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
- Learn about jsonld by playing in the playground here http://json-ld.org/
- Go through the README for the docker extractors template: https://opensource.ncsa.illinois.edu/bitbucket/projects/BD/repos/bd-extractor-template/browse
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 | | DEPLOYED | | | | | | |
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| ncsa.image.ocr | Python | Tesseract | Linux | Rui | ocr | |
|---|
ncsa.cv.facesInna (may be?)eyesprofiles | Python | OpenCV | Linux | |
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Innacvcloseupsfluorescentcomet | Python | pymedici  |
|---|
OpenCVLinuxInnaopencvcvprofilesOpenCVLinuxInnaopencvfluorescentcometpymedici flyhumansilvercometspeckletrackobjectcellprofilertumorsphog | Python | Matlab, mnist-sphog |
|---|
Windows/cellprofilerLianacellprofiler.yeast| bisque.metadata (notes: disabled) | Python | | Linux | | | | |
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| census-section-segmentor | Java |
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PythonWindowscellprofilerimagesphogPython | Matlab, mnist-sphog handwritten/HandwrittenNumbers image.caltech101 | | | | | | | ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | |
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ncsa.bisque.metadata (notes: disabled) | | census-section-segmentor | Java | cv/censusLiana, Innacvriver Python | OpenCV (python), convert (from imagemagick), and Gdalcv/riverLianageoshpExtractorgdalJong LeegeoJong LeegeotiffExtractorgdalJong LeegeoJong Lee | ncsa.image.ponddetect| /humanpref | Marcus, Ankit |
ncsa.xml.greenindexroute, ncsa.csv.greenindexroute | Python |
|---|
Matlabfeature_detection, Ankithumanprefknn_numerals | Python | OpenCV | Linux | | | | Marcus |
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ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | Linux | | |
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Python | Matlab | Linux | Marcusmapshumanpref, Ankitxml.greenindexroute, ncsa.csv.greenindexrouteOpenCVLinuxMarcusmapsgreenrouteMarcusimageknn_numeralsOpenCV | Linux | Marcus | | Marcus | ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | Linux | Marcuscoreaudio/speech2textMarcusaudiopreview| 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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Python | coreaudio/preview simplelanguagePython | numpySimpleLanguage.simplesummaryPython | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least:
nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt.SimpleSummaryncsa.nlp.SNLPSentiment | Java | Stanford CoreNLP tool, java, mavennlp/SNLP/SNLPSentimentExtractorLiana, Marcus(?)nlpwordtablesPython | requests, pika, win32com nlp/WordTablesExtractorLiana | | Kenton, Smruti |
| ncsa.image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | |
|---|
siegfried | Pythonsiegfried/browseGregory Jansen | ncsa.versus.image | Java | Versus | Linux | | core/browse/image/preview | Rob, Sandeep |
| ncsa.pdf.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | | | |
|---|
Smruti PadhyversusKenton, Smrutiimageimage, Sandeepncsa.pdf.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | |
| NOT DEPLOYED |
|---|
| ncsa.image.digitpy | Python | opencv |
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PythoncorepdfpreviewRobvideo.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.)| cv.pdfimages | | pdfimages, from poppler-utils |
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Pythoncorevideo/previewRob | | | | ncsa.cv.caltech101 | Python | Matlab and VLFeat | 64-bit Mac OS |
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| | | | | | | |
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| | | | | NOT DEPLOYED | | | | | | |
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ncsa.image.digitpy | Python | opencvcv/handwritten/SimpleDigitPythoncv.pdfimagespdfimages, from poppler-utilscv/poppler | ncsa.cv.caltech101 | Python | Matlab and VLFeat | 64-bit Mac OS cv/vlfeatPython | Liana, Constantinos |
| LSVA integrated | |
|---|
dbpedia | Natural Language Toolkit (NLTK) and rdflib.Luigi MarinidbpediaLuigi Marini | digestdigest | ncsa.image.geotiffGDAL, Cython| pymedici, subprocess, logging, os, numpy, |
pygeoprocessingpika,requestsRuiLinux | geotiffRui, Mostafa Elag | ncsa.hpc | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | |
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hpc | LSVA | | /ChemCBCExtractor | Yan |
| msc-IsletExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
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Javalsva | LSVA integrated | | /IsletExtractor | Yan |
| msc-MonitorExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
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lsva-integrated movieslice| dailymonitor | Python | requests, pika, openpyxl, xlrd, pymongo | | |
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moviesliceSandeepmri2mesh| msc-PhenotypeExtractor | Python |
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pymedici subprocess logging, os, numpy, shutil, zipfilemrimri2meshMarcus | msc-ChemCBCExtractor | PythonLinuxYanmscChemCBCExtractorYan | msc-IsletExtractorrequests, pika, openpyxl, xlrd, pymongo | Linux | YanmscIsletExtractorYanmscMonitorExtractor| detector | Python | MATLAB, FFMPEG, requests |
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, pika, openpyxl, xlrd, pymongoLinux | YanmscMonitorExtractorYanmsc.dailymonitor| person-tracker | Python | python, MATLAB, FFMPEG requests |
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, pika, openpyxl, xlrd, pymongonot usedmscOldMonitorExtractorAshwini | msc-PhenotypeExtractor, pika, openpyxl, xlrd, pymongoLinux | Yanmsc/PhenotypeExtractorncsa.nlp.SNLP| medici_PTM_thumbnails | Java | | |
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Stanford CoreNLP tool, java, mavennlpSNLP/SNLPExtractorLiana | ncsa.nlp.tika | Python | Tika project page, pymedicinlptikaLiana | person-detector | Python | MATLAB, FFMPEG, requests and pikaperson-detectorpythonSandeep | ncsa.person-tracker | Python | python, MATLAB, FFMPEG requests and pikaperson-trackingpythonSandeep | | Constantinos |
| medici_ptm_3d | Java | | |
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terra.plantcv | Python | pikarequestswheelplantcvYanPTMthumbnailsPTMThumbnailExtractorConstantinos | medici_PTM_metadata | Javaptm/PTMMetadataExtractorConstantinosPtmMetadata(?)
Javaptm/PTMMetadataConstantinosptm_mapsptmPTMMapsExtractor_ptm_3dJavaptmPTM3DExtractorimages_ptmptmImagesPTMExtractorrabbitmq(look like examples)rabbitmq | Name not clear extractors-seabird/ | ScalaseabirdLuigi3dx3d ObjJSONExtractormedici_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 | | 3d/X3DhtmlExtractorConstantinos | ncsa.arcgis.landsat7mosaic | Python | ArcGIS | Windows | Smruti Padhybd-cz/ndviextractorSmrutiarcgis.floodplainArcGISWindowsSmruti Padhybd-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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