1,721,026 research outputs found
rtFIN 2019 - Rigorous study design and reporting standards revisited
No full textWorkshop at 4th Real-time functional imaging and neurofeedback (rtFIN) conference, RWTH Aachen University, in collaboration with Prof. Ben Becker (Chengdu), Stephan Heunis (Jülich) and Amelie Haugg (Zurich
rtFIN 2019 - Rigorous study design and reporting standards revisited
No full textWorkshop at 4th Real-time functional imaging and neurofeedback (rtFIN) conference, RWTH Aachen University, in collaboration with Prof. Ben Becker (Chengdu), Stephan Heunis (Jülich) and Amelie Haugg (Zurich
datalad/datalad-catalog: 1.0.1 - Brand new CLI!
No full text1.0.1 (Fri Sept 1 2023) -- Brand new CLI!
Summary
This is the first major release update since the initial release,
mainly due to breaking changes in the command line interface.
Most of the changes were included in https://github.com/datalad/datalad-catalog/pull/309,
summarised as:
update API to entrypoint per command: create, add, validate, serve, get, set, remove, translate, workflow
introduce datalad-next dependency, at first for constraint system but in future for whatever functionality is useful
refactor most of the code related to the main commands
Some of the important changes to take note of:
Validation is now done according to the schema of a specific catalog (now located at path-to-catalog/schema/*), where previously validation was always done according to the latest schema of the installed package version (which is now the fallback).
Metadata can be passed to any catalog command that takes it as in argument, in different formats: json lines from STDIN, JSON-serialized string, and a file with JSON lines.
pytest fixtures are now located in tests/fixtures.py and exposed to all tests
catalog-get|set provides an extensible set of commands for configuring a catalog and reporting its properties
the handling of config files is refactored:
The main changes relate to how/when a config file is provided.
Previously, config files were specified during instantiation of the WebCatalog class, and a whole lot of obscure code was necessary to determine how this config applies to the catalog or dataset level.
The refactored code receives the config file via the Create() and Add() commands or via the WebCatalog.create() or Node.add_attributes() python methods.
Now, WebCatalog can be instantiated with location alone (no 'action' necessary anymore, and no config_file)
Now, config is set on WebCatalog or Node instances after/during running their respective create() methods and not during instantiation
Translation functionality is refactored, and requires updated to existing translators:
With the new catalog argument, translation occurs to the specific schema version of the catalog (if supported by an available translator); if the catalog argument is not supplied, the expected schema version is the latest supported by the package installation.
The translator matching process is streamlined by keeping track of previously matched and instantiated translators
Functionality to get the supported schema version, source name, and source version have been moved to the translator base class in order to support the abovementioned changes. This means existing and new translators will have to override these functions.
Enhancements and new features
Something is now better than before, e.g. test. #pr (by @jsheunis)
ENH: add a "request access" button for a dataset. PR #235 (by @jsheunis)
NF: Adds metadata translation functionality in dedicated class. PR #246 (by @jsheunis)
ENH: don't install jq dependency on windows. PR #248 (by @jsheunis)
ENH: refactoring config, extractors_used. PR #237 (by @jsheunis)
ENH+BUG: Improving translators and catalog generation. PR #269 (by @jsheunis)
Frontend maintenance. PR #272 (by @jsheunis)
ENH+NF: add javascript customization options via config. PR #283 (by @jsheunis)
ENH: Translator edits. PR #277 (by @jsheunis)
UX: improve user experience when browsing. PR #289 (by @jsheunis)
Bids translator - fix name & license reporting. PR #286 (by @mslw)
ENH: URL parameterization. PR #295 (by @jsheunis)
RF: move from single entrypoint API to entrypoint per command. PR #309 (by @jsheunis)
1.0.0 release. PR #334 (by @jsheunis)
Deprecations and removals
BF: Remove imports of datalad.metadata. PR #240 (by @mslw)
Bug Fixes
BUG/ENH/UX: lots of JS tweaks. PR #299 (by @jsheunis)
[BF] Small fixes to latest cli commands. PR #333 (by @jsheunis)
Fix datacite_gin publication doi translation. PR #325 (by @mslw)
Documentation
DOC: update pipeline docs to agree with latest version of meta-conduct use. PR #258 (by @jsheunis)
ENH: adds acknowledgements to readme and docs. PR #308 (by @jsheunis)
Internal
Switch MacOS Appveyor builds to Monterey. PR #242 (by @mslw)
codespell: typo fixes, config, workflow. PR #257 (by @yarikoptic)
Add a readthedocs configuration file. PR #336 (by @jsheunis)
depend on datalad-next 1.0.0b3 . PR #336 (by @jsheunis)
Tests
Major refactoring of tests in relation to PR #309 (by @jsheunis)
Update datalad.tests.utils imports. PR #320 (by @jwodder)
Authors: 4
John T Wodder (@jwodder)
Michał Szczepanik (@jsheunis)
Stephan Heunis (@jsheunis)
Yaroslav Halchenko (@yarikoptic
Data for: Neu3CA-RT: A Framework for Real-Time fMRI Analysis
No full textNeu3-CA-RT sample Matlab script containing a full explanation of how to run the script and where to find sample dat
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
datalad/datalad-catalog: v1.1.0 - UX improvements and internals
No full text<h3>Summary</h3>
<ul>
<li>This release mostly contains improvements to the UI/UX side of the catalog, such as optimized rendering of components and the addition of new buttons/displays.</li>
<li>A notable addition is the ability to render rich semantic information in a dedicated tab, including (links to) term definitions.</li>
<li>Several internal functions were refactored to remove redundant code or allow</li>
<li>datalad-catalog api calls can now also receive a Python dictionary as metadata input (e.g. <code>add</code> and <code>validate</code>)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/datalad/datalad-catalog/compare/v1.0.1...v.1.1.0</p>
<h3> Enhancements and new features</h3>
<ul>
<li>ENH: adds a "request access" button for a dataset. PR <a href="https://github.com/datalad/datalad-catalog/pull/235">#235</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>ENH: Fine tuning of HTML rendering. PR <a href="https://github.com/datalad/datalad-catalog/pull/347">#347</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>hides fields, including properties, journal, and grant description, if they are not populated, to prevent empty properties from making the rendered page ugly</li>
<li>improves parsing of objects and arrays in the additional display tab so that they can be rendered in a more visually pleasing way.</li>
</ul>
</li>
<li>ENH: Changes approach for setting the required tabs from URL parameters. PR <a href="https://github.com/datalad/datalad-catalog/pull/358">#358</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>discards the use of <code>refs</code> for finding available tabs because of an issue with asynchronous loading of <code>root</code>, the dataset component and its subcomponents, and <code>refs</code>. It can happen that <code>refs</code> might or might not be defined at the time when <code>created()</code> or <code>mounted()</code> is called in the vue app life cycle. For a more useful description, see https://stackoverflow.com/questions/54355375/vue-js-refs-are-undefined-even-though-this-refs-shows-theyre-there.</li>
<li>instead determines the available tabs from the root component data, and accesses this list both on <code>created()</code> and on <code>beforeRouteUpdate()</code> in order to check the provided URL parameter against this list.</li>
</ul>
</li>
<li>ENH: Update icons and social media links by using font-awesome 6.4.2, replacing twitter with X, and adding mastodon. PR <a href="https://github.com/datalad/datalad-catalog/pull/366">#366</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>ENH: Let the binder button display for all datasets and not only for datasets with a github URL; also update the binder link to point to the main branch of the relevant repo. PR <a href="https://github.com/datalad/datalad-catalog/pull/367">#367</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>NF: Introduce a dataset back button. The additions introduce changes to html (to show and hide the back button), to css (for the back button styling together with home button and dataset title), and to JS. The latter handles logic for when to show and hide the back button. Upon <code>create()</code> the superdataset file is fetched in order to store the <code>id</code> and <code>version</code> on the component, and the back button is hidden. Upon internal navigation (using <code>beforeRouteUpdate()</code>), the JS checks if the route that is navigated to is the same as the home page by comparing the new <code>id</code> and <code>version</code> to the stored super id and version. If they are different, show the back button; if they are the same, hide the back button. PR <a href="https://github.com/datalad/datalad-catalog/pull/368">#368</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>ENH: Display "last updated" as 'unknown' if the corresponding field is empty (previously an empty value was displayed as an ugly 'NaN'). PR <a href="https://github.com/datalad/datalad-catalog/pull/369">#369</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>ENH: Content tab UI tweaks. PR <a href="https://github.com/datalad/datalad-catalog/pull/369">#369</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>The cloud icon as a means to download a file is removed</li>
<li>Filename is turned into a link, if the file has an associated URL and only if the URL string contains http</li>
<li>the file size is updated to display correctly (empty string, and not NaN, if the value is empty)</li>
<li>the cursor will only turn into a pointer if the item is a folder or a file with a link.. PR <a href="https://github.com/datalad/datalad-catalog/pull/369">#369</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
</ul>
</li>
<li>ENH: Update functionality wrt subdataset display / behaviour / filtering. PR <a href="https://github.com/datalad/datalad-catalog/pull/373">#373</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>Fixes subdataset filtering to filter on <code>name</code>, <code>givenName</code>, and <code>familyName</code> provided that the property value in each case is not <code>null</code>.</li>
<li>Update subdataset filtering behaviour to only show filtering options when the number of <code>subdatasets > 3</code>. This will hide the filtering options otherwise. Additionally, if the filtering options are hidden, the tags on each subdataset will be deactivated (still visible, but not clickable)</li>
<li>Clears filtering options (filtering text, selected filter tags) when navigating to a subdataset, both from the subdataset view and the content aka file tree view. This prevents the filtering options from remaining and subsequently filtering the subdatasets of the recently selected dataset (after filtering).</li>
</ul>
</li>
<li>ENH: Linked data rendering in <code>additional_display</code> tab. PR <a href="https://github.com/datalad/datalad-catalog/pull/405">#405</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>A new async component is introduced to encapsulate any rendering of <code>additional_tab_display</code>s that have an <code>@context</code> key in their <code>content</code> field. The component was created to remove specific implementation details related to semantics from the overall dataset page rendering (i.e. from the dataset-template component). This allows for future changes to the semantic tab rendering without affecting how the component is invoked.</li>
<li>see previous work by <a href="https://github.com/mslw">@mslw</a> at https://github.com/psychoinformatics-de/sfb1451-projects-catalog/pull/62/files:</li>
</ul>
</li>
<li>ENH: Adds improved logic to the function called when user selects the catalog home button (when the current location is any tab on any dataset page in a catalog). PR <a href="https://github.com/datalad/datalad-catalog/pull/394">#394</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>If there is NO home page set:<ul>
<li>if there is a tab name in the URL, navigate to current</li>
<li>else: don't navigate, only reset</li>
</ul>
</li>
<li>If there IS a home page set:<ul>
<li>if the current page IS the home page:<ul>
<li>if there is a tab name in the URL, navigate to current</li>
<li>else: don't navigate, only reset</li>
</ul>
</li>
<li>if the current page is NOT the home page, navigate to home (reset = clear filters and set tab index = 0)</li>
</ul>
</li>
</ul>
</li>
<li>ENH: adds ability to specify default tab display via dataset-level config file (e.g. <code>"dataset_options"["default_tab"] = "subdatasets"</code>). PR <a href="https://github.com/datalad/datalad-catalog/pull/397">#397</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>the content tab is displayed in position 0</li>
<li>the subdatasets tab is displayed in position 1</li>
<li>other standard / non-standard tabs follow in their original order</li>
<li>if no default tab is specified via the dataset-level config, the content tab is shown</li>
<li>if a different default tab is provided via dataset-level config, that tab will be shown</li>
</ul>
</li>
<li>ENH: Allow python dictionaries to be passed as <code>metadata</code> argument, (e.g. for <code>add</code> and <code>validate</code>). PR <a href="https://github.com/datalad/datalad-catalog/pull/403">#403</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
</ul>
<h3> Deprecations and removals</h3>
<ul>
<li>Removed unused contributors file in repo root. PR <a href="https://github.com/datalad/datalad-catalog/pull/340">#340</a> (by <a href="https://github.com/tmheunis">@tmheunis</a>)</li>
</ul>
<h3> Bug Fixes</h3>
<ul>
<li>BF: Fix double underscore typo in <code>display_schema</code> javascript. PR <a href="https://github.com/datalad/datalad-catalog/pull/402">#402</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>BF: Fix file download url rendering, where the previous state resulted in the download url for a file only containing the first letter of a string (i.e. <code>url_string[0]</code>) because it tested for the existence of an array incorrectly. PR <a href="https://github.com/datalad/datalad-catalog/pull/343">#343</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>BF: Tabs and buttons. PR <a href="https://github.com/datalad/datalad-catalog/pull/350">#350</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>reverts automatic tab switching to its original functionality: displaying the first tab whether it has content or not</li>
<li>fixes the faulty positioning of the "request access" button in the case where no other dataset buttons are displayed</li>
</ul>
</li>
</ul>
<h3> Internal</h3>
<ul>
<li>Add schema utility functions that can be used in a more streamlined way by Python applications. PR <a href="https://github.com/datalad/datalad-catalog/pull/378">#378</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>):<ul>
<li>Adds the ability get the base structure of a valid metadata item (with minimum required fields or all expanded fields), based on the current schema (either in the package data or from an argument-provided catalog). This functionality is contained in the new <code>schema_utils</code> module.</li>
<li>Updates required fields in schemas, specifically removing <code>name</code> from the list of required fields of the dataset schema and adding <code>metadata_sources</code> to the list of required fields of both the dataset and file schemas</li>
</ul>
</li>
<li>Adds ability for <code>schema_utils</code> to return a base metadata item with specific keys excluded. PR <a href="https://github.com/datalad/datalad-catalog/pull/379">#379</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
<li>Have a single implementation of assigning sources by @yarikoptic. PR <a href="https://github.com/datalad/datalad-catalog/pull/356">#356</a></li>
<li>Update <code>versioneer</code> from old 0.18 to 0.23, to fix the build error <code>AttributeError: module 'configparser' has no attribute 'SafeConfigParser'</code> resulting from incompatibility of older version with python 3.12. PR <a href="https://github.com/datalad/datalad-catalog/pull/408">#408</a> (by <a href="https://github.com/jsheunis">@jsheunis</a>)</li>
</ul>
<h3>Authors: 3</h3>
<ul>
<li>Stephan Heunis (@jsheunis)</li>
<li>Tosca Heunis (@tmheunis)</li>
<li>Yaroslav Halchenko (@yarikoptic)</li>
</ul>
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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