Compare revisions

Martin Weise · Martin Weise · Martin Weise · Martin Weise · Martin Weise · Martin Weise
--- a/.docs/.swagger/api-data.yaml
+++ b/.docs/.swagger/api-data.yaml
@@ -14,9 +14,9 @@ externalDocs:
  url: https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services
 servers:
 - url: http://localhost:9093
-  description: Generated server url
+  description: Development instance
 - url: https://test.dbrepo.tuwien.ac.at
-  description: Sandbox
+  description: Staging instance
 paths: {}
 components:
  securitySchemes:

--- a/.docs/.swagger/api-metadata.yaml
+++ b/.docs/.swagger/api-metadata.yaml
--- a/.docs/.swagger/custom.css
+++ b/.docs/.swagger/custom.css
+html,
+body {
+    background: #eee;
+}
+
+.scheme-container {
+    background: none !important;
+    box-shadow: none !important;
+    padding: 0 !important;
+}
\ No newline at end of file
--- a/.docs/.swagger/dist.tar.gz
+++ b/.docs/.swagger/dist.tar.gz
--- a/.docs/.swagger/swagger-site.sh
+++ b/.docs/.swagger/swagger-site.sh
@@ -8,8 +8,8 @@ services[9099]=metadata
 services[3305]=sidecar

 # clean up
-echo "clean up ./dist ./site"
-rm -rf ./dist ./site
+echo "clean up ./site"
+rm -rf ./site

 # ensure target directories are present
 echo "ensure target directory ./site are present"
@@ -17,11 +17,11 @@ mkdir -p ./site

 # extract static site
 echo "extract static site .docs/.swagger/dist.tar.gz"
-tar xzf .docs/.swagger/dist.tar.gz
 for key in "${!services[@]}"; do
  mkdir -p ./site/${services[$key]}
-  echo "extract static site ./dist -> ./site/${services[$key]}"
-  cp -r ./dist/* ./site/${services[$key]}
-  echo "placing .docs/.swagger/api-${services[$key]}.yaml -> ./site/${services[$key]}/api.yaml"
+  echo "extract static site ./swagger-ui.html -> ./site/${services[$key]}"
+  cp .docs/.swagger/swagger-ui.html ./site/${services[$key]}/index.html
+  cp .docs/.swagger/custom.css ./site/${services[$key]}/custom.css
+  sed -i -e "s/__SERVICENAME__/${services[$key]^} Service/g" ./site/${services[$key]}/index.html
  cp ".docs/.swagger/api-${services[$key]}.yaml" "./site/${services[$key]}/api.yaml"
 done
\ No newline at end of file
--- a/.docs/.swagger/swagger-ui.html
+++ b/.docs/.swagger/swagger-ui.html
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8"/>
+    <meta name="viewport" content="width=device-width, initial-scale=1"/>
+    <meta name="description" content="__SERVICENAME__ API description in OpenAPI 3.0"/>
+    <title>__SERVICENAME__ API</title>
+    <link rel="stylesheet" href="https://unpkg.com/swagger-ui-dist@5.11.1/swagger-ui.css"/>
+    <link rel="stylesheet" href="./custom.css"/>
+    <link rel="icon" href="https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/master/.docs/images/signet_white.png" />
+</head>
+<body>
+<div id="swagger-ui"></div>
+<script src="https://unpkg.com/swagger-ui-dist@5.11.1/swagger-ui-bundle.js" crossorigin></script>
+<script src="https://unpkg.com/swagger-ui-dist@5.11.1/swagger-ui-standalone-preset.js" crossorigin></script>
+<script>
+    window.onload = () => {
+      window.ui = SwaggerUIBundle({
+        url: 'api.yaml',
+        dom_id: '#swagger-ui',
+      });
+    };
+</script>
+</body>
+</html>
\ No newline at end of file
--- a/.docs/DEVELOPMENT.md
+++ b/.docs/DEVELOPMENT.md
@@ -25,6 +25,18 @@ mvn -f ./dbrepo-metadata-service/pom.xml clean install -DskipTests

 We practice test-driven development and require contributors to test their code with at least 90% code coverage.

+## Code Documentation
+
+Before creating a merge request, make sure you:
+
+- [x] Generate the [Swagger Docs](#swagger-docs) endpoint documentation
+
+### Swagger Docs
+
+```shell
+bash .swagger/swagger-generate.sh
+```
+
 ## Code Versioning

 ### Branching Strategy

--- a/.docs/deployment-helm.md
+++ b/.docs/deployment-helm.md
@@ -29,7 +29,7 @@ about values, etc.
 ## Limitations

 1. MariaDB Galera does not (yet) support XA-transactions required by the authentication service (=Keycloak). Therefore
-   only a single MariaDB pod can be deployed at once for the [auth database](../system-databases-auth).
+   only a single MariaDB pod can be deployed at once for the [auth database](../system-databases-authentication).

 !!! question "Do you miss functionality? Do these limitations affect you?"


--- a/.docs/images/architecture.drawio
+++ b/.docs/images/architecture.drawio
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      <root>
@@ -581,8 +581,8 @@
      </root>
    </mxGraphModel>
  </diagram>
-  <diagram id="e2fuorb2m_XjboQ7R7_y" name="Data Ingest">
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+  <diagram id="e2fuorb2m_XjboQ7R7_y" name="data-ingest">
+    <mxGraphModel dx="1195" dy="685" grid="1" gridSize="10" guides="1" tooltips="1" connect="1" arrows="1" fold="1" page="1" pageScale="1" pageWidth="1169" pageHeight="827" math="0" shadow="0">
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@@ -648,8 +633,8 @@
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+        <mxCell id="0VJCIkSjTVNNat6pGbHc-8" value="3307/tcp" style="edgeStyle=orthogonalEdgeStyle;rounded=0;orthogonalLoop=1;jettySize=auto;html=1;strokeColor=#000000;startArrow=classic;startFill=1;dashed=1;exitX=0.5;exitY=0;exitDx=0;exitDy=0;exitPerimeter=0;" parent="1" edge="1" source="yvNGLmbJRMNvVS071MuP-1">
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@@ -675,7 +660,7 @@
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        <mxCell id="0VJCIkSjTVNNat6pGbHc-38" value="3306/tcp" style="edgeLabel;html=1;align=center;verticalAlign=middle;resizable=0;points=[];" parent="0VJCIkSjTVNNat6pGbHc-37" vertex="1" connectable="0">
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@@ -687,18 +672,13 @@
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@@ -710,25 +690,25 @@
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--- a/.docs/images/data-ingest.svg
+++ b/.docs/images/data-ingest.svg
--- a/.docs/papers/weise2022dbrepo.bib
+++ b/.docs/papers/weise2022dbrepo.bib
+@article{weise2022dbrepo,
+  title = {DBRepo: a {S}emantic {D}igital {R}epository for {R}elational {D}atabases},
+  volume = {17},
+  ISSN = {1746-8256},
+  url = {https://doi.org/10.2218/ijdc.v17i1.825},
+  DOI = {10.2218/ijdc.v17i1.825},
+  number = {1},
+  journal = {International Journal of Digital Curation},
+  publisher = {Edinburgh University Library},
+  author = {Weise, Martin and Staudinger, Moritz and Michlits, Cornelia and Gergely, Eva and Stytsenko, Kirill and Ganguly, Raman and Rauber, Andreas},
+  year = {2022},
+  month = sep,
+  pages = {11}
+}
\ No newline at end of file
--- a/.docs/papers/weise2022dbrepo.rdf
+++ b/.docs/papers/weise2022dbrepo.rdf
+<rdf:RDF
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:z="http://www.zotero.org/namespaces/export#"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:bib="http://purl.org/net/biblio#"
+ xmlns:foaf="http://xmlns.com/foaf/0.1/"
+ xmlns:link="http://purl.org/rss/1.0/modules/link/"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:prism="http://prismstandard.org/namespaces/1.2/basic/">
+    <bib:Article rdf:about="http://ijdc.net/article/view/825">
+        <z:itemType>journalArticle</z:itemType>
+        <dcterms:isPartOf rdf:resource="urn:issn:1746-8256"/>
+        <bib:authors>
+            <rdf:Seq>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Weise</foaf:surname>
+                        <foaf:givenName>Martin</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Staudinger</foaf:surname>
+                        <foaf:givenName>Moritz</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Michlits</foaf:surname>
+                        <foaf:givenName>Cornelia</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Gergely</foaf:surname>
+                        <foaf:givenName>Eva</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Stytsenko</foaf:surname>
+                        <foaf:givenName>Kirill</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Ganguly</foaf:surname>
+                        <foaf:givenName>Raman</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+                <rdf:li>
+                    <foaf:Person>
+                        <foaf:surname>Rauber</foaf:surname>
+                        <foaf:givenName>Andreas</foaf:givenName>
+                    </foaf:Person>
+                </rdf:li>
+            </rdf:Seq>
+        </bib:authors>
+        <link:link rdf:resource="#item_2"/>
+        <dc:title>DBRepo: a Semantic Digital Repository for Relational Databases</dc:title>
+        <dcterms:abstract>Data curation is a complex, multi-faceted task. While dedicated data stewards are starting to take care of these activities in close collaboration with researchers for many types of (usually file-based) data in many institutions, this is rarely yet the case for data held in relational databases. Beyond large-scale infrastructures hosting e.g. climate or genome data, researchers usually have to create, build and maintain their database, care about security patches, and feed data into it in order to use it in their research. Data curation, if at all, usually happens after a project is finished, when data may be exported for digital preservation into file repository systems.
+We present DBRepo, a semantic digital repository for relational databases in a private cloud setting designed to (1) host research data stored in relational databases right from the beginning of a research project, (2) provide separation of concerns, allowing the researchers to focus on the domain aspects of the data and their work while bringing in experts to handle classic data management tasks, (3) improve findability, accessibility and reusability by offering semantic mapping of metadata attributes, and (4) focus on reproducibility in dynamically evolving data by supporting versioning and precise identification/cite-ability for arbitrary subsets of data.</dcterms:abstract>
+        <dc:date>2022-09-07</dc:date>
+        <z:shortTitle>DBRepo</z:shortTitle>
+        <z:libraryCatalog>DOI.org (Crossref)</z:libraryCatalog>
+        <dc:identifier>
+            <dcterms:URI>
+               <rdf:value>http://ijdc.net/article/view/825</rdf:value>
+            </dcterms:URI>
+        </dc:identifier>
+        <dcterms:dateSubmitted>2024-02-05 13:45:47</dcterms:dateSubmitted>
+        <bib:pages>11</bib:pages>
+    </bib:Article>
+    <bib:Journal rdf:about="urn:issn:1746-8256">
+        <prism:volume>17</prism:volume>
+        <dc:title>International Journal of Digital Curation</dc:title>
+        <dc:identifier>DOI 10.2218/ijdc.v17i1.825</dc:identifier>
+        <prism:number>1</prism:number>
+        <dcterms:alternative>IJDC</dcterms:alternative>
+        <dc:identifier>ISSN 1746-8256</dc:identifier>
+    </bib:Journal>
+    <z:Attachment rdf:about="#item_2">
+        <z:itemType>attachment</z:itemType>
+        <dc:title>Submitted Version</dc:title>
+        <dc:identifier>
+            <dcterms:URI>
+                <rdf:value>https://zenodo.org/record/6637333/files/IDCC22_DBREPO_PREPRINT.pdf</rdf:value>
+            </dcterms:URI>
+        </dc:identifier>
+        <dcterms:dateSubmitted>2024-02-05 13:45:49</dcterms:dateSubmitted>
+        <z:linkMode>1</z:linkMode>
+        <link:type>application/pdf</link:type>
+    </z:Attachment>
+</rdf:RDF>
--- a/.docs/papers/weise2022dbrepo.ris
+++ b/.docs/papers/weise2022dbrepo.ris
+TY  - JOUR
+AU  - Weise, Martin
+AU  - Staudinger, Moritz
+AU  - Michlits, Cornelia
+AU  - Gergely, Eva
+AU  - Stytsenko, Kirill
+AU  - Ganguly, Raman
+AU  - Rauber, Andreas
+TI  - DBRepo: A Semantic Digital Repository for Relational Databases
+T2  - International Journal of Digital Curation
+VL  - 17
+IS  - 1
+SP  - 11
+PY  - 2022
+DA  - 2022/9/7
+PB  - Edinburgh University Library
+AB  - Data curation is a complex, multi-faceted task. While dedicated data
+      stewards are starting to take care of these activities in close
+      collaboration with researchers for many types of (usually file-based) data
+      in many institutions, this is rarely yet the case for data held in
+      relational databases. Beyond large-scale infrastructures hosting e.g.
+      climate or genome data, researchers usually have to create, build and
+      maintain their database, care about security patches, and feed data into
+      it in order to use it in their research. Data curation, if at all, usually
+      happens after a project is finished, when data may be exported for digital
+      preservation into file repository systems. We present DBRepo, a semantic
+      digital repository for relational databases in a private cloud setting
+      designed to (1) host research data stored in relational databases right
+      from the beginning of a research project, (2) provide separation of
+      concerns, allowing the researchers to focus on the domain aspects of the
+      data and their work while bringing in experts to handle classic data
+      management tasks, (3) improve findability, accessibility and reusability
+      by offering semantic mapping of metadata attributes, and (4) focus on
+      reproducibility in dynamically evolving data by supporting versioning and
+      precise identification/cite-ability for arbitrary subsets of data.
+SN  - 1746-8256
+DO  - 10.2218/ijdc.v17i1.825
+UR  - https://doi.org/10.2218/ijdc.v17i1.825
+ER  -
--- a/.docs/papers/weise2022dbrepo.xml
+++ b/.docs/papers/weise2022dbrepo.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<xml><records><record><database name="MyLibrary">MyLibrary</database><source-app name="Zotero">Zotero</source-app><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Weise, Martin</author><author>Staudinger, Moritz</author><author>Michlits, Cornelia</author><author>Gergely, Eva</author><author>Stytsenko, Kirill</author><author>Ganguly, Raman</author><author>Rauber, Andreas</author></authors></contributors><titles><title>DBRepo: a Semantic Digital Repository for Relational Databases</title><secondary-title>International Journal of Digital Curation</secondary-title><short-title>DBRepo</short-title></titles><periodical><full-title>International Journal of Digital Curation</full-title><abbr-1>IJDC</abbr-1></periodical><pages>11</pages><volume>17</volume><number>1</number><issue>1</issue><dates><year>2022</year><pub-dates><date>2022-09-07</date></pub-dates></dates><isbn>1746-8256</isbn><electronic-resource-num>10.2218/ijdc.v17i1.825</electronic-resource-num><abstract>Data curation is a complex, multi-faceted task. While dedicated data stewards are starting to take care of these activities in close collaboration with researchers for many types of (usually file-based) data in many institutions, this is rarely yet the case for data held in relational databases. Beyond large-scale infrastructures hosting e.g. climate or genome data, researchers usually have to create, build and maintain their database, care about security patches, and feed data into it in order to use it in their research. Data curation, if at all, usually happens after a project is finished, when data may be exported for digital preservation into file repository systems.&#xD;We present DBRepo, a semantic digital repository for relational databases in a private cloud setting designed to (1) host research data stored in relational databases right from the beginning of a research project, (2) provide separation of concerns, allowing the researchers to focus on the domain aspects of the data and their work while bringing in experts to handle classic data management tasks, (3) improve findability, accessibility and reusability by offering semantic mapping of metadata attributes, and (4) focus on reproducibility in dynamically evolving data by supporting versioning and precise identification/cite-ability for arbitrary subsets of data.</abstract><remote-database-name>DOI.org (Crossref)</remote-database-name><urls><web-urls><url>http://ijdc.net/article/view/825</url></web-urls><pdf-urls><url>/home/mweise/Zotero/storage/DEL3SNPP/Weise et al. - 2022 - DBRepo a Semantic Digital Repository for Relation.pdf</url></pdf-urls></urls><access-date>2024-02-05 13:45:47</access-date></record></records></xml>
\ No newline at end of file
--- a/.docs/publications.md
+++ b/.docs/publications.md
@@ -6,17 +6,25 @@ hide:

 # Publications

+!!! abstract "How to Cite DBRepo"
+
+    Please cite the following paper:
+
+    Weise, M., Staudinger, M., Michlits, C., Gergely, E., Stytsenko, K., Ganguly, R., & Rauber, A. (2022). DBRepo: a
+    Semantic Digital Repository for Relational Databases. *International Journal of Digital Curation*, 17(1), 11. 
+    DOI: [10.2218/ijdc.v17i1.825](https://doi.org/10.2218/ijdc.v17i1.825)<br />
+
+    [[BibTeX](../papers/weise2022dbrepo.bib)] &nbsp; [[RIS](../papers/weise2022dbrepo.ris)] &nbsp; [[RDF](../papers/weise2022dbrepo.rdf)] &nbsp; [[EndNote](../papers/weise2022dbrepo.xml)]
+
 ## Logos

 DBRepo logo in various formats:

-* [logo.png](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/logo.png)
-* [logo.svg](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/logo.svg)
-
-DBRepo logo (short) in various formats:
+* PNG: [bigger](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/logo.png)
+  ([smaller](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/favicon.png))
+* SVG: [bigger](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/logo.svg)
+  ([smaller](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/favicon.svg))

-* [favicon.svg](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/favicon.svg)
-* [favicon.png](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/raw/dev/dbrepo-ui/static/favicon.png)

 ## Refereed


--- a/.docs/stylesheets/extra.css
+++ b/.docs/stylesheets/extra.css
@@ -9,14 +9,14 @@ figure img.img-border {
    border: 1px solid #b3b3b3;
 }

-.md-main .md-content a:not(.action-button),
-.md-main .md-content a:not(.action-button) {
+.md-main .md-content a:not(.action-button):not([tabindex]),
+.md-main .md-content a:not(.action-button):not([tabindex]) {
    color: var(--md-typeset-color);
    border-bottom: 2px solid var(--md-primary-fg-color);
 }

-.md-main .md-content a:not(.action-button):focus,
-.md-main .md-content a:not(.action-button):hover {
+.md-main .md-content a:not(.action-button):not([tabindex]):focus,
+.md-main .md-content a:not(.action-button):not([tabindex]):hover {
    color: var(--md-typeset-color);
    border-bottom: 2px solid var(--md-primary-fg-color--dark);
 }

--- a/.docs/system-databases-auth.md
+++ b/.docs/system-databases-auth.md
@@ -2,7 +2,7 @@
 author: Martin Weise
 ---

-# Auth Database
+# Authentication Database

 ## tl;dr


--- a/.docs/system-databases-data.md
+++ b/.docs/system-databases-data.md
@@ -25,7 +25,9 @@ author: Martin Weise
 By default, only one Data Database is deployed. You can deploy multiple (different) Data Database instances and make
 them available in the repository as follows:

-```console
+=== "Terminal"
+
+    ```shell
    curl \
       -sSL \
       http://<hostname>/api/container \
@@ -71,7 +73,9 @@ natively.
 Export all databases with `--skip-lock-tables` option for MariaDB Galera clusters as it is not supported currently by
 MariaDB Galera.

-```console
+=== "Terminal"
+
+    ```shell
    mariadb \
        -u <privilegedUsername> \
        -p<privilegedPassword> \
@@ -83,7 +87,9 @@ mariadb \

 ### Restore

-```console
+=== "Terminal"
+
+    ```shell
    mariadb \
        -u <privilegedUsername> \
        -p<privilegedPassword> < dump.sql

--- a/.docs/system-other-search-dashboard.md
+++ b/.docs/system-other-search-dashboard.md
@@ -27,6 +27,12 @@ the [Search Database](../system-databases-search).

 (none)

+!!! question "Do you miss functionality? Do these limitations affect you?"
+
+    We strongly encourage you to help us implement it as we are welcoming contributors to open-source software and get
+    in [contact](../contact) with us, we happily answer requests for collaboration with attached CV and your programming 
+    experience!
+
 ## Security

 (none)
--- a/.docs/system-other-ui.md
+++ b/.docs/system-other-ui.md
@@ -53,7 +53,6 @@ configured as well via the `dbrepo.config.json` values file. The important links
    "page": {
    "information": {
      "links": []
-    }
    },
    ...
 }
@@ -116,6 +115,12 @@ The response looks like this:

 (none)

+!!! question "Do you miss functionality? Do these limitations affect you?"
+
+    We strongly encourage you to help us implement it as we are welcoming contributors to open-source software and get
+    in [contact](../contact) with us, we happily answer requests for collaboration with attached CV and your programming 
+    experience!
+
 ## Security

 (none)
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