Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-06T02:52:36ZEcoinformatics Redmine
Redmine Kepler - Bug #4767 (Resolved): error instantiating actor with port types from KARhttps://projects.ecoinformatics.org/ecoinfo/issues/47672010-02-06T02:52:36ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an Expression actor, give it an input port of type boolean, save it as a KAR into a local repository, then try and drag it onto the canvas. I get an error:</p>
<p>ptolemy.kernel.util.IllegalActionException: TypeAttribute can only be contained by instances of TypedIOPort.<br /> in .Expression.kepler:input and ._type</p> Metacat - Bug #4651 (Resolved): data packages losing data tables (and then finding them again)https://projects.ecoinformatics.org/ecoinfo/issues/46512010-01-07T21:46:52ZOliver Soongsoong@nceas.ucsb.edu
<p>This is on the dev server. I created soong.4 for the Kruger TPCs. soong.4.14 references four data tables containing zipped spatial data, soong.3.1, soong.5.1, soong.10.1, and soong.12.1. A month or so ago, those four data tables seemed to have been lost, and attempts to access them through both Kepler and the web returned file not found XML errors. I left soong.4 alone for daigle to take a look at and created a copy soong.28.5 for me to use. Today, soong.28.5 had the same problem, and the four tables it references, soong.29.2, soong.30.2, soong.31.2, and soong.33.2, are all missing and return file not found XML errors. At the same time, soong.4.14 works again, and soong.3.1, soong.5.1, soong.10.1, and soong.12.1 all exist again.</p> Kepler - Bug #4633 (Resolved): LSID conflictshttps://projects.ecoinformatics.org/ecoinfo/issues/46332009-12-15T01:04:31ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a KAR (KAR2). The LSID bumps as expected. Close the workflow and open KAR1. Make a different change (so it's obviously not the workflow in KAR2) and save the KAR (KAR3). Notice that when the workflow reopens, it looks like KAR2 because it is KAR2 down to the MOML in KAR3.</p>
<p>I'm observing this at r22183 right now.</p> Morpho - Bug #4625 (Resolved): authenticate against KNB, switch source to DEV, and still have accesshttps://projects.ecoinformatics.org/ecoinfo/issues/46252009-12-11T02:07:26ZOliver Soongsoong@nceas.ucsb.edu
<p>I have packages that exist on DEV but not KNB. I start Morpho r4682 with KNB set as the metacat source and authenticate. I can confirm my packages are not on KNB. I then switch the metacat source to dev and open the package list and can see my packages. I can export the packages and extract the data. There was no re-authentication.</p> Morpho - Bug #4624 (New): local/network status icons sometimes (inconsistently) incorrecthttps://projects.ecoinformatics.org/ecoinfo/issues/46242009-12-11T01:44:18ZOliver Soongsoong@nceas.ucsb.edu
<p>A package that only exists remotely gets a network icon but no local icon. After a sync from remote->local, some packages get a local icon but no network icon. If I delete the local copy and close and re-open the package listing (forcing refresh), I see the correct network-only status icon. What's really odd is this happens inconsistently. It will happen to a package.revision consistently, but it may not happen to package.revision+1 or to a different package.</p> Morpho - Bug #4623 (Resolved): docid conflict box needs a button or somethinghttps://projects.ecoinformatics.org/ecoinfo/issues/46232009-12-11T01:26:10ZOliver Soongsoong@nceas.ucsb.edu
<p>I created a package (.1 revision), synced local->remote (.2 revision?), then edited the local EML to produce a docid conflict (another .2 revision). When trying to sync local->remote, a message pops up about a docid conflict and asks how I want to resolve this. There's a radio selector but no "Ok" button or anything like that. The only option is to close the dialog window with the X in the upper right corner, which isn't exactly intuitive. It seems to function properly, though.</p> Morpho - Bug #4622 (Resolved): local copies of zip "data tables" corrupthttps://projects.ecoinformatics.org/ecoinfo/issues/46222009-12-11T00:52:21ZOliver Soongsoong@nceas.ucsb.edu
<p>The example is soong.37.2 on the dev metacat (search for soong). The data package contains zip files as "data tables". The zip files are intact in the cache folder (can be expanded). After syncing remote->local, the zip files in the data folder are corrupt (contents can be listed but not expanded).</p> Metacat - Bug #4612 (Rejected): EML file content out of sync with metacathttps://projects.ecoinformatics.org/ecoinfo/issues/46122009-12-09T00:46:47ZOliver Soongsoong@nceas.ucsb.edu
<p>This is on dev.nceas.ucsb.edu. Search for soong_test. There should be 2 entries for "soong_test 1". One has ID soong_test.3.2 and the other has ID doc.1260314433875.1. Open doc.1260314433875.1 and look at the EML, which should be for soong_test.3.3.</p>
<p>I was testing the ecogrid writer actor in Kepler. I may not have been doing things correctly.</p> Metacat - Bug #4611 (New): searching for soong_test seems to return entries with "soong test" as ...https://projects.ecoinformatics.org/ecoinfo/issues/46112009-12-09T00:31:35ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not sure if this is a "feature" or not. It surprised me. Searching for "soong test" only returns the expected entries, but soong_test returns more than expected.</p> Metacat - Bug #4610 (New): trying to register a dataset when logged in asks for another authentic...https://projects.ecoinformatics.org/ecoinfo/issues/46102009-12-09T00:28:09ZOliver Soongsoong@nceas.ucsb.edu
<p>I log into KNB, then go to Register your dataset online, and it says I must register. The register dataset page seems to be ignoring the existing credentials.</p> Metacat - Bug #4609 (New): when viewed with saved credentials, KNB homepage shows blank entrieshttps://projects.ecoinformatics.org/ecoinfo/issues/46092009-12-09T00:23:12ZOliver Soongsoong@nceas.ucsb.edu
<p>I sign into the KNB, then close the window (but not the browser). The cookie persists, so when I go back to the KNB home page, it picks up the saved credentials from earlier. However, the login space shows no entries (blank username and password, -- choose one -- for the organization), so I can't be sure who I'm logged in as.</p>
<p>This also happens with dev.nceas.ucsb.edu.</p> Morpho - Bug #4461 (New): delete local copy only deletes the most recent stored revision, but thi...https://projects.ecoinformatics.org/ecoinfo/issues/44612009-10-15T18:48:02ZOliver Soongsoong@nceas.ucsb.edu
<p>When deleting a package in the package listing, the current behavior is to delete only the most recent stored copy. However, it just says "Delete". This is particularly confusing when compounded with the fact that after deleting, the entry disappears from the package listing entirely even though earlier copies exist. Only after closing the package listing and reopening it can the user see the previous revision.</p>
<p>A relatively simple fix would be to change Delete to Delete Most Recent Copy. It might also help for users who do want to get rid of an entire package to have a Delete Package entry. It might also help to have the package list refresh after the delete.</p> Morpho - Bug #4460 (New): morpho package listing can be confusing when out of synchttps://projects.ecoinformatics.org/ecoinfo/issues/44602009-10-15T18:43:32ZOliver Soongsoong@nceas.ucsb.edu
<p>This is a UI and clarity issue. Morpho's handling of versions is fine.</p>
<p>In the case of an old local copy and updated online copies, there is no indication in the package listing that there are old copies sitting around (the package listing shows an icon only for the remote copy and no local data). From the perspective of a sometimes offline user, it can appear that work on that old local copy has disappeared.</p>
<p>Similarly, a user who has an old local copy, but signs in and looks at the package listing might be led to believe there is no local data. When that user looks at the package listing offline, it might be surprising to see a local copy. There is also no indication that the data is out of date, even though the (possibly stale) cache might actually contain enough information to flag the local copy as out of date.</p>
<p>Adding something simple like a "stale local copies" icon would help clear this up, instead of using the same blank indication for no local data and local data out of date.</p> Metacat - Bug #4301 (New): sessionid in the URL creates end-user difficultyhttps://projects.ecoinformatics.org/ecoinfo/issues/43012009-08-10T22:34:04ZOliver Soongsoong@nceas.ucsb.edu
<p>Using a plain URL, one cannot access datasets that require authentication. Alternatively, a link of the form <a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=judithk.594">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&docid=judithk.594</a> will function properly when authenticated, although this form is not actually presented in metacat. However, attempting to view the metadata for any of the included data tables will insert a &sessionid= with no value, which causes an error as I think this overrides the (correctly authenticated) value that would otherwise have been passed.</p>
<p>Perversely enough, at the top of any data package is a printed URL of the form <a class="external" href="http://knb.ecoinformatics.org/knb/metacat/judithk.594.26/knb">http://knb.ecoinformatics.org/knb/metacat/judithk.594.26/knb</a>, even though the actual link is <a class="external" href="http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&sessionid=________________________________&docid=judithk.594.26">http://knb.ecoinformatics.org/knb/metacat?action=read&qformat=knb&sessionid=________________________________&docid=judithk.594.26</a> with the actual sessionid embedded in the URL. I think it would be safer and more robust if that sessionid were not explicitly inserted anywhere. From what I recall and have been told, everything should function as intended by simply removing the sessionid from the various URLs.</p> Metacat - Bug #4130 (Resolved): data tables in KNB display dataTable->physical->objectNamehttps://projects.ecoinformatics.org/ecoinfo/issues/41302009-06-08T18:56:18ZOliver Soongsoong@nceas.ucsb.edu
<p>KNB names data tables according to the objectName element within the physical element. By contrast, Kepler's EML 2 Dataset actor displays the entityName. This is mostly confusing for a few dataTables for which the entityName is not the same as the objectName. For example look at judithk.609.27, entityName=Dailyrainl2005.txt and objectName=rainfall2005.txt. I'm not sure which what the best way to handle this is, but it seems more intuitive to refer to the dataTable by the entityName rather than the objectName of the physical container.</p>