Hi Tim, Because LuceneIndex is touched in several places within the code, I started with refactorization of LuceneIndexReaderResourceImpl (see: CTAKES-464 [1])
If you have time, may you also check CTAKES-334 [2]. I started to have it as a prerequisite, because the patch provided actually will make the tests pass (having also UMLS credentials). Alex [1] - https://issues.apache.org/jira/browse/CTAKES-464 [2] - https://issues.apache.org/jira/browse/CTAKES-334 On Wed, Oct 4, 2017 at 8:15 AM, Alexandru Zbarcea <al...@apache.org> wrote: > Thanks Tim, > > I will let you know about the progress. > > Alex > > On Oct 4, 2017 06:34, "Miller, Timothy" <Timothy.Miller@childrens. > harvard.edu> wrote: > >> I had in mind the notes in: >> /ctakes-examples-res/src/main/resources/org/apache/ctakes/ex >> amples/notes/rtf >> >> which I believe are the fake notes Dr. John Green wrote for us. I don't >> know why they are rtf but they are nice, non-toy-length notes. >> Tim >> >> ________________________________________ >> From: Alexandru Zbarcea <al...@apache.org> >> Sent: Tuesday, October 3, 2017 5:32 PM >> To: Apache cTAKES Dev >> Subject: Re: Missing resources for script that extracts markables from a >> corpus for analysis [EXTERNAL] >> >> Hi Tim, >> >> That's great news. If you think there are sample notes that can be used, I >> can start working on the Lucene index and slowly build the UTest for them. >> >> I have created CTAKES-462[1] where we can track this work. >> >> Looking into the ctakes-examples-res, what I can find is: >> $ find . -type f | grep -v "\.class" | grep -v "\.iml" | grep -v "\.jar" | >> grep -v "\.rtf" | grep -v "\.xml" | grep -v "\.bsv" | grep -v "\.piper" >> ./main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt >> ./main/resources/org/apache/ctakes/examples/notes/claudication >> ./main/resources/org/apache/ctakes/examples/notes/shark_bite.txt >> ./main/resources/org/apache/ctakes/examples/notes/edge_cases >> _plaintext_1.txt >> >> ./main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt >> ./main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy >> ./main/resources/org/apache/ctakes/examples/notes/SampleInpu >> tRadiologyNotes.txt >> >> ./main/resources/org/apache/ctakes/examples/notes/smoker/ >> doc1_07543210_sample_past_smoker.txt >> ./main/resources/org/apache/ctakes/examples/notes/smoker/ >> doc2_07543210_sample_past_smoker.txt >> ./main/resources/org/apache/ctakes/examples/notes/smoker/ >> doc2_07543210_sample_current.txt >> ./main/resources/org/apache/ctakes/examples/notes/smoker/ >> doc1_07543210_sample_unknown.txt >> ./main/resources/org/apache/ctakes/examples/notes/smoker/ >> doc1_07543210_sample_current.txt >> ./main/resources/org/apache/ctakes/examples/notes/mother_goose/README >> ./main/resources/org/apache/ctakes/examples/notes/mother_ >> goose/OneMistyMoistyMorning.txt >> ./main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/Peds_RoutBirthNote_1/Peds_RoutBirthNote_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/VascSurg_AAA_Leak_1/VascSurg_AAA_Leak_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/Peds_Dysphagia_1/Peds_Dysphagia_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_LaborProgressNote_1/OBGYN_LaborProgressNote_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_IUD_1/OBGYN_IUD_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_HysterectomyAndBSO_1/OBGYN_HysterectomyAndBSO_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/VascSurg_FollowUp_1/VascSurg_FollowUp_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_PROMCheck_1/OBGYN_PROMCheck_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_Gen_Abscess_1/OBGYN_Gen_Abscess_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/Peds_FebrileSez_1/Peds_FebrileSez_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/VascSurg_RO_AAA_1/VascSurg_RO_AAA_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/VascSurg_RO_DVT_1/VascSurg_RO_DVT_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/GenSurg_UmbilicalHernia_1/GenSurg_UmbilicalHernia_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/VascSurg_PVD_1/VascSurg_PVD_1 >> ./main/resources/org/apache/ctakes/examples/annotation/ >> anafora_annotated/OBGYN_MVAPrego_1/OBGYN_MVAPrego_1 >> >> What notes do you consider I should start with (all) ? >> >> Alex >> >> [1] - https://urldefense.proofpoint.com/v2/url?u=https-3A__issues. >> apache.org_jira_browse_CTAKES-2D462&d=DwIBaQ&c=qS4goWBT7popl >> M69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRR >> NQXipowRLRjx0ibQrHEo8uYx6674h&m=COSkyBpYGrcp_hTAFRRfTx8JCwHA >> zxTM3GMiXKrSbnE&s=jOmot_onPFb31eg689D0ihb5Y4dZTzKcQ40vMCW0Bgk&e= >> >> >> On Mon, Oct 2, 2017 at 6:46 PM, Miller, Timothy <Timothy.Miller@childrens. >> harvard.edu> wrote: >> >> > Yeah, it might be nice to build a lucene index of all the sample notes >> in >> > the ctakes-example module. I'll create a jira for it but probably won't >> be >> > able to get to it right away. >> > Tim >> > >> > ________________________________________ >> > From: Alexandru Zbarcea <al...@apache.org> >> > Sent: Monday, October 2, 2017 5:31 PM >> > To: Apache cTAKES Dev >> > Subject: Re: Missing resources for script that extracts markables from a >> > corpus for analysis [EXTERNAL] >> > >> > Hi Tim, >> > >> > I understand, makes sense. Is it possible to anonymize the data you >> have or >> > come up with a separate body of test data to generate a Lucene index and >> > unit test the code? I think this would have the double benefit of the >> code >> > being tested and showing dev/users how the code is supposed to be used. >> > >> > What do you think? >> > >> > Alex >> > >> > >> > On Mon, Oct 2, 2017 at 9:45 AM, Miller, Timothy < >> > timothy.mil...@childrens.harvard.edu> wrote: >> > >> > > Thanks Alex, >> > > This code is for processing a clinical text data corpus stored as a >> > > lucene index -- data that cannot be redistributed for privacy reasons. >> > > Since it's so related to the coref stuff I thought it should go >> > > alongside the coreference module. But maybe it makes more sense as an >> > > external project since it can't really function without externally >> > > created resources -- what do you think? >> > > Tim >> > > >> > > >> > > On Sun, 2017-10-01 at 19:54 -0400, Alexandru Zbarcea wrote: >> > > > Hi, >> > > > >> > > > I was trying to do a UTest for the >> > > > org.apache.ctakes.coreference.data.PrintMimicMarkables (recently >> > > > added), >> > > > but I couldn't find any of the existing resources that can be used >> > > > for >> > > > this. Can anyone help me pointing to a resource (Lucene index) >> > > > folder. >> > > > >> > > > org.apache.ctakes.coreference.data.PrintMimicMarkables \ >> > > > >> > > > /home/alex/projects/apache/ctakes/ctakes-dictionary-lookup- >> > > > res/target/classes/org/apache/ctakes/dictionary/lookup/rxnorm_index >> > > > \ >> > > > index.out >> > > > >> > > > I was trying with the following lucene folder/resource: >> > > > ./ctakes-coreference- >> > > > res/src/main/resources/org/apache/ctakes/coreference/models/ >> index_med >> > > > _5k >> > > > >> > > > And also the dictionaries: >> > > > ./ctakes-dictionary-lookup- >> > > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/snomed- >> > > > like_codes_sample >> > > > ./ctakes-dictionary-lookup- >> > > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/ >> assertion_ >> > > > cue_phrase_index >> > > > ./ctakes-dictionary-lookup- >> > > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/ >> OrangeBook >> > > > ./ctakes-dictionary-lookup- >> > > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/snomed- >> > > > like_sample >> > > > ./ctakes-dictionary-lookup- >> > > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/ >> drug_index >> > > > >> > > > Any execution looks like: >> > > > 01 Oct 2017 19:50:19 INFO ConstituencyParser - Initializing >> > > > parser... >> > > > Oct 01, 2017 7:50:20 PM >> > > > org.apache.uima.collection.impl.cpm.engine.ArtifactProducer process >> > > > WARNING: Got Exception. (Thread Name: [CollectionReader Thread]::) >> > > > Message: >> > > > docID must be >= 0 and < maxDoc=5000 (got docID=5000) >> > > > Oct 01, 2017 7:50:20 PM >> > > > org.apache.uima.collection.impl.cpm.engine.ArtifactProducer >> run(820) >> > > > WARNING: docID must be >= 0 and < maxDoc=5000 (got docID=5000) >> > > > java.lang.IllegalArgumentException: docID must be >= 0 and < >> > > > maxDoc=5000 >> > > > (got docID=5000) >> > > > at >> > > > org.apache.lucene.index.BaseCompositeReader.readerIndex( >> BaseComposite >> > > > Reader.java:152) >> > > > at >> > > > org.apache.lucene.index.BaseCompositeReader.document(BaseCom >> positeRea >> > > > der.java:115) >> > > > at org.apache.lucene.index.IndexReader.document(IndexReader. >> java:436) >> > > > at >> > > > org.apache.ctakes.core.cr.LuceneCollectionReader.getNext( >> LuceneCollec >> > > > tionReader.java:90) >> > > > at >> > > > org.apache.uima.collection.impl.cpm.engine.ArtifactProducer. >> readNext( >> > > > ArtifactProducer.java:494) >> > > > at >> > > > org.apache.uima.collection.impl.cpm.engine.ArtifactProducer. >> run(Artif >> > > > actProducer.java:711) >> > > > >> > > > Collection process complete called, closing file writer. >> > > > >> > > > I appreciate any of your help, >> > > > Alex >> > >> >
