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 | | | | | | |
|---|
| ncsa.image.ocr | Python | Tesseract | Linux | Rui | ocr | |
|---|
ncsa.cv.faces | Python | OpenCV | Linux | Inna (may be?)cv/browse/opencvLiana | | cv/browse/handwritten/HandwrittenNumbers | |
ncsa.image.caltech101 | | | | | | | |
|---|
| ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | | |
|---|
| ncsa.bisque.metadata (notes: disabled) | Python | | Linux | | | | |
|---|
| census-section-segmentor | Java | | Linux | | |
|---|
ncsa.cv.eyes | Python | OpenCV | Linux | Inna | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/opencv | Liana |
|---|
ncsa.cv.closeups | Python | OpenCV | Linux | InnaopencvprofilesPython| Python | OpenCV (python), convert (from imagemagick), and Gdal | Linux | |
Innaopencvcellprofilerfluorescentcometpymedici 
Windowscv/cellprofilerLianacellprofilerfly Windowscv/cellprofilerLianacellprofilerhuman | | GDAL, Cython, numpy,
pygeoprocessing | Linux |
Windowscv/cellprofilerLianacellprofilersilvercomet WindowscvcellprofilerLianacellprofilerspeckle WindowscvcellprofilerLiana | | Marcus, Ankit |
ncsa.xml.greenindexroute, ncsa. |
|---|
cellprofilertrackobject Windowscv/browse/cellprofilerLianacellprofilertumorPython | | Windows | | Java | CMU Sphinx, ffmpeg, sox | Linux | | |
cvcellprofilerLianacellprofileryeastWindowscvcellprofilerLianaimagesphog| simplelanguage | Python | numpy | |
|---|
Matlab, mnist-sphog Linux | cvhandwritten/HandwrittenNumbers imagecaltech101 | | | | | | | ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | |
|---|
| ncsa.bisque.metadata (notes: disabled) | Python | | Linux | | | |
|---|
census-section-segmentor | Java | | Linux | | cvcensus, Innacvriver PythonOpenCV (python), convert (from imagemagick), and Gdal | Linux | cvrivergeoshpExtractorgdal | LinuxgeoJong Lee | ncsa.geo.tiffExtractorgdalLinuxgeoJong Lee| Gregory Jansen |
| ncsa.versus.image |
|---|
.ponddetectPythonMatlabMarcusmaps/feature_detectionMarcus Ankithumanpref| preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python |
|---|
MatlabLinuxMarcusmapshumanprefMarcus Ankitxml.greenindexroute, ncsa.csv.greenindexroute| pdf.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | | | |
|---|
Python | OpenCV | Linux | Marcusmaps/greenrouteMarcus | ncsa.image.knn_numerals | Python | OpenCV | Linux | Marcus | | Marcusaudio.speech2textJava | CMU Sphinx, ffmpeg, sox | Linux | Marcus | | Marcus | | video.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | |
|---|
ncsa.nlp.simplelanguage | Python | numpynlpSimpleLanguageLiananlpsimplesummaryNatural Language Toolkit (NLTK) for Python, NLTK Data or at least:
nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt.nlpSimpleSummaryLiananlpSNLPSentimentJava | Stanford CoreNLP tool, java, mavennlpSNLP/SNLPSentimentExtractorLiana, Marcus(?)nlpwordtables requests, pika, win32comnlpWordTablesExtractorLianasiegfriedsiegfriedGregory Jansen | ncsa.versus.image | JavaversusKenton, Smruti | | | | | | | |
|---|
| | | | | | | |
|---|
NOT DEPLOYED | | ncsa.image.digitpy (notes: not in the Wiki page) | Python | opencv | | | cv/handwritten/SimpleDigitPython | ncsa.cv.pdfimages (not in the wiki page) | | pdfimages, 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 |
|---|
digest | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | |
|---|
digest | ncsa.image.geotiffGDAL Cython numpy,pygeoprocessing,pika,requests| openpyxl, xlrd, pymongo | Linux | | |
Linux | Ruigeotiffncsa.hpc | Python | | | Rui, Mostafa Elag | | /IsletExtractor | Yan |
| msc-MonitorExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | | |
|---|
hpc | LSVA | | /MonitorExtractor | Yan |
| ncsa.msc.dailymonitor | Python | requests, pika, openpyxl, xlrd, pymongo |
|---|
Java lsva | LSVA integrated | lsva-integrated movieslicePythonmoviesliceSandeep | mri2meshpymedici, subprocess, logging, os, numpy, shutil, zipfilemrimri2meshMarcusmscChemCBCExtractormscChemCBCExtractorYanmscIsletExtractorrequests, pika, openpyxl, xlrd, pymongomscIsletExtractorYan | msc-MonitorExtractor, pika, openpyxl, xlrd, pymongomsc/MonitorExtractorncsa.msc.dailymonitor | Python | requests, pika, openpyxl, xlrd, pymongomscOldMonitorExtractorAshwini | msc-PhenotypeExtractor | Python | requests, pika, openpyxl, xlrd, pymongomscPhenotypeExtractorYan | ncsa.nlp.SNLP | Java | 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 |
extractors-rabbitmq (look like examples) | | | |
|---|
terra.plantcv | Python | pikarequestswheelplantcvYan | medici_PTM_thumbnails | Javaptm/PTMThumbnailExtractorConstantinosPTM_metadataptmPTMMetadataExtractorPtmMetadata(?Name not clear
ptmPTMMetadataptm_mapsptmPTMMapsExtractorptm_3dptmPTM3DExtractorimages_ptmptmImagesPTMExtractorrabbitmq(look like examples)rabbitmq | Name not clear extractors-seabird/ | Scala | | | seabirdLuigi | medici_3d_x3d (one of extractors-3d) | Java | | | 3d/browse/ObjJSONExtractorConstantinos | medici_3d_obj_merger (one of extractors-3d) | Java3dOBJMergerExtractorConstantinos_oni (one of extractors-3d)3dOniExtractorConstantinos | medici_ply_obj (one of extractors-3d) | Java3d/PlyObjExtractorConstantinos | medici_3d_metadata (one of extractors-3d) | Java | | 3dThreeDMetadataExtractorConstantinos | medici_x3d_html (one of extractors-3d) 3d/X3DhtmlExtractorarcgis.landsat7mosaicbd-cz/ndviextractorSmrutiarcgisfloodplainbd-czterex_floodplain/config.pySmruti | medici_book | JavaCATSbooks/BookPreviewExtractorTheerasit Issaranon | medici_image_pyramid | JavaCATSbooks/ImagePreviewPyramidExtractor-shebookTheerasit Issaranon | shebook | Java | | | CATSbooks/browse/SheBookPreviewExtractor/src/BookPreviewExtractorCATSbooks/browse/SheBookPreviewExtractor/src/bookpreviewextractorTheerasit Issaranon | lsva-cedd | JavaCATS-ceddbrowseConstantinoscinemetricsPythonCATS-cinemetricsbrowseConstantinos