EDIT: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852020-04-08T09:02:40ZEDIT Project Management
Redmine feature request #8945 (Resolved): support statistical value type ExactValue (29736701-58c4-48b3-a...https://dev.e-taxonomy.eu/redmine/issues/89452020-04-08T09:02:40ZAndreas Kohlbecker
<p>Unsupported statistical value type: 29736701-58c4-48b3-a9d7-41c74140cac7</p>
<p>Should be quick to fix!!!!</p>
<p>e.g.: <a href="http://test.e-taxonomy.eu/dataportal/preview/caryophyllales_spp/cdm_dataportal/occurrence/426ed193-b652-435e-8c1b-ba84542b0b74">http://test.e-taxonomy.eu/dataportal/preview/caryophyllales_spp/cdm_dataportal/occurrence/426ed193-b652-435e-8c1b-ba84542b0b74</a></p>
bug #8848 (Feedback): Search fails with low data rate network (64kbit/s) network connection due ...https://dev.e-taxonomy.eu/redmine/issues/88482020-02-14T11:46:46ZAndreas Kohlbecker
<p>During testing the taxeditor with low data rate network conditions <a href="see #8812" class="external">64kbit/s</a>, the search fails, since the authentication is missing. The server responds with HTTP status 401.</p>
<p>Debugging revealed that the search is running in a separate thread but the <code>SecurityContextHolderStrategy</code> being used is set to <code>MODE_THREADLOCAL</code> (default). The login dialog is operating in a different thread (main thread?) so that the authentication is not accessible in the search thread.</p>
<p>Interestingly there is no problem with networks connections having a higher data rate.</p>
<p>As solution I suggest to switch to <code>SecurityContextHolder.MODE_GLOBAL</code>, this anyway is the correct strategy for an desktop client application.</p>
bug #8842 (Resolved): CdmServiceRequestExecutor is not stateleass and neither thread save nor acc...https://dev.e-taxonomy.eu/redmine/issues/88422020-02-04T12:59:53ZAndreas Kohlbecker
<p>CdmServiceRequestExecutor uses the field </p>
<pre><code class="java syntaxhl"><span class="kd">private</span> <span class="nc">RemoteInvocation</span> <span class="n">currentRemoteInvocation</span><span class="o">;</span>
</code></pre>
<p>to remember the invocation between the step of serializing the request data and of sending the request in the method <code>AbstractHttpInvokerRequestExecutor.executeRequest(HttpInvokerClientConfiguration config, RemoteInvocation invocation)</code><br>
This method is final and thus can not be overwritten. As workaround <code>currentRemoteInvocation</code> has apparently been introduced in <code>CdmServiceRequestExecutor</code>. This fields, however, causes this bean to be no longer stateless.<br>
Concurrent access from multiple threads can cause things to get mixed up. As consequence cdm entities could be stored in the wrong "session"-cache and the application could miss finding entities in the cache causing them to be loaded twice. <strong>This second situation can be a root cause for MultipleRepresentationExceptions</strong> </p>
bug #8832 (Resolved): Choosing the area for distribution in details view clears the selected statushttps://dev.e-taxonomy.eu/redmine/issues/88322020-01-27T13:31:29ZKatja Luther
<p>When selecting the area for a distribution and the status is already choosen, the status is cleared again. </p>
bug #8812 (Resolved): Connection losses in taxeditor HTTP invoker (RemoteAccessException: Could n...https://dev.e-taxonomy.eu/redmine/issues/88122020-01-16T14:52:18ZAndreas Kohlbecker
<p>A couple of situations exist in which users report problems due to RemoteAccessExceptions ("Could not access HTTP invoker remote service at ...).</p>
<ol>
<li>First of all there is a correlation of these incidents with the network latency. Network latencies > 50ms already seems to be causing problems and connection loss. This has been reported by Katja. The connections to the US are having a much bigger latency (<a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1791">AW_Netzwerklatenzen nach Übersee.mbox</a>)</li>
<li>Connections going through the ZEDAT-VPN seem to be compromised by packet loss (<a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1792">AW_AW_Interessant_Could not access HTTP invoker remote service at .... bei lokalem server.mbox</a>)
<ul>
<li>measuring the packet loss with wireshark shows a packet loss ratio of ~1% ==> Packet loss is not unusual in this case as the VPN access point may choose to drop packages to reduce the throughput for individual clients and connections. This is how rate limiting commonly is realized. </li>
</ul></li>
<li>It seems as if computation intensive and thus long running operations are increasing the risk for the occurrence of these incidents (see <strong>frequently affected operations</strong> below)</li>
</ol>
<a name="Useful-links"></a>
<h3 >Useful links:<a href="#Useful-links" class="wiki-anchor">¶</a></h3>
<ul>
<li><a href="https://www.eclipse.org/jetty/documentation/current/configuring-connectors.html" class="external">Jetty HTTP Connectors</a></li>
</ul>
<a name="frequently-affected-operations"></a>
<h3 >frequently affected operations<a href="#frequently-affected-operations" class="wiki-anchor">¶</a></h3>
<p><strong>Deduplication</strong></p>
<pre>Hallo,
diesmal der Fehler schon bei der Deduplizierung von nur 2 Einträgen (noch von zuhause).
Herzlichen Gruß
Walter
login : w.berendsohn
editor version : 5.11.0
server : api.cybertaxonomy.org (cybertaxonomy.org) / caryophyllales_spp
schema version : 5.11.2.0.20191109
os : Windows 10 10.0 amd64
java : 1.8.0_221
</pre>
<p><strong>Taxon Navigator > Link to Taxon option</strong></p>
<p>Dear Maryam,</p>
<p>please excuse the late reply – our entire university is closed until 5th of January.</p>
<p>I know that the “link with taxon” option is very important especially for you, because while sorting out the imported data you move around in the taxon tree quite a bit. I guess this is indeed a question related to your connection – this function is a rather complicated one, requiring some network traffic.</p>
<p>However, I had similar difficulties in general working with the editor from the US using a weak connection in November – is the “link” function the only problem you face? I think some measures have already been taken to remedy the problems I had. In addition, I understand that a new release is forthcoming in January that may incorporate measures to tackle your problem.</p>
<p>Please don’t hesitate to contact me if you need assistance with any other problems (also with respect to nomenclature etc.). Any progress on the paper?</p>
<p>Best wishes</p>
<p>Walter</p>
<p>From: Maryam malekmohammady <a href="mailto:maryam.malekmohammady@gmail.com">maryam.malekmohammady@gmail.com</a> <br>
Sent: 13 January 2020 23:01<br>
To: VL-BGBM-EditSupport <a href="mailto:EditSupport@BGBM.ORG">EditSupport@BGBM.ORG</a><br>
Cc: Berendsohn, Walter <a href="mailto:W.Berendsohn@bgbm.org">W.Berendsohn@bgbm.org</a><br>
Subject: error</p>
<p>Dear all,</p>
<p>It is a while that "link with taxon" option does not work and I receive this copied error.</p>
<p>My internet is slow and may be it causes this problem.</p>
<p>I also have another problem" when link with taxon option is on and I move a taxon as a synonym to another taxon I have to reopen the classification using the triangle beside Caryophyllales.</p>
<p>I received this error while trying to find Limonium latifolium var. album.</p>
<p>regards<br>
Maryam</p>
<pre>
login : m.malekmohammadi
editor version : 5.11.0
server : api.cybertaxonomy.org (cybertaxonomy.org) / caryophyllales_spp
schema version : 5.11.2.0.20191109
os : Windows 7 6.1 amd64
java : 1.8.0_231
org.eclipse.e4.core.di.InjectionException: org.springframework.remoting.RemoteAccessException: Could not access HTTP invoker remote service at [http://api.cybertaxonomy.org:80/caryophyllales_spp/remoting/taxonnode.service]; nested exception is java.lang.NullPointerException
</pre>
<a name="Simulating-network-latency-and-package-loss"></a>
<h2 >Simulating network latency and package loss<a href="#Simulating-network-latency-and-package-loss" class="wiki-anchor">¶</a></h2>
<ul>
<li><a href="https://wiki.linuxfoundation.org/networking/netem">https://wiki.linuxfoundation.org/networking/netem</a></li>
<li><a href="https://stackoverflow.com/questions/614795/simulate-delayed-and-dropped-packets-on-linux#615757">https://stackoverflow.com/questions/614795/simulate-delayed-and-dropped-packets-on-linux#615757</a></li>
<li><a href="https://unix.stackexchange.com/questions/432925/netem-how-to-delay-packets-sent-to-received-from-some-host#434453" class="external">Netem - how to delay packets sent to/received from some host</a></li>
</ul>
<p>I created a script which simplifies the application of various <code>netem</code> setting to simulate bad network conditions like packet delay, loss and low data transfer rate: <a href="https://gist.github.com/akohlbecker/8bd4b615dceefd3507a85010729fa2b4" class="external">https://gist.github.com/akohlbecker/network-condition-simulator.sh</a></p>
<p>For pure local testing you can start the cdm-server in a docker container and apply the settings to the according network bridge. To find the according interface device check the list of docker networks:</p>
<pre>docker network ls
NETWORK ID NAME DRIVER SCOPE
b7a585babf7f bridge bridge local
fb231843f4b4 caryophyllales_spp_default bridge local
a4b391fdf54d host host local
adf250e35cb8 none null local
6b2b9489586d phycobank_default bridge local
</pre>
<p>In the above example <code>caryophyllales_spp</code> is the name of the container to be used for testing, so the network id is <code>fb231843f4b4</code>. With this information we know that th network bridge should be <code>br-fb231843f4b4</code> which can be proven with <code>ifconfig</code></p>
<a name="Problems-found"></a>
<h3 >Problems found<a href="#Problems-found" class="wiki-anchor">¶</a></h3>
<p>1.</p>
<p>When simulating low bandwidth, 64kbit/s, <code>org.apache.http.NoHttpResponseException .... failed to respond</code> can be observed. This is casued by the server which may refude waiting any longer for packts from the client, the server may close the connection in this case. Usually the http client should be able to detect stale connections, a bug in HttpClient 4.4 is known which causes this Exception (to fail in <a href="https://stackoverflow.com/questions/10558791/apache-httpclient-interim-error-nohttpresponseexception#10600762">https://stackoverflow.com/questions/10558791/apache-httpclient-interim-error-nohttpresponseexception#10600762</a>) --> <strong>TODO</strong> Upgrade httpclient to the latest version.</p>
bug #8562 (Feedback): Remaining issues for preference pageshttps://dev.e-taxonomy.eu/redmine/issues/85622019-09-20T09:14:32ZKatja Luther
<ul>
<li>Menu Labels:<br>
<ul>
<li><del>Multi-Language Support => Application</del></li>
<li>Available Languages => <del>Multi-Language Support + move checkbox of previous Multi-Language Support to this page</del></li>
<li><del>Common Names => Common Name Languages (and/or, if it's too long change the label of the page to "Common Name Languages"</del></li>
</ul></li>
<li><del>General: move „Show Taxonnode Wizard“ to UI->TaxonNavigator</del></li>
<li><del>Supplemental Data: Sources should be moved or cloned to be a sub page of UI because it is only an UI issue, same for „Show UUID and object ID in suppl. Data view“</del></li>
<li>Features: We also need Specimen Features or Occurrence Features. There is a library ticket for the vocabulary issue already. -> as long as there are no specimen features we postpone this issue. </li>
<li><del>Import/Export: An own io menu item for Abcd and other potential io configurator pages</del>
<ul>
<li>maybe Import and Export should be two pages</li>
</ul></li>
<li><del>The general io page should contain the „Show Export/Import Menu“ of the actual „General“ page.-> this preference should also cloned to UI/Navigator</del></li>
<li>area specific status preferences for local preferences -> <a class="issue tracker-5 status-1 priority-10 priority-lowest" title="feature request: Implement preferences with predicate and subject in local preferences (New)" href="https://dev.e-taxonomy.eu/redmine/issues/8309">#8309</a> </li>
<li><del>menu syncronisation distribution prefs local/db side</del>
<ul>
<li><del>discuss where to move the distribution issues: everything belonging to distribution editor -> UI but status/vocabulary selection -> data</del></li>
</ul></li>
<li><del>on local pref distribution status page the selection button is not disabled if db pref does not allow override.</del>
<ul>
<li><del>for the default pref it should be visible whether override is allowed or not</del></li>
</ul></li>
</ul>
<p>====</p>
<p>New issues to be collected at: <a class="issue tracker-4 status-1 priority-11 priority-default" title="bug: New issues for preference pages (New)" href="https://dev.e-taxonomy.eu/redmine/issues/8887">#8887</a></p>