Document AMI tools

[petermr]

No description provided.

[petermr]

AMI tools are written in picocli which documents what each tool does, but not a list of them. Here's the current list, by Java search but it needs checking and testing. Also the commandline is generated by appassembler so soime comands may be missing:

AMIAssertTool.java
// not yet exposed
AMICleanTool.java
// ami-clean cleans specific files or directories in project, explicitly or by regex
// needs testing
AMIDictionaryTool.java
// ami-dictionary makes or modifies dictionaries 
AMIDisplayTool.java
// ami-display not deployed, displays CTree
AMIDownloadTool.java
// ami-download scrapes and downloads. Extensive.
AMIDummyTool.java
// example of a Tool
AMIFilterTool.java
// ami-filters filters images
AMIForestPlotTool.java
// ami-forestplot analyses Forest plot images (specialist but advanced)
AMIGetpapersTool.java
// ami-getpapers convenience wrapper not yet deployed
AMIGraphicsTool.java
// ami-graphics transforms images into objects - complex, hairy
AMIGrobidTool.java
// ami-grobid wrapper for grobid.
AMIImageFilterTool.java
// ami-filter filters images
AMIImageTool.java
// ami-image analyzes images
AMIMakeProjectTool.java
// ami-makeproject makes the project from raw files
AMIMetadataTool.java
// ami-metadata analyzes metadata and transforms it
AMIOCRTool.java
// ami-ocr runs tesseract and/or gocr and transforms result to text
AMIPDFTool.java
// ami-pdf runs PDFBox , collects SVG or Text and analyses
AMIPixelTool.java
// ami-pixel turns bitmaps into graphs (nodes and edges)
AMIRegexTool.java
// ami-regex searches using regex
AMISearchTool.java
// ami-search searches with dictionaries and analyzes results
AMISectionTool.java
// ami-section breaks documents into sections
AMISummaryTool.java
// ami-summary collects summary information
AMISVGTool.java
// ami-svg builds complex objects from SVG
AMITableTool.java
// ami-table extracts tables from documents
AMITransformTool.java
// ami-transform transforms between a wide range of document types
AMIWordsTool.java
// ami-words word frequencies and other tools

Note some of these are prototypes, others very complex. Several can be chained although at present it requires running each job separately in order

[remkop]

Part of this can be automated. As mentioned in #16, picocli can generate man pages for all commands, in unix man page format as well as PDF and HTML. That is the easy part. :-)

More difficult is tutorial type documentation for new users, perhaps similar to AMI-STEM.md.

UPDATE:

I just found https://github.com/petermr/openVirus/wiki/How-ami-search-works/ and I will edit there.

[petermr]

Documentation: One aspect of `picocli`s inheritance is to balance options in AbstractAMITool and the subclasses. There's 20 Options and they appear in every subclass even if they're never used. Q1: is there a way of switching Options off completely in a subclass? Q2: if not, can the docs be switched off?

…

On Sat, Apr 4, 2020 at 11:19 PM Remko Popma ***@***.***> wrote: Part of this can be automated. As mentioned in #16 <#16>, picocli can generate man pages for all commands, in unix man page format as well as PDF and HTML. That is the easy part. :-) More difficult is tutorial type documentation for new users, perhaps similar to AMI-STEM.md <https://github.com/petermr/ami3/blob/master/AMI-STEM.md>. UPDATE: I just found https://github.com/petermr/openVirus/wiki/How-ami-search-works/ and I will edit there. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFTCS4AOAMVAWRFTGIYCA3RK6W6JANCNFSM4LVSZJVQ> .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[remkop]

@petermr I raised a separate ticket #23 for the "too many shared options" problem.