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?) | opencvcveyesOpenCVLinuxInnaopencvcvcloseupsOpenCV| Matlab, mnist-sphog | Linux | |
Inna/opencvLiana | ncsa.cv.profiles | Python | OpenCV | Linux | Inna | https://opensource.ncsa.illinois.edu/bitbucket/projects/CATS/repos/extractors-cv/browse/opencv | Liana |
|---|
ncsa.cellprofiler.fluorescentcomet | Python | pymedici  | Windows | | /handwritten/HandwrittenNumbers | |
ncsa.image.caltech101 | | | | | | | |
|---|
| ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | | |
|---|
| ncsa.bisque.metadata (notes: disabled) | Python | | Linux | | | | |
|---|
| census-section-segmentor | Java | | Linux | | |
|---|
cellprofilercellprofilerflyPython | | Windows | | Python | OpenCV (python), convert (from imagemagick), and Gdal | Linux | | |
cellprofilercellprofilerhuman Windowscv/cellprofilerLianacellprofilersilvercomet | tiffExtractor | Python | gdal | Linux | |
|---|
Windows | cv/cellprofilerLianacellprofilerspeckle | | GDAL, Cython, numpy,
pygeoprocessing | Linux |
Windowscv/cellprofilerLianacellprofilertrackobject WindowscvcellprofilerLianacellprofilertumor WindowscvcellprofilerLiana | | Marcus, Ankit |
ncsa.xml.greenindexroute, ncsa. |
|---|
cellprofileryeast WindowscvcellprofilerLianasphog Matlab, mnist-sphog cvhandwrittenHandwrittenNumbers image.caltech101 | | | | | | | ncsa.bisque.histogram (notes: disabled) | Python | | Linux | | | |
|---|
ncsa.bisque.metadata (notes: disabled)Linux | | census-section-segmentor | Java | | Linux | cvcensus, Innacvriver Python | OpenCV (python), convert (from imagemagick), and Gdal | Linux | | Python | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least: nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt. | | | |
cvrivergeo.shpExtractorPython | gdal | Linux | Jong LeegeoJong LeegeotiffExtractorgdal | Linux | Jong LeegeoJong Lee | ncsa.image.ponddetectMatlabLinuxMarcusmaps/feature_detectionMarcus, Ankit.humanprefPythonMatlabMarcusmaps/humanprefMarcus Ankitxml.greenindexroute, ncsa.csv.greenindexroute| image.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | | | |
|---|
Python | OpenCV | Linux | MarcusmapsgreenrouteMarcus | | 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 | | |
|---|
ncsa.image.knn_numerals | Python | OpenCV | Linux | Marcus | | Marcus |
|---|
ncsa.audio.speech2text | Java | CMU Sphinx, ffmpeg, sox | Linux | Marcus | | Marcus |
|---|
ncsa.nlp.simplelanguage | Python | numpynlpSimpleLanguageLiananlp.simplesummaryPython | Natural Language Toolkit (NLTK) for Python, NLTK Data or at least:
| video.preview (note: check if really deployed. there is an extractor in Hosted VMs list with a similar name.) | Python | | |
|---|
nltk.corpus,nltk.stem.porter and nltk.tokenize.punkt.nlpSimpleSummaryLiananlpSNLPSentimentJavaStanford CoreNLP tool, java, mavennlpSNLP/SNLPSentimentExtractorLiana, Marcus(?)nlpwordtablesPython requests, pika, win32comnlpWordTablesExtractorLiana | siegfriedsiegfriedGregory Jansen | ncsa.versus.image | Java | Versus | Linux | Smruti PadhyversusKenton, Smruti | | | | | | | | | | |
|---|
| | | | NOT DEPLOYED | | | | image.digitpy (notes: not in the Wiki page)Python | opencvcv/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 | | /mri2mesh | Marcus |
| msc-ChemCBCExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux | | |
|---|
digest | Python | | | digest | ncsa.image.geotiff| Yan |
| msc-IsletExtractor | Python |
|---|
GDAL Cython numpypygeoprocessingpika,requestsLinux | RuigeotiffRui, Mostafa Elag | | /IsletExtractor | Yan |
| msc-MonitorExtractor | Python | requests, pika, openpyxl, xlrd, pymongo | Linux |
|---|
ncsa.hpc | Pythonhpc | 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, zipfile mrimri2meshMarcusmscChemCBCExtractormscChemCBCExtractorYanmscIsletExtractor| tracker | Python | python, MATLAB, FFMPEG requests |
|---|
, 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_metadataptmPTMMetadataExtractorName not clear
PtmMetadata(?ptmPTMMetadataptm_mapsptmPTMMapsExtractorptm_3dptmPTM3DExtractor_images_ptmJavaptmImagesPTMExtractorrabbitmq(look like examples)rabbitmq | Name not clear extractors-seabird/ | Scala | | | seabirdLuigi | medici_3d_x3d (one of extractors-3d) | Java | | | 3d/ObjJSONExtractorConstantinos | medici_3d_obj_merger (one of extractors-3d) | Java3dOBJMergerExtractorConstantinos_oni (one of extractors-3d)3dOniExtractorConstantinos | medici_ply_obj (one of extractors-3d) | Java/extractors-3d/browse/PlyObjExtractorConstantinos | medici_3d_metadata (one of extractors-3d) | Java | | 3dThreeDMetadataExtractorConstantinos | medici_x3d_html (one of extractors-3d) | Java3d/X3DhtmlExtractorarcgis.landsat7mosaicArcGISWindowsSmruti Padhybd-cz/ndviextractorSmrutiarcgisfloodplainArcGISWindowsSmruti Padhybd-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