Capturing continued – building a fully functional demo

Another way of using the capturing features of Roxy is for building a demo quickly. For instance by generating a basic search app using the Application Builder, capturing that with Roxy, and then republishing it again after customizing it in every possible way you like. I gave a live demonstration of doing that in the MarkLogic User Group Benelux meetup 'Stop horsing around with NoSQL — How to Build a NoSQL Demo to Impress Your Boss'. This article gives full details on that demo.

Capturing and redeploying an Application Builder app basically comes down to the following steps:

1. Create and deploy a Roxy REST project
2. Use Roxy MLCP features to ingest data
3. Use Roxy to deploy the analyze-data tool
4. Create indexes using the analyze-data tool
5. Create an App-Builder project for the content db of the Roxy project
6. Run through the App-Builder wizard and deploy
7. Use Roxy capture to capture the app-builder project
8. Customize the app-builder code
9. Redeploy to the Roxy project

And that is it. Roughly 7 steps to build a fully running demo, and then you can customize it any way you like, and redeploy as much and anywhere you like.

I’ll run through some details briefly, point to other blog articles of mine that are relevant, and wrap up with links to code, data and recordings of the live demo.

Other capture parameters

My previous blog article ‘Capturing MarkLogic applications with Roxy’ discusses capturing MarkLogic applications in general. It also mentions creating a new Roxy project, and various commands useful for capturing an Application Builder application.

In addition there is one other previously not mentioned capture flag that could be of interest. It is another way to capture configurations, but not all of them at once. Instead it just captures databases and servers matching the current Roxy project. Just use --ml-config instead of --full-ml-config:

./ml local capture --ml-config

This capture command runs faster as it is capturing much less, and you can often find the settings you are looking for easier, as the resulting ml-config file is much smaller. It actually allows targeting specific databases, and servers using extra parameters --databases and --servers:

./ml local capture --ml-config --databases=App-Services,Extensions,Fab --servers=App-Services

Loading data

Using MLCP features of Roxy was discussed briefly as well in my previous article. MLCP allows ingesting data directly from compressed archives, which is very convenient. You can also apply a transform while ingesting. The demo material contains runnable examples of both. Below just a little example of how such a command-line could look like:

./ml local mlcp import -input_file_path ../sample-data/horse-racing/ -input_compressed
-transform_module /ingest/ingest-events-with-geo.xqy -transform_namespace http://marklogic.com/demo

Analyzing data

The analyze-data tool is described in one of my earlier blog articles ‘Analyze your data!‘. Just a very crude tool, and far from flawless, but it can often be useful to get a jumpstart with it, just to get you going quickly.

Customizing app-builder projects

A brief word on customizing app-builder projects: if you intend to push the changes back into the modules database generated by the wizard itself, then make sure to put any customizations into the /application/custom/ folder. Not that there is much reason to push files back there if you can push them to anywhere with Roxy.

Doing so makes sure not only that you can go back to the wizard, make some changes, and redeploy, but also that you can recapture it with Roxy. Roxy will refresh the files in the src/ folder of Roxy, but will leave src/application/custom/ untouched. That means you can go back and forth between the wizard, and your own customizations as many times as you like!

The demo material

The demo material consists of:

• Cheatsheet (890 Kb zip, html slides)
• Cheats (33 Kb zip, various pieces of code and configs)
• Geonames country info (156 Kb xml)
• Horse racing data (70 Mb zip)
• DBPedia triple data (35 Mb zip, ML xml format)

The cheatsheet contains a brief intro, and a long list of all commands and steps you need to go through to run the entire demo yourself. Note that you need to go down on some slides to not miss steps!

The cheats are comprised of a set of various files. It would have take too much time to type everything myself live. The full demo already took about one and half hour with all the cheats.

The latter three provide all of the pieces of data that I used for the demo. I use the Geonames country info for a crude way to show a geospatial map with markers. The horse racing data is the core information. The triples are used to pull in extra info from DBPedia, and use that to add some semantics to the demo.

The recordings

You can watch the recording of the entire live demo with the following two links (we had a break roughly half-way). The quality is not perfect, but it should be understandable:

• MarkLogic User Group Benelux meetup at June 19th, 2014 in Amsterdam, recording part 1 (36 min, moderate quality)
• MarkLogic User Group Benelux meetup at June 19th, 2014 in Amsterdam, recording part 2 (51 min, moderate quality)

Have fun!

XQuery Novelties Revisited

(This is a translation of my article in the Dutch printed magazine <!ELEMENT.)

The latest news on XQuery [1] was presented by me at the XML Holland conference [2] of 2010. All well, but what is the use of XQuery? And why use XQuery over other kinds of alternatives, XML-related or not? I’ll try to answer these questions in this article, and explain why the (relatively new) extensions to XQuery are so interesting.

What is the use of XQuery?

XQuery [3] stands for XML Query Language [4]. That already tells the essence. It is a language to select subsets and substructures from a large set of XML files. The result can be manipulated into something that is suitable to be used in, for example, a subsequent process, or to show in a web browser. XPath [5] is used a lot in XQuery.

All XML standards have their own scope. I’ll name a few. XSLT [6] is a language for transforming XML into some other format. XPointer [7] is an extension of XPath to address nodes more accurately within XML fragments or even subparts of nodes. XLink [8] is a standard to define relationships. XInclude [9] is a standard to compose multiple pieces of XML into one using for instance XLink relationships. And XProc [10] is a standard with which can be described how XML documents should be processed to get to a desired end result. It is expressed itself in XML, and describes the process step by step, also called XML Pipelines. Within XProc you use a.o. XQuery, XSLT, and XInclude languages (and thus indirectly XPath, XPointer and XLink as well) to express what needs to be done exactly within each step.

All these standards are tied together. They are related, and depend on each other. The overlap between some of the mentioned XML standards is summarized quite well in the next image that you can also find at W3Schools [11]:

XQuery vs. XSLT

XQuery has originally a rather specific goal: extract XML fragments from a large(r) collection. This is very different from XSLT, which focusses on transforming XML documents into other XML documents, HTML documents or even documents of other formats.

You would think it should be pretty clear when and why you should use which standard. Yet we often hear the question whether it is best to use XSLT, or best to use XQuery. The point is that these two languages, more than the other ones, have a considerable overlap. There are many tasks you can do in XSLT, that you can also do in XQuery and vice versa. Although this question is in some ways unjustified and not always important, I'll discuss it in a little more detail below here.

If you can tackle something in multiple ways, and both ways do it with similar ease, there is no real reason for rejecting either of the two. Yet you will see that some people prefer XQuery. The syntax of XQuery is much more compact because it is not expressed in XML as XSLT. On the other hand, XSLT is based on a different principle, making doing for instance certain structural changes much easier. In this sense, it is mainly down to personal taste and the specific challenges of the task at hand, which of the two will be used by someone in particular for a given task.

However, XQuery is often used in combination with databases. That affects the balance. Firstly, XSLT fans aren’t always the same people who will be dealing with databases and vice versa. XSLT is more common in the area of document conversions. Secondly, databases entail additional challenges, often of an entirely different order of magnitude. XQuery has extensions that provide help in those areas. But there are no (official) XSLT extensions, and there is no real need for it either.

And that is why comparing XQuery and XSLT is so difficult, and therefore usually futile.

XQuery relatively unknown

The fact that XSLT exists much longer than XQuery, also affects the balance. In the beginning people had not much choice. Later on people got used to the quickly matured XSLT, while XQuery was still a working draft for quite some years. The idea for an "XML Query Language" arose along the emergence of XML, but it took long before it became a W3C Recommendation. XQuery is still relatively new, compared to XSLT and XPath.

One reason for this is that, after the launch of XPath in 1999, people soon became aware that such language could be largely based on XPath. That resulted in the first Working Draft of both XQuery 1.0 and XPath 2.0 in 2001. XSLT could and should of course also benefit. The XSLT 2.0 Working Draft was initiated at the same time. The Recommendations of these three were released more or less simultaneously. We are talking about 2007 by then, that is six years later!

So, XQuery is a Recommendation only since 2007, while XSLT and XPath are Recommendations since 1999, and were pretty popular from the start. XQuery is still catching up on XSLT and XPath. In addition, XML was booming business back then. Innovations in XML standards have slowed down, while new ideas like JSON [12] and NoSQL [13] are getting all the attention.

XQuery needs to catch up with XML databases as well. Various kinds of XML databases emerged after the advent of XML, but the idea of a generic Query Language didn’t appear until several years later. The fact that XQuery reached the Recommendation status only in the recent years, has slowed broad support in commercial database products the years before. A few large parties like IBM were involved in XQuery early on, other parties such as Oracle followed only years later. It was likewise with commercial XML databases: there were some early-adopters, but most of them preferred to wait to see which way the cat would jump.

Relation with databases

The fact that XQuery is used so often in combination with databases, is no coincidence. It is obvious to want to put large collections of XML in an (XML) database. Databases are designed for large-scale storage and efficient extraction. It fits the purpose of XQuery perfectly.

And that's no coincidence either. XQuery (indirectly) emerged out of database languages like SQL. The first ideas for storing XML in databases arose with the advent of XML. Initially people mainly (ab)used relational databases. However, languages like SQL are not equipped to handle XML. So, many extensions and variations arose automatically. By the time the XSLT and XPath Recommendations were a fact, people realized that there was a need for a generic query language as well. This resulted in the Quilt [14] language in 2000, which was renamed to XQuery after adoption by the W3C.

The following chart that I borrowed from sheets of a curriculum about XML and databases [15] (see ch. 10), shows briefly how various database languages merged into XQuery.

That is why it is no coincidence that XQuery and databases go so well together. XQuery is mainly designed and developed for use with databases. W3C has chosen explicitly not to limited it to only databases, making it more general purpose.

Relation with database functionality

Development around XQuery hasn’t stood still during all those years, though. There are quite a number of extensions to XQuery, which significantly increase the power of XQuery. Part of them find their origin in the application of XQuery to databases.

Ronald Bourret has a very informative website in which XML and databases [16] are elaborately discussed. He mentions some basic features that every database must support. Some of the more important are:

• Efficient storage and extraction
• (Full Text) Search
• Transactional updates
• Data integrity and triggers
• Parallel processing and access
• Security and crash recovery
• Version control of data

Storage is of course inherent to databases. A good database also provides facilities for concurrent access and updates, security, and crash recovery. Extraction is covered by XQuery 1.0, the search by the Full-Text standard, updates by the Update Facility standard. And there are extensions for data integrity and versioning as well, though yet unofficial. More on that in the following part.

Extensions on XQuery

XQuery 1.0 relies on XPath 2.0. It is in fact an extension to it. Even XPath, how powerful itself, has certain limitations. It is a language for addressing substructures. It is not really designed for searching. XQuery itself doesn’t provide the right functionality for searching either. It is designed for retrieval and processing. Therefore, an extension to these languages was developed: the "XQuery and XPath Full Text 1.0 [17]" standard, which became a W3C Recommendation [18] in March this year.

XQuery is meant for extraction and processing, not for applying changes. Another extension which became a W3C Recommendation in March this year is the "XQuery Update Facility 1.0 [19]" standard. This is an extension that does allow applying (permanent) changes to XML structures.

Regarding data integrity an (unofficial) proposal [20] was presented at the XML Prague 2010 conference [21]. This extension allows embedding declarations of data collections, indexes and data constraints within your XQuery code. Instead of having to mess around with database configurations, these declarations become part of the application code itself. This makes maintenance much easier. All relevant details gathered in one spot, and within control of the developer him/herself. They would not even need to know much about the database that is actually being used.

Versioning is commonly used for Content Management, but is also used for other purposes such as traceability. Another (unofficial) proposal [22] presented at XML Prague 2010 covers versioning. It is a bit technical, and goes quite deep, but it provides some interesting features. According to the Update Facility standard, all mutations are collected in a so-called ‘Pending Update List’. At the end of an updating script the result of all mutations in that script are committed (stored). This extension describes the idea to preserve all these ‘commit’ moments. To do this effectively, the proposal mentions something called ‘Pending Update List compositions’. These commit moments provide a full history of the XML. Two new XPath ‘axes’ are added, allowing navigation through the full history as integral part of XPath navigation.

Storing all this versioning data requires a lot of disk space, but it is such cheap these days that costs are no longer a problem.

Beyond Scope

But XQuery goes even further. There are currently two extensions that go way beyond database functionality.

The successor of XQuery 1.0 is being developed as we speak: XQuery 1.1, or actually XQuery 3.0 [23], which currently has the W3C Working Draft status. This successor adds a number of features that significantly enhance the expressiveness, such as: try / catch constructs, output statements, group by within a for loop. It also allows calling functions dynamically. In other words: functions as a data type. This takes XQuery to a whole new level.

And as if that were not enough, a standard called "XQuery Scripting Extension 1.0 [24]" is being developed as well. This extension adds several new features that almost make it a (procedural) programming language, for instance: a while loop, redefinition of ,variables and an exit statement. It also builds on top of the XQuery Update Facility standard and allows cumulative (sequential) updates.

All of this makes XQuery very suitable as a ‘scripting’ language, allowing it to compete with languages such as JSP, ASP and PHP. In fact when speaking of web applications it can compete with languages like Java and .Net equally well. It is not for nothing that W3C states:

“XQuery is replacing proprietary middleware languages and Web Application development languages. XQuery is replacing complex Java or C++ programs with a few lines of code…” http://www.w3.org/XML/Query/ [25]

Note: that is an observation, not an opinion!

Programming Language

XQuery 3.0 and the Scripting Extension lift XQuery to a higher level. They give the appearance of a real programming language. It is not a surprise that W3C states that database-specific programming languages are being replaced by XQuery more and more. XQuery is ideally suited as a language for database access, but thanks to these latest enhancements it goes further. XQuery is the glue that can bring all application layers together. It is also powerful enough to support well known Design Patterns [26] without much trouble. Not only the well-known Model-View-Controller [27] pattern, but also other useful patterns, such as Observer, Strategy and others [28].

It is easiest to refer to the application that me and two of my (former) colleagues have made for a programming contest [29] to show the real power of XQuery. The goal was simple: create an application that appeals to XQuery and was well put together. The result was Socialito [30]: a ‘Social Media Dashboard’, in which tweets and other information from your Twitter account is displayed in a highly organized, and customizable manner. The user interface uses HTML and JavaScript (JQuery [31]), but apart from that it uses XQuery exclusively. The data is stored using the XML structure of Twitter itself.

In short, XQuery is not just for "Querying XML" no longer. In XQuery, you can develop application logic and application layers all together. That makes it the core of your entire application. This goes way further than any other XML standard.

Learn more?

Anyone interested in learning more, and keen to see practical applications of XQuery, is kindly invited to sign up for the XML Amsterdam conference of Wednesday 26^th of October at the Regardz Planetarium in Amsterdam. Several Open Standards will be discussed, and there will be multiple presentations on XQuery.

1. latest news on XQuery: http://xmlholland.nl/sites/default/files/Geert Josten-XMLHolland2010.pdf
2. XML Holland conference: http://www.xmlholland.nl/jaarcongres
3. XQuery: http://www.w3.org/TR/xquery/
4. XML Query Language: http://www.w3.org/XML/Query/
5. XPath: http://www.w3.org/TR/xpath20/
6. XSLT: http://www.w3.org/TR/xslt20/
7. XPointer: http://www.w3.org/TR/xptr-framework/
8. XLink: http://www.w3.org/TR/xlink11/
9. XInclude: http://www.w3.org/TR/xinclude/
10. XProc: http://www.w3.org/TR/xproc/
11. W3Schools: https://www.w3schools.com/xml/xpath_intro.asp
12. JSON: http://en.wikipedia.org/wiki/JSON
13. NoSQL: http://en.wikipedia.org/wiki/NoSQL
14. Quilt: http://xml.coverpages.org/quilt_euro.html
15. XML and databases: http://www.inf.uni-konstanz.de/dbis/teaching/ws0708/xml/
16. XML and databases: http://www.rpbourret.com/xml/XMLAndDatabases.htm
17. XQuery and XPath Full Text 1.0: http://www.w3.org/TR/xpath-full-text-10/
18. W3C Recommendation: http://www.w3.org/TR/
19. XQuery Update Facility 1.0: http://www.w3.org/TR/xquery-update-10/
20. proposal: http://www.xmlprague.cz/2010/presentations/Matthias Brantner Extending_XQuery_with_Collections_Indexes_and_Integrity_Constraints.pdf
21. XML Prague 2010 conference: http://www.xmlprague.cz/2010/index.html
22. proposal: http://www.xmlprague.cz/2010/sessions.html
23. XQuery 3.0: http://www.w3.org/TR/xquery-30/
24. XQuery Scripting Extension 1.0: http://www.w3.org/TR/xquery-sx-10/
25. http://www.w3.org/XML/Query/: http://www.w3.org/XML/Query/
26. Design Patterns: http://en.wikipedia.org/wiki/Design_pattern_(computer_science)
27. Model-View-Controller: http://code.google.com/p/xqmvc/
28. Observer, Strategy and others: http://patterns.28msec.com/
29. Programming contest: http://www.28msec.com/contest/results
30. Socialito: http://socialito.my28msec.com/
31. JQuery: http://jquery.com/
32. Personal blog: http://grtjn.blogspot.com/
33. Company blog: http://www.daidalos.nl/blogs/blog/author/Geert/

About the author

Geert Josten joined in July 2000 as an IT consultant at Daidalos. His interest is wide, but he is most active as a content engineer with an emphasis on XML and related standards. He followed the XML standards from the very beginning and actively contributes to the XML community. Geert is also active as Web and Java developer. Read more articles by him on his personal blog [32] and the company blog [33].

PDF to XML conversion with XSLT 2.0

Good old-fashion Content Engineering can save money

XML has brought us many tools for all kinds of tasks. They make a lot of work easy, but developers lazy too. It is harder and harder to find really skilled people these days. New developers haven’t learned from doing things the hard way, even though doing things the hard way still often produces the best results. Here an example of converting PDF to XML using XSLT 2.0 to provide a cheap solution, done the ‘hard’ way.

One of our customers approached us (speaking on behalf of my company, Daidalos). They had some PDF documents with pretty clear layouts. Specific parts of these had to be converted to XML on a regular basis. Obviously, they didn’t want to spend much on it, so we had to look for a cheap solution.

The task seemed simple. Visually identifying the interesting parts, and classifying the information was easy enough. We were hoping to automate the process though. This meant we needed a conversion from PDF to XML with preservation of sufficient layout details to distinguish and classify the interesting bits.

There are plenty tools readily available that help with converting PDF to XML. Most of them cost money, though. The good ones cost a lot of money. We had not that much to spend, so we had to settle for one of the cheapest that could do the trick. Most of the cheaper ones are cheap for a good reason. They were either meant for text extraction only (with a bare minimum of layout), or were good at some aspects of the conversion, but not at what we needed: preservation of sufficient layout details.

One of my colleagues, though, stumbled upon a very small executable called: pdf2html. It is freely available on the internet. It is actually not too well in converting PDF to XML (you need the -xml option), as it occasionally produces ill-formed XML. Nor does it recognize a lot in the PDF. But it does two things pretty well:

1.      identify all text runs within the PDF (with a bit of layout information),
2.      add accurate positioning information to the text runs.

It extracts sufficient information to produce HTML and CSS out of it which mimics the exact textual layout in the PDF. The accurate positioning information is all we need to identify and classify the relevant information. It is this tool that we employed for this task.

This bare conversion to XML was only part of the job though; most of the work still had to be done Just to give an impression of its output, let me show you a sample. The PDF input looked like this:

The XML output like this:

The output is actually quite messy. The largest issues are:

·        Continues text is chunked in separate lines
·        Chunked lines cause hyphenated words to get cut in halves
·        Lines can be chunked in separate text runs as well
·        No hierarchy in the text structure
·        No advanced formatting, like tables and lists
·        No separation of headers, footers, and margin texts
·        No images, or other draws layout, not even table borders

In short: it looks like a literal translation from the PDF text floats to XML, and text floats only. Making sense out of this mess is a real challenge. And I went for it.

As said, the output has one really valuable asset: the positioning information. This positioning information helps coping with most of the above problems. It just needs a careful approach. By applying general enhancements you can get a more logical separation of the information. Once there, you can add meaning to the information.

I roughly took the following steps in mentioned order to apply general enhancement of the raw XML output:

1.      Isolating text runs in different zones (like header and footer)
2.      Gathering text runs on the same ‘line’ (ignoring columns here)
3.      Translate indentation to hierarchy (helps finding lists, provides bare table/column handling)
4.      Merging of lines to build paragraphs

For the first step you need to manually ‘measure’ the height of both. But once known, you can separate text runs belonging to headers, from those belonging to footers, and from those belonging to the body. I simply wrapped them in new elements named ‘header’, ‘footer’, and ‘body’.

The second step is not very difficult either. Search within each page for text runs that have the same top position. Wrap them in a ‘line’ element. A  simple xsl:for-each-group on the ‘top’ attribute did the trick.

The third step is a bit similar to the second step, but instead of looking at the top position, you look at the ‘left’ attribute of each line. Lines starting more to the right than above ones are wrapped in nested ‘block’ elements. Having separated header and footer earlier makes sure their contents doesn’t get mixed with text from the body.

At this point the output has already improved much. It more or less looks like this:

The fourth step requires a bit more effort, but involves not much more than joining the contents of adjacent ‘line’ elements. The ‘block’ elements help to identify where paragraphs should start and end. This is also a good opportunity to resolve hyphenation of words. Take any hyphen at the end of a line, cut it off, and concatenate with the following line without adding an extra space in between. Not entirely fail-safe, but the loss is marginal.

With just four small steps, the output can be greatly enhanced, making it much easier to isolate the interesting information, and add meaning to it. From here it takes only about 20 lines of real XSLT code to get to this end result:

In the end I needed only about 800 lines of XSLT code to get to this result. And nearly half of them are empty lines and comments. With roughly 250 actual lines of code more I was able to produce two more XML extracts of which one involved interpreting complex tabular information.

I’m not saying this approach can crack all your PDF to XML problems. But I do hope to have shown, that doing something the ‘hard’ way doesn’t have to be that really hard. And it can produce high quality results, perhaps even higher that using a more advanced PDF to XML tool.