Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-09-19T22:12:03ZEcoinformatics Redmine
Redmine VegBank - Bug #5493 (In Progress): tomcat crashes frequentlyhttps://projects.ecoinformatics.org/ecoinfo/issues/54932011-09-19T22:12:03ZNick Brandbrand@nceas.ucsb.edu
<p>Tomcat frequently gets into a state where it stops serving pages and needs to be restarted. This has been happening for a while now, first on the RHEL4 server (vegbank), and now on the new Ubuntu 10.04 virtual server (vegbankvm).</p>
<p>Most recently the tomcat service has been manually restarted on 7/30, 8/19, 8/21, 8/27, and 9/19.</p>
<p>I attempted to stop the frequent crashing by increasing the allocated memory in tomcat from 2GB to 4GB, but it crashed a couple days after the change, so I restored the 2GB setting.</p> VegBank - Bug #5478 (New): after querying plants, communities, or plots, link back to searchhttps://projects.ecoinformatics.org/ecoinfo/issues/54782011-08-30T01:28:18ZMichael Leemlee@nceas.ucsb.edu
<p>When searching for something, web sites often want you to be able to modify your search terms easily and search again. We should do that. Now, you have to use the back button.</p>
<p>Seems like we could include part of the search page (fancy option) or at least offer a backlink to it, with the form filled out, ideally.</p> VegBank - Bug #5391 (New): build process into war file does not generate faq.htmlhttps://projects.ecoinformatics.org/ecoinfo/issues/53912011-05-04T20:38:40ZMichael Leemlee@nceas.ucsb.edu
<p>the initial build process that generated the war file did not generate a faq.html file in web/general. This is handled in web/build.xml and needs to be called.</p> InfoVeg - Bug #5388 (New): Migrate CF projects to Archive DBhttps://projects.ecoinformatics.org/ecoinfo/issues/53882011-04-29T16:00:04ZForbes Boylemboyle@unc.edu
<p>CF projects need to be QC'd and migrated.</p> InfoVeg - Bug #5384 (New): Collections spreadsheets verificationhttps://projects.ecoinformatics.org/ecoinfo/issues/53842011-04-29T15:40:29ZForbes Boylemboyle@unc.edu
<p>We want to be able to browse for a collection spreadsheet and determine what percentage of the updated specimens are integrated into the Analysis DB.</p> InfoVeg - Bug #5383 (New): Updating GUIDs for taxon observationshttps://projects.ecoinformatics.org/ecoinfo/issues/53832011-04-29T15:38:56ZForbes Boylemboyle@unc.edu
<p>This will allow better annotation and updating of our taxa, says MLee. Will also help upgrade to Weakley 2010.</p> VegBank - Bug #5211 (New): Colorado data not entered correctlyhttps://projects.ecoinformatics.org/ecoinfo/issues/52112010-10-20T13:17:10ZMichael Leemlee@nceas.ucsb.edu
<p>The taxonomy was not updated as originally requested, there are some problems with the cover values, there are some problems with the metadata, and the community names assigned are strangely rendered.</p>
<p>(from Peet email 10/20/2010)</p> InfoVeg - Bug #5159 (New): auto filter for sensitive specieshttps://projects.ecoinformatics.org/ecoinfo/issues/51592010-08-21T21:36:13ZMichael Leemlee@nceas.ucsb.edu
<p>Today (Sept 3, 2009), Alan and I [Michael] had a productive conversation about how and for<br />which species we should fuzz plot locations. I described our current<br />approach, which rounds plot locations to the nearest 0.01 degree for<br />Lat and Long to approximate a 1km fuzzing, 0.1 degree for 10km fuzzing<br />and 1 degree for 100km fuzzing. Alan asked a great question as to<br />what radius this resulted in. It yields the centroid of a 0.01, 0.1,<br />or 1 degree box, which amounts to a DIAMETER of a little less than the<br />1km, 10km, and 100km.</p>
<p>I ran a quick algorithm for all plots in our database and found that<br />if we say we are fuzzing 100 km (1 degree), the average distance from<br />those points to our plots is 34.7km. If we are trying for 10km (0.1<br />deg), we get 3.7km. If we try to 1km (0.01 deg), we get 380m. We<br />would expect a smaller number than what we are aiming for, but clearly<br />these are a bit low.</p>
<p>So we probably should either round to the nearest 0.02, 0.2, and 2<br />degree boxes, or actually write an algorithm that will pick a point at<br />random within the specified radius. I don't think that should be too<br />hard.</p>
<p>Next, and the key item, Alan said that he didn't think all rare<br />species should be fuzzed. There are plenty that have no economical<br />value, are not of interest to poachers, and are difficult to get to in<br />any case. He said that the key ones to block are Panax, some orchids,<br />some lillies, carniverous species except Utricularia. I'm probably<br />missing some. Also we need to fuzz locations for all bogs plots given<br />the possible existence of bog turtles there, though those don't turn<br />up in our data. I have fuzzed all of Brenda's bog plots in project 73<br />already in the community summary pages. Alan said he could come up<br />with a list of species for us without taking too much effort, as well<br />as an appropriate fuzzing. He expressed a desire to fuzz more than<br />10km but less than 100km, which we might want to consider, as well.</p> InfoVeg - Bug #5105 (In Progress): have x- specimens maphttps://projects.ecoinformatics.org/ecoinfo/issues/51052010-07-28T17:36:55ZMichael Leemlee@nceas.ucsb.edu
<p>example X-UNCC, X-WNC, etc.</p>
<p>reported by Carol Ann</p> VegBank - Bug #4796 (New): receipt of plots with accession codes after loadinghttps://projects.ecoinformatics.org/ecoinfo/issues/47962010-02-16T16:49:37ZMichael Leemlee@nceas.ucsb.edu
<p>Don says: Would it be possible in the future, that whenever someone uploaded their data into VegBank, they could somehow be sent a table of their own plot codes and the VegBank accession code?</p>
<p>Michael: we could certainly add this to the receipt.</p> VegBank - Bug #4502 (New): standardized online data entry form for plotshttps://projects.ecoinformatics.org/ecoinfo/issues/45022009-10-22T19:17:19ZMichael Leemlee@nceas.ucsb.edu
<p>This is vastly complex and difficult to assure that data are complete and things like network interruptions don't cause lost data. I think this is a poor use of time and will under the best circumstances result in poor data entry interface.</p>
<p>Source is section 2.6.2 number 9 of requirements document, page 60</p> VegBank - Bug #4501 (New): map fields and upload data into the NVC Plot DBhttps://projects.ecoinformatics.org/ecoinfo/issues/45012009-10-22T19:17:09ZMichael Leemlee@nceas.ucsb.edu
<p>I have no idea how wide in scope this is. Without knowing something about the incoming data, it's impossible to start programming. This is very vauge. I think time would be better spent getting standard formats like VEGX working. We could also add TurboVeg or other specific formats, but other undefined formats can use VegBranch</p>
<p>Source is section 2.6.2 number 10 of requirements document, page 64</p> VegBank - Bug #4500 (New): Implement a shared login between NVCRS and VegBankhttps://projects.ecoinformatics.org/ecoinfo/issues/45002009-10-22T19:17:01ZMichael Leemlee@nceas.ucsb.edu
<p>This is more complex than it seems and requires simultaneous coding on VegBank and NVCRS to accomodate. Questions:<br />1) when a user registers on NVCRS, do they register on VegBank simultaneously? <br /> a) What if they are already on VegBank? <br /> b) Provide a check box to also register on VegBank? <br /> c) Can two accounts be ''linked'' based on the same email address? What if someone registers with an alias on one system, but not the other? (e.g. <a class="email" href="mailto:jane_user@email.unc.edu">jane_user@email.unc.edu</a> vs. <a class="email" href="mailto:J_User@unc.edu">J_User@unc.edu</a>)<br />2) When a user updates his/her password, do both systems get updated? - security implications here<br />3) When a user logs into VegBank, does s/he get logged in to NVCRS automatically? or checkbox?<br />4) When a user logs into NVCRS, does s/he get logged into VegBank automically? Or checkbox to ''Also login to VegBank?''<br />5) The real can of worms: What about other fully compliant databases? Are we going to add these, too?</p>
<p>Source is section 2.1.3 number 12 of requirements document, page 16</p> VegBank - Bug #4499 (New): Refresh VegBank from Public DBhttps://projects.ecoinformatics.org/ecoinfo/issues/44992009-10-22T19:16:50ZMichael Leemlee@nceas.ucsb.edu
<p>We will need to have VegBank query the NVCRS to get a list of updates. We need to define the scope of what's getting updated. Presumably, this means new community types, as well as their status, old types and new statuses, correlations of communities, and plot annotations to communities. Should not include plot data.</p>
<p>Source is section 2.3.5 number 21 of requirements document, page 48</p> VegBank - Bug #4498 (New): Provide raw data for summary tables in distributed queryhttps://projects.ecoinformatics.org/ecoinfo/issues/44982009-10-22T19:16:43ZMichael Leemlee@nceas.ucsb.edu
<p>VegBank will need to provide raw data for summary table of plots to be aggregated into a summary for plots from multiple databases.</p>
<p>Source is section 2.6.10 number 42 of requirements document, page 77</p>