Hi again, Another possible assists ...
Ctakes uses Apache OpenNLP. It looks like they have put some effort into Portuguese systems: https://sourceforge.net/projects/opennlp/files/models-1.5/ The files with the prefix pt- should be for Portuguese. I think. So you could probably get tokenization and part of speech into ctakes. However, that won't be as good as an English translation. Sean -----Original Message----- From: Manuel Lamy [mailto:[email protected]] Sent: Thursday, January 25, 2018 6:02 PM To: [email protected] Subject: Re: Problem using CPE and XMI Writer CAS Consumer [EXTERNAL] Hello Sean, Thanks for the awesome inputs as always! *SNOMED* Afaik SNOMED doesn't exist in the Portuguese language yet. As per my research and this reference[1], SNOMED-CT is only translated for Australian English, Danish, Dutch, Spanish, Swedish, and USA/UK English. Did you hear about SNOMED-CT translated to Portuguese somewhere? I may have to come with a solution for this. It's possible for me to build a mechanism that tries to translate all SNOMED-CT from English to Portuguese, or from the Spanish since it's a close language from Portuguese. I can use many sources, such as ICD-9/10, DBpedia or/and a direct translation tool. However, this path will not be easy to take on my own. But it's a possibility though. I have to think about it. *Bat files in Development Version* I was trying to run the bat files that were inside the module ctakes-distribution of my Dev Version. I guess that was my problem after all. *Translation* Yes, I know cTAKES won't translate for me. I was thinking in using an offline translator and adding it to my pipeline. I have yet to find a translator that is half as good as the Google Translator though. I don't want to rely in an online translator. *Wiki Documentation* Thanks for your compliment. Sure, I would love to help. I like to express myself as clear as possible. However, my knowledge about the system is still limited. I only started using cTAKES a couple of months ago. But if I can help with something just ask me, I would be glad to help. Thanks a lot Sean. Best regards, Manuel Lamy [1] - https://urldefense.proofpoint.com/v2/url?u=https-3A__www.snomed.org_snomed-2Dct_snomed-2Dct-2Dworldwide_translations-2Dof-2Dsnomed-2Dct&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=Dglu7v-Nns-ao41Lbn-oe6MAFF2cEWlkJ-8NQmHv7Xk&e= 2018-01-25 20:43 GMT+00:00 Finan, Sean <[email protected]>: > Hi Manuel, > > Thank you for the information. I have a couple of response lines … > > > > I need to do it because cTAKES seems to not work with the Portuguese > language at all > - Yes and no … You can create a dictionary of terms in the > Portuguese language. This would allow ctakes to at least recognize these > terms and save them for posterity. However, the more advanced processing > available for English (negation, uncertainty detection, etc.) will not be > available. If you can find other nlp projects that work with Portuguese it > may be possible to insert them into a ctakes pipeline. The instructions > for creating a custom dictionary are here (language selection is not > documented but it is on the gui, download the umls with portugese snomed if > you can): > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Dictionary-2BCreator-2BGUI&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=AD732kchCeJtdn_QfNegFdrzKsmW8uw7Nhb-GWg1VRQ&e= > > > What I have in mind is to create a pipeline system that first translates > the texts from Portuguese to English > - Probably a good way to go if you have a decent > translation tool. > > > From my research, I couldn't find anything relevant in this topic. > - We definitely could use more documentation. > > > Well, since this is the user version, I don't have the > runPiperSubmitter.bat available > - Correct. It is a tool that was created after the 4.0 > release. > > > When I try to run the bat files inside the bin of the Dev Version, I > have the results shown in the image attached to this e-mail. > - Your attachments were scrubbed so I can’t see them. > However, I have a guess: did you run a “maven package”, unzip the created > installation file and run from the bin/ directory there? Or are you > running with the bin/ inside your development sandbox? The second method > won’t work and will give you the “class not found” errors that you are > seeing. If you want to run using Intellij, turn on the profile > “runPiperGui” and compile. Maven should launch the gui after compilation. > > > Well, first of all, my objective is to share my experiences with cTAKES, > in order to share with the community what I'm going through. This way I can > contribute to the community and probably help others who are going through > the same as me. > - Excellent. Would you be willing to write documentation > for the ctakes wiki? Your emails are clear and extremely well formatted! > > > 1. Is this feasible? Am I aiming for something that I simply can't rely > in cTAKES only to do, because I have to translate the texts first? > > - Ctakes won’t translate for you, but if you can find a tool that > will then processing with ctakes should be possible. > > 1. Why don't I have a TypeSystem.xml file to feed CVD first, in the > Development Version? I can only find it in the User Version, under > /resources. > > - The typesystem.xml file is in the ctakes-type-system project > until you “maven package” and create an “installation”. If you just run > from your developer environment you can point to the TypeSystem.xml in > ctakes-type-system/src/main/resources/… > > 1. Why do we have options in CVD for other languages, but it clearly > only works for the English language? > > - The cvd is a tool that is part of Apache UIMA. It is more > generic than ctakes and can read xmi files created by other systems. I > have no idea what the details are concerning its language support. > > 1. Any other hint you can give me, concerning the big picture of what > I'm trying to build here? > > - Not really, sorry. The multi-lingual goes outside my area of > knowledge. > > Sean > > > From: Manuel Lamy [mailto:[email protected]] > Sent: Thursday, January 25, 2018 2:28 PM > To: [email protected] > Subject: Re: Problem using CPE and XMI Writer CAS Consumer [EXTERNAL] > > Hello Sean, > > Before all, thansk a lot for the quick and detailed answer. Awesome > support by you. > > I'll give you a structured answer to be the more objective and concise > possible. I guess it's important to tell you what I'm trying to achieve in > order for you to help me. > > My Project > > I'm actually making a project with cTAKES in a partnership with a > Portuguese hospital. > > My goal is to create reports of the narrative parts of the EMRs of this > hospital, in order to report the symptoms, diseases and clinical procedures > found in each EMR. > > What I have in mind is to create a pipeline system that first translates > the texts from Portuguese to English, and then creates these reports based > on the translated texts. > > I'm not even sure yet I can create a pipeline system of this style with > cTAKES. I need to do it because cTAKES seems to not work with the > Portuguese language at all (despite that option being shown in the > languages list when using CVD and that's confusing). So, well, I will > translate it, I guess it's my best bet. > > But just a note, I think it should exist more support and documentation > about how to work with cTAKES in different languages than English. From my > research, I couldn't find anything relevant in this topic. Not even one > reference telling clearly that cTAKES only works with English language and > not with the others. > > Version of cTAKES > > Naturally, I'm running the development version of cTAKES. I'm using > Intellij. I'm using the latest version of cTAKES, trunk, that corresponds > to version 4.0.1-SNAPSHOT. > > So, I guess so far so good, just as you said, I'm using trunk. > > I did everything as per the guide "Developer Install Guide", concerning > the Intellij instructions. The guide I used can be found here: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=e2yD-cLW1Dlpq29Om7A73a4xDPGLDUZSudPClFUEzBU&e= > cTAKES+4.0+Developer+Install+Guide<https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=jykKf1NthK-1Y45BRzYVVVAYQK6939NDMIg-lhY2wLQ&e=. > proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_ > confluence_display_CTAKES_cTAKES-2B4.0-2BDeveloper- > 2BInstall-2BGuide&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjX > OytMmgM0&s=CVSlmO5-wIWG9Bh-dTmpXoUGF5sgLWD2jp4sbGZ8vh8&e=> > > > Behavior of cTAKES when running pipelines > > Well, I did what you told me. I ran the Default Clinical Pipeline and the > Piper File Submitter as per the wiki's. I have the User and Development > versions both in my machine. > > Now, I tried to run those pipelines in the User and Development versions. > I ran the respective bat files: > > > * For the Default Clinical Pipeline I ran 'bin/runClinicalPipeline -i > inputDirectory --xmiOut outputDirectory --user umlsUsername --pass > umlsPassword' > * For the Piper File Submitter, I ran the 'bin/runPiperSubmitter' > Well, the results of running these two bat files were quite differents for > the User and Development versions. > > User Version > > Default Clinical Pipeline > > In this version, I went to bin directory and just ran the line > 'bin/runClinicalPipeline -i inputDirectory --xmiOut outputDirectory > --user umlsUsername --pass umlsPassword' with my parameters. > > It worked well and created the XMI output files where it was supposed. And > I could open them in CVD, first opening a TypeSystem.xml file and then the > generated XMI files I wanted. > > Piper File Submitter > > Well, since this is the user version, I don't have the > runPiperSubmitter.bat available. Is this normal? That's comprehensible and > I guess normal, for what I understand from this quote " If you are running > from a development environment (checked out trunk from SVN) they can also > be run using the Piper File Submitter GUI." But you tell me. > > Well, I can say the User Version did what I wanted in this step, but I > thought that would be nice to replicate it in the Development version, > since I guess I'll have to use it in the future in order to implement all I > want for my project described in the beggining of this e-mail. And the > problems arose in the Development version.... > > Development Version > > Well, in this version, I tried to replicate what I did in the User > version, thinking to myself it would output the same result. I was wrong. > > > Default Clinical Pipeline and Piper File Submitter > > When I try to run the bat files inside the bin of the Dev Version, I have > the results shown in the image attached to this e-mail. > > Yes, could not find or load PiperFileRunner and PiperRunnerGui. Is it > supposed to happen in the Development Version? Am I doing something wrong > in here? i just followed the guides you have available. All my Development > Version installation was per the guide. > > > My objective with this e-mail > > Well, first of all, my objective is to share my experiences with cTAKES, > in order to share with the community what I'm going through. This way I can > contribute to the community and probably help others who are going through > the same as me. > > In second place, I would like to know your opinion about the feasability > of what I'm trying to make here. My goal is build a pipeline system like: > > > * EMRs in Portuguese already in txt files in a directory -> > Translation to English -> Process all of the texts with Clinical Pipeline > -> Output XMI in order to open them in CVD > This is what I aim with cTAKES. So I have the following questions: > > > 1. Is this feasible? Am I aiming for something that I simply can't rely > in cTAKES only to do, because I have to translate the texts first? > 2. Why don't I have a TypeSystem.xml file to feed CVD first, in the > Development Version? I can only find it in the User Version, under > /resources. > 3. Why do we have options in CVD for other languages, but it clearly > only works for the English language? > 4. Any other hint you can give me, concerning the big picture of what > I'm trying to build here? > Any additional information you need from my side, just tell me. > > Thanks one more time for the quick answers and support Sean. > > Best regards, > > Manuel > > > 2018-01-25 15:35 GMT+00:00 Finan, Sean <[email protected] > <mailto:[email protected]>>: > Hi Manuel, > > My first comment is that you are running ctakes in a somewhat “ancient” > manner, or better put, the xml descriptor workflow has been pretty much > deprecated. > > You should try to run ctakes 4.0. If you are software savvy then I advise > that you try the development version that is in trunk. You’ve probably > been on the ctakes download page, but just a reminder : > https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=NmTVdyQzJ4PMX8X5CEfmrRCPBn_0nupPPMBQtp_4Fg8&e=<https://urldefense.proofpoint.com/ > v2/url?u=http-3A__ctakes.apache.org_&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s= > eR4BZrqJcoxN9dwsWE5PUw9qwMAju7w9zOOzqMHT95U&e=> > > The ctakes wiki has some useful information, and the 4.0 entry is here: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=gd_IcjGK3Jvad4c-PYkuLSNXVjLBeSR-VrMEJ19Qrck&e=< > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_ > confluence_display_CTAKES_cTAKES-2B4.0&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s= > IgvR2Z9rgstXIbo3scW0DsWkA59X0ANVuYeO5P5lrwI&e=> > > To start playing with ctakes I suggest that you try to run the default > clinical pipeline, following the instructions here: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=e2yD-cLW1Dlpq29Om7A73a4xDPGLDUZSudPClFUEzBU&e= > Default+Clinical+Pipeline<https://urldefense.proofpoint.com/ > v2/url?u=https-3A__cwiki.apache.org_confluence_display_ > CTAKES_Default-2BClinical-2BPipeline&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s= > hvwwTI35sq53mx3R9TsPtHEF3p2G29qCmVime1NsgKU&e=> > > Those instructions will start the default clinical pipeline from a command > line. If you have the development version from trunk then there is a gui > available to run pipelines: > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=e2yD-cLW1Dlpq29Om7A73a4xDPGLDUZSudPClFUEzBU&e= > Piper+File+Submitter+GUI<https://urldefense.proofpoint.com/ > v2/url?u=https-3A__cwiki.apache.org_confluence_display_ > CTAKES_Piper-2BFile-2BSubmitter-2BGUI&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjX > OytMmgM0&s=HKBfRNAlLaLk9c-sPqupZpQzAc5ddcWbbXvWxRiWwBw&e=> > > There are also many other pipeline configurations available in trunk to > run more advanced / involved pipelines. They are not in the 4.0 release. > The pipelines (including 4.0 default) are all defined using the replacement > for those xml descriptor files. The replacements are called “piper files”. > https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=-ifPT1RLQFSC5JfXB8KiXFFpaWXiwmATZ3ZiEDqR0Mk&e=<https:// > urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache. > org_confluence_display_CTAKES_Piper-2BFiles&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjX > OytMmgM0&s=E7wf87y0Ldqo_pGw2sYdC_DPEeqsmnLYPMkrM5LIz8w&e=> > > I hope that you find the pipers easier to understand and use than the old > xml descriptors. > > Anyway, if you run the ctakes 4.0 default clinical pipeline as outlined in > the wiki page it will use the new FileTreeReader and FileTreeXmiWriter > combination. > > Give it a whirl and let me know how things go. > > Sean > > > From: Manuel Lamy [mailto:[email protected]<mailto:[email protected]>] > Sent: Thursday, January 25, 2018 9:09 AM > To: [email protected]<mailto:[email protected]> > Subject: Re: Problem using CPE and XMI Writer CAS Consumer [EXTERNAL] > > Hello Sean, > > First of all, thanks for your quick answer. > > I'm probably making some confusion over here, so I have the following > questions. > > > 1. A CAS Consumer is defined by a XML file. What you are implying is > that I should go to my consumer XML (__XmiWriterCasConsumer.xml) and change > it's <implementationName> tag to 'org.apache.ctakes.core.cc<htt > ps://urldefense.proofpoint.com/v2/url?u=http-3A__org. > apache.ctakes.core.cc&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc > pKGd4f7d4gTao&m=AApC_ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=77ECYie_ > 8Zy3RN9ARtzl51dBaHan8dijiNX2p0IkjIA&e=>.FileTreeXmiWriter' instead of ' > org.apache.ctakes.core.cc<https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=6E81rE-QEYoyyKHrR6ZHlSurpOHAb_6oRM7SieeLSiU&e=. > com/v2/url?u=http-3A__org.apache.ctakes.core.cc&d= > DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=77ECYie_ > 8Zy3RN9ARtzl51dBaHan8dijiNX2p0IkjIA&e=>.XmiWriterCasConsumer'? Funny > enough, it gives me a classNotFoundException if I do this. Would like to > have your confirmation if I'm doing the right thing please. The class is > well defined in that path though. > 2. Concerning the reader, I make the same analogy. Should I go to my > descriptor and change it's <implementationName> tag from ' > org.apache.ctakes.core.cr<https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=6E81rE-QEYoyyKHrR6ZHlSurpOHAb_6oRM7SieeLSiU&e=. > com/v2/url?u=http-3A__org.apache.ctakes.core.cr&d= > DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=-ag_dLUKFN_aLQ4irY_ > xU_CLzGNrDn6NfV62R5ojs8k&e=>.FilesInDirectoryCollectionReader' to ' > org.apache.ctakes.core.cr<https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=6E81rE-QEYoyyKHrR6ZHlSurpOHAb_6oRM7SieeLSiU&e=. > com/v2/url?u=http-3A__org.apache.ctakes.core.cr&d= > DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=-ag_dLUKFN_aLQ4irY_ > xU_CLzGNrDn6NfV62R5ojs8k&e=>.FileTreeReader'? > I did these two things and the error is the same concerning the new > consumer 'FileTreeXmiWriter', as you can see in the first image attached to > this e-mail. > > I would also like to ask you another question: > > > 3. Why does my class 'FileTreeXmiWriter' has a lot of unresolved > classes? You can see it in the second image attached to this e-mail. I > can't seem to import them right. I tried to import the extension of this > class only to check the result, and look how it solved the import to me. > 'apache' is not recognized. I'm just kinda baffled with the hierarchy > defined for this project. If you could give me a little bit of > clarification in this topic and how to solve it I would be appreciated. > > Thanks for your attention! I'm really looking forward to put this to work. > cTAKES seems awesome. It just needs these little tweaks. > > Best regards, > > Manuel > > > > > > 2018-01-24 22:26 GMT+00:00 Finan, Sean <[email protected] > <mailto:[email protected]><mailto: > [email protected]<mailto:[email protected] > >>>: > Hi Manuel, > > Your image got scrubbed by a server, but the problem may have been fixed > in a recent xmi writer. The latest xmi writer is in ctakes core and is > named FileTreeXmiWriter. One possible cause for a problem in the writer is > if the document has some unexpected character or character combination. A > document reader should be massaging documents before they are processed and > sent to the writer. The most recent file reader is named FileTreeReader > and is also in ctakes core. > > Sean > > > > From: Manuel Lamy [mailto:[email protected]<mailto:[email protected]>< > mailto:[email protected]<mailto:[email protected]>>] > Sent: Wednesday, January 24, 2018 5:10 PM > To: [email protected]<mailto:[email protected]><mailto:d > [email protected]<mailto:[email protected]>> > Subject: Problem using CPE and XMI Writer CAS Consumer [EXTERNAL] > > Hello guys, > > I'm having problems running the CPE using a XMI Writer CAS Consumer. > However, it works with other consumers. > > Problem > > In the figure below, you can see my setup and the error I'm obtaining: > > [Imagem inline 2] > > Logs > > Concerning logs, I'm obtaining this from Intellij: > > org.apache.uima.resource.ResourceInitializationException > at org.apache.uima.collection.impl.CollectionProcessingEngine_ > impl.initialize(CollectionProcessingEngine_impl.java:81) > at org.apache.uima.impl.UIMAFramework_impl._ > produceCollectionProcessingEngine(UIMAFramework_impl.java:438) > at org.apache.uima.UIMAFramework. > produceCollectionProcessingEngine(UIMAFramework.java:918) > at org.apache.uima.tools.cpm.CpmPanel.startProcessing( > CpmPanel.java:573) > at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel. > java:105) > at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713) > Caused by: org.apache.uima.resource.ResourceConfigurationException > at org.apache.uima.collection.impl.cpm.container.CPEFactory. > pro<https://urldefense.proofpoint.com/v2/url?u=http-3A__l.cpm.container. > CPEFactory.pro&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=Kd-RE-JiMaX2AlLA310idXB- > Dyqrbh68kZ24-2ZFEe0&e=>duceIntegratedCasProcessor(CPEFactory.java:1093) > at org.apache.uima.collection.impl.cpm.container.CPEFactory. > getCasProcessors(CPEFactory.java:547) > at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init( > BaseCPMImpl.java:253) > at org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>( > BaseCPMImpl.java:127) > at org.apache.uima.collection.impl.CollectionProcessingEngine_ > impl.initialize(CollectionProcessingEngine_impl.java:73) > ... 5 more > Caused by: java.lang.Exception: The component XMI Writer CAS Consumer > cannot be created. (Thread Name: Thread-5) > ... 10 more > > Attempted Solutions > > I only found one guy with the same problem as me. The solution proposed in > the thread, by Sean Finan, was to change the xml of my consumer > (__XmiWriterCasConsumer.xml), particularly the content of the tag > <implementationName>, from > <implementationName>org.apache.ctakes.core.cc<https:// > urldefense.proofpoint.com/v2/url?u=http-3A__org.apache. > ctakes.core.cc&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=77ECYie_ > 8Zy3RN9ARtzl51dBaHan8dijiNX2p0IkjIA&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=jykKf1NthK-1Y45BRzYVVVAYQK6939NDMIg-lhY2wLQ&e=. > proofpoint.com/v2/url?u=http-3A__apache.ctakes.core.cc&d= > DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=55lXUJ1MFPyBhpVH4sCBuEZD- > InGrPRtD4YTvCJpMFo&s=zBsJhrOUC6BXHsKiMP4cEZTtjqB73N9V-kjGKPhqaNA&e=>. > XmiWriterCasConsumerCtakes</implementationName> > > to > > <implementationName>org.apache.uima.tools.components. > XmiWriterCasConsumer</implementationName> > > > > However, this didn't work. The error is exactly the same. I'm out of ideas > about what to do. I would like to have the report of CPE in XMI, in order > to read it with CVD. You can see the thread here: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201701.mbox_-25&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=VZfX5xii1KxsUcRxcVLFxR6hIhkAwYMQuJyh_SHu7KE&e= > [email protected]%3E< > https://urldefense.proofpoint.com/v2/url?u=http- > 3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201701.mbox_- > 253C29cefd1fa1b44ce4a8dc92ec8b1cd882-40CHEXMAIL1A.CHBOSTON. > ORG-253E&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=AApC_ > ctDoYjWBegXtxXpnBYO1T5L0I1tSjXOytMmgM0&s=_6v4jkcWzpMVtIWPH- > 1GkFuXpcYGRYdjs3sGzVLuEPA&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UOqyIzWZMiqyTVgWAmnNt4cTeil7s4oY_RwVgTy1XI8&s=6E81rE-QEYoyyKHrR6ZHlSurpOHAb_6oRM7SieeLSiU&e=. > com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod- > 5Fmbox_ctakes-2Ddev_201701.mbox_-253C29cefd1fa1b44ce4a8dc92ec8b > 1cd882-40CHEXMAIL1A.CHBOSTON.ORG-253E&d=DwMFaQ&c=qS4goWBT7poplM69zy_ > 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > 55lXUJ1MFPyBhpVH4sCBuEZD-InGrPRtD4YTvCJpMFo&s= > vzHmir9t5IBncKpumZCOCqviJeDNNVl4ZkjEiK9AMp8&e=><https:// > urldefense.proofpoint.com/v2/url?u=http-3A__mail- > 2Darchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201701.mbox_- > 253C29cefd1fa1b44ce4a8dc92ec8b1cd882-40CHEXMAIL1A.CHBOSTON. > ORG-253E&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m= > N5zX2YGt7jbGKsiWAN7z5tdADmV2PwJdHTvvx2oZ2fM&s=5c-Yr8TMBg7- > VyEjwF7gJlT1xP3LpHC6dvnZbihxDPg&e=> > > > > Result Expected > > Running the CPE process and have outputs as XMI files. > > > > Result Obtained > > Running the CPE results in an error, specifically for the consumer > __XMIWriterCasConsumer. > > > > Conclusion > > Do any of you guys had this problem before? Do you have a suggestion about > how can it be solved? Thanks a lot > > > > Best regards, > > Manuel > >
