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videos:indexing_xml_records

Video 7: Indexing XML Records

The seventh VuFind instructional video explains how to import XML records using XSLT, with an emphasis on records that were harvested via OAI-PMH.

Video is available as an mp4 download or through YouTube.

Update Notes

:!: This video was recorded using VuFind 6.1. In VuFind 8.0, changes were made which impact the content of this video:

  • The ojs-multirecord.xsl file has been removed, and the standard ojs.xsl file has been updated to handle both the single-record and multi-record cases. All of the information in this video about the advantages and disadvantages of each technique still applies, but it is no longer necessary to make changes to ojs.properties in order to support the multi-record case. The only changes you need to make are in oai.ini, to control how records are harvested.
  • All of the other example XSLT files have been adjusted to support multi-record indexing, so you can apply this technique to records harvested from other systems as well.

Transcript

This is a raw machine-generated transcript; it will be cleaned up as time permits.

welcome to the seventh do you find tutorial video this is a continuation of last month's video about oai-pmh where we learned how to harvest Excel records using tools bundled with view find this month we are going to look at what to do with those records once we have them and to talk about indexing XML generally the first thing that I should emphasize is that Mark XML is a special exception you can use view find standard mark indexing tools which we talked about several months ago to import binary mark and Mark XML and that is much easier than trying to use the tools we talked about today to index mark which is of course extremely complex so don't overdo your your work by trying to load mark using XSLT there are other tools available but for everything else what we talked about today should be helpful so I've already mentioned XSLT so that was a bit of a spoiler if you find uses XSLT for loading xml data into solar so first i should talk a little bit about what XSLT is it's short for extensible stylesheet language transformations and it's a declarative programming language where you build an XML document that tells the XSLT engine how to transform one XML document into another XML document um there are several versions of XSLT I believe the language is up to version 3.0 right now but PHP is built-in XSLT processor only supports version 1.0 of the language obviously I'm not going to teach you XSLT today in five minutes it's a bit of a project to learn so if you do go off and read a tutorial about it be sure you find one about the original version of the language and not the later ones that add a lot of additional features it's perhaps a little unfortunate that PHP doesn't support newer XSLT versions but this is compensated for quite a bit by the fact that there are bindings between XSLT and PHP so you can write custom functions in PHP and use them in your XSLT so whenever there's missing functionality and XSLT you can usually cover that gap with the PHP function and view find comes packed with a number of example functions for common needs and lots of examples of XSLT as well so for today's example I'm going to harvest in ojs journal called expositions which is hosted at Villanova ojs is the open journal system and open source journal hosting platform and it supports oai-pmh so this is a good example of a real world system that you can harvest from an index interview find and if you find includes some sample configurations and an XSLT for harvesting from evade ojs and indexing the resulting data so again it's it's a pretty good simple real world example so I'm going to go to the command line where I'm in my view find home directory and just show a couple of files to give you a taste of what this all looks like so all of you find sample XSLT sheets in the import / XSL subdirectory you find home and as you can see we actually have three different flavors of ojs XSLT s we have n LM o j sx SL which uses the National Library of medicines metadata standard which is a bit richer than the default o aidc dublin core data but for today's demonstration i'm just going to use a j s XSL which indexes the dublin core we also have a je s multi-record which i will show you a little later so stay tuned for that but to get things started I'm just going to show you what the OJS XSL looks like as I mentioned an XSLT is just an XML document and it really works by pattern matching using XPath which is a way of specifying particular locations within an XML document so within an XSLT anything that you see that's prefixed with XSL : is an XSLT command and anything else is actually output that the XSLT is going to create so the XSLT is in view find are all designed to create solar documents for indexing which always have a top-level ad tag that contains Doc tags that contain fields that need to be added to solar documents so the XSL T's are mostly defining solar fields and containing rules using XSLT to fill those fields with the appropriate data so for example to get our unique ID we're pulling from in XSL tab I mean an XML tag called identifier we have a hard-coded record format so this is just putting this literal value into every record which would enable us to create an OG a specific a record driver if we wanted to we have an all fields field to index all of the text within the XML document which uses some XSLT functions to extract that text we use variables which XSLT supports to pass in institution and collection values I will show you momentarily how these variables get set and XSLT supports looping for multi values so for example this code here populates view finds language field by looping through every dublin core language tag in the document and for any non-empty values it calls a PHP function which translates to the strings from two letter or three-letter codes into all textual representations again I obviously can't go into great depth about all how all of this works here but hopefully this this gives you a little taste and if you go off and read an XSLT tutorial or two it should make even more sense so the XSLT is only part of what view find needs to do XML indexing the other part being a properties file for the import tool which tells it not only which XSLT to use but also what custom PHP functions to make available and what values to set for any custom variables that are used within the XSLT so let's look at a s dot properties file that goes with that XSLT i just showed you and all of the import properties files live in the import director and they all contain lots of comments explaining in detail what all of the settings mean but just to go through the highlights of course there's an XSLT setting this tells us which XSLT to use and as I teased earlier you see with ojs you actually have a choice of the regular ojs XSL which will index one a dublin core record at a time or the OJS multi record XSL which can index a grouping of dublin core records all in one file the multi-record is much faster it just requires some extra work when you harvest and I'm going to show you how to use both of these today we'll start one at a time and we'll work our way up to multi-record you also can expose specific PHP functions directly into the XSLT by just creating a list of functions here by default none of the package configurations do this but it is a possibility if you want to make PHP functions available to your XSLT you can also create a class full of custom functions and expose all of them to your X and sub t and most of view finds examples just to use a view find XSLT import view find class full of static functions for exposing custom behavior like that string mapping I showed you in the language import moving on down there's the ability to pass the custom classes to XSLT using their fully qualified names with the namespace but all of you finds configurations truncate off the namespace and just expose the base class name which makes the XSLT a little shorter and more readable so every time I call the view find function I just say you find : : function name instead of having to type you find slash XSLT slashing or slash to be fun so best truncate custom class finally there's a parameter section and this is where you set the values that are exposed as variables to the XSLT so I showed you earlier that the institution and collection fields in the solar index are getting set to variables and the variables are set here so by default you're going to get institution and collection set to ojs so before I can show you any more of the actual importing process we're going to need some records to play with so let me set up the oai-pmh harvesting for expositions I'm going to edit my local harvest oai ini file which we set up on last month's video and just go to the bottom and create a new section I'm going to call it expositions so that when I run the harvest all of my records will go into a directory called expositions under my local harvest directory the URL is HTTP expositions journals villanova you /ai metadata prefix is oai DC because dublin core and now some new settings that i didn't show you last time first of all inject ID equals identifier as i mentioned when we talked about oai-pmh when we harvest using that protocol we get both records and header data if you find needs a unique identifier for everything in index dublin core that we get back from a IP mhm doesn't necessarily have any kind of identifier in it but the oai-pmh headers will always have a unique ID for every record so by setting inject ID equals identifier here we're telling the harvester take the ID from the oai-pmh header create an identifier tag inside the XML that you're going to harvest and save to disk put the ID value in there and this is how the XSLT I showed you earlier was able to pull an ID from the identifier tag and use it in the index so this is a really important feature of view files harvester that enables you to harvest just about anything and reliably be able to index it in solar with a unique ID the IDS that you get back from oai-pmh are often extremely verbose and they would make for ugly and unreadable URLs so we also have some settings called ID search and ID replace which let us use regular expressions to transform the identifiers at the same time that we're injecting them so in the case of ojs the ids have this long prefix oai : o JSP KP dot s fu CA : we don't want to show that to our users so we're going to replace it with expositions - so this way everything that we index from expositions will have a distinctive prefix on the ID so we don't have to worry about expositions records clashing with records from other sources the other thing about this is that the there are several slashes in some of the IDs and slashes in IDs can create problems because slashes have a special meaning in URLs and it requires extra configuration of your webserver to make things behave nicely so let's just get rid of all the slashes as well so we're gonna say ID search bracket bracket equals type slash pipe ID replace bracket bracket equals - so let me explain all of this in whole now that I've typed it all in I do search and ID replace or repeatable settings in the file you can have as many pairs of search and replace as you need to transform your IDs you just have to be sure the brackets on the end of ID search and ID replace so that when the configuration is read the multiple values are processed correctly an ID search as I mentioned is a regular expression it uses the purl style regular expressions supported in PHP and those regular expressions require you to start and end the expression for the pattern you're matching with the same character so in this first example where we're getting rid of the oai ojs prefix i surrounded it with matching /iz because that is a fairly common convention for regular expressions but for the second pair where we want to turn forward slashes into dashes I can surround the forward slash with forward slashes that would confuse the regular expression engine so I just used pipe characters instead so that it has matching characters on the beginning and end of the expression that don't conflict with the internal part I could have chosen a different character here it doesn't really matter but I think I just look pretty so there you go so with all of that in place we're now ready to harvest expositions so now I just need to run of view finds oai-pmh harvests to get the expositions content so I run PHP harvest slash Argus dot PHP and I tell it I want to harvest expositions and now I wait and it pulls down a whole bunch of records 285 records one for each record in expositions each of them is an XML file and they are all in my local harvest expositions directory so now we're ready to put all these pieces together we have a directory full of XML files in dublin core format we have an xslt and we have a properties file so there is a command-line tool that comes with you find called import XSL PHP so it's PHP import / import - XSLT HP and this has a nice - - test - only mode that you can use if you want to see what it does without actually writing anything into solar so I'm going to use that for the first run here just to demonstrate what's happened so the first parameter to this command is the name of an XML file so I'm going to choose just one is these files more or less at random so I chose local harvest expositions one five eight eight six eight five one nine two expositions article 2486 that big number at the front is actually just a timestamp the the harvester cuts the time of harvest on every file downloads the second parameter is the name of the properties file I've configured to do the import and I don't need to tell it the path to that file I just need to tell it the file name because like many things in view find what it's going to do is its first going to look in view find local dur slash import to see if we have a local customized properties file if it doesn't find that it's then going to fall back and look in if you find home slash import and use the default one so since I haven't customized anything yet it's just going to to go for the defaults so I'm going to run this command and it outputs a solar document which itted by transforming the input so as you can see like in all fields it's just a whole bunch of text it extracted all the free text from the XML taking the tags off of it there's that hard-coded record format of ojs the ID is that identifier that we injected and as you can see it's prefixed with expositions like we told it to be and the slash that would have been here has become a dash so all my regular expressions worked and here's my University and ojs that came in from those variables that were set in the properties file and a whole bunch of other stuff so let's repeat that command but just take the test only off to actually index it into solar the exit import does not immediately commit changes to solar so if you just run this command and try to search for a record it won't show up instantly the way to ensure that solar is all the way up to date is to run the utility MIT PHP script to send a solar commit so I'm gonna do that just so I can demonstrate that this actually worked so now if I go to my browser I loaded up this search for all records prior to indexing and you can see there there were 250 records at that time but if I repeat the search now there are now 251 and as you can see in the institution facet we have one from my University which was what and from that Oh Jas properties file so if I click on that to filter down here is the nonviolence article that we indexed from the XML so that's really great but we have more than 200 of these records we don't want to have to index them by hand one at a time fortunately there is a script called this slash batch import excess LSH which will take the name of a directory under your local harvest path and the name of a property file and it will loop through and index every single file in that directory using that configuration thus saving you lots and lots of typing and as it does the indexing it also creates a subdirectory of your harvest directory called processed and it moves those files into the process directory so at the end of this process after all two hundred-plus files have been indexed I should have an empty expositions directory with a process subdirectory containing all the hundreds of records that got indexed the batch process is also smart enough that if anything should go during the index it will not move files that failed to import correctly so if I had one bad record in this batch all the good ones would get successfully indexed and moved into the processed directory but the bad one would stay there and I could then for example run that test mode I showed you on the one record to see exactly what the error message is that was preventing the transformation or to see oh there's a missing required field or something to troubleshoot that and fix it the other thing that will be left in the expositions directory is a file called last harvest dot txt which will just contain the date of the last time we ran the oai-pmh harvester which allows incremental updates which I believe I mentioned last time but that means that if I ran the harvest again tomorrow and two new records had been added to ojs it would only harvest those two and then I could index those and I wouldn't have to reenact the other 200 so now the the index process has completed and if I just do a directory listing of local artists expositions you'll see that I'm not lying to you all that's left here is the last harvest text and a processed directory so let's go back over to view finder browser and refresh these results and sure enough here are 285 records they're all searchable they all have links back to ojs to read the full article success but you may have noticed I had to ramble for quite a lot of time while those 200 records indexed because indexing things one at a time actually takes quite a while and if you have thousands or tens of thousands of records it's even worse and that is why the multi record function I talked about is really handy so what I'm going to do is I'm going to remove the whole local harvest expositions directory so we can start over and I can show you how much faster this is if we do records and batches instead of wanting to talk so first I'm going to edit my oai harvesting configuration in local harvest I died and I all I need to do is add one more setting at the bottom of this called combined records equals true and what that is going to do is tell the harvester instead of writing one dublin core record into each file you want to create one file for every batch of records that come back over IP MH and you're going to wrap them in a tag called collection if you want to use a different tag name there's another setting you can use for that but for this example just turning on combined records and accepting the default tag of collection is good enough the other thing we need to do is set up the OJS properties file to use the combined XSLT sign so let's copy the default import Oh Jo stop properties into local import because as with everything else files inside local are going to override defaults in the core code and let's edit local import okay I stopped properties I'm just going to comment out a JSX SL and uncomment ojs multi-record XSL so let's just take a quick look at that other XSLT to see what the differences are so I'm gonna edit import / XSL ojs multi-record XSL and so this uses template matching so it's going to match the top-level collection tag and then it's going to loop through the collection looking for a IDC and apply templates to each of them in turn and then there's this Oh a IDC template and this code is quite similar to the single record code it just matches within the scope of a single Oh a IDC instead of globally looking for particular tags and this is really probably a better way to approach all XSLT writing the difference between multi record and single record is that I wrote the single record one when I didn't know what I was doing and somebody else he's better at XSLT than me wrote the multi record one so welcome contributions of multi record import scripts for other metadata formats as well but I do offer the single and multi record options because there are scenarios where each can be useful we'll talk about that a little more momentarily in any case I've now shown you the multi record XSLT I've reconfigured the oai-pmh harvester to harvesting groups and I've configured ojs properties to use the multi record XSLT so everything should be aligned correctly so let's run the oai-pmh harvester again so HP harvest underscore oai dot PHP so harvest expositions and the harvest should take the same amount of time we're still harvesting the same 285 records but if I look inside Local Harvest expositions this time there are only three files there because the oai server provided us with three batches of records and each of those got saved to a single file and now if I were to run single file import XSL dot PHP script in test only mode on one of these files you will see that the output is much longer than before because now instead of just having one record transformed to solar we now have a whole collection of records of them to be precise so it goes on and on but the advantage of this is you remember how long it took to batch import the expositions and every file contained the only one record let me show you how much faster it is when there are only three files containing 100 records each harvest slash batch important XSL physicians directory ojs doc figuration file one two three word up so that was a dramatic improvement in performance the only disadvantage to doing things this way that I can see is that as I mentioned the import script will skip files that fail the import so if I had one corrupted record in this ajs instance and I ran this batch import one of these three files would fail and I would know there was a problem with one of the hundred records within that file but it would be hard to figure out which one had caused the problem so doing single record importing may be valuable for troubleshooting purposes if nothing else and I would suggest that if you do a batch import and you run into trouble try doing a single import that will probably help you pinpoint the causes of your problems I should also note that as I said most of the example XSL teas are things I wrote that are designed for a single record at a time there's still some work to be done creating batch import XSL teas for all the format's I showed you ojs because that's one where this work has already been done if anyone needs multi record import for another format that's something I would welcome contributions of so that it could be shared with everyone else using the project and I expect that over time our repertoire will expand and improve so that's it for this month thank you for listening and we'll have more next time

videos/indexing_xml_records.txt · Last modified: 2021/09/10 11:22 by demiankatz