

73 

+

74def test_csv_plugin_adds_rows_multiple_files_strict_mode(): 

+

75 mock_pm = PermissionsManager() 

+

76 path1 = "/".join([get_git_root("."), "dsi/data", "wildfiredata.csv"]) 

+

77 path2 = "/".join([get_git_root("."), "dsi/data", "yosemite5.csv"]) 

+

78 

+

79 plug = Csv(filenames=[path1, path2], strict_mode=True, perms_manager=mock_pm) 

+

80 try: 

+

81 plug.add_rows() 

+

82 except TypeError: 

+

83 # Strict mode will throw TypeError if enabled and csv headers don't match 

+

84 assert True 

+

85 

+

86 

+

87def test_csv_plugin_leaves_active_metadata_wellformed(): 

+

88 path = "/".join([get_git_root("."), "dsi/data", "wildfiredata.csv"]) 

+

89 

+

90 term = Terminal() 

+

91 term.load_module("plugin", "Csv", "consumer", filenames=[path]) 

+

92 term.load_module("plugin", "Hostname", "producer") 

+

93 term.transload() 

+

94 

+

95 columns = list(term.active_metadata.values()) 

+

96 assert all([len(columns[0]) == len(col) for col in columns]) # all same length 

+
+ + + diff --git a/htmlcov/d_6361f3bb962fa186_test_permissions_py.html b/htmlcov/d_6361f3bb962fa186_test_permissions_py.html new file mode 100644 index 00000000..ab094839 --- /dev/null +++ b/htmlcov/d_6361f3bb962fa186_test_permissions_py.html @@ -0,0 +1,212 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/permissions/tests/test_permissions.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/permissions/tests/test_permissions.py: + 100% +

+ +

+ 86 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1import git 

+

2import os 

+

3from glob import glob 

+

4 

+

5from dsi.core import Terminal 

+

6from dsi.permissions.permissions import PermissionsManager 

+

7 

+

8 

+

9def get_git_root(path): 

+

10 git_repo = git.Repo(path, search_parent_directories=True) 

+

11 git_root = git_repo.git.rev_parse("--show-toplevel") 

+

12 return git_root 

+

13 

+

14 

+

15def print_and_y(s): 

+

16 print(s) 

+

17 return "y" 

+

18 

+

19 

+

20def test_multiple_perms_fails_by_default(monkeypatch): 

+

21 monkeypatch.setattr("builtins.input", print_and_y) # mock input 

+

22 term = Terminal() 

+

23 bueno_path = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

24 os.chmod(bueno_path, 0o664) 

+

25 term.load_module("plugin", "Bueno", "consumer", filenames=bueno_path) 

+

26 term.load_module("plugin", "Hostname", "consumer") 

+

27 term.transload() 

+

28 pq_path = "/".join([get_git_root("."), "dsi/data", "dummy_data.pq"]) 

+

29 term.load_module("driver", "Parquet", "back-end", filename=pq_path) 

+

30 assert not term.artifact_handler(interaction_type="put") 

+

31 

+

32 

+

33def test_multiple_permissions_register_correctly(monkeypatch): 

+

34 monkeypatch.setattr("builtins.input", print_and_y) # mock input 

+

35 term = Terminal(allow_multiple_permissions=True) 

+

36 bueno_path = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

37 os.chmod(bueno_path, 0o664) 

+

38 term.load_module("plugin", "Bueno", "consumer", filenames=bueno_path) 

+

39 term.load_module("plugin", "Hostname", "consumer") 

+

40 

+

41 term.transload() 

+

42 

+

43 for env_col in ("uid", "effective_gid", "moniker", "gid_list"): 

+

44 uid, gid, settings = tuple(term.perms_manager.column_perms[env_col]) 

+

45 assert isinstance(uid, int) 

+

46 assert isinstance(gid, int) 

+

47 assert settings == "0o660" 

+

48 

+

49 for bueno_col in ("foo", "bar", "baz"): 

+

50 uid, gid, settings = tuple(term.perms_manager.column_perms[bueno_col]) 

+

51 assert isinstance(uid, int) 

+

52 assert isinstance(gid, int) 

+

53 assert settings == "0o664" 

+

54 

+

55 pq_path = "/".join([get_git_root("."), "dsi/data", "dummy_data.pq"]) 

+

56 term.load_module("driver", "Parquet", "back-end", filename=pq_path) 

+

57 assert term.artifact_handler(interaction_type="put") 

+

58 

+

59 

+

60def test_squash_permissions_register_correctly(monkeypatch): 

+

61 monkeypatch.setattr("builtins.input", print_and_y) # mock input 

+

62 term = Terminal(squash_permissions=True) 

+

63 bueno_path = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

64 os.chmod(bueno_path, 0o664) 

+

65 term.load_module("plugin", "Bueno", "consumer", filenames=bueno_path) 

+

66 term.load_module("plugin", "Hostname", "consumer") 

+

67 

+

68 term.transload() 

+

69 

+

70 for env_col in ("uid", "effective_gid", "moniker", "gid_list"): 

+

71 uid, gid, settings = tuple(term.perms_manager.column_perms[env_col]) 

+

72 assert isinstance(uid, int) 

+

73 assert isinstance(gid, int) 

+

74 assert settings == "0o660" 

+

75 

+

76 for bueno_col in ("foo", "bar", "baz"): 

+

77 uid, gid, settings = tuple(term.perms_manager.column_perms[bueno_col]) 

+

78 assert isinstance(uid, int) 

+

79 assert isinstance(gid, int) 

+

80 assert settings == "0o660" 

+

81 

+

82 pq_path = "/".join([get_git_root("."), "dsi/data", "dummy_data.pq"]) 

+

83 term.load_module("driver", "Parquet", "back-end", filename=pq_path) 

+

84 assert term.artifact_handler(interaction_type="put") 

+

85 

+

86 

+

87def test_permissions_output_correctly(monkeypatch): 

+

88 monkeypatch.setattr("builtins.input", print_and_y) # mock input 

+

89 term = Terminal(allow_multiple_permissions=True) 

+

90 bueno_path = "/".join([get_git_root("."), "dsi/data", "bueno1.data"]) 

+

91 os.chmod(bueno_path, 0o664) 

+

92 

+

93 term.load_module("plugin", "Bueno", "consumer", filenames=bueno_path) 

+

94 term.load_module("plugin", "Hostname", "consumer") 

+

95 term.transload() 

+

96 

+

97 pq_path = "/".join([get_git_root("."), "dsi/data", "dummy_data.pq"]) 

+

98 term.load_module("driver", "Parquet", "back-end", filename=pq_path) 

+

99 

+

100 assert term.artifact_handler(interaction_type="put") 

+

101 

+

102 pm = PermissionsManager() 

+

103 written_paths = glob("/".join([get_git_root("."), "dsi/data"]) + "/dummy_data*.pq") 

+

104 for path in written_paths: 

+

105 uid, gid, settings = pm.get_file_permissions(path) 

+

106 if settings == "0o664": # the bueno file 

+

107 old_uid, old_gid, old_settings = pm.get_file_permissions(bueno_path) 

+

108 assert uid == old_uid 

+

109 assert gid == old_gid 

+

110 assert settings == old_settings 

+

111 assert ( 

+

112 path.find(str(uid)) != -1 

+

113 and path.find(str(gid)) != -1 

+

114 and path.find(settings) != -1 

+

115 ) 

+
+ + + diff --git a/htmlcov/d_b38de40496d1c270_test_core_py.html b/htmlcov/d_b38de40496d1c270_test_core_py.html new file mode 100644 index 00000000..ac1776a8 --- /dev/null +++ b/htmlcov/d_b38de40496d1c270_test_core_py.html @@ -0,0 +1,129 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/tests/test_core.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/tests/test_core.py: + 100% +

+ +

+ 23 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1import git 

+

2from dsi.core import Terminal 

+

3 

+

4 

+

5def get_git_root(path): 

+

6 git_repo = git.Repo(path, search_parent_directories=True) 

+

7 git_root = git_repo.git.rev_parse("--show-toplevel") 

+

8 return (git_root) 

+

9 

+

10 

+

11def test_terminal_module_getter(): 

+

12 a = Terminal() 

+

13 plugins = a.list_available_modules('plugin') 

+

14 drivers = a.list_available_modules('driver') 

+

15 assert len(plugins) > 0 and len(drivers) > 0 

+

16 

+

17 

+

18def test_unload_module(): 

+

19 a = Terminal() 

+

20 a.load_module('plugin', 'GitInfo', 'producer', 

+

21 git_repo_path=get_git_root('.')) 

+

22 assert len(a.list_loaded_modules()['producer']) == 1 

+

23 a.unload_module('plugin', 'GitInfo', 'producer') 

+

24 assert len(a.list_loaded_modules()['producer']) == 0 

+

25 

+

26 

+

27def test_unload_after_transload_fails(): 

+

28 a = Terminal() 

+

29 a.load_module('plugin', 'Hostname', 'producer') 

+

30 a.transload() 

+

31 a.unload_module('plugin', 'Hostname', 'producer') 

+

32 assert len(a.list_loaded_modules()['producer']) == 1 

+
+ + + diff --git a/htmlcov/d_f83834e4fc976fad_test_gufi_py.html b/htmlcov/d_f83834e4fc976fad_test_gufi_py.html new file mode 100644 index 00000000..8aa50ddf --- /dev/null +++ b/htmlcov/d_f83834e4fc976fad_test_gufi_py.html @@ -0,0 +1,116 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_gufi.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_gufi.py: + 100% +

+ +

+ 15 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1from dsi.drivers.gufi import Gufi 

+

2from dsi.permissions.permissions import PermissionsManager 

+

3 

+

4isVerbose = False 

+

5 

+

6 

+

7def test_artifact_query(): 

+

8 dbpath = "db.db" 

+

9 index = "gufi_indexes" 

+

10 prefix = "/usr/local/bin" 

+

11 table = "sample" 

+

12 column = "sample_col" 

+

13 mock_pm = PermissionsManager() 

+

14 store = Gufi(prefix, index, dbpath, table, column, 

+

15 isVerbose, perms_manager=mock_pm) 

+

16 sqlstr = "select * from dsi_entries" 

+

17 rows = store.get_artifacts(sqlstr) 

+

18 store.close() 

+

19 assert len(rows) > 0 

+
+ + + diff --git a/htmlcov/d_f83834e4fc976fad_test_sqlite_py.html b/htmlcov/d_f83834e4fc976fad_test_sqlite_py.html new file mode 100644 index 00000000..a4548b4f --- /dev/null +++ b/htmlcov/d_f83834e4fc976fad_test_sqlite_py.html @@ -0,0 +1,155 @@ + + + + + Coverage for /home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_sqlite.py: 100% + + + + + +
+
+

+ Coverage for /home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_sqlite.py: + 100% +

+ +

+ 41 statements   + + + +

+

+ « prev     + ^ index     + » next +       + coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+ +
+
+
+

1import git 

+

2 

+

3from dsi.drivers.sqlite import Sqlite, DataType 

+

4from dsi.permissions.permissions import PermissionsManager 

+

5 

+

6isVerbose = True 

+

7 

+

8 

+

9def get_git_root(path): 

+

10 git_repo = git.Repo(path, search_parent_directories=True) 

+

11 git_root = git_repo.git.rev_parse("--show-toplevel") 

+

12 return (git_root) 

+

13 

+

14 

+

15def test_wildfire_data_sql_artifact(): 

+

16 dbpath = "wildfire.db" 

+

17 mock_pm = PermissionsManager() 

+

18 store = Sqlite(dbpath, perms_manager=mock_pm) 

+

19 store.close() 

+

20 # No error implies success 

+

21 assert True 

+

22 

+

23 

+

24def test_wildfire_data_csv_artifact(): 

+

25 csvpath = '/'.join([get_git_root('.'), 'dsi/data/wildfiredata.csv']) 

+

26 dbpath = "wildfire.db" 

+

27 mock_pm = PermissionsManager() 

+

28 store = Sqlite(dbpath, perms_manager=mock_pm) 

+

29 store.put_artifacts_csv(csvpath, "simulation", isVerbose=isVerbose) 

+

30 store.close() 

+

31 # No error implies success 

+

32 assert True 

+

33 

+

34 

+

35def test_yosemite_data_csv_artifact(): 

+

36 csvpath = '/'.join([get_git_root('.'), 'dsi/data/yosemite5.csv']) 

+

37 dbpath = "yosemite.db" 

+

38 mock_pm = PermissionsManager() 

+

39 store = Sqlite(dbpath, perms_manager=mock_pm) 

+

40 store.put_artifacts_csv(csvpath, "vision", isVerbose=isVerbose) 

+

41 store.close() 

+

42 # No error implies success 

+

43 assert True 

+

44 

+

45 

+

46def test_artifact_query(): 

+

47 dbpath = "wildfire.db" 

+

48 mock_pm = PermissionsManager() 

+

49 store = Sqlite(dbpath, perms_manager=mock_pm) 

+

50 _ = store.get_artifact_list(isVerbose=isVerbose) 

+

51 data_type = DataType() 

+

52 data_type.name = "simulation" 

+

53 result = store.sqlquery("SELECT *, MAX(wind_speed) AS max_windspeed FROM " + 

+

54 str(data_type.name) + " GROUP BY safe_unsafe_fire_behavior") 

+

55 store.export_csv(result, "query.csv") 

+

56 store.close() 

+

57 # No error implies success 

+

58 assert True 

+
+ + + diff --git a/htmlcov/favicon_32.png b/htmlcov/favicon_32.png new file mode 100644 index 00000000..8649f047 Binary files /dev/null and b/htmlcov/favicon_32.png differ diff --git a/htmlcov/index.html b/htmlcov/index.html new file mode 100644 index 00000000..b55b86f4 --- /dev/null +++ b/htmlcov/index.html @@ -0,0 +1,137 @@ + + + + + Coverage report + + + + + +
+
+

Coverage report: + 100% +

+ +
+ +
+

+ coverage.py v7.2.7, + created at 2023-12-19 16:49 -0700 +

+
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Modulestatementsmissingexcludedcoverage
/home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_gufi.py1500100%
/home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_sqlite.py4100100%
/home/qwofford/Projects/jaey/dsi/dsi/permissions/tests/test_permissions.py8600100%
/home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_env.py7300100%
/home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_file_consumer.py6500100%
/home/qwofford/Projects/jaey/dsi/dsi/tests/test_core.py2300100%
Total30300100%
+

+ No items found using the specified filter. +

+
+ + + diff --git a/htmlcov/keybd_closed.png b/htmlcov/keybd_closed.png new file mode 100644 index 00000000..ba119c47 Binary files /dev/null and b/htmlcov/keybd_closed.png differ diff --git a/htmlcov/keybd_open.png b/htmlcov/keybd_open.png new file mode 100644 index 00000000..a8bac6c9 Binary files /dev/null and b/htmlcov/keybd_open.png differ diff --git a/htmlcov/status.json b/htmlcov/status.json new file mode 100644 index 00000000..0fb823d0 --- /dev/null +++ b/htmlcov/status.json @@ -0,0 +1 @@ +{"format":2,"version":"7.2.7","globals":"5ebaf789ae33a85c3243c242b20819f5","files":{"d_f83834e4fc976fad_test_gufi_py":{"hash":"4403e77df9f85fb6202a45010a52fb81","index":{"nums":[0,1,15,0,0,0,0,0],"html_filename":"d_f83834e4fc976fad_test_gufi_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_gufi.py"}},"d_f83834e4fc976fad_test_sqlite_py":{"hash":"2b2467482b4175233919e43d34890008","index":{"nums":[0,1,41,0,0,0,0,0],"html_filename":"d_f83834e4fc976fad_test_sqlite_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/drivers/tests/test_sqlite.py"}},"d_6361f3bb962fa186_test_permissions_py":{"hash":"1df971e574319c0667a348694802615d","index":{"nums":[0,1,86,0,0,0,0,0],"html_filename":"d_6361f3bb962fa186_test_permissions_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/permissions/tests/test_permissions.py"}},"d_54b267feee0cd80c_test_env_py":{"hash":"2a996270b9ee66f0cdc95e881cad0cbd","index":{"nums":[0,1,73,0,0,0,0,0],"html_filename":"d_54b267feee0cd80c_test_env_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_env.py"}},"d_54b267feee0cd80c_test_file_consumer_py":{"hash":"5564e8be0cfecfbb49b1b6fa2b2aa5ee","index":{"nums":[0,1,65,0,0,0,0,0],"html_filename":"d_54b267feee0cd80c_test_file_consumer_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/plugins/tests/test_file_consumer.py"}},"d_b38de40496d1c270_test_core_py":{"hash":"c3a647a4e886930a79be2a80d8636c8f","index":{"nums":[0,1,23,0,0,0,0,0],"html_filename":"d_b38de40496d1c270_test_core_py.html","relative_filename":"/home/qwofford/Projects/jaey/dsi/dsi/tests/test_core.py"}}}} \ No newline at end of file diff --git a/htmlcov/style.css b/htmlcov/style.css new file mode 100644 index 00000000..11b24c4e --- /dev/null +++ b/htmlcov/style.css @@ -0,0 +1,309 @@ +@charset "UTF-8"; +/* Licensed under the Apache License: http://www.apache.org/licenses/LICENSE-2.0 */ +/* For details: https://github.com/nedbat/coveragepy/blob/master/NOTICE.txt */ +/* Don't edit this .css file. Edit the .scss file instead! */ +html, body, h1, h2, h3, p, table, td, th { margin: 0; padding: 0; border: 0; font-weight: inherit; font-style: inherit; font-size: 100%; font-family: inherit; vertical-align: baseline; } + +body { font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; font-size: 1em; background: #fff; color: #000; } + +@media (prefers-color-scheme: dark) { body { background: #1e1e1e; } } + +@media (prefers-color-scheme: dark) { body { color: #eee; } } + +html > body { font-size: 16px; } + +a:active, a:focus { outline: 2px dashed #007acc; } + +p { font-size: .875em; line-height: 1.4em; } + +table { border-collapse: collapse; } + +td { vertical-align: top; } + +table tr.hidden { display: none !important; } + +p#no_rows { display: none; font-size: 1.2em; } + +a.nav { text-decoration: none; color: inherit; } + +a.nav:hover { text-decoration: underline; color: inherit; } + +.hidden { display: none; } + +header { background: #f8f8f8; width: 100%; z-index: 2; border-bottom: 1px solid #ccc; } + +@media (prefers-color-scheme: dark) { header { background: black; } } + +@media (prefers-color-scheme: dark) { header { border-color: #333; } } + +header .content { padding: 1rem 3.5rem; } + +header h2 { margin-top: .5em; font-size: 1em; } + +header p.text { margin: .5em 0 -.5em; color: #666; font-style: italic; } + +@media (prefers-color-scheme: dark) { header p.text { color: #aaa; } } + +header.sticky { position: fixed; left: 0; right: 0; height: 2.5em; } + +header.sticky .text { display: none; } + +header.sticky h1, header.sticky h2 { font-size: 1em; margin-top: 0; display: inline-block; } + +header.sticky .content { padding: 0.5rem 3.5rem; } + +header.sticky .content p { font-size: 1em; } + +header.sticky ~ #source { padding-top: 6.5em; } + +main { position: relative; z-index: 1; } + +footer { margin: 1rem 3.5rem; } + +footer .content { padding: 0; color: #666; font-style: italic; } + +@media (prefers-color-scheme: dark) { footer .content { color: #aaa; } } + +#index { margin: 1rem 0 0 3.5rem; } + +h1 { font-size: 1.25em; display: inline-block; } + +#filter_container { float: right; margin: 0 2em 0 0; } + +#filter_container input { width: 10em; padding: 0.2em 0.5em; border: 2px solid #ccc; background: #fff; color: #000; } + +@media (prefers-color-scheme: dark) { #filter_container input { border-color: #444; } } + +@media (prefers-color-scheme: dark) { #filter_container input { background: #1e1e1e; } } + +@media (prefers-color-scheme: dark) { #filter_container input { color: #eee; } } + +#filter_container input:focus { border-color: #007acc; } + +header button { font-family: inherit; font-size: inherit; border: 1px solid; border-radius: .2em; color: inherit; padding: .1em .5em; margin: 1px calc(.1em + 1px); cursor: pointer; border-color: #ccc; } + +@media (prefers-color-scheme: dark) { header button { border-color: #444; } } + +header button:active, header button:focus { outline: 2px dashed #007acc; } + +header button.run { background: #eeffee; } + +@media (prefers-color-scheme: dark) { header button.run { background: #373d29; } } + +header button.run.show_run { background: #dfd; border: 2px solid #00dd00; margin: 0 .1em; } + +@media (prefers-color-scheme: dark) { header button.run.show_run { background: #373d29; } } + +header button.mis { background: #ffeeee; } + +@media (prefers-color-scheme: dark) { header button.mis { background: #4b1818; } } + +header button.mis.show_mis { background: #fdd; border: 2px solid #ff0000; margin: 0 .1em; } + +@media (prefers-color-scheme: dark) { header button.mis.show_mis { background: #4b1818; } } + +header button.exc { background: #f7f7f7; } + +@media (prefers-color-scheme: dark) { header button.exc { background: #333; } } + +header button.exc.show_exc { background: #eee; border: 2px solid #808080; margin: 0 .1em; } + +@media (prefers-color-scheme: dark) { header button.exc.show_exc { background: #333; } } + +header button.par { background: #ffffd5; } + +@media (prefers-color-scheme: dark) { header button.par { background: #650; } } + +header button.par.show_par { background: #ffa; border: 2px solid #bbbb00; margin: 0 .1em; } + +@media (prefers-color-scheme: dark) { header button.par.show_par { background: #650; } } + +#help_panel, #source p .annotate.long { display: none; position: absolute; z-index: 999; background: #ffffcc; border: 1px solid #888; border-radius: .2em; color: #333; padding: .25em .5em; } + +#source p .annotate.long { white-space: normal; float: right; top: 1.75em; right: 1em; height: auto; } + +#help_panel_wrapper { float: right; position: relative; } + +#keyboard_icon { margin: 5px; } + +#help_panel_state { display: none; } + +#help_panel { top: 25px; right: 0; padding: .75em; border: 1px solid #883; color: #333; } + +#help_panel .keyhelp p { margin-top: .75em; } + +#help_panel .legend { font-style: italic; margin-bottom: 1em; } + +.indexfile #help_panel { width: 25em; } + +.pyfile #help_panel { width: 18em; } + +#help_panel_state:checked ~ #help_panel { display: block; } + +kbd { border: 1px solid black; border-color: #888 #333 #333 #888; padding: .1em .35em; font-family: SFMono-Regular, Menlo, Monaco, Consolas, monospace; font-weight: bold; background: #eee; border-radius: 3px; } + +#source { padding: 1em 0 1em 3.5rem; font-family: SFMono-Regular, Menlo, Monaco, Consolas, monospace; } + +#source p { position: relative; white-space: pre; } + +#source p * { box-sizing: border-box; } + +#source p .n { float: left; text-align: right; width: 3.5rem; box-sizing: border-box; margin-left: -3.5rem; padding-right: 1em; color: #999; } + +@media (prefers-color-scheme: dark) { #source p .n { color: #777; } } + +#source p .n.highlight { background: #ffdd00; } + +#source p .n a { margin-top: -4em; padding-top: 4em; text-decoration: none; color: #999; } + +@media (prefers-color-scheme: dark) { #source p .n a { color: #777; } } + +#source p .n a:hover { text-decoration: underline; color: #999; } + +@media (prefers-color-scheme: dark) { #source p .n a:hover { color: #777; } } + +#source p .t { display: inline-block; width: 100%; box-sizing: border-box; margin-left: -.5em; padding-left: 0.3em; border-left: 0.2em solid #fff; } + +@media (prefers-color-scheme: dark) { #source p .t { border-color: #1e1e1e; } } + +#source p .t:hover { background: #f2f2f2; } + +@media (prefers-color-scheme: dark) { #source p .t:hover { background: #282828; } } + +#source p .t:hover ~ .r .annotate.long { display: block; } + +#source p .t .com { color: #008000; font-style: italic; line-height: 1px; } + +@media (prefers-color-scheme: dark) { #source p .t .com { color: #6a9955; } } + +#source p .t .key { font-weight: bold; line-height: 1px; } + +#source p .t .str { color: #0451a5; } + +@media (prefers-color-scheme: dark) { #source p .t .str { color: #9cdcfe; } } + +#source p.mis .t { border-left: 0.2em solid #ff0000; } + +#source p.mis.show_mis .t { background: #fdd; } + +@media (prefers-color-scheme: dark) { #source p.mis.show_mis .t { background: #4b1818; } } + +#source p.mis.show_mis .t:hover { background: #f2d2d2; } + +@media (prefers-color-scheme: dark) { #source p.mis.show_mis .t:hover { background: #532323; } } + +#source p.run .t { border-left: 0.2em solid #00dd00; } + +#source p.run.show_run .t { background: #dfd; } + +@media (prefers-color-scheme: dark) { #source p.run.show_run .t { background: #373d29; } } + +#source p.run.show_run .t:hover { background: #d2f2d2; } + +@media (prefers-color-scheme: dark) { #source p.run.show_run .t:hover { background: #404633; } } + +#source p.exc .t { border-left: 0.2em solid #808080; } + +#source p.exc.show_exc .t { background: #eee; } + +@media (prefers-color-scheme: dark) { #source p.exc.show_exc .t { background: #333; } } + +#source p.exc.show_exc .t:hover { background: #e2e2e2; } + +@media (prefers-color-scheme: dark) { #source p.exc.show_exc .t:hover { background: #3c3c3c; } } + +#source p.par .t { border-left: 0.2em solid #bbbb00; } + +#source p.par.show_par .t { background: #ffa; } + +@media (prefers-color-scheme: dark) { #source p.par.show_par .t { background: #650; } } + +#source p.par.show_par .t:hover { background: #f2f2a2; } + +@media (prefers-color-scheme: dark) { #source p.par.show_par .t:hover { background: #6d5d0c; } } + +#source p .r { position: absolute; top: 0; right: 2.5em; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; } + +#source p .annotate { font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; color: #666; padding-right: .5em; } + +@media (prefers-color-scheme: dark) { #source p .annotate { color: #ddd; } } + +#source p .annotate.short:hover ~ .long { display: block; } + +#source p .annotate.long { width: 30em; right: 2.5em; } + +#source p input { display: none; } + +#source p input ~ .r label.ctx { cursor: pointer; border-radius: .25em; } + +#source p input ~ .r label.ctx::before { content: "▶ "; } + +#source p input ~ .r label.ctx:hover { background: #e8f4ff; color: #666; } + +@media (prefers-color-scheme: dark) { #source p input ~ .r label.ctx:hover { background: #0f3a42; } } + +@media (prefers-color-scheme: dark) { #source p input ~ .r label.ctx:hover { color: #aaa; } } + +#source p input:checked ~ .r label.ctx { background: #d0e8ff; color: #666; border-radius: .75em .75em 0 0; padding: 0 .5em; margin: -.25em 0; } + +@media (prefers-color-scheme: dark) { #source p input:checked ~ .r label.ctx { background: #056; } } + +@media (prefers-color-scheme: dark) { #source p input:checked ~ .r label.ctx { color: #aaa; } } + +#source p input:checked ~ .r label.ctx::before { content: "▼ "; } + +#source p input:checked ~ .ctxs { padding: .25em .5em; overflow-y: scroll; max-height: 10.5em; } + +#source p label.ctx { color: #999; display: inline-block; padding: 0 .5em; font-size: .8333em; } + +@media (prefers-color-scheme: dark) { #source p label.ctx { color: #777; } } + +#source p .ctxs { display: block; max-height: 0; overflow-y: hidden; transition: all .2s; padding: 0 .5em; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Ubuntu, Cantarell, "Helvetica Neue", sans-serif; white-space: nowrap; background: #d0e8ff; border-radius: .25em; margin-right: 1.75em; text-align: right; } + +@media (prefers-color-scheme: dark) { #source p .ctxs { background: #056; } } + +#index { font-family: SFMono-Regular, Menlo, Monaco, Consolas, monospace; font-size: 0.875em; } + +#index table.index { margin-left: -.5em; } + +#index td, #index th { text-align: right; width: 5em; padding: .25em .5em; border-bottom: 1px solid #eee; } + +@media (prefers-color-scheme: dark) { #index td, #index th { border-color: #333; } } + +#index td.name, #index th.name { text-align: left; width: auto; } + +#index th { font-style: italic; color: #333; cursor: pointer; } + +@media (prefers-color-scheme: dark) { #index th { color: #ddd; } } + +#index th:hover { background: #eee; } + +@media (prefers-color-scheme: dark) { #index th:hover { background: #333; } } + +#index th[aria-sort="ascending"], #index th[aria-sort="descending"] { white-space: nowrap; background: #eee; padding-left: .5em; } + +@media (prefers-color-scheme: dark) { #index th[aria-sort="ascending"], #index th[aria-sort="descending"] { background: #333; } } + +#index th[aria-sort="ascending"]::after { font-family: sans-serif; content: " ↑"; } + +#index th[aria-sort="descending"]::after { font-family: sans-serif; content: " ↓"; } + +#index td.name a { text-decoration: none; color: inherit; } + +#index tr.total td, #index tr.total_dynamic td { font-weight: bold; border-top: 1px solid #ccc; border-bottom: none; } + +#index tr.file:hover { background: #eee; } + +@media (prefers-color-scheme: dark) { #index tr.file:hover { background: #333; } } + +#index tr.file:hover td.name { text-decoration: underline; color: inherit; } + +#scroll_marker { position: fixed; z-index: 3; right: 0; top: 0; width: 16px; height: 100%; background: #fff; border-left: 1px solid #eee; will-change: transform; } + +@media (prefers-color-scheme: dark) { #scroll_marker { background: #1e1e1e; } } + +@media (prefers-color-scheme: dark) { #scroll_marker { border-color: #333; } } + +#scroll_marker .marker { background: #ccc; position: absolute; min-height: 3px; width: 100%; } + +@media (prefers-color-scheme: dark) { #scroll_marker .marker { background: #444; } } diff --git a/index.html b/index.html new file mode 100644 index 00000000..6c2c7621 --- /dev/null +++ b/index.html @@ -0,0 +1,160 @@ + + + + + + + The Data Science Infrastructure Project (DSI) — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+ +
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation.html b/installation.html new file mode 100644 index 00000000..21874e18 --- /dev/null +++ b/installation.html @@ -0,0 +1,134 @@ + + + + + + + Installation — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Installation

+
    +

  1. Create or activate a DSI virtual environment.

    2. +

  2. cd into the project space root

    3. +

  3. python -m pip install .

    4. +

  4. [Optional] If you are running DSI Unit tests python -m pip install pytest gitpython coverage-badge pytest-cov.

    5. +

  5. [Optional] If you are HTML documentation python -m pip install sphinx sphinx_rtd_theme

    6. +
+
+

How to create and activate a virtual environment

+

We recommend Miniconda for virtual environment management (https://docs.conda.io/en/latest/miniconda.html). To create and activate a Miniconda virtual environment:

+
    +

  1. Download and install the appropriate Miniconda installer for your platform.

    2. +

  2. If this is the first time creating a DSI virtual environment: conda create -n 'dsi' python=3.11. The -n name argument can be anything you like.

    3. +

  3. Once the virtual environment is created, activate it with conda activate dsi, or whatever name you picked in the preceding step.

    4. +

  4. Proceed with Step 2 in the “Installation” section.

    5. +

  5. When you’ve completed work, deativate the conda environment with conda deactivate.

    6. +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/introduction.html b/introduction.html new file mode 100644 index 00000000..da1d2fab --- /dev/null +++ b/introduction.html @@ -0,0 +1,146 @@ + + + + + + + Introduction — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Introduction

+

The goal of the Data Science Infrastructure Project (DSI) is to provide a flexible, AI-ready metadata query capability which returns data subject to strict, POSIX-enforced file security. The data lifecycle for AI/ML requires seamless transitions from data-intensive/AI/ML research activity to long-term archiving and share data repositories. DSI enables flexible, data-intensive scientific workflows that meet researcher needs.

+_images/data_lifecycle.png +

DSI system design is driven by experiences which satisfy User Stories. DSI uses Object Oriented design principles to encourage modularity and to support contributions by the user community.

+
+

Implementation

+

The DSI system is composed of three fundamental parts:

+_images/three_easy_pieces.png +
+

DSI Core Middleware

+

DSI’s core middleware is focused on delivering user-queries on unified metadata which are distributed across many files and security domains. DSI currently supports Linux, and is tested on RedHat- and Debian-based distributions. The DSI Core middleware is a home for DSI Plugins and an interface for DSI Drivers.

+
+
+

Plugin Abstract Classes

+

Plugins transform an arbitrary data source into a format that is compatible with our middleware. We call the parsed and queriable attributes “metadata” (data about the data). Metadata share the same security profile as the source data.

+

Plugins can operate as data consumers or data producers. A simple data consumer might parse an application’s output file and place it into a middleware compatible data structure: Python built-ins and members of the popular Python collection module. A simple data producer might execute an application to supplement existing data and queriable metadata.

+

Plugins are defined by a base abstract class, and support child abstract classes which inherit the properties of their ancestors.

+_images/PluginClassHierarchy.png +
+
+

Driver Abstract Classes

+

Drivers are an interface between the User and the Core, or an interface between the Core and a storage medium. Drivers can operate as Front-ends or Back-ends, and a Driver contributor can choose to implement one or both. Driver front-ends are built to deliver an experience which is compatible with a User Story. A simple supporting User Story is a need to query metadata by SQL query. Because the set of queriable metadata are spread across filesystems and security domains, a supporting Driver Back-end is required to assemble query results and present them to the DSI core middleware for transformation and return, creating an experience which is compatible with the User Story.

+_images/user_story.png +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 00000000..ac9c1176 Binary files /dev/null and b/objects.inv differ diff --git a/permissions.html b/permissions.html new file mode 100644 index 00000000..86608dfc --- /dev/null +++ b/permissions.html @@ -0,0 +1,264 @@ + + + + + + + Permissions — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Permissions

+

DSI is capable of consuming information from files, environments, and in-situ processes which may or may not have the same permissions authority. To track this information for the purposes of returning user queries into DSI storage, we utilize a permissions handler. The permissions handler bundles the authority by which information is read and adds this to each column data structure. Most relational database systems require that types are enforced by column, and DSI extends this idea to require that permissions are enforced by column. By tracking the permissions associated with each column, DSI can save files using the same POSIX permissions authority that initially granted access to the information, therefore preserving POSIX permssions as files are saved.

+

By default, DSI will stop users from saving any metadata if the length of the union of the set of column permissions is greater than one. This prevents users from saving files that might have complex security implications. If a user enables the allow_multiple_permissions parameter of the PermissionsManager, then the number of files that will be saved is equal to the length of the union of the set of column permissions in the middleware data structures being written (an example of this behavior follows). There will be one file for each set of columns read by the same permissions authority.

+

By default, DSI will always respect the POSIX permissions authority by which information was read. If the user wishes to override this behavior and write all of their metadata to the same file with a unified UID and GID, they can enable the squash_permissions parameter of the PermissionsManager. The user should be very certain that the information they are writing is protected appropriately in this case.

+

An example helps illustrate these scenarios:

+ + + + + + + + + + + + + + + + + + + +

Col A

Col B

Col C

Perm D

Perm D

Perm F

Row A1

Row B1

Row C1

Row A2

Row B2

Row C2

+

By default, DSI will refuse to write this data structure to disk because len(union({D,D,F})) > 1

+

If a user enables the allow_multiple_permissions parameter, two files will be saved:

+
>>> $ cat file1
+>>> | Col A  | Col B  |
+>>> ===================
+>>> | Perm D | Perm D |
+>>> | Row A1 | Row B1 |
+>>> | Row A2 | Row B2 |
+>>> $ get_perms(file1)
+>>> Perm D
+>>> $ cat file2
+>>> | Col C  |
+>>> ==========
+>>> | Perm F |
+>>> | Row C1 |
+>>> | Row C2 |
+>>> $ get_perms(file2)
+>>> Perm F
+
+
+

If a user enables allow_multiple_permissions and squash_permissions, then a single file will be written with the user’s UID and effective GID and 660 access:

+
>>> $ cat file
+>>> | Col A  | Col B  | Col C  |
+>>> ============================
+>>> | Perm D | Perm D | Perm F |
+>>> | Row A1 | Row B1 | Row C1 |
+>>> | Row A2 | Row B2 | Row C2 |
+>>> $ get_perms(file)
+>>> My UID and Effective GID, with 660 access controls.
+
+
+
+
+exception dsi.permissions.permissions.ColumnNotRegisteredError(key: str)
+
+ +
+
+class dsi.permissions.permissions.Permission(uid: int, gid: int, settings: str)
+

A simple dataclass to represent POSIX file permissions

+
+ +
+
+exception dsi.permissions.permissions.PermissionNotFoundError(perm: Permission)
+
+ +
+
+class dsi.permissions.permissions.PermissionsManager(allow_multiple_permissions=False, squash_permissions=False)
+

A class to handle and register the mapping from columns +to their permissions. Uses flyweights so that each unique +permission is shared and only stored in memory once.

+
+
+get_column_perms(key: str) → Permission
+

Get the Permission of a given column

+
+ +
+
+get_file_permissions(fpath: str) → tuple[int, int, str]
+

Given a filepath, returns (uid, gid, settings)

+
+ +
+
+get_perm(uid, gid, settings) → Permission
+

If a perm already exists, return it. Else create it.

+
+ +
+
+get_permission_columnlist_mapping() → dict[dsi.permissions.permissions.Permission, list[str]]
+

Returns a mapping from unique Permission to list of columns.

+
+ +
+
+get_process_permissions() → tuple[int, int, str]
+

In the event of data not coming from a file, +default to (uid, egid, 660)

+
+ +
+
+has_multiple_permissions() → bool
+

Returns whether or not the collection has multiple permissions.

+
+ +
+
+register_columns(keys: list[str], perm: Permission) → None
+

Links a list of column names to a given permission

+
+ +
+
+register_columns_with_file(keys: list[str], fp: str) → None
+

Gets a file’s Permission and links it to the given columns

+
+ +
+
+set_file_permissions(file_mapping: dict[str, list[str]]) → None
+

Given a mapping from filename to list of columns, set each file +to its column’s permissions. (All columns of a file share perms)

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/plugins.html b/plugins.html new file mode 100644 index 00000000..f1da4b8e --- /dev/null +++ b/plugins.html @@ -0,0 +1,316 @@ + + + + + + + Plugins — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Plugins

+

Plugins connect data-producing applications to DSI middleware. Plugins have “producer” or “consumer” functions. A Plugin consumer function deals with existing data files or input streams. A Plugin producer deals with generating new data. Plugins are modular to support user contribution. Plugin contributors are encouraged to offer custom Plugin abstract classes and Plugin implementations. A contributed Plugin abstract class may extend another plugin to inherit the properties of the parent. In order to be compatible with DSI middleware, Plugins should produce data in Python built-in data structures or data structures sourced from the Python collections library. Plugin extensions will be accepted conditional to the extention of plugins/tests to demonstrate the new Plugin capability. We can not accept pull requests that are not tested.

+_images/PluginClassHierarchy.png +
+
+class dsi.plugins.metadata.Plugin(path)
+

Plugin abstract class for DSI core product.

+

A Plugin connects a data producer to a compatible middleware +data structure.

+
+
+abstract add_to_output(path)
+

Initialize Plugin setup.

+

Read a Plugin file. Return a Plugin object.

+
+ +
+ +
+
+class dsi.plugins.metadata.StructuredMetadata(**kwargs)
+

plugin superclass that provides handy methods for structured data

+
+
+add_to_output(row: list) → None
+

Adds a row of data to the output_collector and guarantees good structure. +Useful in a plugin’s add_rows method.

+
+ +
+
+schema_is_set() → bool
+

Helper method to see if the schema has been set

+
+ +
+
+set_schema(column_names: list, validation_model=None) → None
+

Initializes columns in the output_collector and column_cnt. +Useful in a plugin’s pack_header method. +Also registers column permissions if filename is set.

+
+ +
+ +
+
+class dsi.plugins.env.Environment(**kwargs)
+

Environment Plugins inspect the calling process’ context.

+

Environments assume a POSIX-compliant filesystem and always collect UID/GID +information.

+
+ +
+
+class dsi.plugins.env.GitInfo(git_repo_path='./', **kwargs)
+

A Plugin to capture Git information.

+

Adds the current git remote and git commit to metadata.

+
+
+add_rows() → None
+

Adds a row to the output with POSIX info, git remote, and git commit

+
+ +
+
+pack_header() → None
+

Set schema with POSIX and Git columns

+
+ +
+ +
+
+class dsi.plugins.env.Hostname(**kwargs)
+

An example Environment implementation.

+

This plugin collects the hostname of the machine, and couples this with the POSIX +information gathered by the Environment base class.

+
+
+add_rows() → None
+

Parses environment provenance data and adds the row.

+
+ +
+
+pack_header() → None
+

Set schema with keys of prov_info.

+
+ +
+ +
+
+class dsi.plugins.env.SystemKernel(**kwargs)
+

Plugin for reading environment provenance data.

+

An environment provenance plugin which does the following: +1. System Kernel Version +2. Kernel compile-time config +3. Kernel boot config +4. Kernel runtime config +5. Kernel modules and module config +6. Container information, if containerized

+
+
+add_rows() → None
+

Parses environment provenance data and adds the row.

+
+ +
+
+static get_cmd_output(cmd: list, ignore_stderr=False) → str
+

Runs a given command and returns the stdout if successful.

+

If stderr is not empty, an exception is raised with the stderr text.

+
+ +
+
+get_kernel_bt_config() → dict
+

Kernel boot-time configuration is collected by looking at /proc/cmdline.

+

The output of this command is one string of boot-time parameters. This string is +returned in a dict.

+
+ +
+
+get_kernel_ct_config() → dict
+

Kernel compile-time configuration is collected by looking at /boot/config-(kernel version) +and removing comments and empty lines.

+

The output of said command is newline-delimited option=value pairs.

+
+ +
+
+get_kernel_mod_config() → dict
+

Kernel module configuration is collected with the “lsmod” and “modinfo” commands.

+

Each module and modinfo are stored as a key-value pair in the returned dict.

+
+ +
+
+get_kernel_rt_config() → dict
+

Kernel run-time configuration is collected with the “sysctl -a” command.

+

The output of this command is lines consisting of two possibilities: +option = value (note the spaces), and sysctl: permission denied … +The option = value pairs are added to the output dict.

+
+ +
+
+get_kernel_version() → dict
+

Kernel version is obtained by the “uname -r” command, returns it in a dict.

+
+ +
+
+get_prov_info() → str
+

Collect and return the different categories of provenance info.

+
+ +
+
+pack_header() → None
+

Set schema with keys of prov_info.

+
+ +
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 00000000..071f9710 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,165 @@ + + + + + + Python Module Index — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Python Module Index
    • +
  • +
    • +
+
+
+
+
+ + +

Python Module Index

+ +
+ d +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
 
+ d
+ dsi +
    + dsi.core +
    + dsi.drivers.filesystem +
    + dsi.drivers.gufi +
    + dsi.drivers.parquet +
    + dsi.drivers.sqlite +
    + dsi.permissions.permissions +
    + dsi.plugins.env +
    + dsi.plugins.metadata +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 00000000..a5764f42 --- /dev/null +++ b/search.html @@ -0,0 +1,125 @@ + + + + + + Search — DSI 0.0.0 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
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  • Search
    • +
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+
+
+
+
+ + + + +
+ +
+ +
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+ +
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+
+
+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 00000000..bb74ae2e --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["core", "drivers", "index", "installation", "introduction", "permissions", "plugins"], "filenames": ["core.rst", "drivers.rst", "index.rst", "installation.rst", "introduction.rst", "permissions.rst", "plugins.rst"], "titles": ["Core", "Drivers", "The Data Science Infrastructure Project (DSI)", "Installation", "Introduction", "Permissions", "Plugins"], "terms": {"The": [0, 3, 4, 5, 6], "dsi": [0, 1, 3, 5, 6], "middlewar": [0, 1, 5, 6], "defin": [0, 1, 4], "termin": [0, 2], "concept": 0, "an": [0, 1, 4, 5, 6], "instanti": 0, "i": [0, 1, 3, 4, 5, 6], "human": 0, "machin": [0, 6], "interfac": [0, 1, 4], "person": 0, "set": [0, 4, 5, 6], "up": 0, "onli": [0, 5], "need": [0, 4], "know": 0, "how": [0, 2], "thei": [0, 5], "want": [0, 1], "ask": 0, "question": 0, "what": 0, 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