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(MOST RECENT WORK AT THE TOP)November 9, 1995 - ThursdayIntroduced JSP to the KnowledgeManager app and its associated database datastructures, and copied the source tree to his account on patella. Also createda new Sybase database for him to work with.November 1, 1995 - WednesdayFinished up the modifications to FrameBuilder, called the result version 1.61,and sent Dave and John a note that it's ready to use.Did the first round of modifications to the FrameBuilder "Author's Guide".document. It feels like I'm having to apologize a lot less this time around,now that it isn't so eccentric.October 31, 1995 - TuesdayRevamped the file saving operations in FrameBuilder, so it works more likea regular program. Corrected a few bugs, like references to an old menuitem name that got changed, and the fact that "New Frame" didn't used tocheck for unsaved modifications before blowing everything away. It's allmuch cleaner now.October 30, 1995 - MondayChanged the way names are assigned and edited in FrameBuilder, with simplechecks for misplaced space characters and improvements to the way thedialogs are linked. Also included support for Cut/Copy/Paste in the editmenu, which works also on contour shapes themselves. Next, will work onorthogonalizing everything and improving file handling.October 26, 1995 - ThursdayRe-arranged the files on the image server to work with the newest version ofthe browser, so that a single split frame can refer to multiple (3 right now)data areas generated by different authors. Uploaded v2.4b3 of the browserdemo, but it's 68K only right now; I discovered a defect that stops it coldwhen certain frames are loaded.Fought with TCP/IP networking on Bob's PB5300, and gave up for the momentwhile Apple investigates why they shipped Open Transport on his machineinstead of MacTCP.September 19, 1995 - TuesdayAdded textual-attribute-display window to KMan.September 13, 1995 - WednesdayMade some extensive mods to the browser's pointing quiz module (pquiz.c)."Show Answer" now uses a generic routine from the image-interaction moduleto draw outlines, instead of having the code in two places; it's smaller,more maintainable, and follows the outline-on time delay mechanism too.The quiz questions themselves come in random order instead of alphabetically,and are chosen by looking at the Contours menu instead of directly manipulatingthe linked list of contours. The code is lots simpler now. And finally, atthe end of a quiz, the scoring results are shown.September 12, 1995 - TuesdaySpent a lot of time going through FrameBuilder (my barebones SuperCardimage-outlining utility) and writing up a specfor possible future use if someone decideds to do the job for real or for anon-Mac environment.September 5, 1995 - TuesdayStarted learning the basics of perl, trying to make a filter to mungethrough my source files inserting logging statements to implement a"coverage monitor" -- a way to find out what parts of a program have beenexercised in a particular run or series of runs. Perl is good because itlets me do global substitutions to a group of files, and I had thought I'dbe able to use the same script to do the same thing on both Unix and theMac; but MacPerl doesn't work the way I thought it would, so it'll take somethinking. (The coverage monitor idea works like a charm, though).September 4, 1995 - MondayAwoke to an extremely loud and heavy thunderstorm and drenching rain, upin the North Cascades about 15 miles from Mount Baker. Everyone was in arush to go back home all of a sudden...wonder why?August 31, 1995 - ThursdayImproved the file & disk sharing setup in the Farr lab, removing dependenceon the in-house LocalTalk cable plant; a hard-disk problem manifested itselfhalfway through the job, but Norton seemed to cure it. Hopefully they'll getbetter capability and throughput and fewer headaches -- time will tell.Checked out get an idea of what kinds of HTML editors are out there for the Mac, andwas quite pleased. There were lots of HyperCard/SuperCard-based tools, whichI'm not interested in at all, but I did load and test Webtor, HTML Editor,and HTML Pro. The last seemed to fitbest with my idea of how such an editor should work, and also had thecleanest interface and was the most streamlined in its performance andmemory usage. I did manage to fool it into generating erroneous HTML, soit's not completely solid, but at least it's there so I don't have towrite it myself.Finally, I figured out some more vi commands to help me edit text (a mappingto add the "> " to each line of an attributed text block, and a macro tobreak up a long line with multiple hard returns).August 30, 1995 - WednesdayChanged KMan's login dialog to allow a database name to be specified.Created a "kbtest" database on synapse with enough stuff in it so thatit's a usable testbed.August 29, 1995 - TuesdayEnabled remote access between synapse (as a server) and tarsus (as a client)and was able to do a sp_helpdb directly on both machines without having torun isql twice. This means that, if we set it up properly, a single processcan log in to its normal dataserver host and query ALL databases on ALLhosts, which ought to make it faster and easier to figure out what'savailable (by reading the sysservers table to find out what servers arethere, and doing sp_helpdb on each of them).August 28, 1995 - MondayReinstated the restriction against duplicate term names; the database willwork fine, I think, but the interface depends on terms being unique becauseso much of what it does is name-based instead of ID-based. Allowing multipleduplicate terms will take some thinking and design work.August 24, 1995 - ThursdayImplemented the "Add Synonym" command in Knowledge Manager. It's verysimple, presenting a one-field dialog;it infers the author field fromthe value in the regular concept entry dialog's "modified by" field, andleaves most of the other fields (Authority, UMLSID, etc.) blank. The termis immediately visible for editing in the term inspector after a successfuladdition into the database, so those fields can be set if desired.Removed the restriction on duplicate term names; they're now allowed, butif the concept-entry procedure sees that one of your new names is alreadypresent, it allows you to back out and think about it or cancel the wholeoperation (or you can forge ahead and create duplicates if you wish). Ithink this may be a source of trouble eventually, but we have to do it if wewant an author to be able to create two separate concepts called "ventricle"with different concept ID's and definitions. (It just occurs to me that manyoperations, like locating a term in the hierarchy, work by name and not by IDso they'll display behavior that some authors may not expect when collisionsin the name space are present).KMan bugfix: the term insertion was allowing the entry of a blank preferredname, which interfered with everything down the road. I put a restriction inthe stored procedure to enforce this, and a similar check in the centry module.KMan bugfix: find-in-hierarchy was opening trees up properly, but leavingthem marked as "collapsed", so that double-clicking an ancestor in thedisplay caused double entries to crop up. Fixed in panhandler.August 18, 1995 - FridayGot Dennis's IIcx to start up again after last night's power shutdown (sittingcold all night resulted in the infamous hard drive "stiction" problem).August 16, 1995 - WednesdayWrote up some HTML describing the Knowledge Manager design andimplementation for Dr. Rosse/NLM/whoever else wants to know. They don't yetapproach the level of actual "documentation", but they do answer a lot ofquestions about what it is and how it's put together. It would also be agood place to talk about design decisions, tradeoffs, and limitations, andthat's what'll be going into it in the near future.The project has been going on since mid-April, and in these four months hasgrown to a little over 2700 lines of code. It's at the point now where allthe major functionality is in place and works, but it has not been extensivelytested and there are some things it should do that still aren't there (likeediting text attributes). It'll be mostly new features going in now, though,rather than basic design.August 14-15, 1995 - Monday & TuesdayAdded a new operation to KMan, the "find-in-hierarchy" command functionality.It's just an option in the general find dialog, when checked the program willattempt to locate the target term in context in the hierarchy tree (openingup the intervening subtrees if necessary). It uses a recursive method callwhich I'm not too happy with, but reasonable nesting levels shouldn't use uptoo much stack.I've arrived at a development cycle that seems to work very well: I determinethe next two or three features or hurdles that need doing, then spend timein the office reading any necessary information in the NextLibrary so I willknow how to go about it; then I lay out the basic structure and do the initialcoding at home from Das Mac. I can come back the next day after having thoughtthrough it again and double-checked my initial implementation ideas, andput it all through the compiler and put the finishing touches on it. Not beingable to compile and test immediately after the initial coding means I havemore time to think through the job without getting bogged down in details.Also, using the Mac at work as the code editing station means I do a lot lesswindow-swapping and can concentrate on the task at hand more easily.August 10, 1995 - ThursdayFixed a nasty bug in the browser's new NetGetDescription() routine, whichwas adding 1 to the returned address of a newly-allocated handle instead ofadding 1 to the requested size, as was intended. Changed contour-menu actionso all information is retrieved for a structure by name, instead of justhighlighting the shape in the image window.Got the browser's videodisc driver to work on the PB540c; it works on themodem port when the modem is set to "Normal", but doesn't work on the printerport (which tests out busy all the time). I don't know why. The 8100 in F509is exactly the opposite.August 7, 1995 - MondaySpent all afternoon making extensive modifications to the routines whichimplement the tree insertion/deletion/movement operations. It was a whilebefore I realized why the addition of a "root" node was requiring suchlarge changes; what I arrived at was the fact that it violates one of thedesign assumptions that made the original program so clean. Basically, itwas clear from the outset that all the relevant information about a treemember was to be contained visually in the display; for any term that youcould see in a given hierarchy, you could always count on seeing thefollowing things: the name of the hierarchy, the preferred name of theterm, its parent, any and all siblings, and whether there were any childrenyet to be retrieved. But artificially hiding the "root" item means thatpractically all the routines that manipulate the data must also take thespecial case into account, using different methods to infer the requiredinformation instead of accessing it directly from the display.The code isn't any uglier -- I'm doing some modularization as I go along,pulling common code sequences into their own utility routines, so in someways it's better than it was. But I don't like the special cases much, northe implicit knowledge the code has to have about the contents of the database.Ah well, if the world were perfect we wouldn't need custom programs at all.This is a good reminder, though, to think more about the scope of a modificationat the design stage before jumping into implementation.This is an important consideration for the next design change: that of usinga special database field to indicate semantic types instead of the "Role" field.To all appearances this should clean things up a lot, but it might have arippling effect in the code too. Especially, it will be necessary to thinkabout how that information is to be displayed; we have to do more than justsupply a checkbox to show the status of the flag. If tree-traversal queriesare to use the value of the flag to allow/disallow links from appearing inthe display, we have to make the user choose at the time they enter a givenhierarchy (switching the flag on and off during traversal would give ahopelessly confusing display, IMHO). And right now, it only makes sensewhen accessing the "isa" hierarchy -- should we special case that? Anothercoded assumption about the contents of the database...August 4, 1995 - FridayRemoved the "root" level from the hierarchy displays in KMan; but didn'tdeal with all the cases of inserting/moving children of root yet.KMan presents a dialog at startup asking for a host/user combination, incase the user wants to override the defaults.Checked out MifMucker, a FrameMaker-to-HTML converter. It failed immediatelyon John's example file, not too surprising; there are many tools for doingthis but I doubt if any of them is really robust yet. In any case, there'sno way the Web is going to show annotated images with lines and contoursand such (we already know this!) so I think the real solution is going tobe to change the labels so they're readable on the screen and then doscreenshots. A lot of work, and inelegant, but fairly uncomplicated.July 31, 1995 - MondaySpent most of the afternoon (before Dave's going-away party) trying tofigure out AH's Mailstrom problems. After trying many things, I sent tohelp@cac and Mark Mcnair suggested the inbox might be corrupted in a waythat would confuse the client side; it appears that may be the case alongabout the 5th message down, we'll try fixing that tomorrow and see if it hasany effect. If it is, I guess that'll be another mark in favor of using Pine.July 27-28, 1995 - Thursday/FridayDesigned and implemented an export module for the Knowledge Navigator. Thisis a set of routines and dialog boxes that allows the user to select fromamong different possible output formats, and have the program write datadirectly to static files for printing or sending to NLM. The formats arespecified in a report-wrting syntax that the user can change or override,rather than being fixed in C or Lisp code. This module will be a lot better than having a collection of command linescripts to use in preparing data to go to NLM, because the user can basicallydecide what they want to see and then create the files directly. It alsomeans that the job of building hierarchies in the correct order with thecorrect indentations only has to be done in one place. One point to make aboutthis module was the fact that I did the design and writing as a sort ofreaction after reading parts of Steve McConnell's book "Code Complete". Asa result of actually performing advance planning and specification, and usingsome of McConnell's advice concerning coding practices, the whole thing wenttogether far faster and with fewer conundrums than is usual with me. It wasa pleasure to piece it all together and have it working so quickly. The bookdoesn't really prescribe any particular Method, instead it points out severalmethods that people use for various stages of real-world programming jobsand urges the reader to think about each stage carefully before proceedingto the next. I find it helps a lot, by reducing the amount of time I spendmoving back and forth between decision-making and problem-solving. My onlypoint of departure from the book method was that I neglected to write up mydesign notes into a form that could be used by others to figure out theoperation of the module, something I should do but there's no place for itanywhere yet. Maybe I'll put it in a technical documentation section ofsome web pages on the Knowledge Manager.Fixed an interesting problem on the PowerMac 8100 in the microscope lab.Photoshop and Netscape were groaning under the difficult task of opening anew view window for some reason -- they'd do everything normally (includingthe appearance of dialog boxes and splash pages, managing menus, that stuff)but if you tried to open a new document window the watch cursor would freezefor anywhere between 1 and 3 MINUTES and then you'd get the window and beable to continue working. Very weird. It happened with barebones extensionsand even with them all turned off. I finally decided that I'd try installingQuickDraw GX (which wasn't there) and that fixed the problem; then I usedthe Extensions Manager to turn GX off, and the problem stayed fixed. Iconjecture that some other part of the system code thought GX was installed(maybe it had been, and was removed in some messy way).July 24, 1995 - MondayOver the last couple of work days, I've finally got around to patching upthe Atlas navigation code. I don't say "re-wrote", because it was not thecomplete overhaul that I'd like to do -- but I got rid of the very worstpart, which was the "hidden" windows. The original Atlas showed every windowon the screen all the time, and then we changed it so some navigation windowswould disappear but stay in memory for later...a method I never liked at all.Now the needed information concerning navigation is preserved but the contentsof the window (and the window structure itself) is thrown away when thewindow is not showing.This means that navigation proceeds correctly (well, I think so, but haven'ttested it completely yet) regardless of how the navigation frames are marked.Most importantly, the user can go back to previous levels of the frame listinstead of going all the way to the top and then down again. Also, framesCAN be marked as static (either by the author, or by a user during a givensession) so they won't go away. This implements the "multiple frames" ideamuch more cleanly than it has in the past and saves memory unless it'sdirectly needed for viewing a frame.There's still the difficulty of falling off the end of a frame list onto theorthogonal view, but I haven't resolved whether I want to code this as aspecific case yet. In general the basic operation is much cleaner and lesswasteful but the code really begs to be re-thought and re-written, which Idoubt will ever happen. There are many more important things to do thanrebuilding code that already does what it's supposed to. (I think I couldmake it faster, but other than that the user would see no difference and Ihave yet to hear any complaints about this part of the program's performance).July 14, 1995 - FridayAdded the necessary logic to the Atlas software to allow it to play movieseither directly, in its internal player windows, or through an externalplayer utility via Apple Events.Improved error handling in the serial I/O code in hopes of making it workon the PowerPC. For some reason the OS always reports that the port is alreadyin use, so the videodisc driver feature doesn't work on the newer machines.But then, neither does Kermit, so I don't feel too bad.July 11, 1995 - TuesdayFinished entering the "tributary of" data.July 10, 1995 - MondayImplemented the "Expand All Subtrees" button, and put in a check so thata term can't be added to a subtree more than once. Also entered a couplemore pages of "tributary of" hierarchy data.July 3, 1995 - MondayAdded code to allow the user to change term names and other fields in theTerm inspector, and improved validation of the data entry (to disallowspecial characters and report to the user what's required of them).June 28, 1995 - WednesdayDeleted 3 extra copies of TeachText from the Mac in the postdoc office, sonow text files will open without the -39 error; and consumed most of theafternoon with other departmental support duties.June 27, 1995 - Tuesday(sorry -- it's been a while since I reported in)Knowledge Manager now has a Term Inspector window (distinct from the Conceptinspector) to show database fields for individual terms. It also has controlsfor re-ordering child links in relation to their siblings.June 5, 1995 - MondayKnowledge Manager's "Insert Term as Child" operation working.Fixed an old bug in the image server that would allow the use of ".." ina file specifier, thus letting anyone in the world download any file on theserver. Now it's restricted to browser-related files only.Filled out all the departmental Mac support web pages, as a sort of outlineof what help is available and where to get it. (which see)June 1, 1995 - ThursdayKnowledge Manager now lets the user interactively add terms to the database,with improved error-checking and messaging when (for instance) a potentialnew term is already present.May 31, 1995 - WednesdayImplemented operation tracking mechanism in the Knowledge Manager, so I canfind out which commands people are using to do their work.May 30, 1995 - TuesdayFound and implemented a way for the Atlas to switch out and bring Netscapeto the fore when being used as an external viewer.May 26, 1995 - FridayKnowledge Manager operations in working order:- pasting a subtree as a root node- maintaining the order of child nodesAlso, made miscellaneous improvements in the way the Find dialog works(term entry field automatically selected for you, double-clicking a termcloses the dialog, etc.) and made a great improvement to the way childnodes are fetched when a subtree is expanded...the old way stored a listof ID's in a temporary array, the new way uses a stored procedure whichuses a join to replace all the intermediate processing.May 24, 1995 - WednesdayPut the finishing touches on the browser-navigation documents, put themon the web, and sent out notices.May 23, 1995 - TuesdayKnowledge Manager can now delete whole subtrees, thanks to a nifty littleprocedure which iteratively marks all of a given parent's descendants. I'mreally liking those stored procedures more and more.May 22, 1995 - MondayKnowledge Manager's term search dialog now fills the concept-inspectorinformation when you double-click a term, correctly resolving synonyms.Also, you can insert a term from the concept inspector as a root node inthe currently-displayed hierarchy.May 19, 1995 - FridayFinished the bulk of the documents outlining navigational strategies andquestions, and placed them on the Web in my home page.May 16, 1995 - TuesdayCut & Paste subtrees working in the Knowledge Manager;it does it by moving theselected subtree in or out of a "pasteboard" which is just another term inthe tree structure.May 12, 1995 - FridayKnowledge Manager works entirely from the active Sybase database on TARSUS,no static files are needed. Navigation works cleanly. The next step is tostart work on the Cut, Paste, and Delete operations on sub-trees.May 2, 1995 - TuesdayKnowledge Manager now retrieves a synonym list in the concept inspectorpanel, and updates the Role popup properly; and I built a "Find" panel whichlets you search the term list in the database for a wildcarded string, witha radio button to tell whether hits should be displayed in the inspectorpanel or in the hierarchy itself (but neither of those options actually worksyet, right now it just retrieves the proper list of names from the databaseand lets you click on one of them).May 1, 1995 - MondaySpent quite a bit of time constructing the document that Jim and Scott and Idiscussed which will afford discussion on a specification for navigationwithin the Atlas. I didn't actually write the document, but I did set outall of the sections and points that I think are germaine to the problem.Got the Knowledge Manager's database access routines working; now when youclick on a term in a hierarchy, the concept inspector fills in all theinfo from the "terms" table correctly.April 27, 1995 - ThursdayInstalled LaserWriter Bridge on the Sage lab computer to allow their Macs toshare a localtalk-only printer. Seems to work OK, time will tell.April 26, 1995 - WednesdayShowed the newest Atlas software to the DigAnat group with JWS. As a resultof some discussion over presentation of text information, I changed the nameof the "Glossary" window to "Attributes".Discussed deliverables and more specific data handling protocols with Jim,Shelley, and CR. Plan is to make the output match his input and try it outwith Shelley and I actually proofreading the output.Showed working indented-hierarchy tree browser to Jim, discussed implementationoptions for editing functions.Learned about Exabyte-tape handling and figured out how to pipe the output ofMacDump to it.April 24, 1995 - MondayInstalled MacDump on Cortex and Shelley's PowerMac, tested various setupsand operations.April 17, 1995 - Monday3:20 PM -- Knowledge Manager can now load and navigate a group of hierarchies,opening and closing subtrees with a double-click.April 14, 1995 - FridayHelped Ellen, a new staff member, wade through the process of creatingan accounton MAX.April 13, 1995 - ThursdaySpent practically all day figuring out how to make the knowledge managerstart up and open a file when you double-click it in Workspace Manager.April 12, 1995 - WednesdayGot the Knowledge Manager to the point where it will show a list ofhierarchies in a browser, and load the proper indented list into thebrowser when you click one of them. Just works with static files.I still haven't thought of a good way to let the user drag terms around thehierarchies. I'm thinking of making it purely a noun-verb operation, selectinga single line in the hierarchy and allowing a variety of operations:(1) double-click for opening/closing the subtree below the selected node(2) menu command to add empty line before/after the selection(3) changing the hierarchical level of the selected node (L/R arrow keys?)(4) either "cutting" the term for later pasting in a different position,perhaps with a multiple-object pasteboard, or two different browsers (yuk),or some other mechanismAdded details of networking strategies and protocols to the Atlastechnical documentation web page.Also fixed a small problem with Sandi's PURCH93 database.Bill says thata new system based on Sybase is planned for the 95-97 biennium startingthis summer. That'll be nice.April 11, 1995 - TuesdayAdded a couple of fixes to v2.3 of the Atlas software, to make the handlingof multiple movies kinder to the user.Sent the first iteration of the UMLS data extensions off to the NLM.April 10, 1995 - MondayAssimilated the UMLS/SNOMED identifiers sent by Mohamed into the databaseand took care of another small problem or two; e.g. about 100 terms containingtwo space characters in a row, 6 of which were identical to other terms whenthe spaces were removed.April 5, 1995 - WednesdayFound the missing library that was preventing Metrowerks C from generatinga PowerPC native Browser with QuickTime support (see 3/31/95). Spoke withChuck from HSCER about what needs to be done before sending this fix out.There are some logic issues about when certain dialogs should appear and whatthey should say, and some more important questions of design and integration(the QuickTime movies, if viewed as just another Browser datatype, show upin a window which is conceptually almost exactly like an image window, sowe're going to have to solve the problem of how "multiple images" fits into the navigation/window-management strategy. But probably none of this needsto be pursued just in order to get a fix shipped in the next couple of weeks.)April 4, 1995 - TuesdayGathered log files from the last year's Browser usage and set up a workingdirectory with some tools for analyzing them. It's all on neuron, in /usr/people/skandha/logs.April 3, 1995 - MondaySet up a source & data backup procedure to automate the process of takingweekly snapshots of the UMLS contract data sources.Altered the rule list for CR's terms table to make the "Preferred Term"role be "Preferred Name" instead, which is more in keeping with UMLS usage.March 30-31, 1995 - Thursday/FridayFinished alpha-test version of Atlas program with direct QuickTime playerwindows. Had to convert to MetroWerks C for the 68K version, because THINK Cv5.0.4 headers are too incompatible with the new ones to work without lotsof changes. However, the MW PowerPC compiler somehow would not resolve theQuickTime library calls so for now the fix will be 68K-only, running underemulation on PowerMacs. No big deal, running native doesn't really buy muchanyway because we spend most of our time in mixed-mode MacTCP or in QuickDrawroutines.March 29, 1995 - WednesdayFinished first draft of data-file generation utilities for writing themachine-readable sources to send to NLM containing names and links from ourdatabase. Had to roll my own tools to generate indented hierarchies, pushingthe data this way and that, because XLisp dies with bus errors/other assortedanomalous behavior when the size of a tree exceeds about 100 nodes. No bigdeal, it works for now and in the future we won't be doing it this way (I hope).March 22, 1995 - WednesdayMet with HSCER programmer to talk about possible strategies for dealing with problems the IBA has when installed under At Ease.We'll probably rush a bare-bones QuickTime player mechanism intothe existing code and ship it that way, in two to three weeks ifall goes well.Instituted a new window in the Atlas program, called the "Info"window, which displays persistent (non-dialog) messages separatelyfrom the Glossary mechanism. Compiled latest version of the programas 2.2b1.March 21, 1995 - TuesdayExtended the capabilities of the C and Lisp programs for parsing and loadingUMLS contract data, to deal with certain anomalies in the input stream andto make provisional test output files.Modified the FrameBuilder program, from 1.4 to 1.5, to allow the authorto paste text from the clipboard into the FRAME-INFO field in the optionsdialog; JWS will use this for showing descriptive text about his histologicalsections.March 20, 1995 - MondayWrote the Lisp code for taking parsed terminology data files and enteringthe data to the Sybase tables. (Functions CR-PREFERRED-TERM, CR-SYNONYM,and CR-ADD-LINK.)March 17, 1995 - FridayWrote "ih-parse", a C program to take the "Generic" formatted files fromWordPerfect and get them into a form that a Lisp reader can deal witheasily. It figures out what hierarchy is being built, locates preferredterms, synonyms, and semantic types, and puts out well regulated fileswithout pesky stray characters. 2b1af7f3a8