Apr. 22, 2015:

• Meet at 2pm, location TBA
• Tae Woo: finished with finals, done with coursework!! w00t! Fixed some bugs with GreenFIE-HD: some offsets were 0-based instead of 1-based and vice versa. Still more bugs to work on, but it's coming.
• Christopher: spoke with Justin (parents both Tawainese, is a Taiwan RM) vis a vis Jiapu project; Justin will finish 240 during Summer Term; finished finals; fixed gray background problem; strange problem with hover handler (stopped working for some reason), but it's fixed by changing it to mouse-enter/mouse-leave events; fixed another strange issue with highlighting that he fixed
• Dr. Embley: convert-to-GedcomX program now works; it will need some refactoring, but not quite yet; has bounding-box success! Currently working on cross-tool integration; has found an off-by-one error in the OSMX document coming from somewhere upstream in the tool chain. There will be a host of other issues. Blocker: resource URL is not being passed downstream.
• Dr. Liddle: wrote final, gave finals, graded finals (still reconciling, wrapping up grading); Jenkins is working properly
• Dr. Woodfield: has been working on the build; is beginning to use the wrappers; other program runs fine; needs a large data set to be able to generate soft-constraint distributions (Dr. Embley will check on whether we can get this data)
• Sidebars:
  • Demo COMET updates
  • Tool chain inconsistencies/issues
  • Woodfield's build
  • Directory structure adjustments (Liddle/Embley)
  • Liddle/Almquist tomorrow at 10am (communicating with ListReader)

Apr. 15, 2015:

• Happy tax day, everyone!
• Tae Woo: was busy with finals, but worked on OSMX to JSON project a bit; tried to update Alpha and had a failure.
• Dr. Packer: looked at the test failures in the one file, and was able to resolve the test case that seemed most important; will check in before end of day; needs to debug Dr. E's installation of ListReader
• Christopher: given ListReader's input, should be able to populate the fields now; annotation is working; send seems to be okay, now needs to integrate with backend service; now gets text from offsets (so ListReader doesn't have to supply text); this only works on the PDF document type; reduced PDF image growth rate so it doesn't jump too much; having trouble diagnosing the gray background-on-hover issue; there is a cosmetic issue with ListReader training
• Dr. Embley: got thin line finished with end-to-end tool; working on thick line; getting ready for big presentation
• Dr. Liddle: did a ton more refactoring, especially on OntologyEditor, but all throughout the Alpha project; worked with Dr. Embley on a number of programming issues
• Sidebars:
  • Alpha update with Tae Woo
  • Find issue with gray backgrounds; see ListReader cosmetic training issue
  • Offline: Liddle/Almquist should meet on backend ListReader integration (Christopher will schedule separately with Dr. Liddle)
  • Liddle/Embley look at OntoSoar on Linux

Apr. 8, 2015: Starting April 28, DEG meetings will be Tuesdays at 2pm.

• Tae Woo: busy with class projects this week; learned about “expected value”, precision/recall, and thinks perhaps this could help with his project
• Dr. Packer: building Alpha as we speak; has Netbeans 8; will look at test-case errors next time
• Christopher: lots of class projects this week; found a way to populate form, but getting empty string when sending it back
• Dr. Woodfield: spent a lot of time learning the Ontology Workbench; needs to learn more about Netbeans now
• Dr. Embley: thin thread works all the way through: extraction from page to GedcomX!
• Dr. Liddle: lots of time refactoring; lots of time with other DEG members
• Dr. Lonsdale: made progress with OntoSoar, and now has committed; got locations working and can associate them with different types of life events; has christening and other events in new ontology working; still left: multiple-word locations (e.g. “Salt Lake City”) and 4-ary relationships; will be gone the next four weeks
• Sidebars:
  • Liddle/Kim: Netbeans 8 and Java 8
  • Woodfield/Liddle: wrappers-consuming project setup
  • Liddle/Embley: keep Reema's stuff??
  • Liddle/Embley: access to file assets while running on dithers (server) instead of workstation

Apr. 1, 2015:

• Dr. Packer: working with Dr. Embley on ListReader
• Christopher: added “Execute ListReader” button to UI; working on train ListReader and populate form
• Dr. Woodfield: got Netbeans running with JDK 8; unable to get into Jenkins
• Dr. Embley: quarterly goal for Q1 was to get a thin thread through all steps in the ensemble; hasn't quite completed the very last piece: GedcomX; Q2 goal is a full thread with all the tools (OntoSoar, ListReader, COMET, GreenFIE-HD, all producing GedcomX output)
• Dr. Liddle: worked with Drs. Embley and Lonsdale quite a bit; did a ton of refactoring work
• Dr. Lonsdale: finally got Maven, Soar, Ontos, and Netbeans all playing nicely with each other [next week is last Wednesday he'll be here for a while – getting back in town May 6]
• Tae Woo: made progress on programming GreenFIE-HD; calculating precision and recall (working on some bugs still); has some recovery issues right now
• Sidebars:
  • ListReader test cases for Java 8 (Liddle, Packer) – AStar code no longer is relevant – likewise CRF; likely need to work on HMM code: see rev. 5865, 5866
  • Dr. Woodfield needs access to Jenkins (Liddle, Woodfield) – done
  • The Alpha refactor & wrappers (everyone)
  • RegEx highlighting for COMET (Embley, Almquist, Liddle)
  • User Story 4 for OntoSoar (Embley, Lonsdale, Liddle)

Mar. 25, 2015:

• Dr. Lonsdale: made some progress on Soar setup – version number was a big issue; still not to the point where we can build at-will and be fully integrated with the rest of the Alpha project tree
• Tae Woo: hasn't made much progress this week, but finished OsmxToJson so it emits correct JSON now
• Dr. Packer: has reduced DEG hours, and is spending more time with Dr. Embley to get ListReader to run on his machines
• Dr. Woodfield: decided that modifying the XSD won't be helpful; syntax checking at the XML level isn't particularly helpful; working on Netbeans install (noted Wiki instructions are old)
• Christopher: made the red delete button smaller; multiple fields turning grey doesn't have an easy solution (might be a Bootstrap issue); for populating fields with ListReader annotations, has an idea of how to get the fields, but it needs more discussion
• Dr. Embley: mounting a steep learning curve, getting into wrappers; have agreement with Randy on GedcomX interface; highlighting demo is working well
• Dr. Liddle: worked with Embley & Lonsdale on various implementation issues and the ensemble layout
• Sidebars:
  • KAE build
  • Netbeans build issues with Dr. Woodfield
  • Christopher: how to get fields from labels
  • Ensemble directory structure

Mar. 18, 2015:

• Dr. Liddle: made good progress on PDFIndexer issues (fixed bug, redid character bounding boxes to match PDFBox 2.0.0-SNAPSHOT)
• Dr. Packer: finished testing HMM with production mode scripts; worked on 3 pages of example; looking for smooth transition path
• Dr. Woodfield: looked at the object wrapper stuff, made progress understanding it; looked at long-term view of how to use the constraint checking tool; needs to figure out how to use the code
• Christopher: Got rid of hover issues and added “annoying popup” on navigation away from page; also resized the delete button
• Dr. Embley: almost fully resolved on GEDCOMX with Randy; worked with Liddle to access pages; doing lots of programming
• Dr. Lonsdale: spent too much time trying to get SOAR built properly in both Eclipse and Netbeans to no avail (will meet with Liddle on Friday)
• Tae Woo: just about finished coding for the import (needs about an hour's worth of work still); evaluator should be done within about a week after that; need to begin integration with COMET (will meet with Embley/Liddle after next week's meeting)
• Sidebars:
  • PDFIndexer changes
  • ListReader (potential complication)
  • Ensemble directory structure, URLs

Mar. 11, 2015:

• Tae Woo: has done un-nest operation, bidirectionally; need to re-nest and emit JSON
• Dr. Packer: working on text string passing between ListReader & COMET; adding text is a bit harder than previously thought
• Christopher: resource ID seems to be the best way forward – see sidebar; some bug fixes; working on 288, 299
• Dr. Woodfield: dynamic constraint checking may be difficult, and it could be lower-hanging fruit to run after saving from annotator?
• Dr. Embley: did a demo for John from PDF through FROnTIER, to COMET, merger, inferencing for gender etc., Duke to de-duplicate, final output through Peter's code to produce GEDCOMX (which isn't even close to what we want). Nearly finished mock-up of the GEDCOMX that we do want. Figured out how to get bounding boxes into it (4-corner relative or pixel-based). We could actually take our work and put it into FamilySearch.
• Dr. Liddle: helped various people with programming; progress studying web components and Polymer (interesting possibilities for us); discussed architecture of Fe6 management console thoroughly with Dr. Embley
• Dr. Lonsdale: figured out that it's not OSMXDocumentLoader causing grief, but something in the classpath settings somewhere
• Sidebars:
  • JSON being passed between COMET and ListReader (both Dr. Packer and Christopher have discussion items)
    • How important is it to have text string in what's sent to ListReader? Answer: not very. Let's punt on passing text back and forth.
    • COMET needs to know source ID or resource object, or some way to get to it; using only a path will cause half of the other things to break that depend on the full resource.
  • Hosting FamilySearch data extensions
  • Current priorities
  • Bounding boxes
  • Refactoring projects in the SVN repository (e.g. OntoSoar bound up with other modules)

Mar. 4, 2015:

• Welcome back Peter! And Liddle!
• Dr. Liddle: got some work done getting object-existence rules into the converter.
• Peter: happy about having thesis paper accepted to AAAI where it was well received.
• Dr. Lonsdale: coding frenzy - ocean = OntoSoar running on Eclipse Lunar; upgraded to Soar 9.4; got everything to build in Eclipse, also on NetBeans. Had to comment out an OSMX test in loader code. Document loader in OntoSoar has some issues with changes in the library. Needs permission to commit code to SVN repository.
• Tae Woo: busy with class projects and being sick; working on unnesting records; next up will be sorting by offset, then dealing with parent1/parent2 merge situations
• Dr. Packer: turned a version of ListReader to Christopher to play with; next up is adding text to the JSON
• Christopher: hasn't yet been able to use the new ListReader; just changed it to work with the new format; discussed using parameter instead of file with Dr. Packer; has ListReader highlighting working
• Dr. Embley: did some coding (not quite a coding frenzy, snow falling) dealing with the full line from PDF to GEDCOMX; will need to deal with jobs soon (directory structure, etc.)
• Dr. Woodfield: working on constraints, regular expressions, adding semantics
• Sidebars:
  • SVN repo access for lonz
  • Annotator2 popup on hover needs to go away
  • How to deal with bounding boxes (begin by setting up a tool that post-processes OSMX files to read bounding-box info from XML files)
  • What Dr. Embley is promising to hand over to Randy Wilson
  • ListReader: demo, also Dr. Packer & Christopher on parameter discussion

Feb. 25, 2015:

• Discussed Fe6 Architecture (quarterly goals and the current status of each in the progress reports below)
• Dr. Liddle: in Hawaii (but coded object-existence rules)
• Dr. Lonsdale: OntoSoar running under Eclipse, needs new target ontology
• Tae Woo: Coding osmx2json – import done; unnest, merge, nest, export lacking
• Dr. Packer: got passed major bug, coordinating with Christopher about transferring info back and forth
• Christopher: highlighting largely working, will turn attention to ListReader interface
• Dr. Woodfield: questions about mismatch in conceptual models
• Dr. Embley: Fe6 architecture; object-existence rules (w/ Dr. Liddle), functional for single-entry fields
• Sidebars:
  • (email) Christopher and Dr. Packer: ListReader interface via file transfer vs. parameter passing
  • (next week) bounding boxes – pass through vs. determine during FamilyTree generation
  • (next week) artifacts during highlighting (two fields with identical annotations, focus field highlighted after initial hover, multiple entry fields grey after initial hover, pencil-+-x still shows in annotator2)

Feb. 19, 2015:

• Dr. Liddle is out of town
• Discussed Luther Tychonievitch's RootsTech presentation: “From Purple Prose to Machine-Checkable Proofs: Levels of rigor in family history tools”

Feb. 12, 2015:

• Today is RootsTech developer conference; no Dr. Embley today
• Dr. Liddle: IRB has approved my proposal; got some programming done with Dr. Embley; fixed OntologyEditor w.r.t. relationship connections; spent some time working with Christopher
• Dr. Embley presented at FHTW
• Tae Woo: has been programming on getting form JSON ready for the next phase in the pipeline; is implementing it in a way that works just for his thesis; issue: sometimes COMET freezes when advancing to next page; next up is getting various JSON structures finalized
• Christopher: hover highlighting is mostly working, but there are some special cases that still need work; deprecated standard mode, so forms now default to grid mode; has questions about adding to nested fields (two similar user stories may need coalescing)
• Dr. Woodfield: made progress on CS 340; nearing the end of screens, JS, backend; persistence is up next; two things from conference yesterday: (1) thinking about a mechanism to apply probabilistic constraints to the Church's One Tree to Rule Them All; (2) need a declarative mechanism for specifying rules and constraints. It's time for a new modeling standard.
• Sidebars:
  • Christopher: demo highlighting, user stories on nested fields
  • Tae Woo: how to really convert to form JSON

Feb. 5, 2015:

• Dr. Lonsdale: AAAI conference was really good (1000 people); our talk went well – Peter did a great job
• Dr. Woodfield: still being inundated by CS 340; Dr. L & Dr. L may be able to serve as advisers to CS MS students
• Dr. Packer: has gotten back into the code, and BigInteger fix seems to be working and working reasonably quickly; will continue with change to JSON instead of OSMX, keeping track of labels to send info back to annotator to highlight different parts of query string
• Christopher: has highlight functionality working (calling function from console); finding what is needed in the DOM on hover is interesting, and needs some more work
• Dr. Embley: RootsTech development summit is next Wednesday, so won't be to DEG meeting; our FHTW workshop paper was accepted; working on a paper with George Nagy; did some programming; have object existence rules been deployed to annotator2? (needs to be checked)
• Dr. Liddle: worked with Dr. Embley on some bugs & coding issues; got IRB application submitted
• Sidebars:
  • Work out example for Christopher to test highlighting
  • Work out example for calling ListReader ???
  • Embley presentation outline
• Notes:
  • Liddle perhaps should fix OntologyEditor order bug for objects in relationship connections
  • Liddle definitely should fix PDFIndexer/annotator vertical axis issue
  • Tool names:
    • The annotator will be called COMET: Click-Only (or at least Mostly) Extraction Tool
    • The form-based extraction tool ensemble will be called Fe5: Fe == Iron ⇒ strong; 5 is version number, and we have ideas for versions 6 and 7; here are the phases:
      • 1. Extract with multiple extraction tools
      • 2. Merge extracted records into filled-in forms
      • 3. Resolve: human looks at form, corrects as needed
      • 4. Accuracy check: we may just let the ensemble do the job automatically, or we may need to keep people involved
      • 5. Learning: feedback loop to improve the tools, and with Tae Woo's work learn new extraction rules so the tools keeps getting better
      • 6. Family Tree creation and check (Dr. Woodfield's work)
      • 7. Generate the full WoK-HD that we've talked about in the past (add back in the query components, etc.)

Jan. 28, 2015:

• Dr. Lonsdale is in Texas with OntoSOAR paper
• Dr. Liddle: NSF proposal has advanced to “recommended” status; working on IRB clearance now
• Tae Woo: has been programming; successfully converts OSMX to record, and now needs to convert records to JSON
• Dr. Packer: has a couple of papers ready to resubmit; next week will be back to programming ListReader
• Dr. Woodfield: same as last week (making progress)
• Christopher: has been working on hover highlighting; has something that should be highlighting, but just getting border, not color; general highlight is mostly working, and pretty close for single entries on highlighting; but hover isn't working
• Dr. Embley: has been working with Thomas on papers; got some programming and inference work done this week; will work on export to GedComX
• Sidebars:
  • XSD import/include (the difference between the two is a namespace issue)
  • Highlight demo/discussion, product backlog discussion
  • Thinking of names for ensemble, annotator tool
  • Thomas had some ideas on making the interface work a lot faster

Jan. 21, 2015:

• Congratulations, Joseph, on passing your thesis defense
• Joseph: passed defense, got paperwork done
• Dr. Lonsdale: wants to sidebar on Maven problem (784 TNRB, 9:30am Thursday)
• Tae Woo: has been programming on OsmxToJson, especially converting record part; figured out some solutions, feels we have it; needs deploy of annotator2
• Dr. Packer: has been working with Dr. Embley on the paper; should be done next week with those; ListReader development follows
• Christopher: has split the highlighting story into three; has something for general highlighting and knows the basic idea for single entry and multiple entry
• Dr. Liddle: has been doing miscellaneous things and refactoring osmx2.xsd
• Dr. Embley: we have the Springer book Towards the Multilingual Semantic Web, submitted FHTW paper, met with Dr. Lonsdale; wants to talk about recruiting students
• Dr. Woodfield: still working on CS 340 for another few weeks
• Sidebars:
  • Rejuvenating the group: could Scott be the pseudo adviser plus a real adviser
  • OSMX2 .xsd discussion
  • New flow for downstream that takes as input all the OSMX documents that are produced along the way (solves the problem with gender we had discussed)

Jan. 14, 2015:

• Joseph to present thesis defense dry run
• Scrum meeting afterwards if time

Jan. 7, 2015:

• Joseph: worked on presentation for defense enabled probability output features (incl. from command line)
• Dr. Liddle: got IS 411 started again; refined the deployment scripts; heads-up on maven assembly plugin and build process
• Dr. Lonsdale: got back yesterday
• Tae Woo: still struggling with converting OSMX to JSON
• Dr. Packer: working with Dr. Embley, responding to paper feedback, some more coding
• Christopher: getting back to classes; fixed adding new record with A/a key; working on highlighting for GreenFIE
• Dr. Woodfield: mostly has worked on CS 340
• Dr. Embley: working with Thomas on the paper; will resubmit soon
• Sidebars:
  • Tae Woo's issue with OSMX-to-JSON conversion and page issues/page boundaries/complex annotations/edited text, etc.
    • Note: complex annotations need to be refactored in the OSMX xsd; JSON correctly associates resources with annotation components; OSMX does not.
    • Note: Dr. Embley needs to add a user story to fix JSON to OSMX to deal with AnnotatedComponent required attributes (id, type, inResource).
  • Bug for appending annotation from multiple pages [NOTE: unable to replicate this issue on Mac/Chrome with annotator2]
  • Think about FHT Workshop & Jiapu (can Dave write abstract?)