|
MMTx Detailed Trouble Report (Trouble Report #) |
| Field | Field Data |
|---|---|
| ID | 1 |
| Category | mmtxT |
| Synopsis | Missing machine output fields |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Thu Oct 25 09:30:00 EST 2001 |
| Closed-Date | Tue Mar 19 07:11:27 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | Actually, I have some more, but I guess they are intended: both in the candidates and the mapping lines, the second part in mmtx is missing, metamap parts such as "[[1,1],[1,1],0],[[2,2],[2,2],0]],yes,no" doe not appear in mmtx. |
| How-To-Repeat | echo "Obstructive Sleep Apnea" | mmtx -q |
| Notes | See TR #13 for same problem. Not able to duplicate here yet. I get all info. |
| ID | 2 |
| Category | mmtxT |
| Synopsis | Machine output differences |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Thu Oct 25 09:31:00 EST 2001 |
| Closed-Date | Fri Mar 15 10:19:35 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | with the -q option, the string "basic research" results in: MMTx: echo "basic research" | mmtx -a -q => utterance('00000000.tx.1',"basic research"). and MetaMap: echo "basic research" | metamap -a -q => utterance('00000000.tx.0', "basic research"). MMTx: echo "basic research \"a" | mmtx -a -q => utterance('00000000.tx.0', "basic research "a"). and MetaMap: echo "basic research \"a" | metamap -a -q => utterance('00000000.tx.1',"basic research ""a") |
| How-To-Repeat | see above |
| Notes | Fixed in MMTx V2.0 |
| ID | 3 |
| Category | mmtxT |
| Synopsis | Result and parsing differences |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Wed Oct 31 09:32:00 EST 2001 |
| Closed-Date | Fri Mar 15 10:21:18 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | $ echo "Raynaud's disease" | mmtx results in: Phrase: "Raynaud ' s disease" Meta Candidates (10) 902 Raynaud's Disease [Disease or Syndrome] 861 Secondary disease, NOS [Disease or Syndrome] 812 Disease [Disease or Syndrome] 779 SS <1> (Sezary Syndrome) [Neoplastic Process] 779 SS <2> (Sicca Syndrome) [Disease or Syndrome] 756 DIS (Diagnostic interview schedule) [Intellectual Product] 756 Second [Quantitative Concept] 741 seconds [Temporal Concept] 719 Secondary <2> (Secondary to) [Temporal Concept] 719 secondary <1> (Metastatic to) [Functional Concept] Meta Mapping (861) 861 Secondary disease, NOS [Disease or Syndrome] ----------------------------------------------------------------------- $ echo "Raynaud's disease" | metamap results in (as it should): Phrase: "Raynaud's disease" Meta Candidates (3): 1000 Raynaud's Disease [Disease or Syndrome] 861 Disease [Disease or Syndrome] 805 DIS (Diagnostic interview schedule) [Intellectual Product] Meta Mapping (1000): 1000 Raynaud's Disease [Disease or Syndrome] |
| How-To-Repeat | see above |
| Notes | Fixed in MMTx V2.0 |
| ID | 4 |
| Category | mmtxT |
| Synopsis | Strings not processing |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Sun Jan 13 09:34:00 EST 2002 |
| Closed-Date | Fri Mar 15 10:22:03 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | FYI: the strings "beta-2 beta-3" and "n-nitro n-nitrosoguanidine" take ages to map, and actually, mmtx will die before mapping :-( |
| How-To-Repeat | echo "beta-2 beta-3" | mmtx |
| Notes | Problem fixed in MMTx V2.0 |
| ID | 5 |
| Category | mmtxT |
| Synopsis | Strings not processing continued |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Jan 14 09:35:00 EST 2002 |
| Closed-Date | Fri Mar 15 10:22:51 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | with regard to the two phrases I emailed yesterday. Mmtx seems to go into an infinite loop. Is it possible to let it time out if no mammping has been found? See TR #4 |
| How-To-Repeat | echo "beta-2 beta-3" | mmtx |
| Notes | Fixed in MMTx V2.0 |
| ID | 6 |
| Category | mmtxT |
| Synopsis | Differences between MetaMap and MMTx |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | suspended |
| Class | sw-bug |
| Arrival-Date | Wed Mar 06 09:36:00 EST 2002 |
| Closed-Date | --- |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | FYI: the sentence " the mean incidence of the 10 year period was 1.0 per 100,000 children per year." |
| How-To-Repeat | echo "the mean incidence of the 10 year period was 1.0 per 100,000 children per year." | mmtx |
| Notes | Working with Lan and User Initial response is that there is no real difference. ----------- Looks like Version 2.2 will have shape identification. |
| ID | 7 |
| Category | mmtxT |
| Synopsis | Request for modifications |
| Severity | non-critical |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | change-request |
| Arrival-Date | Wed Jan 30 09:39:00 EST 2002 |
| Closed-Date | Wed Oct 16 11:21:44 EDT 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | NOTE: Submitted for user: - Is there an interface to the brill tagger? We do not currently provide enough documentation (minus the source code) to provide someone to build a tagger client. - Is there an unistall script? Such a script would also drop the databases. - Is there a way to update MMTx databases short of creating new databases and re-loading the entire models. At issue are users that have customized the UMLS where they are constantly changing that data to suite their needs. User has an application database that changes every few days. - When making a custom UMLS, what MRSO term types get filtered out? |
| How-To-Repeat | --- |
| Notes | Submitted for user per email notes 1) Reference TR#16 2) Version 2.2 should have this 3) Reference TR#19 4) Will provide user with a copy of the Filtering paper. |
| ID | 8 |
| Category | mmtxT |
| Synopsis | Installation Errors |
| Severity | critical |
| Priority | high |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Feb 22 09:42:01 EST 2002 |
| Closed-Date | Fri Mar 15 10:26:03 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | Errors during installation with respect to DB_MMTxDBTest_01_strict |
| How-To-Repeat | install program |
| Notes | Fixed problems, tested, and released - MMTx V2.0.B |
| ID | 9 |
| Category | mmtxT |
| Synopsis | Error starting up MMTx |
| Severity | critical |
| Priority | high |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Feb 22 09:44:00 EST 2002 |
| Closed-Date | Thu Jun 06 13:32:10 EDT 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.4 MySQL Version: |
| Description | I just installed MMTx, 2.0 and when I invoke it, I get the error: "Main method is not public". How do I resolve this? |
| How-To-Repeat | run mmtx |
| Notes | Work-around in V2.0.C and full fix awaiting repackaging of MMTx. This is caused by stricter checking done in Java 1.4 |
| ID | 10 |
| Category | mmtxT |
| Synopsis | General MMTx Question |
| Severity | non-critical |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | question |
| Arrival-Date | Mon Feb 25 09:51:00 EST 2002 |
| Closed-Date | Wed Oct 09 11:06:27 EDT 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | Can anyone answer this? Actually, can anyone tell me how to suppress the regular output and just get pipe delimited output, with the options that I want? I tried "--nmm --pipedOutput".? |
| How-To-Repeat | N/A |
| Notes | This is being evaluated. We have discussed doing this in the past - the only issue is the repetative nature of the output. -------------------- Looks like Version V2.2 will have this option. |
| ID | 11 |
| Category | mmtxT |
| Synopsis | Question on MMTx |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Tue Feb 26 09:52:00 EST 2002 |
| Closed-Date | Tue Jul 29 14:20:57 EDT 2008 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | The options scheme is very familiar to Unix programmers, so I personally like it. It's also similar to the KSS API, also familiar. What's not clear is if there are any dependencies between the options. For example if I toggle X on, does it have any impact on any of the other toggles, or are they all mutually independent in their effects? I am experimenting and it seems like some of them do have dependencies... |
| How-To-Repeat | N/A |
| Notes | We've looked at this, but no work done to date. Need to look at MetaMap and MMTx to determine the interdependencies of options. ------------ Same as TR #26 |
| ID | 12 |
| Category | mmtxT |
| Synopsis | Machine output inconsistencies |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Tue Feb 26 09:53:00 EST 2002 |
| Closed-Date | Wed Oct 16 11:20:53 EDT 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | it seems if I turn off mappings or candidates, that the output still shows a heading for them, but lists them as zero or none, rather than just omitting mapping/candidate information completely... NOTE: Dependent on TR #11 & TR #26 |
| How-To-Repeat | --- |
| Notes | Need to contact user and see what options they are using. |
| ID | 13 |
| Category | mmtxT |
| Synopsis | Machine output data missing |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Thu Feb 28 09:54:00 EST 2002 |
| Closed-Date | Wed Mar 27 07:12:36 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | using just the -q option, I am not getting any info after the semantic type lists, for each candidate in a mapping (i.e., not getting match map list, overmatch y or n, etc.). This is fine for my purposes right now, but just wondering if this is a bug? |
| How-To-Repeat | --- |
| Notes | This is the same as Marc's problem. Not able to duplicate with my environment yet - I get all of the info. |
| ID | 14 |
| Category | mmtxT |
| Synopsis | Output wrong |
| Severity | critical |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Mar 04 09:55:00 EST 2002 |
| Closed-Date | Wed Mar 27 07:12:53 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | Not sure why, but if I give the string "Lyme Disease" to mmtx, it does not map it to the correct concept (same), but instead maps it to "Disease". |
| How-To-Repeat | echo "Lyme Disease" | mmtx |
| Notes | This has been fixed by Guy and now we are just awaiting results from user testing. |
| ID | 15 |
| Category | mmtxT |
| Synopsis | Need option to display MMTx version information |
| Severity | non-critical |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | change-request |
| Arrival-Date | Mon Mar 04 09:56:00 EST 2002 |
| Closed-Date | Fri Mar 15 10:36:03 EST 2002 |
| Release | V2.0.B |
| Environment | Operating System: Solaris OS Version: Solaris 5.8 Java Version: Java 1.3 MySQL Version: 3.23.47 |
| Description | It would be nice to be able to type mmtx --version and receive information on what version I'm running. |
| How-To-Repeat | --- |
| Notes | Incorporated into MMTx V2.0.C |
| ID | 16 |
| Category | mmtxT |
| Synopsis | Question on using Brill Tagger |
| Severity | non-critical |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Fri Mar 15 20:13:00 EST 2002 |
| Closed-Date | Wed May 15 11:10:02 EDT 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | NOTE: Submitted for user: I don't see much of a problem getting the tagger up and wrapped, although you might consider making the lisp wrapper available as well with some documentation (I still have to figure out how to get you up from the socket servers to CORBA-based interfaces--see our AMIA paper from a few years ago on a laboratory test knowledge mediator using lisp<-->java connectivity through PARC's ILU object broker). I've been looking at Brill-style taggers over the past few months to support digital library work we are doing in-house, of which there are also open-source distributions available. As you point out, the tagset and the availability of tagged training texts are significant issues. From some preliminary investigation, it seems like there is widespread use of the treebank tagset or extensions thereof, and there aren't health care oriented training texts available. I'm curious as to if and how the team will be addressing this. Look forward to your comments after the AMIA deadline. |
| How-To-Repeat | N/A |
| Notes | --- |
| ID | 17 |
| Category | mmtxT |
| Synopsis | Question |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Thu Mar 21 09:43:00 EST 2002 |
| Closed-Date | Tue Apr 02 13:28:06 EST 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 1. How can I filter/skip some obviously non-medical concepts (although they are listed in UMLS)? For example, (1) "Fig." inside this text should not be marked as "Fig [Food]": This condition is called a succenturiate lobe (Fig. 6-5 ) and may be problematic if that lobe of placenta is inadvertently left within the uterus at the time of delivery. (2) Likewise, "al" shouldn't be "Aluminum [Element, Ion, or Isotope]" These studies provide strong evidence of the interconnectiveness of maternal and fetal fluid spaces across the membranes and placenta (Kilpatrick et al, 1991). I'd like to know a way to filter those abbreviations. |
| How-To-Repeat | N/A |
| Notes | --- |
| (1) "Fig." inside this text should not be marked as "Fig [Food]" | side this text should not be marked as "Fig [Food]": |
| This condition is called a succenturiate lobe (Fig. 6-5 ) and may | is called a succenturiate lobe (Fig. 6-5 ) and may be |
| problematic if that lobe of placenta is inadvertently left within the uter | that lobe of placenta is inadvertently left within the uterus |
| at the time of deliver | delivery. |
| 2. The other question is why MMTx includes "(" in the phrase? In the abo | estion is why MMTx includes "(" in the phrase? In the above |
| example (2), "placenta (Kilpatrick et al" was analyzed as a phrase. Can MM | lacenta (Kilpatrick et al" was analyzed as a phrase. Can MMTx |
| separate the | --- |
| --- | |
| I believe that a bug fix on this is being tested, but mainly because the text wasn't broken into two phrases. As you your specific question about the parenthesis, the parser sometimes includes punctuation that we would normally not consider to be part of a phrase because it does not harm for our subsequent processing. Do you have a particular reason for wanting it excluded? |
|
| ID | 18 |
| Category | mmtxT |
| Synopsis | Parsing question/problem |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Thu Mar 21 09:45:00 EST 2002 |
| Closed-Date | Tue Jul 29 14:02:05 EDT 2008 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 2. The other question is why MMTx includes "(" in the phrase? In the above example (2), "placenta (Kilpatrick et al" was analyzed as a phrase. Can MMTx separate them? |
| How-To-Repeat | echo "placenta (Kilpatrick et al" | mmtx echo "Nerve conduction velocity (NCV)" |mmtx echo "Magnetic Resonance Imaging (MRI)"|mmtx |
| Notes | The bigger question on the fix is if it should be fixed? If it is, it needs to be done on MetaMap as well. This problem accounted for the bulk of the non tagger differences between MMTx and MetaMap. |
| ID | 19 |
| Category | mmtxT |
| Synopsis | update metamap dataset on-the-fly |
| Severity | serious |
| Priority | medium |
| Responsible | cliff |
| State | closed |
| Class | support |
| Arrival-Date | Thu Mar 21 15:27:00 EST 2002 |
| Closed-Date | Thu Mar 28 14:08:32 EST 2002 |
| Release | V2.0B |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | I'm looking for a synopsis on how to update the metamap dataset for single concepts. Longer-term this would be a useful feature to incorporate. For the present, some documentation on what tables need to be updated would be great! |
| How-To-Repeat | --- |
| Notes | 3/22/02: In reply to TR #19: The Data File Builder (dfbuilder) module of MMTx might be what you are looking for. The dfbuilder was designed to allow you to create your own data set(s) or to modify the UMLS distribution files. I would recommend that you look at the Data File Builder documentation (http://mmtx.nlm.nih.gov/dfBuilder.shtml) and see if that will do what you are looking for. If it doesn't, or, if you need more information to proceed, please provide us with more specifics on the types of updates you are trying to do and we will work with you. Response from our Data File Builder specialist (Cliff): In the UMLS, information about a concept is spread over several files. So how to modify a few concepts depends on which attributes of the concept they want to update. Assuming they want to add or remove troublesome synonyms they could modify the 0Suppress1 file and follow the example of our filtering and mark them suppressible. Subsequently building a moderate or strict model would assure the desired terms were removed. They would start with the complete UMLS and run the Data File Builder. If they want to try this more details can be provided. I suggest looking at the documentation on the Data File Builder, then sending us a more detailed description of the 'updates' they would like to make and we may be able to suggest a process to achieve their goals. Reply: I will review the Data File Builder documentation. Bill Hole should have a copy of our UMLS vocabulary server report that details what we have done. We support the following editing functions against umls: create concept Add atoms to existing concept transpose atoms from one concept to another delete atoms from one concept to another merge one concept into another concept split a concept out of an existing concept delete concepts. In order to integrate metamap, we need to update metamap tables appropriately for each of these operations, as opposed to running dfbuilder in batch mode. Answered 4/3/02: Changes to concepts, particularly ones that include MeSH terms, can have subtle and possibly hard to trace consequences for MetaMap data files. For example, splitting entry terms from a MeSH concept into separate UMLS concepts can change not only the CUI reported for each of the words in the *words*.txt files, but also the treecodes reported for that concept. We have not done the necessary analysis to be able to provide a synopsis of how to update the MetaMap data files based on changes to individual concepts. Your study of the dfbuilder scripts and programs will probably yield the information you seek. If you pass your findings on to us we will make them available to other researchers on our upcoming 'contrib.' page on the MMTx web site. |
| ID | 20 |
| Category | mmtxT |
| Synopsis | missing dfbuilder script 0Suppress1 |
| Severity | serious |
| Priority | medium |
| Responsible | cliff |
| State | closed |
| Class | question |
| Arrival-Date | Mon Mar 25 12:01:00 EST 2002 |
| Closed-Date | Wed Mar 27 07:11:43 EST 2002 |
| Release | V2.0B |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 0Suppress1 script missing from mmtx/dfbuilder/scripts directory |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 21 |
| Category | mmtxT |
| Synopsis | Installation error |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Mar 25 12:56:00 EST 2002 |
| Closed-Date | Fri May 03 13:47:32 EDT 2002 |
| Release | --- |
| Environment | Operating System: Linux OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | We are following the web guidelines required for the set up of the MMTx program. In order to run MMTx we have run ./bin/install.sh but we get this message: In Class program.MMTxinstall: main must be public and static Would you be able to help us with this issue, namely: what does this message mean? and what, can we do in order to proceed with the installation of the software? |
| How-To-Repeat | --- |
| Notes | Looks like we missed the installation program when we were setting up the work-around to run in Java 1.4. follow-up 4/2/02: We just have one more query with regard to MMTx installation. Indeed, we are having some trouble in the final phase of the installation of the software. As you may see in the output file we get when we try to run ./bin/install.sh (please see document attached) As referred in the output file, if the problem is the root of Java password, please let us know how we can introduce a new password in the root user Java. With regard the files you sent us,after installing it, we realised that our Java version is 1.3 so we ended up not using the additional file you so kindly sent us. |
| ID | 22 |
| Category | mmtxT |
| Synopsis | Follow-up Question #1 |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Wed Mar 27 07:18:00 EST 2002 |
| Closed-Date | Thu Mar 28 13:37:35 EST 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 1. What are the 'C.......' that appear in the word files, and what is the logic to emit them in GleanMRCON.processLine? Answer: C....... occurs in some data for optimization purposes. As an example, the line abdomen|S0003328|C....... in a word index file means that the word "abdomen" occurs in the string S0003328 ('Palpation of abdomen'). The presence of C....... signals that the given string is also the concept name. No further searching is necessary to obtain the concept name. On the other hand, the entry abdomen|S0288461|C0000735 means that "abdomen" occurs in S0288461 ('abdomen neoplasm'), a string for concept C0000735 with preferred name 'Abdominal Neoplasms'. |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 23 |
| Category | mmtxT |
| Synopsis | Follow-up Question #2 |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Wed Mar 27 07:19:00 EST 2002 |
| Closed-Date | Thu Mar 28 13:36:47 EST 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 2. In FilterMRCONSO.filterNmStrDups, it appears that there is no particular criterion as to which record is kept when duplicates are discovered. Looks like the first record processed is kept, and the dups are discarded. Answer: That's exactly correct; we keep the first occurrence of a string in the mrconso file (a join of MRCON and MRSO) that is indistinguishable from other strings within a concept. Since preferred forms occur in this file before non-preferred forms, this has the effect of keeping the preferred forms. |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 24 |
| Category | mmtxT |
| Synopsis | Follow-up Question #3 |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Wed Mar 27 07:19:00 EST 2002 |
| Closed-Date | Thu Mar 28 13:34:54 EST 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 3. Any particular reason for the use of another unique name for semantic types instead of just using the unique Tcodes? Answer: Yes, we find the mnemonics much easier to understand when we manually review output. |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 25 |
| Category | mmtxT |
| Synopsis | Follow-up Question #4 |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | question |
| Arrival-Date | Wed Mar 27 07:19:00 EST 2002 |
| Closed-Date | Thu Mar 28 13:33:30 EST 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | 4. Why isn't jlvg used for normalization? NLSStrings looks to be more lightweight, was it just easier to include? Answer: NLSStrings is a descendent of a corresponding Prolog module used by MetaMap and similar programs developed in the Natural Language Systems program. It predates lvg, is tailored to our specific needs, and is more efficient than lvg (the last time I checked). I'm also fairly certain that lvg doesn't have the full functionality required for the specific kind of normalization we're doing; in particular, it doesn't respect word order and the kinds of normalization involving NOS and NEC are different (MetaMap continues to filter out NOS but no longer does so with NEC). |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 26 |
| Category | mmtxT |
| Synopsis | Explanation of options with interdependencies |
| Severity | serious |
| Priority | medium |
| Responsible | alan |
| State | closed |
| Class | doc-bug |
| Arrival-Date | Wed Mar 27 09:05:01 EST 2002 |
| Closed-Date | Tue Jul 29 14:21:20 EDT 2008 |
| Release | 2.0.C |
| Environment | Operating System: Solaris OS Version: 2.8 Java Version: Java 1.2 MySQL Version: 3.23.39 |
| Description | The documentation needs to include adequate option descriptions along with explanations of how they interact. ---------- Same as TR#11 |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 27 |
| Category | mmtxT |
| Synopsis | -h needs to be translated into English |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | doc-bug |
| Arrival-Date | Wed Mar 27 09:08:00 EST 2002 |
| Closed-Date | Tue Jun 04 14:14:33 EDT 2002 |
| Release | 2.0.C |
| Environment | Operating System: Solaris OS Version: 2.8 Java Version: Java 1.2 MySQL Version: 3.23.39 |
| Description | The output from -h is unreadable. It needs to be written so that options are organized into groups (see the web site), so that columns are straight, and so that debug options are somehow isolated (perhaps with a new option?). |
| How-To-Repeat | mmtx -h |
| Notes | This has been done in a sample file and made available to the user for comment. All we are waiting to do at this point is to install into the MMTx code. |
| ID | 28 |
| Category | mmtxT |
| Synopsis | MMTx hangs when running the following |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Mar 29 06:34:00 EST 2002 |
| Closed-Date | Wed May 15 11:12:23 EDT 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | Executing mmtx on the following text: Weight Reduction^Excess body weight-body mass index causes it to hang indefinitely...... Thought I should let you know. I don't think we have yet installed any of the bug fixes for v 2.0 on our machines....maybe they would fix this, I don't know. ----------------- Output differs greatly from MetaMap |
| How-To-Repeat | run text through MMTx |
| Notes | I believe it works in the current release 2.0.C. I get the proper answer when I run it through - please see if you can update to the 2.0.C version and run it and see if you are getting the same results. I've tested this query in both V2.0.B and V2.0.C and get the same results. Are you using any options? I only tried it with the default options set. ----------------------------- |
| ID | 29 |
| Category | mmtxT |
| Synopsis | MMTx doesn't work after applying updates for V2.0.C |
| Severity | serious |
| Priority | high |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Apr 01 06:48:01 EST 2002 |
| Closed-Date | Wed Apr 03 13:14:10 EST 2002 |
| Release | --- |
| Environment | Operating System: Solaris OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | We installed patches to version 2.0.C today. I just tried to run the text again and now it doesn't hang, but gives the following java error: Using Database: DB_01_strict Weight Reduction^Excess body weight-body mass index ^D Processing 00000000.tx.0: Weight Reduction^Excess body weight-body mass index Exception in thread "main" java.lang.NoSuchMethodError at lexicalization.LexicalLookup.makeLexicalElementOf(LexicalLookup.java:1307) at lexicalization.LexicalLookup.matchMultiWords(LexicalLookup.java:941) at lexicalization.LexicalLookup.lexicalLookup(LexicalLookup.java:331) at lexicalization.LexicalLookup.lexicalLookupAux(LexicalLookup.java:239) at lexicalization.LexicalLookup.lexicalLookupAux(LexicalLookup.java:212) at programs.MMTx.processSentence(MMTx.java:310) at programs.MMTx.processDocumentX(MMTx.java:1161) at programs.MMTx.processCollectionX(MMTx.java:876) at programs.MMTx.run(MMTx.java:1049) at programs.MMTx.main(MMTx.java:1235) |
| How-To-Repeat | --- |
| Notes | Thanks for the quick return on the info. It looks like you are running a very early version of MMTx. In reference to your question on how to tell which version - unfortunately, until V2.0.C there really isn't except to look at the dates of the files. In looking at the dates of the class files from the listing provided. Most of your classes are from the November 2001 timeframe which was the timeframe when we had the early V1.0.? where ? is one of A-I. I'm "guessing" from the date, that it is V1.0.I since that would have been the latest version available in late-November. What I'd like to do I guess is build a tar file to replace all of your existing files. This would have the benefit of not forcing you to go back through the installation process. I just need to know if you changed any of the source files before I setup the tar file for you. Sorry for all the confusion, but, that does explain why I'm not able to duplicate some of the problems you were seeing. PS: We will also need to work on the script that you are using to run MMTx with. The updated files should have a new one ready for you. |
| ID | 30 |
| Category | mmtxT |
| Synopsis | Exception occurred when parsing a sentence |
| Severity | serious |
| Priority | high |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Wed Apr 03 10:34:00 EST 2002 |
| Closed-Date | Mon Apr 08 07:19:56 EDT 2002 |
| Release | V2.0 |
| Environment | Operating System: Windows NT/2000 OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | When parsing this sentence: In a joint U.S. Centers for Disease Control and Prevention and Thai Ministryof Public Health trial, 397 asymptomatic Thai women were randomized to receive either placebo or AZT in the last month of pregnancy(300 mg tablets orallytwice dailyfrom 36 weeks until labor, one tablet at the onset of labor, and one tablet every3 hours until delivery). MMTx generated this error: Something went wrong: java.lang.ArrayIndexOutOfBoundsException java.lang.ArrayIndexOutOfBoundsException at mm.Candidate.doCandidatePosCheck(Candidate.java:797) at candidateGeneration.CandidateGeneration.computeMetaCandidates(Candida teGeneration.java:484) at candidateGeneration.CandidateGeneration.createCandidates(CandidateGen eration.java:222) at programs.MMTx.mapPhrase(MMTx.java:469) at programs.MMTx.processPhrase(MMTx.java:412) at programs.MMTx.processSentence(MMTx.java:347) at programs.MMTx.processDocumentX(MMTx.java:1154) at programs.MMTx.processCollectionX(MMTx.java:874) at programs.MMTx.run(MMTx.java:1041) at programs.MMTx.main(MMTx.java:1228) 04/05/02: I have downloaded V2.0C and tried the same test, but still failed. It seemed that my original 02/15/2002 version is V2.0A. I upgraded from V2.0A directly to V2.0C. This should be fine, right? Since V2.0B it's only a fix for database installation process. Anyway, I have listed all files under my mmtx/classes directory. Attached please find this file. For some newer class files, it might because I recompiled some source code. But I didn't break any original functionality. For that mm/Candidate.class, which caused the exception, I only changed one line in the source code so that my test could be passed. Answer: When you say "I have downloaded V2.0C" and upgraded over V2.0A what exactly do you mean? Did you download the full V2.0C distribution and reinstall? Or did you download the upgrade for V2.0C and upgrade? Also, the changing one line raises a yellow flag on my side. Could you forward me the source code of the file you changed and I'll try running with that file to see if I can replicate your problem. 04/05/02: I downloaded only the upgrade files, i.e., "Version 2.0.C of MMTx Classes and Source Update (85kb)", then did the upgrade. Attached please find Candidate.java. You can search "Huang" for the line I changed in order to pass my test. I didn't have enough time to dig into more deeply into the code. Answer: The upgrade was only designed to take you from V2.0B to V2.0C and only included those files. I've compiled and ran with your changed file and your right it isn't changing the behavior. It runs fine on my system and without the error. Under both Solaris and Windows 2000. I believe the error is coming in because of the old version mixed with the new version. The only two solutions I can offer are the following: 1) Do a complete reinstall with the V2.0.C source & classes distribution. 2) Download the complete V2.0.C source & classes distribution, tar the contents into a new directory and copy over the source files and class files into your existing mmtx directory. |
| How-To-Repeat | --- |
| Notes | Initially, I'm not able to reproduce on the Solaris platform with V2.0.B or V2.0.C. Need to check on the PC side to see if it is platform specific. 4/4/02: Unable to reproduce on Windows platform. ------------------ I'm in the process of reloading my PC with MMTx and then I will try running your file through. I don't get the same error on the Sun Solaris platform, so, I need to check to see if it is something specific to the PC. If you are running from a version on 2/15, you might want to consider upgrading if any of the changes outlined on the download page apply to the kinds of work you are doing. I'll let you know when I've had a chance to run on the PC side. |
| ID | 31 |
| Category | mmtxT |
| Synopsis | fullVars from GenerateMMVariants does not match MetaMap tables |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | suspended |
| Class | sw-bug |
| Arrival-Date | Wed Apr 03 15:58:00 EST 2002 |
| Closed-Date | --- |
| Release | 2.0.A |
| Environment | Operating System: Solaris OS Version: Solris 2.8 Java Version: Java 1.3 MySQL Version: |
| Description | I have attempted to validate the variant generation that is part of the MMTx Data File Builder. There are differences for which I do not know the significance. Here are my observations, please let me know if they are significant. The full01.txt is distributed with MMTx and is a join of the variant tables used by MetaMap. The fullVars_02_custom.txt was produced by GenerateMMVariants on a Linux box. I have sorted them, removed the final pipe from the former and compared the resulting files. Those files can be found in /home/cliff/projects/data_file_builder/variants The files used were full01.sorted.stripped -- Herein known as Lan's fullVars_02_custom.sorted -- Herein known as Guy's 1) Size: Lan's 1 592 620 Guy's 1 812 481 2) Common Records: 8631 3) Numbers: Lan's about 207 000 Guy's about 94 000 Lan set the second column of numbers to none, guy set column two to the value in column 4. 4) None: Lan used it 982 021 times Guy never used it. 5) Example 1: I picked a word at random where I found some common rows and compared the treatement from both files. The indented values come from Guy's file. The plus indicated a record unique to that file. Lan's version does not have noun to verb transitions. Guy's version has some duplicate records, that may not pose a problem in the database. There are some differences even for similar records. absence|noun|absence|noun|0|NULL|1|1|1|1| absence|noun|absences|noun|1|i|1|1|1|1| absence|noun|absent|adj|3|d|1|1|1|1| absence|noun|absence|noun|0|NULL|1|1|1|1 absence|noun|absences|noun|1|i|1|1|1|1 absence|noun|absent|adj|3|d|1|1|1|1 +absence|noun|absented|verb|7|ddi|1|0|0|1 +absence|noun|absenting|verb|7|ddi|1|0|0|1 +absence|noun|absents|verb|7|ddi|1|0|0|1 +absence|noun|absent|verb|6|dd|1|0|0|1 absent|adj|absence|noun|3|d|1|1|1|1| absent|adj|absences|noun|4|id|1|1|1|1| absent|adj|absent|adj|0|NULL|1|1|1|1| absented|verb|absents|verb|1|i|1|1|1|1| (a) absented|verb|absent|verb|1|i|1|1|1|1| absent|adj|absence|noun|3|d|1|1|1|1 absent|adj|absences|noun|4|di|1|1|1|1 absent|adj|absent|adj|0|NULL|1|1|1|1 +absented|verb|absented|verb|0|NULL|1|1|1|1 +absented|verb|absented|verb|0|NULL|1|1|1|1 --duplicate +absented|verb|absenting|verb|2|ii|1|1|1|1 absented|verb|absents|verb|2|ii|1|1|1|1 differs from (a) absented|verb|absent|verb|1|i|1|1|1|1 6) Example 2: The recording of the history is reversed for these to files. Guy's has some new variants, are they valid? ocular|adj|eye|noun|2|s|1|1|1|1 ocular|adj|eyes|noun|3|is|1|1|1|1 ocular|adj|ocular|adj|0|NULL|1|1|1|1 ocular|adj|oculi|noun|4|id|1|1|1|1 ocular|adj|oculus|noun|3|d|1|1|1|1 ocular|adj|ophthalmia|noun|7|dss|1|1|1|1 ocular|adj|ophthalmic|adj|4|ss|1|1|1|1 ocular|adj|optic|adj|4|ss|1|1|1|1 ocular|adj|eye|noun|2|s|1|1|1|1 ocular|adj|eyes|noun|3|si|1|1|1|1 ocular|adj|ocular|adj|0|NULL|1|1|1|1 ocular|adj|oculi|noun|4|di|1|1|1|1 ocular|adj|oculus|noun|3|d|1|1|1|1 +ocular|adj|ophthalmiac|noun|7|ssd|1|1|1|1 +ocular|adj|ophthalmiacs|noun|8|ssdi|1|1|1|1 ocular|adj|ophthalmia|noun|7|ssd|1|1|1|1 +ocular|adj|ophthalmias|noun|8|ssdi|1|1|1|1 ocular|adj|ophthalmic|adj|4|ss|1|1|1|1 ocular|adj|optic|adj|4|ss|1|1|1|1 eye|noun|eye|noun|0|NULL|1|1|1|1 eye|noun|eyes|noun|1|i|1|1|1|1 eye|noun|ocular|adj|2|s|1|1|1|1 eye|noun|oculi|noun|6|ids|1|1|1|1 eye|noun|oculus|noun|5|ds|1|1|1|1 eye|noun|ophthalmia|noun|5|ds|1|1|1|1 eye|noun|ophthalmic|adj|2|s|1|1|1|1 eye|noun|optic|adj|2|s|1|1|1|1 eye|noun|eye|noun|0|NULL|1|1|1|1 eye|noun|eyes|noun|1|i|1|1|1|1 eye|noun|ocular|adj|2|s|1|1|1|1 eye|noun|oculi|noun|6|sdi|1|1|1|1 eye|noun|oculus|noun|5|sd|1|1|1|1 +eye|noun|ophthalmiac|noun|5|sd|1|1|1|1 +eye|noun|ophthalmiacs|noun|6|sdi|1|1|1|1 eye|noun|ophthalmia|noun|5|sd|1|1|1|1 +eye|noun|ophthalmias|noun|6|sdi|1|1|1|1 eye|noun|ophthalmic|adj|2|s|1|1|1|1 eye|noun|optic|adj|2|s|1|1|1|1 7) Example 3: I picked out a number to show differences. For numbers Lan has second column with none, and an extra row with none in column four: 105058|none|105058|adj|0|NULL|1|1|1|1 105058|none|105058|adv|0|NULL|1|1|1|1 +105058|none|105058|none|0|NULL|1|1|1|1 105058|none|105058|noun|0|NULL|1|1|1|1 105058|none|105058's|noun|1|i|1|1|1|1 105058|none|105058|verb|0|NULL|1|1|1|1 105058|adj|105058|adj|0|NULL|1|1|1|1 105058|adv|105058|adv|0|NULL|1|1|1|1 105058|noun|105058|noun|0|NULL|1|1|1|1 105058|noun|105058's|noun|1|i|1|1|1|1 105058|verb|105058|verb|0|NULL|1|1|1|1 99994|none|99994|adj|0|NULL|1|1|1|1 99994|none|99994|adv|0|NULL|1|1|1|1 +99994|none|99994|none|0|NULL|1|1|1|1 99994|none|99994|noun|0|NULL|1|1|1|1 99994|none|99994's|noun|1|i|1|1|1|1 99994|none|99994|verb|0|NULL|1|1|1|1 99994|adj|99994|adj|0|NULL|1|1|1|1 99994|adv|99994|adv|0|NULL|1|1|1|1 99994|noun|99994|noun|0|NULL|1|1|1|1 99994|noun|99994's|noun|1|i|1|1|1|1 99994|verb|99994|verb|0|NULL|1|1|1|1 8) Example 4: This abbreviation showed some similarities, but the treatment seemed to be substantially different. Lans: abo's|noun|abo|noun|1|i|1|1|1|1 abos|noun|abo|noun|1|i|1|1|1|1 abo's|noun|aborted|verb|6|ide|1|0|0|0 abos|noun|aborted|verb|6|ide|1|0|0|0 abo's|noun|aborter|noun|8|dde|1|0|0|0 abos|noun|aborter|noun|8|dde|1|0|0|0 abo's|noun|abortion|noun|2|e|1|1|1|0 abos|noun|abortion|noun|2|e|1|1|1|0 abo's|noun|abortions|noun|3|ie|1|1|1|0 abos|noun|abortions|noun|3|ie|1|1|1|0 abo's|noun|abort|verb|5|de|1|0|0|0 abos|noun|abort|verb|5|de|1|0|0|0 abo's|noun|abo's|noun|0|NULL|1|1|1|1 abos|noun|abo's|noun|0|p|1|1|1|1 abo's|noun|absent bed occupancy|noun|2|e|1|1|1|0 abos|noun|absent bed occupancy|noun|2|e|1|1|1|0 abo's|noun|absent bed occupant|noun|2|e|1|1|1|0 abos|noun|absent bed occupant|noun|2|e|1|1|1|0 abo's|noun|antibodies|noun|3|ie|1|1|1|0 abos|noun|antibodies|noun|3|ie|1|1|1|0 abo's|noun|antibody|noun|2|e|1|1|1|0 abos|noun|antibody|noun|2|e|1|1|1|0 abo's|noun|preventive substance|noun|4|se|1|1|1|0 abos|noun|preventive substance|noun|4|se|1|1|1|0 abo's|noun|sensitizing substance|noun|4|se|1|1|1|0 abos|noun|sensitizing substance|noun|4|se|1|1|1|0 abo's|noun|substance sensibilisatrice|noun|4|se|1|1|1|0 abos|noun|substance sensibilisatrice|noun|4|se|1|1|1|0 Guy's: ABO's|noun|ABO|noun|1|i|1|1|1|1 ABOs|noun|ABO|noun|1|i|1|1|1|1 ABO's|noun|aborted|verb|7|iadi|1|0|0|0 ABOs|noun|aborted|verb|7|iadi|1|0|0|0 ABO's|noun|aborter|noun|9|iadd|1|0|0|0 ABOs|noun|aborter|noun|9|iadd|1|0|0|0 ABO's|noun|aborters|noun|10|iaddi|1|0|0|0 ABOs|noun|aborters|noun|10|iaddi|1|0|0|0 ABO's|noun|aborting|verb|7|iadi|1|0|0|0 ABOs|noun|aborting|verb|7|iadi|1|0|0|0 ABO's|noun|abortionist|noun|6|iad|1|0|0|0 ABOs|noun|abortionist|noun|6|iad|1|0|0|0 ABO's|noun|abortionists|noun|7|iadi|1|0|0|0 ABOs|noun|abortionists|noun|7|iadi|1|0|0|0 ABO's|noun|abortion|noun|3|ia|1|1|0|0 ABOs|noun|abortion|noun|3|ia|1|1|0|0 ABO's|noun|abortions|noun|4|iai|1|1|0|0 ABOs|noun|abortions|noun|4|iai|1|1|0|0 ABO's|noun|aborts|verb|7|iadi|1|0|0|0 ABOs|noun|aborts|verb|7|iadi|1|0|0|0 ABO's|noun|abort|verb|6|iad|1|0|0|0 ABOs|noun|abort|verb|6|iad|1|0|0|0 ABO's|noun|ABO's|noun|0|NULL|1|1|1|1 ABOs|noun|ABOs|noun|0|NULL|1|1|1|1 ABO's|noun|ABOs|noun|2|ii|1|1|1|1 ABOs|noun|ABO's|noun|2|ii|1|1|1|1 ABO's|noun|antibodies|noun|4|iai|1|1|0|0 ABOs|noun|antibodies|noun|4|iai|1|1|0|0 ABO's|noun|antibody|noun|3|ia|1|1|0|0 ABOs|noun|antibody|noun|3|ia|1|1|0|0 ABO's|noun|ectrotic|adj|5|ias|1|1|0|0 ABOs|noun|ectrotic|adj|5|ias|1|1|0|0 |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 32 |
| Category | mmtxT |
| Synopsis | different output for "activated" between mmtx and skr |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Tue Apr 30 06:31:00 EDT 2002 |
| Closed-Date | Tue Jul 29 14:02:23 EDT 2008 |
| Release | V2.0.C |
| Environment | Operating System: Linux OS Version: redhat 7.0. problem also on OS X Java Version: Java 1.3 MySQL Version: 3.23.49a |
| Description | skr and mmtx differ in mapping between "activated". mmtx does not find any mapping, skr finds "Activate" as concept. |
| How-To-Repeat | echo "activate" | MMTx -a -q |
| Notes | --- |
| ID | 33 |
| Category | mmtxT |
| Synopsis | machine output not consistent, related to verb inflections |
| Severity | critical |
| Priority | high |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Tue Apr 30 06:34:00 EDT 2002 |
| Closed-Date | Thu May 30 09:06:45 EDT 2002 |
| Release | V2.0.C |
| Environment | Operating System: Linux OS Version: redhat 7.0. problem also on OS X Java Version: Java 1.3 MySQL Version: 3.23.49a |
| Description | machine output is not always consistent when there is no mapping found. echo "activate" | MMTx -a -q results in: utterance('00000000.tx.1',"activated"). phrase('activated',[verb([lexmatch([activated]),inputmatch([activated]),tag(verb),tokens([activated])])]). candidates([]).mappings([]). 'EOU'. the mappings ios behind the candidates, and not on a new line!!. same problem with talking, signaling, deleted, disrupts, oxidized, i.e. some verb inflections lead to this problematic output |
| How-To-Repeat | echo "activate" | MMTx -a -q |
| Notes | Problem in MMTx.java where newline wasn't being placed after zero candidates list found. Should be in new release 2.0.D |
| ID | 34 |
| Category | mmtxT |
| Synopsis | mmtx / skr inconsistency, related to hyphens? |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Tue Apr 30 07:28:01 EDT 2002 |
| Closed-Date | Thu Apr 24 12:12:40 EDT 2003 |
| Release | V2.0.C |
| Environment | Operating System: Linux OS Version: redhat 7.0. problem also on OS X Java Version: Java 1.3 MySQL Version: 3.23.49a |
| Description | take "interleukin-10" and compare mmtx and skr: SKR finds "Interleukin-10", but SKR only finds "Interleukins, NOS". In machine output: it seems that MMTx inserts a space in front of the hyphen MMTx output after MMTx -a -q: utterance('00000000.tx.1',"interleukin-10"). phrase('interleukin -10',[head([lexmatch([interleukin]),inputmatch([interleukin]),tag(noun),tokens([interleukin])]),not_in_lex([inputmatch([-10]),tag(unknown),tokens([-,10])])]). candidates([ev(-827,'Interleukin, NOS','Interleukins',[interleukin],[aapp,imft],[[[1,1],[1,1],0]],yes,no),ev(-755,'ILS','ILS',[ils],[aapp,phsu],[[[1,1],[1,1],3]],yes,no)]). mappings([map(-827,[ev(-827,'Interleukin, NOS','Interleukins',[interleukin],[aapp,imft],[[[1,1],[1,1],0]],yes,no)])]). 'EOU'. SKR output: utterance('00000000.tx.1',"interleukin-10"). phrase('interleukin-10',[mod([lexmatch([interleukin]),inputmatch([interleukin]),tag(noun),tokens([interleukin])]),punc([inputmatch([-]),tokens([])]),shapes([inputmatch(['10']),features([integer]),tokens(['10'])])]). candidates([ev(-1000,'Interleukin-10','Interleukin-10',[interleukin,'10'],[aapp,imft],[[[1,1],[1,1],0],[[2,2],[2,2],0]],yes,no),ev(-861,'Interleukin, NOS','Interleukins',[interleukin],[aapp,imft],[[[1,1],[1,1],0]],yes,no)]). mappings([map(-1000,[ev(-1000,'Interleukin-10','Interleukin-10',[interleukin,'10'],[aapp,imft],[[[1,1],[1,1],0],[[2,2],[2,2],0]],yes,no)])]). 'EOU'. |
| How-To-Repeat | echo "activate" | MMTx -a -q |
| Notes | --- |
| ID | 35 |
| Category | mmtxT |
| Synopsis | error on file generation when creating custom knowledge source |
| Severity | serious |
| Priority | high |
| Responsible | cliff |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri May 17 14:38:00 EDT 2002 |
| Closed-Date | Thu Jun 06 13:30:52 EDT 2002 |
| Release | 2.0D |
| Environment | Operating System: Windows NT/2000 OS Version: win2k Java Version: Java 1.4 MySQL Version: 3.23.42 |
| Description | Problem 1: 1)Running 05GenerateMWIfiles, always get 0 size file for cui_concept, cui.concept.st and concept_st.txt 2)the first line of file "cui_concept" is strange, like this: C.......|X C0000005|A1BG C0000005|alpha-1-B glycoprotein C0000007|A2M C0000007|alpha-2-macroglobulin 2) Running LoadDataFiles, can not load table "concept_cui" and "concept_st", check the file "concept_cui.txt.0" and "concept_cui.txt" having strange format: X |C....... A1BG |C0000005 alpha-1-B glycoprotein |C0000005 A2M |C0000007 alpha-2-macroglobulin |C0000007 A2MP |C0000008 It seems there is a extra "\n" after the first field. |
| How-To-Repeat | Run all procedures to 05GenerateMWIFiles Run LoadDataFiles |
| Notes | Add special condition to filter out extraneous ^Ms from java output files. |
| ID | 36 |
| Category | mmtxT |
| Synopsis | BuildDataFiles fails because of bad path |
| Severity | critical |
| Priority | high |
| Responsible | will |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri May 31 11:08:01 EDT 2002 |
| Closed-Date | Wed Oct 09 10:59:55 EDT 2002 |
| Release | 2.0.D |
| Environment | Operating System: Windows NT/2000 OS Version: Java Version: Java 1.3 MySQL Version: |
| Description | If the installation of MMTx in a directory below the top level of a device, the path offered for the creation of the workspace is wrong. Instead of /cygwin/e/MYTOP/mmtx/... you get E:MYTOPmmtx/... This also affects LoadDataFiles and the dfbuilder.profile. These all need double back slashes \\ replacement by the setup script because they are going to be interpreted in a shell environment that will consume single back slashes. |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 37 |
| Category | mmtxT |
| Synopsis | Test of email alias |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Jun 03 07:10:00 EDT 2002 |
| Closed-Date | Mon Oct 07 09:59:28 EDT 2002 |
| Release | V2.0.D |
| Environment | Operating System: Solaris OS Version: Solaris 2.8 Java Version: Java 1.3 MySQL Version: 3.23.49 |
| Description | Just wanted to test to see if Lan receives this email via mail alias on SKR1. |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 38 |
| Category | mmtxT |
| Synopsis | installation scripts gives error |
| Severity | critical |
| Priority | medium |
| Responsible | will |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Wed Jun 05 10:37:00 EDT 2002 |
| Closed-Date | Thu Jun 06 13:25:41 EDT 2002 |
| Release | V2.0.D |
| Environment | Operating System: MacOS-X OS Version: 10.1.5 Java Version: Java 1.3 MySQL Version: 3.23.46 |
| Description | installation script gives error: JGM: Database mmtx does not exist - creating ... ERROR -- Unable to create Database mmtx exitting application Root access is available, in MySQL, the strict, mmtx and lexicon databases have been created. However, no tables are in those databases. Log file is: ----------------------------------------------------------- Welcome to the MMTx Installation script We will be walking you through the following: 0) Validating environment, 1) Setting up the pathing in the config directory files, 2) Unloading the data files, 3) Setting up the mmtxUser MySQL user, 4) Creating necessary databases in MySQL, 5) Loading necessary tables in MySQL and, 6) Running an initial test to verify operations. Note: The installation script uses some GNU CYGWIN programs that have been distributed along with this script. These commands are only used when this installation is on a Windows platform. The command that have been distributed include tar, gunzip, rm, find, hosthame, and cmp. The CYGWIN package is licensed under the GNU Public License. The entire CYGWIN package, along with the sources to these commands can be found at http://sources.redhat.com/cygwin/. ----------------------------------------------------------- NOTE: This script requires root privilege in MySQL! Continue[Y/y or N/n] [N]? File Found :/usr/bin/tar Is this the correct instantiation to use? [Y/y or N/n] [Y]? File Found :/usr/bin/gunzip Is this the correct instantiation to use? [Y/y or N/n] [Y]? File Found :/bin/rm Is this the correct instantiation to use? [Y/y or N/n] [Y]? File Found :/usr/bin/cmp Is this the correct instantiation to use? [Y/y or N/n] [Y]? 1) Setting up the pathing in the config directory files: Full pathname of the mmtx PARENT directory [/Users/weeber/MMTx]: Specify the Database Server Host name that you will be using. The default is the database engine or server (mysql or some other db) will be on the same machine that the MMTx sofware is on. Database HostName [localhost]: Running Setup ... -- Updating hostname in config/mmtxRegistry.cfg ... Done -- Updating hostname in resources/mysql.cmd ... Done 2) Unloading the data files: Done 3) Setting up the mmtxUser MySQL user: Change the mmtxUser default password (Y/y or N/n) [N]? -- You have elected to use the default password: 'defaultPass' 3 & 4) Finish setting up mmtxUser and creating Databases: Database root user[root]: Does the database have a password set for user internal (Y/y or N/n) [N]? Enter the Mysql Root password The following MMTx elements are already installed: -- Nothing currently installed -- Making sure we have a clean MySQL first ... Done -- Adding user and tables to MySQL ... Done 5) Loading necessary tables in MySQL: PLEASE NOTE: This step takes some time due to the large amount of data loaded and the creation of indexes. We will be automatically going through all of the databases you downloaded. The estimates are based on a Sun Sparc Ultra 60. The Windows estimates are based on a 400 MHZ PENTIUM II, running NT2000. -- mmtx ~1 hour and 40 minutes -- Strict Model (default) ~55 minutes [45 minutes on Windows] -- Moderate Model (optional) ~1 hour and 40 minutes -- Relaxed Model (optional) ~2 hours -- Lexicon ~20 minutes [42 minutes on Windows -- Loading mmtx tables ... -- Creating the Variants tables and the Semantic Types table... |
| How-To-Repeat | --- |
| Notes | Stuffit expander incorrectly extracts GNU tar archives. |
| ID | 39 |
| Category | mmtxT |
| Synopsis | Data file builder when generating variant files |
| Severity | serious |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Jun 07 04:27:00 EDT 2002 |
| Closed-Date | Thu Apr 24 12:14:00 EDT 2003 |
| Release | V2.0.D + patch from Willy |
| Environment | Operating System: MacOS-X OS Version: 10.1.5 Java Version: Java 1.3 MySQL Version: 3.23.46 |
| Description | when usiong the data file builder to extract only MESH from the UMLS, the generation of variant files (executing 01GenerateVariants in the directory 03variants) results in an error. Note that the java programs are not killed. Output is written in the directory subInputDir. The contens of those files look like: ...... bikunin|-2147483632 curcacycline A|-2147483632 didimethylsulfoxide|-2147483632 spoliation|-2147483632 ..... The error message is: ** Configuration Error: Can't find bundle for base name data.config.lvg, locale en_US ** Error: problem of opening/reading config file: 'data.config.lvg'. Use -x option to specify the config file path. java.lang.NullPointerException at Lvg.Lib.Configuration.GetConfiguration(Configuration.java:59) at Lvg.Api.LvgApi.Init(LvgApi.java:225) at Lvg.Api.LvgApi. at variantGeneration.LexicalTools. at variantGeneration.PGvSlave.generateVariants(PGvSlave.java:308) at variantGeneration.PGvSlave.generateVariants(PGvSlave.java:213) at variantGeneration.PGvWorker.run(PGvWorker.java:100) at variantGeneration.PGvWorker.main(PGvWorker.java:330) java.lang.NullPointerException at Lvg.Lib.Configuration.GetConfiguration(Configuration.java:59) at Lvg.Api.LvgApi.Init(LvgApi.java:225) at Lvg.Api.LvgApi. at variantGeneration.LexicalTools. at variantGeneration.PGvSlave.generateVariants(PGvSlave.java:308) at variantGeneration.PGvSlave.generateVariants(PGvSlave.java:213) at variantGeneration.PGvWorker.run(PGvWorker.java:100) at variantGeneration.PGvWorker.main(PGvWorker.java:330) |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 42 |
| Category | mmtxT |
| Synopsis | Fruitful data not in proper format. |
| Severity | non-critical |
| Priority | medium |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Aug 09 12:31:00 EDT 2002 |
| Closed-Date | Thu Apr 24 12:19:13 EDT 2003 |
| Release | 2.2.A |
| Environment | Operating System: MMTx: Solaris MySQL:Solaris OS Version: 2.8 Java Version: Java 1.4 MySQL Version: |
| Description | The lvg installations yields an error with the checked in data. Fruitful.data yields the following message from MySQL: -- Loading data into Fruitful table ... Exception: java.lang.NumberFormatException: n+s Line: 0 - !kung|!Kung|128|1|Gn|1|n+s|0| ***Error: problem of reading file. -- Total Inserted Record: 0 Guy told us that this did not matter for Variant Generation. The file has been replaced with an empty file which generates no errors. Valid data should be checked in, or this problem can be closed if the data is really not needed. |
| How-To-Repeat | Run mmtx install and choose to install the data file builder. |
| Notes | --- |
| ID | 43 |
| Category | mmtxT |
| Synopsis | MMTx fails verification test during install, but otherwise runs normally |
| Severity | serious |
| Priority | medium |
| Responsible | will |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Mon Aug 19 14:35:00 EDT 2002 |
| Closed-Date | Wed Oct 09 10:59:26 EDT 2002 |
| Release | MMTx V2.2.A |
| Environment | Affects Solaris 2.8, Red Hat Linux 7.2, Mac OS/X 10.1, Windows NT, and possibly others. |
| Description | MMTx fails verification test during install but runs correctly afterwards from command line. |
| How-To-Repeat | run sh ./bin/install.sh on UNIX or ./bin/install.bat on windows from MMTx directory. |
| Notes | Removed leading "./" from "config" in CLASSPATH: CLASSPATH=./classes:./config:./lib/mmtx.jar: ... becomes: CLASSPATH=classes:config:./lib/mmtx.jar: ... However, the real fix is to use ClassLoader.getSystemResourceAsStream(String) instead. I modified GlobalBehavior.readRegistryFile(String) and GobalBehavior.readConfigFile(String) to use getSystemResourceAsStream(String). |
| ID | 45 |
| Category | mmtxT |
| Synopsis | Errors on database actions not reported. |
| Severity | serious |
| Priority | medium |
| Responsible | will |
| State | closed |
| Class | change-request |
| Arrival-Date | Fri Aug 30 10:30:01 EDT 2002 |
| Closed-Date | Wed Oct 09 13:33:05 EDT 2002 |
| Release | --- |
| Environment | Operating System: MMTx: Solaris MySQL:Solaris OS Version: 2.8 Java Version: Java 1.4 MySQL Version: |
| Description | Encountered this problem when error in building the paths for datafiles on the PC resulted in verification errors at the end of the installation. The DbUtil class sends SQL commands to MySQL but ignores the failure status returned by the API class MySqlUtil. This made tracking down the error very difficult. |
| How-To-Repeat | Here is a suggested solution to be added after r2.2: Provided a local version of the execute function to call the function in the parent class and check the response and report it to System.error. Replace several calls to super.execute with this.execute to get this checking behavior for all accesses to this function. The reasons for the use of super in this situation was unclear. Here is the required code: // ================================================|Public Method Header|==== /** * Method execute * An overide of the MySqlUtil method that checks for success and reports * failure * * @param statement A SQL statement for the database to execute. * @return success The value return from the super class. */ // ================================================|Public Method Header|==== public boolean execute( String statement ) { boolean success = false; if ( success = super.execute(statement)) { return success; } else { System.out.println("Execution of the following command "+ "failed: " + statement); return success; } } |
| Notes | --- |
| ID | 46 |
| Category | mmtxT |
| Synopsis | Permission Problem--MMTx hangs if not root or mmtx user |
| Severity | serious |
| Priority | high |
| Responsible | guy |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Oct 04 22:07:00 EDT 2002 |
| Closed-Date | Tue Nov 23 11:14:51 EST 2004 |
| Release | 2.2.A |
| Environment | Operating System: MMTx: Linux MySQL:Linux OS Version: RH 7.3 Java Version: Java 1.3 MySQL Version: |
| Description | Updated to 2.2.A, deleted old Tables during update. When running mmtx from command line, processing hangs silently after output line "Processing 'user-enter phrase'" . . . if the command is run by a user other than mmtx or root [software installed under mmtx user account]. No error messages appear using -w or -9 Had initially installed previous version with mmtxUser to have password mmtx. Looking at the config.log file for 2.2.a, no password appears for the mmtxUser. Upgrade to 2.2.a was uneventful--tests at end of install were successful. |
| How-To-Repeat | Run mmtx from an account other than root or the mmtx account where the software is installed. |
| Notes | MMTx 2.2.C contains fix to JDBM which now ignores the transaction log. In Version 2.4, MySQL has been replaced with BerkeleyBtrees |
| ID | 47 |
| Category | mmtxT |
| Synopsis | mmtxUser password clash when running both 2.0 and 2.2 |
| Severity | non-critical |
| Priority | low |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Tue Oct 08 14:50:01 EDT 2002 |
| Closed-Date | Tue Dec 03 11:03:16 EST 2002 |
| Release | 2.0, 2.2 |
| Environment | Operating System: MMTx: Linux MySQL:Linux OS Version: RH 7.3 Java Version: Java 1.3 MySQL Version: |
| Description | 2.0 has no password policy, 2.2 requires mmtxUser of 8 chars. 2.0 will not work after a 2.2 install if a user changes from having a password to no password, or has a password less than 8 chars and wants to maintain a password. Fix is to update the password in the 2.0 mmtxRegistry. |
| How-To-Repeat | Install 2.2, change password, or select no password when password exists for 2.0. 2.0 will be broken. |
| Notes | --- |
| ID | 48 |
| Category | mmtxT |
| Synopsis | Install script can not connect to the databases. |
| Severity | critical |
| Priority | high |
| Responsible | will |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Fri Oct 18 15:41:00 EDT 2002 |
| Closed-Date | Tue Jan 07 09:39:41 EST 2003 |
| Release | 2.2.A |
| Environment | Operating System: MMTx: Linux MySQL:Linux OS Version: Linux 2.4.19 Java Version: Java 1.3 MySQL Version: 3.23.52 |
| Description | I can not install metamap! install script fails at the point given below. (my mysqld deamon is working and I am using the correct root password) ----------- Creating & loading necessary databases ... java.lang.Exception: Not able to connect to the database. Check the following common causes: 1) Is the database server (deamon) running? 2) Does the root have a password, and if so, was it correctly specified? at gov.nih.nlm.nls.mmtx.install.MMTxInstall.createDatabases(MMTxInstall.java:812) at gov.nih.nlm.nls.mmtx.install.MMTxInstall.main(MMTxInstall.java:1736) Installation is not complete: Not able to connect to the database. Check the following common causes: 1) Is the database server (deamon) running? 2) Does the root have a password, and if so, was it correctly specified? |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 49 |
| Category | mmtxT |
| Synopsis | MMTx Trouble Report |
| Severity | serious |
| Priority | medium |
| Responsible | jim |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Sun Oct 20 20:09:00 EDT 2002 |
| Closed-Date | Mon Oct 21 07:39:51 EDT 2002 |
| Release | --- |
| Environment | Operating System: MMTx: MySQL: OS Version: Java Version: MySQL Version: |
| Description | --- |
| How-To-Repeat | --- |
| Notes | --- |
| ID | 50 |
| Category | mmtxT |
| Synopsis | unable to properly install MMTx on Windows Me |
| Severity | critical |
| Priority | high |
| Responsible | cliff |
| State | closed |
| Class | sw-bug |
| Arrival-Date | Wed Oct 30 20:09:00 EST 2002 |
| Closed-Date | Fri Nov 08 11:15:01 EST 2002 |
| Release | not running... downloaded mmtx_V2[1].A.jar |
| Environment | Operating System: MMTx: Windows NT/2000 MySQL:Win |