XQuery Collection - Cant get multiple files from a directory - xquery

I'm trying to get all the filenames from a directory that have a specific string in the XML elements. I'm using this code for that:
for $x in collection('file:///C:/Sricpts/Software20180101-V1.1.1/workspace/Data_PreProcessing?select=*.xml')
where matches($x, 'INSERT INTO')
return $x
However when I run the code it gives that error:
[FODC0002] Resource 'C:/Program Files (x86)/BaseX/file:/file:///C:/Sricpts/Software20180101-V1.1.1/workspace/Data_PreProcessing?select=*.xml' does not exist.
How can I solve this problem?
Many thanks!

If you use BaseX, there is no need to specify a file filter. All XML documents that occur in the specified directory will be added to your collection:
for $x in collection('file:///C:/Sricpts/Software20180101- V1.1.1/workspace/Data_PreProcessing')
where matches($x, 'INSERT INTO')
return $x
If you want to have more control over the documents to be chosen, you can take advantage of the File Module:
let $root := 'C:\Sricpts\Software20180101- V1.1.1\workspace\Data_PreProcessing'
for $path in file:list($root, true(), '*.xml')
let $doc := doc($root || $path)
where matches($doc, 'INSERT INTO')
return $doc

Related

How to execute XQuery on all XML documents in the folder

I need to make sure a particular node exists in many XML files. I have to switch the context each time I want to query another document.
Is there any way I can execute XQuery on all documents in the directory without switching the context?
I may be a little late, but most probably the following XQuery will do what you wish, it returns the path to each XML-File that does not contain a specific element:
let $path := "."
for $file in file:list( $path, true(), '*.xml')
let $path := $path || "/" || $file
where not(
exists(fetch:xml($path)/foo/bar[text() = "Text"])
)
return $path
If you were only interested if there were XML-files in a specific that do or do not contain a specific element the following query might be useful:
declare variable $path := "/Users/michael/Code/foo";
every $doc in file:list($path, true(), '*.xml') (: returns a sequence of file-names :)
=> for-each(concat($path,"/", ?)) (: returns a sequence of full paths to each file :)
=> for-each(fetch:xml#1) (: returns a sequence of documents :)
satisfies exists(
$doc/*/*[text() = "Text"]
)
Hope this helps ;-)

eXist-db serialize is expand-xincludes=no ignored?

In eXist-db 4.4, Xquery 3.1, I am compressing a number of XML files to a .zip in a directory. The compression process uses serialize().
The XML files have some large xincludes which according to the documentation are automatically processed in serializing. I have attempted to 'turn off' the xinclude serialization in two places in the code (prologue declare and map), but the serializer is still outputting all xincludes:
declare option exist:serialize "expand-xincludes=no";
declare function zip:get-entries-for-zip()
{
(: get documents prefixed by 'MS609' :)
let $pref := "MS609"
(: get list of document names :)
let $doclist := xmldb:get-child-resources($globalvar:URIdata)[starts-with(., $pref)]
(: output serialized entries :)
let $entries :=
for $n in $doclist
return
<entry name="{$n}" type='text' method='store'>
{serialize(doc(concat($globalvar:URIdata, "/", $n)), map { "method": "xml", "expand-xincludes": "no"})}
</entry>
return $entries
};
The XML data with xincludes to reproduce this problem can be found here http://medieval-inquisition.huma-num.fr/downloads under the description "BM MS609 Edition (tei-xml)".
Many thanks in advance.
The expand-xincludes serialization parameter is specific to eXist and, as such (or at least at present), cannot be set using the fn:serialize() function. Instead, use the util:serialize() function:
util:serialize($document, "expand-xincludes=no")
Alternatively, since you're ultimately interested in zipping the contents of a collection, you can skip the explicit serialization step, declare your serialization options in the query's prolog (or set it inline using util:declare-option()), and simply provide the compression:zip() function the URI path(s) to the collections/documents you want to zip. For example:
xquery version "3.1";
declare option exist:serialize "expand-xincludes=no";
let $sources := "/db/apps/my-app/my-data" (: or a sequence of paths to individual docs:) ! xs:anyURI(.)
let $preserve-collection-structure := false()
let $zip := compression:zip($sources, $preserve-collection-structure),
return
xmldb:store("/db", "my-data.zip", $zip)
For more on serialization options in eXist, see my earlier answer to a similar question: https://stackoverflow.com/a/49290616/659732.

Recursive copy of a folder with XQuery

I have to copy an entire project folder inside the MarkLogic server and instead of doing it manually I decided to do it with a recursive function, but is becoming the worst idea I have ever had. I'm having problems with the transactions and with the syntax but being new I don't find a true way to solve it. Here's my code, thank you for the help!
import module namespace dls = "http://marklogic.com/xdmp/dls" at "/MarkLogic/dls.xqy";
declare option xdmp:set-transaction-mode "update";
declare function local:recursive-copy($filesystem as xs:string, $uri as xs:string)
{
for $e in xdmp:filesystem-directory($filesystem)/dir:entry
return
if($e/dir:type/text() = "file")
then dls:document-insert-and-manage($e/dir:filename, fn:false(), $e/dir:pathname)
else
(
xdmp:directory-create(concat(concat($uri, data($e/dir:filename)), "/")),
local:recursive-copy($e/dir:pathname, $uri)
)
};
let $filesystemfolder := 'C:\Users\WB523152\Downloads\expath-ml-console-0.4.0\src'
let $uri := "/expath_console/"
return local:recursive-copy($filesystemfolder, $uri)
MLCP would have been nice to use. However, here is my version:
declare option xdmp:set-transaction-mode "update";
declare variable $prefix-replace := ('C:/', '/expath_console/');
declare function local:recursive-copy($filesystem as xs:string){
for $e in xdmp:filesystem-directory($filesystem)/dir:entry
return
if($e/dir:type/text() = "file")
then
let $source := $e/dir:pathname/text()
let $dest := fn:replace($source, $prefix-replace[1], $prefix-replace[2])
let $_ := xdmp:document-insert($source,
<options xmlns="xdmp:document-load">
<uri>{$dest}</uri>
</options>)
return <record>
<from>{$source}</from>
<to>{$dest}</to>
</record>
else
local:recursive-copy($e/dir:pathname)
};
let $filesystemfolder := 'C:\Temp'
return <results>{local:recursive-copy($filesystemfolder)}</results>
Please note the following:
I changed my sample to the C:\Temp dir
The output is XML only because by convention I try to do this in case I want to analyze results. It is actually how I found the error related to conflicting updates.
I chose to define a simple prefix replace on the URIs
I saw no need for DLS in your description
I saw no need for the explicit creation of directories in your use case
The reason you were getting conflicting updates because you were using just the filename as the URI. Across the whole directory structure, these names were not unique - hence the conflicting update on double inserts of same URI.
This is not solid code:
You would have to ensure that a URI is valid. Not all filesystem paths/names are OK for a URI, so you would want to test for this and escape chars if needed.
Large filesystems would time-out, so spawning in batches may be useful.
A an example, I might gather the list of docs as in my XML and then process that list by spawning a new task for every 100 documents. This could be accomplished by a simple loop over xdmp:spawn-function or using a library such as taskbot by #mblakele

How to tidy-up Processing Instructions in Marklogic

I have a content which is neither a valid HTML nor a XML in my legacy database. Considering the fact, it would be difficult to clean the legacy, I want to tidy this up in MarkLogic using xdmp:tidy. I am currently using ML-8.
<sub>
<p>
<???†?>
</p>
</sub>
I'm passing this content to tidy functionality in a way :
declare variable $xml as node() :=
<content>
<![CDATA[<p><???†?></p>]]>
</content>;
xdmp:tidy(xdmp:quote($xml//text()),
<options xmlns="xdmp:tidy">
<assume-xml-procins>yes</assume-xml-procins>
<quiet>yes</quiet>
<tidy-mark>no</tidy-mark>
<enclose-text>yes</enclose-text>
<indent>yes</indent>
</options>)
As a result it returns :
<p>
<? ?†?>
</p>
Now this result is not the valid xml format (I checked it via XML validator) due to which when I try to insert this XML into the MarkLogic it throws an error saying 'MALFORMED BODY | Invalid Processing Instruction names'.
I did some investigation around PIs but not much luck. I could have tried saving the content without PI but this is also not a valid PI too.
That is because what you think is a PI is in fact not a PI.
From W3C:
2.6 Processing Instructions
[Definition: Processing instructions (PIs) allow documents to contain
instructions for applications.]
Processing Instructions
[16] PI ::= '' Char*)))?
'?>'
[17] PITarget ::= Name - (('X' | 'x') ('M' | 'm') ('L' |
'l'))
So the PI name cannot start with ? as in your sample ??†
You probably want to clean up the content before you pass it to tidy.
Like below:
declare variable $xml as node() :=
<content><![CDATA[<p>Hello <???†?>world</p>]]></content>;
declare function local:copy($input as item()*) as item()* {
for $node in $input
return
typeswitch($node)
case text()
return fn:replace($node,"<\?[^>]+\?>","")
case element()
return
element {name($node)} {
(: output each attribute in this element :)
for $att in $node/#*
return
attribute {name($att)} {$att}
,
(: output all the sub-elements of this element recursively :)
for $child in $node
return local:copy($child/node())
}
(: otherwise pass it through. Used for text(), comments, and PIs :)
default return $node
};
xdmp:tidy(local:copy($xml),
<options xmlns="xdmp:tidy">
<assume-xml-procins>no</assume-xml-procins>
<quiet>yes</quiet>
<tidy-mark>no</tidy-mark>
<enclose-text>yes</enclose-text>
<indent>yes</indent>
</options>)
This would do the trick to get rid of all PIs (real and fake PIs)
Regards,
Peter

To remove the node but keep the value inside intact through XQuery

I have a content.xml modelled as below
<root>
<childnode>
Some text here
</childnode>
</root>
I am trying to remove the <childnode> and update the content.xml with only the value of it
so the output looks like
<root>
Some Text here
</root>
I wrote a function to perform this but anytime I run it it gives me error as "unexpected token: modify". I was thinking of a way to accomplish this without using functx functions.
xquery version "1.0";
declare namespace request="http://exist-db.org/xquery/request";
declare namespace file="http://exist-db.org/xquery/file";
declare namespace system="http://exist-db.org/xquery/system";
declare namespace util="http://exist-db.org/xquery/util";
declare namespace response="http://exist-db.org/xquery/response";
declare function local:contentUpdate() {
let $root := collection('/lib/repository/content')//root/childNode
let $rmChild := for $child in $root
modify
(
return rename node $child as ''
)
};
local:updateTitle()
Thanks in advance
There are multiple problems with your query:
Updating functions must be declared as updating.
You're calling another function than you defined (probably you didn't notice as there still have been syntax errors).
Rename node expects some element (or processing instruction, attribute) as target, the empty string is not allowed.
At least BaseX doesn't allow updating statements when defining code as XQuery 1.0. Maybe exist doesn't care about this, try adding it if you need to know.
You do not want to rename, but replace all <childnode />s with its contents, use replace node.
This code fixes all these problems:
declare updating function local:contentUpdate() {
let $root := collection('/lib/repository/content')
return
for $i in $root//childnode
return
replace node $i with $i/data()
};
local:contentUpdate()
eXist-db's XQuery Update syntax is documented at http://exist-db.org/exist/update_ext.xml. Note that this syntax predates the release of the XQuery Update Facility 1.0, so the syntax is different and remains unique to eXist-db.
The way to do what you want in eXist-db is as follows:
xquery version "1.0";
declare function local:contentUpdate() {
let $root := doc('/db/lib/repository/content/content.xml')/root
return
update value $root with $root/string()
};
local:contentUpdate()
The primary changes, compared to your original code, are:
Inserted the eXist-db syntax for your update
Prepended '/db' to your collection name, as /db is the root of the database in eXist-db; replaced the collection() call with a doc() call, since you stated you were operating on a single file, content.xml
Changed //root to /root, since "root" is the root element, so the // (descendant-or-self) axis is extraneous
Replaced updateTitle() with the actual name of the function, contentUpdate
Removed the extraneous namespace declarations
For more on why I used $root/string(), see http://community.marklogic.com/blog/text-is-a-code-smell.

Resources