use https over http where possible (#159)

* Fix link to jaspersoft repo
* Update links to references and resources
* xmlns in htmls
* License
* Test fixtures
* Css/less

CHANGELOG.asciidoc

@@ -16,10 +16,10 @@ All notable changes to this project will be documented in this file.
 
 == Format and Versioning Scheme
 
-The format is based on http://keepachangelog.com/en/1.0.0/[Keep a Changelog].
+The format is based on https://keepachangelog.com/en/1.0.0/[Keep a Changelog].
 
 SciPaMato is an application. Therefore, the versioning scheme is _not_ adhering
-to http://semver.org/spec/v2.0.0.html[Semantic Versioning], which is mostly
+to https://semver.org/spec/v2.0.0.html[Semantic Versioning], which is mostly
 targeting software components or libraries. Nevertheless, I'm sticking with
 three part version numbers (e.g. 1.0.0), increasing the second number for
 bigger changes and the third number for relatively small changes and bug fixes.
@@ -561,7 +561,7 @@ NOTE: References to user stories are in the form Iteration/Story-Number.
 - dependency bumps: wicket-spring-boot, jOOQ, PostgreSQL JDBC Driver, spring-cloud
 - 08/20 - Public: reduce columns/column sizes in result view (abbreviated
   authors, journal instead of location)
-- 08/12 - Public: Add http://blog.apps.npr.org/pym.js/[pym.js] to support
+- 08/12 - Public: Add https://blog.apps.npr.org/pym.js/[pym.js] to support
   loading SciPaMaTo-Public within a responsive iframe
 - 08/21 - Public: Styling of  NewStudy page
 
@@ -800,7 +800,7 @@ the table in your database instances (`alter table schema_version rename to flyw
 - Introduced Project Lombok for Getters/Setters, Equals/HashCode and Builders
 - Rebased the database creation scripts. Now not adding papers or searches anymore, only reference data
 - switched from markdown to asciidoc for wiki pages
-- Created ChangeLog according to http://keepachangelog.com/en/1.0.0/[Keep a Changelog]
+- Created ChangeLog according to https://keepachangelog.com/en/1.0.0/[Keep a Changelog]
 - use OktHttp with feign
 - various improvements in wiki pages, javadoc, sonar suggested code changes
 - dependency updates: spring-boot-starter, wicket, wicket-spring-boot-starter, jOOQ, postgres-jdbc-driver, spring-boot-admin, assertJ

README.adoc

@@ -25,10 +25,10 @@ https://projects.spring.io/spring-security/[Spring Security]
 * https://projectlombok.org/[Lombok]
 * Presentation Layer
 ** https://wicket.apache.org/[Apache Wicket] with
-http://getbootstrap.com/[Bootstrap]
+https://getbootstrap.com/[Bootstrap]
 ** https://github.com/MarcGiffing/wicket-spring-boot[wicket-spring-boot-starter]
 ** https://github.com/l0rdn1kk0n/wicket-bootstrap[wicket-bootstrap]
-** http://community.jaspersoft.com/[JasperReport] for PDF generation
+** https://community.jaspersoft.com/[JasperReport] for PDF generation
 ** https://github.com/OpenFeign/feign[Feign] as HTTP client to PubMed
 ** jaxb for XML parsing
 * Persistence Layer
@@ -40,15 +40,15 @@ http://getbootstrap.com/[Bootstrap]
 ** https://www.testcontainers.org/[Testcontainers] (running integration tests against the dockerized db)
 ** https://projects.spring.io/spring-batch/[Spring Batch] for pushing data from the core to the public database
 * Caching
-** JCache with http://www.ehcache.org/[Ehcache3]
+** JCache with https://www.ehcache.org/[Ehcache3]
 
 [[architecture-documentation]]
 == Architecture Documentation
 
-I started using http://structure101.com/[Structure101] to assess and track the architecture of SciPaMaTo.
+I started using https://structure101.com/[Structure101] to assess and track the architecture of SciPaMaTo.
 Many thanks to the friendly people of Structure101 to provide a free license for SciPaMaTo as an open source project!
 
-image:http://structure101.com/images/s101_170.png[Structure101]
+image:https://structure101.com/images/s101_170.png[Structure101]
 
 [[user-documentation]]
 == User Documentation

build.gradle.kts

@@ -80,7 +80,7 @@ allprojects {
         mavenCentral()
         jcenter()
         maven { url = uri("https://dl.bintray.com/mockito/maven/") }
-        maven { url = uri("http://jaspersoft.jfrog.io/jaspersoft/third-party-ce-artifacts") }
+        maven { url = uri("https://jaspersoft.jfrog.io/jaspersoft/third-party-ce-artifacts") }
     }
 }
 

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/AbstractPage.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <head>
     <title wicket:id="pageTitle"></title>
 </head>
@@ -10,4 +10,4 @@
     <wicket:child/>
     <wicket:container id="footer-container" wicket:id="footer-container"/>
 </body>
-</html>
+</html>

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/component/table/column/AbstractClickablePropertyColumn$LinkPanel.html

@@ -1,6 +1,6 @@
 <!DOCTYPE html>
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <a wicket:id="link"><span wicket:id="label"></span></a>
 </wicket:panel>
-</html>
+</html>

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/component/table/column/LinkIconColumn.java

@@ -5,7 +5,7 @@
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
  *
- *     http://www.apache.org/licenses/LICENSE-2.0
+ *     https://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/component/table/column/LinkIconPanel.html

@@ -6,7 +6,7 @@
   ~ you may not use this file except in compliance with the License.
   ~ You may obtain a copy of the License at
   ~
-  ~     http://www.apache.org/licenses/LICENSE-2.0
+  ~     https://www.apache.org/licenses/LICENSE-2.0
   ~
   ~ Unless required by applicable law or agreed to in writing, software
   ~ distributed under the License is distributed on an "AS IS" BASIS,
@@ -15,10 +15,10 @@
   ~ limitations under the License.
   -->
 
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <a wicket:id="link">
         <i wicket:id="image"></i>
     </a>
 </wicket:panel>
-</html>
+</html>

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/component/table/column/LinkIconPanel.java

@@ -5,7 +5,7 @@
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
  *
- *     http://www.apache.org/licenses/LICENSE-2.0
+ *     https://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
@@ -78,4 +78,4 @@ protected AjaxLink<Void> getLink() {
     }
 
     protected abstract void onClickPerformed(@NotNull AjaxRequestTarget target);
-}
+}

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/pages/login/AbstractLoginPage.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <body>
     <wicket:extend>
         <form wicket:id="form">
@@ -40,4 +40,4 @@ <h2 class="form-signin-heading" wicket:id="header">Please sign in</h2>
         </form>
     </wicket:extend>
 </body>
-</html>
+</html>

common/common-wicket/src/main/java/ch/difty/scipamato/common/web/pages/login/AbstractLogoutPage.html

@@ -1,10 +1,10 @@
 <!DOCTYPE html>
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <body>
     <wicket:extend>
         <form wicket:id="form">
             <input type="submit" value="Logout"/>
         </form>
     </wicket:extend>
 </body>
-</html>
+</html>

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/TestAbstractPage.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <body>
     <wicket:extend>
         <div class="panel panel-default">
@@ -11,4 +11,4 @@
         </form>
     </wicket:extend>
 </body>
-</html>
+</html>

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/TestAbstractPanel.html

@@ -1,4 +1,4 @@
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <div wicket:id="fooLabel"></div>
     <input wicket:id="foo"/>
@@ -7,4 +7,4 @@
     <input wicket:id="baz" type="checkbox"/>
     <span wicket:id="bazLabel"></span>
 </wicket:panel>
-</html>
+</html>

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/TestCoponents.kt

@@ -26,7 +26,7 @@ class TestApplicationProperties : ApplicationProperties {
     override fun getDefaultLocalization() = "en"
     override fun getBrand() = "SciPaMaTo"
     override fun getTitleOrBrand() = "SciPaMaTo"
-    override fun getPubmedBaseUrl() = "http://pubmed/"
+    override fun getPubmedBaseUrl() = "https://pubmed/"
     override fun getCmsUrlSearchPage() = "http://localhost:8081/"
     override fun getRedirectFromPort() = 8080
     override fun getMultiSelectBoxActionBoxWithMoreEntriesThan() = 4

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/component/table/column/ClickablePropertyColumnTestPanel.html

@@ -1,5 +1,5 @@
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <table class="dataview" wicket:id="table"></table>
 </wicket:panel>
-</html>
+</html>

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/component/table/column/LinkIconColumnTestPanel.html

@@ -1,5 +1,5 @@
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <table class="dataview" wicket:id="table"></table>
 </wicket:panel>
-</html>
+</html>

common/common-wicket/src/test/kotlin/ch/difty/scipamato/common/web/pages/AbstractMenuBuilderTest.kt

@@ -109,7 +109,7 @@ internal class AbstractMenuBuilderTest {
     fun assertExternalLinkWithIcon() {
         menuBuilder.addExternalLink(
             navbar,
-            "http://test.com",
+            "https://test.com",
             "mylabel",
             GlyphIconType.adjust,
             Navbar.ComponentPosition.LEFT
@@ -120,21 +120,21 @@ internal class AbstractMenuBuilderTest {
         assertThat(links).hasSize(1)
         val theLink = links[0]
 
-        assertThat(theLink.defaultModelObjectAsString).isEqualTo("http://test.com")
+        assertThat(theLink.defaultModelObjectAsString).isEqualTo("https://test.com")
         assertThat(theLink.get("label").defaultModelObject).isEqualTo("mylabel")
         assertThat((theLink.get("icon") as Icon).type).isEqualTo(GlyphIconType.adjust)
     }
 
     @Test
     fun assertExternalLinkWithoutIcon() {
-        menuBuilder.addExternalLink(navbar, "http://foo.com", "otherlabel", null, Navbar.ComponentPosition.LEFT)
+        menuBuilder.addExternalLink(navbar, "https://foo.com", "otherlabel", null, Navbar.ComponentPosition.LEFT)
 
         val links = getExternalLinksFrom(navbar)
 
         assertThat(links).hasSize(1)
         val theLink = links[0]
 
-        assertThat(theLink.defaultModelObjectAsString).isEqualTo("http://foo.com")
+        assertThat(theLink.defaultModelObjectAsString).isEqualTo("https://foo.com")
         assertThat(theLink.get("label").defaultModelObject).isEqualTo("otherlabel")
         val icon = theLink.get("icon") as Icon
         assertThat(icon.type).isNull()

core/core-entity/src/main/java/ch/difty/scipamato/core/entity/CoreEntity.java

@@ -26,7 +26,7 @@ public abstract class CoreEntity extends ScipamatoEntity {
      * e.g. {@literal [\\w\\u00C0-\\u024f]}
      * <p>
      * Thanks to hqx5 for his answer to the following <a href=
-     * "http://stackoverflow.com/questions/4043307/why-this-regex-is-not-working-for-german-words">stackoverflow
+     * "https://stackoverflow.com/questions/4043307/why-this-regex-is-not-working-for-german-words">stackoverflow
      * question </a>
      */
     protected static final String RE_W = "\\w\\u00C0-\\u024f";

core/core-entity/src/main/java/ch/difty/scipamato/core/entity/Paper.java

@@ -105,8 +105,8 @@ public class Paper extends IdScipamatoEntity<Long> implements CodeBoxAware, News
      * referenced below:
      *
      * @see <a href=
-     *     "http://blog.crossref.org/2015/08/doi-regular-expressions.html">
-     *     http://blog.crossref.org/2015/08/doi-regular-expressions.html</a>
+     *     "https://www.crossref.org/blog/dois-and-matching-regular-expressions/">
+     *     https://www.crossref.org/blog/dois-and-matching-regular-expressions/</a>
      */
     private static final String DOI_REGEX = "^10\\.\\d{4,9}/[-._;()/:A-Z0-9]+$";
 
@@ -169,7 +169,7 @@ public String getFieldName() {
     private Long number;
 
     /**
-     * Digital Object Identifier (see http://www.doi.org)
+     * Digital Object Identifier (see https://www.doi.org)
      * <p>
      * /^10.\d{4,9}/[-._;()/:A-Z0-9]+$/i
      */

core/core-persistence-jooq/src/integration-test/kotlin/ch/difty/scipamato/core/persistence/TestApplication.kt

@@ -33,7 +33,7 @@ open class TestApplication {
             override fun getDefaultLocalization() = "de"
             override fun getBrand() = "scipamato"
             override fun getTitleOrBrand() = brand
-            override fun getPubmedBaseUrl() = "http://pubmed/"
+            override fun getPubmedBaseUrl() = "https://pubmed/"
             override fun getCmsUrlSearchPage() = "http://localhost/paper/number"
             override fun getRedirectFromPort() = 8080
             override fun getMultiSelectBoxActionBoxWithMoreEntriesThan() = 4

core/core-persistence-jooq/src/main/java/ch/difty/scipamato/core/persistence/ConditionalSupplier.java

@@ -28,9 +28,9 @@
  * @see <a href=
  *     "https://gist.github.com/ggalmazor/93bdcf8b124304a19266#file-gistfile1-java">https://gist.github.com/ggalmazor/93bdcf8b124304a19266#file-gistfile1-java</a>
  * @see <a href=
- *     "http://www.programania.net/diseno-de-software/functional-trick-to-compose-conditions-in-jooq/">http://www.programania.net/diseno-de-software/functional-trick-to-compose-conditions-in-jooq/</a>
+ *     "https://www.programania.net/diseno-de-software/functional-trick-to-compose-conditions-in-jooq/">https://www.programania.net/diseno-de-software/functional-trick-to-compose-conditions-in-jooq/</a>
  * @see <a href=
- *     "http://stackoverflow.com/questions/19803058/java-8-stream-getting-head-and-tail">http://stackoverflow.com/questions/19803058/java-8-stream-getting-head-and-tail</a>
+ *     "https://stackoverflow.com/questions/19803058/java-8-stream-getting-head-and-tail">https://stackoverflow.com/questions/19803058/java-8-stream-getting-head-and-tail</a>
  */
 @SuppressWarnings("SpellCheckingInspection")
 public class ConditionalSupplier {
@@ -93,4 +93,4 @@ private static <T> Tuple2<Optional<T>, Seq<T>> splitAtHead(final Stream<T> strea
         final Iterator<T> it = stream.iterator();
         return Tuple.tuple(it.hasNext() ? Optional.of(it.next()) : Optional.empty(), Seq.seq(it));
     }
-}
+}

core/core-pubmed-api/src/main/resources/pubmed_180101.dtd

@@ -3,7 +3,7 @@
 2017-10-06
 
 This DTD supports both the E-utilities and ftp service data dissemination methods. 
-It is based on http://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd
+It is based on https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_170101.dtd
 
 Additions/Changes since 170101 DTD: 
 

core/core-sync/src/intTestDisabled/java/ch/difty/scipamato/core/sync/jobs/newstudypagelink/NewStudyPageLinkItemWriterIntegrationTest.java

@@ -20,7 +20,7 @@ class NewStudyPageLinkItemWriterIntegrationTest
     private static final int    SORT_EXISTING  = 1;
     private static final int    SORT_NEW       = 20;
     private static final String TITLE          = "foo";
-    private static final String URL            = "http://a.b";
+    private static final String URL            = "https://a.b";
     private static final String TITLE_EXISTING = "Web Suche";
 
     private PublicNewStudyPageLink newNewStudyPageLink, existingNewStudyPageLink;

core/core-web/src/main/java/ch/difty/scipamato/core/web/code/CodeEditHeaderPanel.html

@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!--suppress WicketForgeHtmlIdInspection, HtmlFormInputWithoutLabel -->
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <div class="row">
         <div class="col-md-6">
@@ -30,4 +30,4 @@
         </div>
     </div>
 </wicket:panel>
-</html>
+</html>

core/core-web/src/main/java/ch/difty/scipamato/core/web/code/CodeEditTranslationPanel.html

@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!--suppress WicketForgeHtmlIdInspection, HtmlFormInputWithoutLabel -->
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <div wicket:id="translations" class="row">
         <div class="col-md-6">
@@ -14,4 +14,4 @@
         </div>
     </div>
 </wicket:panel>
-</html>
+</html>

core/core-web/src/main/java/ch/difty/scipamato/core/web/code/CodeListFilterPanel.html

@@ -1,6 +1,6 @@
 <!DOCTYPE html>
 <!--suppress WicketForgeHtmlIdInspection, HtmlFormInputWithoutLabel -->
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <form wicket:id="filterForm" role="form">
         <div class="row">
@@ -22,4 +22,4 @@
         </div>
     </form>
 </wicket:panel>
-</html>
+</html>

core/core-web/src/main/java/ch/difty/scipamato/core/web/code/CodeListResultPanel.html

@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!--suppress WicketForgeHtmlIdInspection -->
-<html xmlns:wicket="http://wicket.apache.org">
+<html xmlns:wicket="https://wicket.apache.org">
 <wicket:panel>
     <table class="dataview" wicket:id="results"></table>
 </wicket:panel>
-</html>
+</html>