Metamap | First iteration of the 'metamaps ' platform
kandi X-RAY | Metamap Summary
kandi X-RAY | Metamap Summary
First iteration of the 'metamaps' platform. A tool for knowledge cartography.
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Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of Metamap
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QUESTION
I've been playing around with metaclasses to try and get a good feel of them. A really simple (and pointless) one I came up with is the following:
...ANSWER
Answered 2021-Jun-10 at 12:16I realize this may create more trouble than it solves, but if you don't plan to derive anything from MappingMeta, this seems to get around the problem (in that your code above runs).
QUESTION
I am parsing an XMI/XML data structure into a pandas dataframe by first decomposing it into a dictionary. When I encounter a named tuple in a list in my XMI, there appear to be a maximum of two named tuples in my list (although the majority only have one).
To handle this case, I am doing the following:
...ANSWER
Answered 2020-May-03 at 02:33- Iterate over
Negationnamedtuples- for each thing in
negation.modifier- add a row using the negation attributes and the things attributes
- for each thing in
Or instead of parsing XML to namedtuples to dictionaries skip the middle part and create a single dictionary - {'begin':[row0,row1,...],'end':[row0,row1,...],'negtrigger':[row0,row1,...],'negtype':[row0,row1,...]} - from the XML
QUESTION
I am trying to return a Map from a scala method as below.
I have two different Maps with some matching keys. I need to find the matching keys between them and pick the values out of them and put them in another Map in the way I wanted. Below is the code I wrote for the aforementioned action.
...ANSWER
Answered 2019-May-01 at 08:10map preserves the collection type. You can map a List to another List, and, in the end, cast your List directly to a Map
QUESTION
I am trying to get a service running in minikube (MetaMap Tagger service, medpost-skr).
I have the following Docker file that runs fine on its own:
...ANSWER
Answered 2019-Apr-03 at 19:24The issue was that these services were being started as background processes. Starting them in the foreground was the solution.
QUESTION
We keep encountering a java.lang.OutOfMemoryError: Java heap space error when running MetaMap (with Java API and UIMA wrapper).
Unfortunately, the logs are not very informative, so we don't know which file it's puking on.
In the past, we've had issues with MetaMap creating huge circular annotations when it's encountered the pipe (|) symbol. However, the file set we're using (MIMIC notes) don't contain any pipe symbols. Are there other characters that may be exhibiting similar behavior to the pipe symbol?
We could increase system RAM to circumvent the heap space issue (it's actually not able to use the maximum set heap, which is set to 6 GB, since system RAM is limited), but we would prefer to know what is causing the issue, especially since then the output file size is more manageable.
* EDIT *
Just to clarify: We have increased memory resources for the JVM and that does help to actually push the data through (this was tested on a local VM). The problem MetaMap has is that it creates enormous circular annotations that eat up the JVM resources (and on our current system, the OS RAM is not optimal).
As noted in my comment below, we preprocess the files to strip them of any characters that throw errors. The heap space error is kind of annoying though, since unlike for other errors we've encounter (e.g., spaces surrounding a lone period, as in text . text), these just throw a parsing error with the text that threw the error. In the case of the pipe symbol, we found it by increasing RAM (on the VM we were initially testing this on) and then looking at the annotations in the UIMA viewer. We were able to identify the problematic files, since the output file size of the XMI with circular annotations is enormous.
We are running some tests on the VM again to see if we can identify the issue, but if anyone has MetaMap experience to help us identify any problem characters or character sequences, that would be desirable.
* EDIT 2 *
Memory should not be an issue. We are running the app using export JAVA_TOOL_OPTIONS='-Xms2G -Xmx6G -XX:MinHeapFreeRatio=25 -XX:+UseG1GC'
there is a fundamental issue with circular annotations we are trying to resolve. This is gobbling up resources and puking.
...ANSWER
Answered 2019-Jan-04 at 19:09I would like to add recommendations from oracle trouble shooting article
Exception in thread thread_name: java.lang.OutOfMemoryError: Java heap space
The detail message Java heap space indicates object could not be allocated in the Java heap. This error does not necessarily imply a memory leak
Possible causes:
Simple configuration issue, where the specified heap size
is insufficient for the application.
- Application is unintentionally holding references to objects, and this prevents the objects from being garbage collected.
- Excessive use of finalizers.
One other potential source of this error arises with applications that make excessive use of finalizers. If a class has a finalize method, then objects of that type do not have their space reclaimed at garbage collection time
After garbage collection, the objects are queued for finalization, which occurs at a later time. finalizers are executed by a daemon thread that services the finalization queue. If the finalizer thread cannot keep up with the finalization queue, then the Java heap could fill up and this type of OutOfMemoryError exception would be thrown.
One scenario that can cause this situation is when an application creates high-priority threads that cause the finalization queue to increase at a rate that is faster than the rate at which the finalizer thread is servicing that queue.
QUESTION
I am trying to compile, in Visual Studio 2015, a DLL that I am making which acts as a C-compatible wrapper around some functionality from OpenVDB, making it usable in an existing C project. When I build, however, I get the following Linker Errors:
...ANSWER
Answered 2017-Jun-26 at 16:11It turned out to be a combination of a couple problems:
- My OpenVDB binaries were compiled with OPENVDB_3_ABI_COMPATIBLE defined, and so were using the boost version of shared_ptr instead of the std version, but I hadn't defined OPENVDB_3_ABI_COMPATIBLE when trying to build my project, so it was trying to build using the std version; hence, undefined externals.
- I hadn't defined OPENEXR_DLL and HALF_EXPORTS, which is evidently required when building with those libraries, unbeknownst to me.
- I was compiling with the /MT option instead of the /MDd option used by half.lib
In the end, all I needed to do was define OPENEXR_DLL, HALF_EXPORTS, and OPENVDB_3_ABI_COMPATIBLE, and switch the build option to /MDd.
QUESTION
I'm developing an application that parses a text file and looks for times between certain sent actions, a simple visual aid in short.
My issue is that the sorting on the StackedBarCharts x-axis has gone awry, as shown by the image linked below;
The relevant code for generating these charts;
...ANSWER
Answered 2017-Jun-07 at 21:03Found the solution after an extensive amount of banging my head against the wall of not understanding:
- First of all, don't programatically skip adding any values to the original series. Add all 0-values ranging between the values you want to keep. This is for sorting purposes.
- Remove all 0-values when you've finalized the adding of new data.
This is the snippet of code I've used to remove the 0-values, modify for your own purposes as you wish.
QUESTION
I have a document with an Map field, similar to this:
...ANSWER
Answered 2017-Jun-01 at 08:36 DBObject queryObject = new BasicDBObject("someUniqueField", "value");
BasicDBObject newMap = new BasicDBObject("metaMap.k2", "new-v2");
newMap.put("metaMap.k3", "v3");
DBObject updateObject = new BasicDBObject("$set", newMap);
mongoTemplate.getCollection("collectionName").update(queryObject, updateObject);
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