This page is for the refactoring of the existing extractors. The original wiki page Hosted VMs is still used for the deployments.
As we figure out who's working on what, please start with the following steps for the extractor(s) you chose:
- be able to run the extractor
- add a README, specifically a readme.md (i.e. in markdown), with information on how to install dependencies and run the extractor (in its current shape)
- start looking at dbpedia extractor for template on how to dockerize it
- ... more to come
Steps to take for every extractor in this list:
- Docker containers
- JSONLD
- Extractor info registration
- Use pyclowder (for python extractors)
- Add status messages to all extractors and fix level granularity
- Make status constants (DONE, ERROR)
- Arcgis multiprocessing extractor
- Register on on demand execution queues
- Add on demand key binding to configuration file: messageType = "*.file.text.plain", "extractors."+extractorName
- Standardize around python logging
- Figure out what to log and what format to follow
Add logstash to docker compose- Add sample input/ouput to git repository
- Add icon for tools catalog to git repository
- Add entry to Tools catalog, with icon
ID (Extractor Name from config file, same as queue name) | Programming Language | Software | OS | Assigned To | Link to repo | Who wrote or worked on the code |
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| DEPLOYED | | | | | | |
|---|
| ncsa.image.ocr | Python | Tesseract | Linux | Rui | ocr | |
|---|
ncsa.cv.faces | Python | OpenCV | Linux | Inna (may be?) | opencvcveyesOpenCVLinuxInnaopencvcvcloseupsOpenCVLinuxInnaopencvcvprofilesOpenCVLinuxInnaopencvfluorescentcometpymedici 
flyhumancellprofilersilvercomet| Matlab, mnist-sphog | Linux |
Windows/cellprofilerLianacellprofiler.speckle| bisque.histogram (notes: disabled) | Python | | Linux | |
|---|
Windowshttps://opensource.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/cellprofilerLiana | ncsa.cellprofiler.trackobject | Python | | Windows | | | bisque.metadata (notes: disabled) | Python | | Linux | | | | |
|---|
| census-section-segmentor | Java | | Linux | | |
|---|
cellprofilercellprofilertumorPythonWindows | | (python), convert (from imagemagick), and Gdal | Linux | | |
cellprofilercellprofileryeast Windowscv/cellprofilerLianaimagesphog Matlab, mnist-sphog Gregory Jansencv/handwritten/HandwrittenNumbers caltech101 | | | Gregory Jansen | | | ncsa.bisque.histogram (notes: disabled) | Python | | Python | GDAL, Cython, numpy,
pygeoprocessing |
| bisque.metadata (notes: disabled) census-section-segmentor | Java | | Linux | | | cvcensusLiana Innacvriver Python | OpenCV (python), convert (from imagemagick), and GdalSmruti PadhycvriverLiana | | Marcus, Ankit |
ncsa.xml.greenindexroute, ncsa. |
|---|
geoshpExtractorgdalJong LeegeoJong LeegeotiffExtractorgdal | Linux | | OpenCV | Linux | | | | Marcus |
ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | Linux | | |
|---|
Jong LeegeoJong LeeimagegeotiffGDAL, Cython, numpy,
pygeoprocessing | Linux | RuigeotiffRui, Mostafa Elagimageponddetect| simplelanguage | Python | numpy |
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MatlabLinuxMarcusmapsfeature_detectionMarcus, Ankit | | SimpleLanguage | Liana |
| ncsa.nlp.simplesummary | Python | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least: nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt. | | | |
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ncsa.image.humanpref | Python | Matlab | Linux | MarcusmapshumanprefMarcus, Ankitxml.greenindexroute, ncsa.csv.greenindexroutePython | OpenCV | Linux | Marcusmapsgreenrouteimageknn_numeralsOpenCV | LinuxMarcus | | Marcus | ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | Linux | Marcuscoreaudio/speech2textMarcus | ncsa.audio.previewcore/browse/audio/preview nlpsimplelanguagePythonnumpy nlp/SimpleLanguageLiananlp.simplesummaryPython | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least: nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt. | | | image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | | | |
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Gregory JansennlpSimpleSummaryLiananlp.SNLPSentimentJava | Stanford CoreNLP tool, java, mavennlpSNLPSNLPSentimentExtractorLiana, Marcus(?) | | preview | Rob |
| ncsa.video.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) |
|---|
ncsa.nlp.wordtablesrequests, pika,win32comnlp/WordTablesExtractorLiana | siegfried | PythonsiegfriedGregory JansenversusimageJava | Versus | Linux | | pdfimages | | pdfimages, from poppler-utils | | | |
|---|
Smruti PadhyversusKenton, Smruti | ncsa.image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | |
| ncsa.cv.caltech101 | Python | Matlab and VLFeat | 64-bit Mac OS |
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coreimage/previewRob, Sandeep | ncsa.pdf.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.)core/pdf/previewRob | ncsa.video.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Pythoncore/video/previewRob | | | | | | | | |
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NOT DEPLOYED | | | ncsa.image.digitpy | Python | opencv | | cv/handwritten/SimpleDigitPython | | Liana, Constantinos |
| LSVA integrated |
|---|
ncsa.cv.pdfimagespdfimages, from poppler-utilscv/poppler cv.caltech101Matlab and VLFeat64-bit Mac OS cv/vlfeat dbpedia Natural Language Toolkit (NLTK) and rdflib.| pymedici, subprocess, logging, os, numpy, shutil, zipfile | | |
Luigi MarinidbpediaLuigi Marini | | Marcus |
| msc-ChemCBCExtractor |
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digest | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | |
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digest | ncsa.hpc | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | | |
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hpc | LSVA | | /IsletExtractor | Yan |
| msc-MonitorExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
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Javalsva | LSVA integrated | | /MonitorExtractor | Yan |
| ncsa.msc.dailymonitor | Python | requests, pika, openpyxl, xlrd, pymongo |
|---|
lsva-integrated | | Ashwini |
| msc-PhenotypeExtractor |
|---|
ncsa.movieslice | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | | |
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moviesliceSandeep | mri2mesh | Python | pymedici, subprocess, logging, os, numpy, shutil, zipfilemrimri2meshMarcus | msc-ChemCBCExtractorrequests,pikaopenpyxl, xlrd, pymongoLinuxYanmscChemCBCExtractorYanmscIsletExtractorrequests, pika, openpyxl, xlrd, pymongo | Linux | | MATLAB, FFMPEG, requests and pika | | | |
YanmscIsletExtractorYanmscMonitorExtractor| tracker | Python | python, MATLAB, FFMPEG requests |
|---|
, pika, openpyxl, xlrd, pymongoLinux | YanmscMonitorExtractorYanncsamsc.dailymonitor| plantcv | Python | pika
requests |
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, pika, openpyxl, xlrd, pymongonot usedmsc/OldMonitorExtractorAshwini | msc-PhenotypeExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | | Yan |
| medici_PTM_thumbnails | Java | | | | |
|---|
YanmscPhenotypeExtractorYan | | Constantinos |
| medici_PTM_metadata |
|---|
ncsa.nlp.SNLPStanford CoreNLP tool, java, mavennlpSNLP/SNLPExtractorLiana | ncsa.nlp.tika | Python | Tika project page, pymedicinlptikaLiana | person-detector | Python | MATLAB, FFMPEG, requests and pikaperson-detector/pythonSandeep | ncsa.person-tracker | Python | python, MATLAB, FFMPEG requests and pikaperson-trackingpythonSandeep | | Constantinos |
| medici_images_ptm | Java | | |
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terra.plantcv | Python | pikarequestswheelplantcv/browseYan | medici_PTM_thumbnails | Javaptm/PTMThumbnailExtractorConstantinos | medici_PTM_metadata | Java | ptm/PTMMetadataExtractorConstantinos | Name not clear
PtmMetadata(?ptmPTMMetadataptm_mapsptmPTMMapsExtractorptm_3dptmPTM3DExtractorimages_ptmptmImagesPTMExtractorrabbitmq(look like examples)rabbitmq | Name not clear extractors-seabird/ | ScalaseabirdLuigi | medici_3d_x3d (one of extractors-3d) | Java | | | extractors3dObjJSONExtractorConstantinos | medici_3d_obj_merger (one of extractors-3d) | Java | | | 3d/OBJMergerExtractorConstantinosoni (one of extractors-3d)3dOniExtractorConstantinosply_obj (one of extractors-3d)3dPlyObjExtractorConstantinos | medici_3d_metadata (one of extractors-3d) | Java3d/ThreeDMetadataExtractorConstantinos | medici_x3d_html (one of extractors-3d) | Java | | 3dX3DhtmlExtractorConstantinos | ncsa.arcgis.landsat7mosaic | Python | ArcGIS | Windows | Smruti Padhybd-cz/ndviextractorSmrutiarcgis.floodplainArcGISWindowsSmruti Padhy-bd-cz/browse/terex_floodplain/config.pySmruti | medici_book | Javabooks/BookPreviewExtractorTheerasit Issaranon | medici_image_pyramid | JavaCATSbooks/ImagePreviewPyramidExtractor-shebookTheerasit Issaranon | shebook | JavaCATSbooks/SheBookPreviewExtractor/src/BookPreviewExtractor CATSbooks/SheBookPreviewExtractor/src/bookpreviewextractorTheerasit Issaranon | lsva-cedd | JavaCATSceddConstantinos.cinemetricsPython/CATS/repos-cinemetricsbrowseConstantinosimagemetadataPythonCATSextractors-coreimagemetadataMax. Rob | | | | | | | | |
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