Merge develop

openatlas/database/link.py

@@ -174,11 +174,10 @@ def get_all_links_for_network(
         FROM model.link l
         JOIN model.entity de ON l.domain_id = de.id
         JOIN model.entity re ON l.range_id = re.id
-        WHERE de.openatlas_class_name IN  %(system_classes)s
-            AND re.openatlas_class_name IN  %(system_classes)s;
+        WHERE de.openatlas_class_name IN %(system_classes)s
+            AND re.openatlas_class_name IN %(system_classes)s;
         """,
         {'system_classes': tuple(system_classes)})
-    # Todo: return list(g.cursor) would be better but triggers an API error
     return [dict(row) for row in g.cursor.fetchall()]
 
 
@@ -202,5 +201,4 @@ def get_links_by_id_network(ids: list[int]) -> list[dict[str, Any]]:
         WHERE l.range_id IN %(ids)s OR l.domain_id IN %(ids)s;
         """,
         {'ids': tuple(ids)})
-    # Todo: return list(g.cursor) would be better but triggers an API error
     return [dict(row) for row in g.cursor.fetchall()]

openatlas/static/manual/faq.html

@@ -105,48 +105,48 @@ <h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this heading"></
 <section id="how-to-manage-multiple-projects-or-case-studies">
 <h2>How to manage multiple projects or case studies<a class="headerlink" href="#how-to-manage-multiple-projects-or-case-studies" title="Permalink to this heading"></a></h2>
 <p>Tag: technical</p>
-<p>There are two main approaches how to deal with multiple projects or case
-studies.</p>
+<p>There are two main approaches on how to deal with multiple projects or case
+studies:</p>
 <section id="multiple-instances">
 <h3>Multiple instances<a class="headerlink" href="#multiple-instances" title="Permalink to this heading"></a></h3>
-<p>If every project has their own instance (installation) of OpenAtlas than you
+<p>If every project has their own instance (installation) of OpenAtlas then you
 don’t have to worry about separating the data later. But it would also mean
 that data can’t be used together, at least not directly.</p>
 </section>
 <section id="shared-instance">
 <h3>Shared instance<a class="headerlink" href="#shared-instance" title="Permalink to this heading"></a></h3>
-<p>Projects (or case studies) can use the same instance which can be especially
-useful if they share data, e.g. information about places or persons.</p>
+<p>Projects (or case studies) can use the same instance which can be useful if
+they share data, such as information about places or persons.</p>
 <p>For data separation a custom <a class="reference internal" href="entity/type.html"><span class="doc">Type</span></a> can be created,
 usually called <strong>Case study</strong>, which can be:</p>
 <ul class="simple">
-<li><p>attached to multiple classes (probably most of them)</p></li>
-<li><p>set to <strong>multiple</strong> use so that e.g. a place can be part of multiple case
+<li><p>Attached to multiple classes (probably most of them)</p></li>
+<li><p>Set to <strong>multiple</strong> use so that a place can be part of multiple case
 studies</p></li>
-<li><p>set to <strong>required</strong> so that users don’t forget to enter it</p></li>
+<li><p>Set to <strong>required</strong> so that users don’t forget to choose at least one</p></li>
 </ul>
 <p>Later on, e.g. when running analyses or developing a presentation site for one
-case study, this type can be used to separate the data via the
-<a class="reference internal" href="technical/api.html"><span class="doc">API</span></a>.</p>
+case study, data can be filtered by case studies to separate the data sets
+via the <a class="reference internal" href="technical/api.html"><span class="doc">API</span></a>.</p>
 </section>
 </section>
 <section id="how-does-data-access-work">
 <h2>How does data access work<a class="headerlink" href="#how-does-data-access-work" title="Permalink to this heading"></a></h2>
 <p>Tag: design decision</p>
-<p>In OpenAtlas it can be chosen if and when to make data public but:</p>
+<p>If and when data saved in OpenAtlas is shared can be chosen at any point, but:</p>
 <ul class="simple">
 <li><p>All registered users have access to all model data</p></li>
 <li><p>Either <strong>all</strong> data is made public via the <a class="reference internal" href="technical/api.html"><span class="doc">API</span></a> or <strong>none</strong></p></li>
-<li><p>Presentation sites can filter which data (e.g. which case study) to show
+<li><p>Presentation sites can filter which data (e.g. which case study) is shown
 via the API</p></li>
 <li><p>Showing images is a special case because it also depends on licenses and the
 <a class="reference internal" href="admin/iiif.html"><span class="doc">IIIF</span></a> server</p></li>
 </ul>
 <p>There is no option (or plans to add one) to <strong>hide</strong> parts of the data for
-specific users. Reasons for this is that it would conflict with one of our core
-values (open) but there are also practical reasons, e.g. to avoid duplicates.
-If a strict separation is needed, using multiple OpenAtlas instances would
-likely be a better alternative.</p>
+specific users as that conflicts with one of our core value - to be open.
+Furthermore, there are practical reasons, e.g. to avoid duplicates.
+If a strict separation is needed, using multiple OpenAtlas instances might
+be a better solution.</p>
 </section>
 <section id="how-to-enter-professions">
 <h2>How to enter professions<a class="headerlink" href="#how-to-enter-professions" title="Permalink to this heading"></a></h2>
@@ -157,36 +157,36 @@ <h2>How to enter professions<a class="headerlink" href="#how-to-enter-profession
 This group consists of people with the same profession. Say you want to
 enter our lead developer Alex into the database: create a group named
 ‘OpenAtlas’ and connect him to that group in the respective form. Here you
-can also pick the role he has in that group from a list of types. For a more
+can pick the role he has in that group from a list of types. For a more
 detailed tutorial on how to enter professions, have a look
 <a class="reference internal" href="examples/profession.html"><span class="doc">here</span></a>.</p>
 </section>
 <section id="how-to-make-files-available-for-the-public">
 <span id="public-sharing-label"></span><h2>How to make files available for the public<a class="headerlink" href="#how-to-make-files-available-for-the-public" title="Permalink to this heading"></a></h2>
-<p>In case it is planned to share files with the public, e.g. at a presentation
-site or a public archive, several criteria have to be met.</p>
+<p>If you plan on sharing files with the public, e.g. on a presentation
+site or a public archive, several criteria have to be met:</p>
 <section id="criteria-checked-by-the-software">
 <h3>Criteria checked by the software<a class="headerlink" href="#criteria-checked-by-the-software" title="Permalink to this heading"></a></h3>
 <ul class="simple">
 <li><p>The file must exist</p></li>
 <li><p>A license has to be specified</p></li>
-<li><p>It has to be marked with <strong>public sharing allowed</strong></p></li>
+<li><p>The file has to be marked with <strong>public sharing allowed</strong></p></li>
 </ul>
-<p>In case these criteria aren’t met, a file won’t be:</p>
+<p>In case these criteria aren’t met, a file:</p>
 <ul class="simple">
-<li><p>Shared via the <a class="reference internal" href="technical/api.html"><span class="doc">API</span></a></p></li>
-<li><p>Won’t show up on presentation sites developed by the OpenAtlas team</p></li>
-<li><p>Won’t be included in case the long time archiving
-system <a class="reference external" href="https://arche.acdh.oeaw.ac.at/">ARCHE</a> is used</p></li>
+<li><p>Will not be shared via the <a class="reference internal" href="technical/api.html"><span class="doc">API</span></a></p></li>
+<li><p>Will not show up on presentation sites developed by the OpenAtlas team</p></li>
+<li><p>Will not be included in long-term archiving via
+<a class="reference external" href="https://arche.acdh.oeaw.ac.at/">ARCHE</a></p></li>
 </ul>
-<p>But be aware that although the file itself won’t be shared, the file
-information (e.g. filename) will still be available (e.g. shown on a
+<p>Be aware that although the file itself won’t be shared, the file
+information (such as filenames, etc.) will still be available (e.g. shown on a
 presentation site).</p>
-<p>At <strong>file</strong> -&gt; <strong>list</strong> at the top you find counts for:</p>
+<p>At <strong>file</strong> -&gt; <strong>list</strong> you find counts for:</p>
 <ul class="simple">
-<li><p>public files</p></li>
-<li><p>public files with a missing license</p></li>
-<li><p>public files with a license but without creator (which many licenses require)</p></li>
+<li><p>Public files</p></li>
+<li><p>Public files with a missing license</p></li>
+<li><p>Public files with a license but without creator (which many licenses require)</p></li>
 </ul>
 </section>
 <section id="criteria-checked-by-users">
@@ -209,15 +209,15 @@ <h2>Why can’t a free text field be added via custom types<a class="headerlink"
 <p>Tag: design decision</p>
 <p>A free text entry field would lead to lots of unstructured data.
 Unstructured data can not be processed automatically and would result in it
-not being presented nor searchable in the OpenAtlas system as well as in a
-presentation site that presents your data. Therefore, we made the decision, not
-to include free text types into the OpenAtlas system. Solutions to this problem
-are very case specific, but you could:</p>
+neither being presented nor searchable in the OpenAtlas system as well as in a
+presentation site. Therefore, we made the decision, not to include free text
+types into the OpenAtlas system. Solutions to this problem are very case
+specific, but you could:</p>
 <ul class="simple">
-<li><p>use the already provided description fields to enter any type of free text
-(keep in mind that this also comes with restrictions on how to present this
-data at a presentation site)</p></li>
-<li><p>create a new tree of project specific types for as many cases as possible
+<li><p>Use the provided description field to enter any type of free text
+(keep in mind that this also comes with restrictions on how to present the
+data on a presentation site)</p></li>
+<li><p>Create a new tree of project specific types for as many cases as possible
 and structure your data with them – for a step by step tutorial how to
 create new types, click <a class="reference internal" href="examples/types.html"><span class="doc">here</span></a>.</p></li>
 </ul>
@@ -234,11 +234,10 @@ <h2>Why can’t longer texts be formatted<a class="headerlink" href="#why-can-t-
 be used by other systems via the <a class="reference internal" href="technical/api.html"><span class="doc">API</span></a>, and these systems are
 not necessarily able to handle these formats.</p>
 <p>Another reason is that these formats might change over time. All in all it is
-more important for us that acquired data is as interoperable, as long as
+more important that acquired data is as interoperable for as long as
 possible.</p>
-<p>Of course the situation is different for e.g. presentation sites for OpenAtlas
-data. There it would be possible to e.g. add manual formatted texts where
-needed.</p>
+<p>For presentation sites and the alike it is possible to add e.g. manually
+formatted texts, etc. where needed.</p>
 </section>
 </section>
 

openatlas/static/manual/features.html

@@ -110,16 +110,16 @@ <h1>Features<a class="headerlink" href="#features" title="Permalink to this head
 <section id="model">
 <h2>Model<a class="headerlink" href="#model" title="Permalink to this heading"></a></h2>
 <p>The data model specifies the structure in which the information is stored
-within the database. The use of an ontology, for example, allows the data to be
+within the database. The use of an ontology allows the data to be
 combined more easily with information from other projects and is consistent
 with the <a class="reference external" href="https://www.go-fair.org/fair-principles/">FAIR principles</a>.</p>
 <p>The OpenAtlas <a class="reference internal" href="model/index.html"><span class="doc">Model</span></a> is based on the international standard of
 <a class="reference external" href="https://www.cidoc-crm.org/">CIDOC CRM</a>, an ontology widely used within the
 field of humanities.</p>
 <ul class="simple">
 <li><p><a class="reference internal" href="entity/type.html"><span class="doc">Types</span></a> can be used to adapt for specific research topics</p></li>
-<li><p><a class="reference internal" href="entity/reference_system.html"><span class="doc">Reference Systems</span></a> for
-Linked Open Data (LOD)</p></li>
+<li><p><a class="reference internal" href="entity/reference_system.html"><span class="doc">Reference Systems</span></a> help create Linked Open
+Data (LOD)</p></li>
 <li><p>Mapping <a class="reference internal" href="tools/map.html"><span class="doc">spatial</span></a> and
 <a class="reference internal" href="ui/date.html"><span class="doc">temporal</span></a> uncertainty</p></li>
 <li><p><a class="reference internal" href="examples/archaeological_data.html"><span class="doc">Archaeological finds</span></a>
@@ -130,7 +130,7 @@ <h2>Model<a class="headerlink" href="#model" title="Permalink to this heading">
 </section>
 <section id="user-interface">
 <h2>User Interface<a class="headerlink" href="#user-interface" title="Permalink to this heading"></a></h2>
-<p>The user interface allows for easy and quick entry of information into the
+<p>The user interface (UI) allows for easy and quick entry of information into the
 database, while the data is mapped in the background according to the
 specifications of the data model (see above).
 Due to the use of <a class="reference internal" href="entity/type.html"><span class="doc">types</span></a>, this can be designed
@@ -188,8 +188,8 @@ <h2>Data Exchange<a class="headerlink" href="#data-exchange" title="Permalink to
 </section>
 <section id="user-management">
 <h2>User Management<a class="headerlink" href="#user-management" title="Permalink to this heading"></a></h2>
-<p>The User Management Features allows the activation of users for the own
-OpenAtlas instance. These can also be divided into different user groups with
+<p>The User Management Features allows the activation of users for your
+OpenAtlas instance. They can be divided into different user groups with
 different permissions. In addition, the user interface can be adapted to the
 user’s own preferences via settings.</p>
 <ul class="simple">

openatlas/static/manual/overview.html

@@ -96,8 +96,8 @@
 <h1>Overview<a class="headerlink" href="#overview" title="Permalink to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 </div>
-<p>The overview page can be reached when clicking on the logo at the upper left.
-When logged in following is displayed:</p>
+<p>The overview page can be reached by clicking on the logo in the upper left
+corner. When logged in following information is displayed:</p>
 <ul class="simple">
 <li><p>An overview table of already entered entities</p></li>
 <li><p>Links to manual, <a class="reference internal" href="model/index.html"><span class="doc">Model</span></a> and <a class="reference internal" href="tools/network.html"><span class="doc">Network visualization</span></a></p></li>

openatlas/static/manual/tools/anthropological_analyses.html

@@ -115,11 +115,11 @@ <h2>Sex Estimation<a class="headerlink" href="#sex-estimation" title="Permalink
 <p>Sex estimation on the method published by <em>Ferembach et al. 1979</em>
 (D. Ferembach, I. Schwidetzky, and M. Stloukal, Empfehlungen für die
 Alters- und Geschlechtsdiagnose am Skelett. Homo 30, 1979, 1-32).</p>
-<p>For this method, features of the bones, primarily in the skull and pelvis, are
-examined. In addition to the features proposed in Ferembach et al. possibilities
-to assess the margo supramastoideus, os sacrum, and the robustness of the
-humerus and femur were supplemented. Therefore, the following features can be
-accessed:</p>
+<p>Features of the bones, primarily in the skull and pelvis, are
+examined when following this method. In addition to the features proposed in
+Ferembach et al. possibilities to assess the margo supramastoideus, os
+sacrum, and the robustness of the humerus and femur were supplemented.
+Therefore, the following features can be accessed:</p>
 <p><strong>Skull</strong></p>
 <ul class="simple">
 <li><p>Glabella  (W = 3)</p></li>
@@ -174,8 +174,8 @@ <h2>Sex Estimation<a class="headerlink" href="#sex-estimation" title="Permalink
 <li><p><strong>male</strong> 2</p></li>
 <li><p><strong>not preserved</strong> (no assigned value)</p></li>
 </ul>
-<p>The product is then divided by the sum of the weighting values used.
-The result is called sex ratio and can take values between -2 and 2.
+<p>The product of all features is then divided by the sum of the weighting values
+used. The result is called sex ratio and can take values between -2 and 2.
 The following types are assigned:</p>
 <ul class="simple">
 <li><p>-2 to -0.7:           <strong>female</strong></p></li>

openatlas/static/manual/tools/image_annotation.html

@@ -106,29 +106,30 @@ <h1>Image annotation<a class="headerlink" href="#image-annotation" title="Permal
 <div class="toctree-wrapper compound">
 </div>
 <p>The image annotation feature allows for marking areas on an image and adding
-a text and/or link it to an entity. E.g. a person on a group picture or an
-artifact at an excavation site image.</p>
+a text and/or link to an entity. In that way a person in a group picture
+or an artifact on an excavation photo can be linked to the entity in OpenAtlas.</p>
 <p>Prerequisite for image annotation is an enabled and configured
 <a class="reference internal" href="../admin/iiif.html"><span class="doc">IIIF</span></a> server.</p>
 <section id="usage">
 <h2>Usage<a class="headerlink" href="#usage" title="Permalink to this heading"></a></h2>
-<p>At a <a class="reference internal" href="../entity/file.html"><span class="doc">File</span></a> detail view click on the <strong>Enable IIIF view</strong> button
-below the image if it wasn’t converted already.</p>
-<p>Once the image was converted you can click on the <strong>Annotate</strong> link below the
+<p>In a <a class="reference internal" href="../entity/file.html"><span class="doc">File</span></a>’s detail view, click the <strong>Enable IIIF view</strong> button
+below the image, if it is not converted already.
+Once the image is converted click the <strong>Annotate</strong> link below the
 image and the annotation view will open in a new tab.</p>
-<p>In the image annotation view you can see the image in an IIIF viewer and a form
-for new annotations and a list of already entered annotations with links to
-edit or delete them.</p>
+<p>In the image annotation view you can see the image in an IIIF viewer as
+well as a form for new annotations including a list of already saved
+annotations. Links to edit or delete previous annotations are als porvided.</p>
 <p><strong>Form fields</strong></p>
 <ul class="simple">
-<li><p><strong>IIIF image view</strong> - here you can use the rectangle draw button on the left
-side to mark an area.</p></li>
-<li><p><strong>Annotation</strong> - you can enter a description here</p></li>
-<li><p><strong>Entity</strong> - you can link an entity here</p></li>
+<li><p><strong>IIIF image view</strong> - click the button on the left to draw a rectangle
+to mark the desired area.</p></li>
+<li><p><strong>Annotation</strong> - enter a description</p></li>
+<li><p><strong>Entity</strong> - link to an entity</p></li>
 </ul>
 <p>Be aware that the <strong>Entity</strong> selection only offers entities that are already
-linked to the file. This is to guarantee that the entity is also linked via
-the model (which the image annotation is not part of).</p>
+linked to the file. This guarantees that each selectable entity is also
+linked to the file via the model. Immage annotation does not create new
+model links in the background!</p>
 </section>
 </section>