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path: root/src/Text/Pandoc/Readers/JATS.hs
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2021-11-20Capture `alt-text` in JATS figures (#7703)Albert Krewinkel1-2/+13
Co-authored-by: Aner Lucero <4rgento@gmail.com>
2021-05-09Change reader types, allowing better tracking of source positions.John MacFarlane1-3/+8
Previously, when multiple file arguments were provided, pandoc simply concatenated them and passed the contents to the readers, which took a Text argument. As a result, the readers had no way of knowing which file was the source of any particular bit of text. This meant that we couldn't report accurate source positions on errors or include accurate source positions as attributes in the AST. More seriously, it meant that we couldn't resolve resource paths relative to the files containing them (see e.g. #5501, #6632, #6384, #3752). Add Text.Pandoc.Sources (exported module), with a `Sources` type and a `ToSources` class. A `Sources` wraps a list of `(SourcePos, Text)` pairs. [API change] A parsec `Stream` instance is provided for `Sources`. The module also exports versions of parsec's `satisfy` and other Char parsers that track source positions accurately from a `Sources` stream (or any instance of the new `UpdateSourcePos` class). Text.Pandoc.Parsing now exports these modified Char parsers instead of the ones parsec provides. Modified parsers to use a `Sources` as stream [API change]. The readers that previously took a `Text` argument have been modified to take any instance of `ToSources`. So, they may still be used with a `Text`, but they can also be used with a `Sources` object. In Text.Pandoc.Error, modified the constructor PandocParsecError to take a `Sources` rather than a `Text` as first argument, so parse error locations can be accurately reported. T.P.Error: showPos, do not print "-" as source name.
2021-03-24Fix DocBook reader mathml regression...John MacFarlane1-3/+5
...caused by the switch in XML libraries. Also fixed a similar issue in JATS. Closes #7173.
2021-02-18DocBook, JATS, OPML readers: performance optimization.John MacFarlane1-21/+3
With the new XML parser, we can avoid the expensive tree normalization step we used to do. This gives a significant speed boost in docbook and JATS parsing (e.g. 9.7 to 6 ms).
2021-02-16Rename Text.Pandoc.XMLParser -> Text.Pandoc.XML.Light...John MacFarlane1-33/+25
..and add new definitions isomorphic to xml-light's, but with Text instead of String. This allows us to keep most of the code in existing readers that use xml-light, but avoid lots of unnecessary allocation. We also add versions of the functions from xml-light's Text.XML.Light.Output and Text.XML.Light.Proc that operate on our modified XML types, and functions that convert xml-light types to our types (since some of our dependencies, like texmath, use xml-light). Update golden tests for docx and pptx. OOXML test: Use `showContent` instead of `ppContent` in `displayDiff`. Docx: Do a manual traversal to unwrap sdt and smartTag. This is faster, and needed to pass the tests. Benchmarks: A = prior to 8ca191604dcd13af27c11d2da225da646ebce6fc (Feb 8) B = as of 8ca191604dcd13af27c11d2da225da646ebce6fc (Feb 8) C = this commit | Reader | A | B | C | | ------- | ----- | ------ | ----- | | docbook | 18 ms | 12 ms | 10 ms | | opml | 65 ms | 62 ms | 35 ms | | jats | 15 ms | 11 ms | 9 ms | | docx | 72 ms | 69 ms | 44 ms | | odt | 78 ms | 41 ms | 28 ms | | epub | 64 ms | 61 ms | 56 ms | | fb2 | 14 ms | 5 ms | 4 ms |
2021-02-10Add new unexported module T.P.XMLParser.John MacFarlane1-2/+7
This exports functions that uses xml-conduit's parser to produce an xml-light Element or [Content]. This allows existing pandoc code to use a better parser without much modification. The new parser is used in all places where xml-light's parser was previously used. Benchmarks show a significant performance improvement in parsing XML-based formats (especially ODT and FB2). Note that the xml-light types use String, so the conversion from xml-conduit types involves a lot of extra allocation. It would be desirable to avoid that in the future by gradually switching to using xml-conduit directly. This can be done module by module. The new parser also reports errors, which we report when possible. A new constructor PandocXMLError has been added to PandocError in T.P.Error [API change]. Closes #7091, which was the main stimulus. These changes revealed the need for some changes in the tests. The docbook-reader.docbook test lacked definitions for the entities it used; these have been added. And the docx golden tests have been updated, because the new parser does not preserve the order of attributes. Add entity defs to docbook-reader.docbook. Update golden tests for docx.
2020-10-08Extend fix to #6719 to JATS readerJohn MacFarlane1-13/+13
2020-09-13Fix hlint suggestions, update hlint.yaml (#6680)Christian Despres1-6/+6
* Fix hlint suggestions, update hlint.yaml Most suggestions were redundant brackets. Some required LambdaCase. The .hlint.yaml file had a small typo, and didn't ignore camelCase suggestions in certain modules.
2020-06-28JATS reader: parse abstract element into metadata field of same name (#6482)Albert Krewinkel1-0/+9
Closes: #6480
2020-04-28Support new Underline element in readers and writers (#6277)Vaibhav Sagar1-2/+2
Deprecate `underlineSpan` in Shared in favor of `Text.Pandoc.Builder.underline`.
2020-04-15Use the new builders, modify readers to preserve empty headersdespresc1-5/+7
The Builder.simpleTable now only adds a row to the TableHead when the given header row is not null. This uncovered an inconsistency in the readers: some would unconditionally emit a header filled with empty cells, even if the header was not present. Now every reader has the conditional behaviour. Only the XWiki writer depended on the header row being always present; it now pads its head as necessary.
2020-04-15Adapt to the newest Table type, fix some previous adaptation issuesdespresc1-3/+3
- Writers.Native is now adapted to the new Table type. - Inline captions should now be conditionally wrapped in a Plain, not a Para block. - The toLegacyTable function now lives in Writers.Shared.
2020-04-15Implement the new Table typedespresc1-25/+24
2020-04-15JATS reader: handle "label" element in section title.John MacFarlane1-1/+7
Closes #6288.
2020-03-29Clean up some fmaps (#6226)Joseph C. Sible1-3/+3
* Avoid fmapping when we're just binding right after anyway * Clean up unnecessary fmaps in the LaTeX reader
2020-03-22Finer grained imports of Text.Pandoc.Class submodules (#6203)Albert Krewinkel1-1/+1
This should speed-up recompilation after changes in `Text.Pandoc.Class`, as the number of modules affected by a change will be smaller in general. It also offers faster insights into the parts of `T.P.Class` used within a module.
2020-03-15Use implicit Prelude (#6187)Albert Krewinkel1-2/+0
* Use implicit Prelude The previous behavior was introduced as a fix for #4464. It seems that this change alone did not fix the issue, and `stack ghci` and `cabal repl` only work with GHC 8.4.1 or newer, as no custom Prelude is loaded for these versions. Given this, it seems cleaner to revert to the implicit Prelude. * PandocMonad: remove outdated check for base version Only base versions 4.9 and later are supported, the check for `MIN_VERSION_base(4,8,0)` is therefore unnecessary. * Always use custom prelude Previously, the custom prelude was used only with older GHC versions, as a workaround for problems with ghci. The ghci problems are resolved by replacing package `base` with `base-noprelude`, allowing for consistent use of the custom prelude across all GHC versions.
2020-03-13Update copyright year (#6186)Albert Krewinkel1-1/+1
* Update copyright year * Copyright: add notes for Lua and Jira modules
2020-02-07Resolve HLint warningsAlbert Krewinkel1-2/+2
All warnings are either fixed or, if more appropriate, HLint is configured to ignore them. HLint suggestions remain. * Ignore "Use camelCase" warnings in Lua and legacy code * Fix or ignore remaining HLint warnings * Remove redundant brackets * Remove redundant `return`s * Remove redundant as-pattern * Fuse mapM_/map * Use `.` to shorten code * Remove redundant `fmap` * Remove unused LANGUAGE pragmas * Hoist `not` in Text.Pandoc.App * Use fewer imports for `Text.DocTemplates` * Remove redundant `do`s * Remove redundant `$`s * Jira reader: remove unnecessary parentheses
2020-02-07Various minor cleanups and refactoring (#6117)Joseph C. Sible1-1/+1
* Use concatMap instead of reimplementing it * Replace an unnecessary multi-way if with a regular if * Use sortOn instead of sortBy and comparing * Use guards instead of lots of indents for if and else * Remove redundant do blocks * Extract common functions from both branches of maybe Whenever both the Nothing and the Just branch of maybe do the same function, do that function on the result of maybe instead. * Use fmap instead of reimplementing it from maybe * Use negative forms instead of negating the positive forms * Use mapMaybe instead of mapping and then using catMaybes * Use zipWith instead of mapping over the result of zip * Use unwords instead of reimplementing it * Use <$ instead of <$> and const * Replace case of Bool with if and else * Use find instead of listToMaybe and filter * Use zipWithM instead of mapM and zip * Inline lambda wrappers into the real functions * We get zipWithM from Text.Pandoc.Writers.Shared * Use maybe instead of fromMaybe and fmap I'm not sure how this one slipped past me. * Increase a bit of indentation
2019-11-12Switch to new pandoc-types and use Text instead of String [API change].despresc1-34/+42
PR #5884. + Use pandoc-types 1.20 and texmath 0.12. + Text is now used instead of String, with a few exceptions. + In the MediaBag module, some of the types using Strings were switched to use FilePath instead (not Text). + In the Parsing module, new parsers `manyChar`, `many1Char`, `manyTillChar`, `many1TillChar`, `many1Till`, `manyUntil`, `mantyUntilChar` have been added: these are like their unsuffixed counterparts but pack some or all of their output. + `glob` in Text.Pandoc.Class still takes String since it seems to be intended as an interface to Glob, which uses strings. It seems to be used only once in the package, in the EPUB writer, so that is not hard to change.
2019-03-02JATS reader: Support fig-group block element (#5317).John MacFarlane1-1/+4
2019-03-01Remove license boilerplate.John MacFarlane1-18/+0
The haddock module header contains essentially the same information, so the boilerplate is redundant and just one more thing to get out of sync.
2019-02-23JATS reader: fix parsing of figures.John MacFarlane1-18/+27
This ensures that a figure containing a single image is parsed as a pandoc "implicit figure" (i.e., a Para with a single Image whose title attribute begins with `fig:`). More complex figures will still be parsed as divs. Closes #5321.
2019-02-15JATS reader: handle citations with multiple references.John MacFarlane1-7/+10
The rid attribute can have a space-separated list of ids. Closes #5310.
2019-02-04Add missing copyright notices and remove license boilerplate (#5112)Albert Krewinkel1-2/+2
Quite a few modules were missing copyright notices. This commit adds copyright notices everywhere via haddock module headers. The old license boilerplate comment is redundant with this and has been removed. Update copyright years to 2019. Closes #4592.
2018-10-24Use foldl' instead of maximum to account for empty listsAlexander Krotov1-4/+2
2018-07-02JATS reader: fix typo ("lable" instead of "label")Alexander Krotov1-1/+1
2018-04-25Added licensing headers for DocBook, EPUB, JATS, OPML readers.John MacFarlane1-0/+30
See #4592.
2018-03-29Removed unused extensions (#4506)Anabra1-1/+1
2018-03-18Use NoImplicitPrelude and explicitly import Prelude.John MacFarlane1-0/+2
This seems to be necessary if we are to use our custom Prelude with ghci. Closes #4464.
2018-01-19hlint code improvements.John MacFarlane1-1/+0
2017-12-23JATS reader: handle author-notes.John MacFarlane1-5/+6
2017-12-23JATS reader: code refactoring.John MacFarlane1-63/+48
2017-12-23JATS reader: include institute metadata.John MacFarlane1-2/+11
2017-12-23JATS reader: process author metadata.John MacFarlane1-5/+27
2017-12-23JATS reader: better citation handling.John MacFarlane1-3/+79
We now convert a ref-list element into a list of citations in metadata, suitable for use with pandoc-citeproc. We also convert references to pandoc citation elements. Thus a JATS article with embedded bibliographic information can be processed with pandoc and pandoc-citeproc to produce a formatted bibliography.
2017-12-22Improve support for code language in JATSHamish Mackenzie1-2/+19
2017-12-20Add Basic JATS reader based on DocBook readerHamish Mackenzie1-0/+387