Vfrdtyky

I need help on the optimization of a batch-file to get multiple xml tags of over a thousand xml files into a .txt or .csv.

The .xml's are all in the same format. They are clinical studies and look like this:

    <?xml version="1.0" encoding="UTF-8"?>

<clinical_study rank="373">

  <!-- This xml conforms to an XML Schema at:

    https://clinicaltrials.gov/ct2/html/images/info/public.xsd -->

  <required_header>

    <download_date>ClinicalTrials.gov processed this data on May 25, 2017</download_date>

    <link_text>Link to the current ClinicalTrials.gov record.</link_text>

    <url>https://clinicaltrials.gov/show/NCT00146471</url>

  </required_header>

  <id_info>

    <org_study_id>Kep-F10.3.01</org_study_id>

    <nct_id>NCT00146471</nct_id>

  </id_info>

  <brief_title>Efficacy and Safety of Levetiracetam in the Inpatient Treatment of Alcohol Withdrawal Syndrome</brief_title>

  <official_title>Efficacy and Safety of Levetiracetam in the Inpatient Treatment of Alcohol Withdrawal Syndrome [Sicherheit Und Wirksamkeit Von Levetiracetam (Keppra) für Die Behandlung Des stationären Alkoholentzugsyndroms]</official_title>

  <sponsors>

    <lead_sponsor>

      <agency>Charite University, Berlin, Germany</agency>

      <agency_class>Other</agency_class>

    </lead_sponsor>

  </sponsors>

  <source>Charite University, Berlin, Germany</source>

  <oversight_info>

    <has_dmc>Yes</has_dmc>

  </oversight_info>

  <brief_summary>

    <textblock>

      The purpose of this study is to evaluate the efficacy and safety of levetiracetam for

      treating alcohol withdrawal syndrome (AWS) in inpatients (vs. placebo). The primary come-out

      parameter is the reduction of the total needed amount of diazepam for add-on treatment of

      acute alcohol withdrawal symptoms. The secondary come-out parameter are - safety criteria

      (AE) - reduction of alcohol withdrawal score over the days.

    </textblock>

  </brief_summary>

  <overall_status>Completed</overall_status>

  <start_date>January 2006</start_date>

  <completion_date type="Actual">September 2007</completion_date>

  <primary_completion_date type="Actual">July 2007</primary_completion_date>

  <phase>Phase 3</phase>

  <study_type>Interventional</study_type>

  <has_expanded_access>No</has_expanded_access>

  <study_design_info>

    <allocation>Randomized</allocation>

    <intervention_model>Parallel Assignment</intervention_model>

    <primary_purpose>Treatment</primary_purpose>

    <masking>Double Blind (Participant, Care Provider, Investigator)</masking>

  </study_design_info>

  <primary_outcome>

    <measure>To evaluate the efficacy and safety of levetiracetam for treating alcohol withdrawal syndrome in inpatients. The primary come-out parameter is the reduction of the amount of diazepam for add-on treatment of acute alcohol withdrawal</measure>

    <time_frame>during trial</time_frame>

  </primary_outcome>

  <secondary_outcome>

    <measure>Secondary come-out parameters are - safety criteria (AE) - reduction of alcohol withdrawal score over the days</measure>

    <time_frame>during trial</time_frame>

  </secondary_outcome>

  <number_of_arms>2</number_of_arms>

  <enrollment type="Actual">120</enrollment>

  <condition>Alcohol Withdrawal Syndrome</condition>

  <arm_group>

    <arm_group_label>2</arm_group_label>

    <arm_group_type>Active Comparator</arm_group_type>

  </arm_group>

  <arm_group>

    <arm_group_label>1: Diazepam plus Placebo</arm_group_label>

    <arm_group_type>Placebo Comparator</arm_group_type>

  </arm_group>

  <intervention>

    <intervention_type>Drug</intervention_type>

    <intervention_name>Levetiracetam</intervention_name>

    <description>1500-2000 mg daily add-on or Placebo Diazepam as needed</description>

    <arm_group_label>2</arm_group_label>

    <other_name>KEPPRA</other_name>

  </intervention>

  <intervention>

    <intervention_type>Drug</intervention_type>

    <intervention_name>Placebo</intervention_name>

    <description>1500-2000 mg daily add-on or Placebo Diazepam as needed</description>

    <arm_group_label>1: Diazepam plus Placebo</arm_group_label>

  </intervention>

  <eligibility>

    <criteria>

      <textblock>

        Inclusion Criteria:



          -  Ages eligible for study: 18-65 years.



          -  Meets criteria for alcohol dependence according to DSM-IV/ICD-10



          -  Known withdrawal symptoms in the past in case of discontinuation of alcohol

             consumption



          -  Hospital admission for alcohol detoxification



          -  Able to provide a written informed consent.



          -  Able to follow verbal and written instructions (incl. a sufficient knowledge of

             German language).



          -  Must be medically acceptable for study treatment. No past or present physical

             disorder that is likely to deteriorate during participation. No ECG abnormality which

             would likely worsen during participation and no clinical laboratory abnormality that

             would also suggest deterioration during treatment.



          -  Have a negative urine drug screen for benzodiazepines or heroine or methadone



        Exclusion Criteria:



          -  Current diagnosis of any other substance dependence syndrome other than alcohol

             dependence (excluding nicotine and caffeine dependence).



          -  History of idiopathic epilepsy.



          -  Patient with any current clinically significant psychiatric disorder (acute

             suiciality) or developmental disorder (including organic mental disorder), like

             psychotic disorders.



          -  Patients with the following complications of alcoholism (lifetime): acute delirium

             tremens, hallucinatory alcoholic state, Korsakoff`s syndrome, Wernicke

             encephalopathy, decomposed liver cirrhosis (Child B, C), suspected cirrhosis with the

             following clinical symptoms detected at clinical exam: signs of portal hypertension

             and signs of hepato-cellular failure, thrombocytopenia.



          -  Subjects with known sensitivity of previous adverse reaction to levetiracetam



          -  Contra-indication (hypersensitivity to levetiracetam or pyrrolidone derivatives) or

             known non-response to levetiracetam.



          -  History of severe GI disease which might render absorption of the medication

             difficult or produce medical instability of the patient which would include active

             peptic ulcer disease, ulcerative colitis, regional colitis, or evidence by history or

             physical exam of GI bleeding.



          -  Patients with any clinically significant acute or chronic progressive neurological,

             gastrointestinal, cardiovascular, hepatic, renal, haematological, endocrine,

             dermatological or respiratory disease, such as diabetes, severe infection, acute

             alcoholic hepatitis, or any other medical condition with significant worsening of the

             clinical situation of the patient that might interfere with the evaluation of study

             medication.



          -  Female patients pregnant, breast-feeding or of child bearing age and not protected by

             effective contraceptive such as implants, injectables, combined oral contraceptives,

             some IUDS, sexual abstinence, sterilization or vasectomized partner.



          -  Actually continuous use of pharmacological agents that are known to lower the seizure

             threshold or augment or decrease the alcohol withdrawal syndrome.



          -  Subjects with known sensitivity of previous adverse reaction to diazepam or clonidine



          -  Contra-indication or known non-response to diazepam or clonidine

      </textblock>

    </criteria>

    <gender>All</gender>

    <minimum_age>18 Years</minimum_age>

    <maximum_age>65 Years</maximum_age>

    <healthy_volunteers>No</healthy_volunteers>

  </eligibility>

  <overall_official>

    <last_name>Martin Schaefer, MD</last_name>

    <role>Principal Investigator</role>

    <affiliation>Charité Campus Mitte, Klinik für Psychiatrie und Psychotherapie</affiliation>

  </overall_official>

  <location>

    <facility>

      <name>MLU Halle-Wittenberg</name>

      <address>

        <city>Halle</city>

        <state>Sachen/Anhalt</state>

        <zip>06097</zip>

        <country>Germany</country>

      </address>

    </facility>

  </location>

  <location>

    <facility>

      <name>Charité - Universitätsmedizin Berlin, Campus Charité Mitte, Klinik für Psychiatrie und Psychotherapie</name>

      <address>

        <city>Berlin</city>

        <zip>10117</zip>

        <country>Germany</country>

      </address>

    </facility>

  </location>

  <location>

    <facility>

      <name>Psychiatrische Klinik der Charité im St.-Hedwig Krankenhaus</name>

      <address>

        <city>Berlin</city>

        <zip>10559</zip>

        <country>Germany</country>

      </address>

    </facility>

  </location>

  <location>

    <facility>

      <name>Klinik für Psychiatrie und Suchtmedizin, Kliniken Essen Mitte</name>

      <address>

        <city>Essen</city>

        <zip>45136</zip>

        <country>Germany</country>

      </address>

    </facility>

  </location>

  <location>

    <facility>

      <name>Zentrum für Seelische Gesundheit</name>

      <address>

        <city>Rhede</city>

        <zip>46414</zip>

        <country>Germany</country>

      </address>

    </facility>

  </location>

  <location_countries>

    <country>Germany</country>

  </location_countries>

  <reference>

    <citation>Krebs M, Leopold K, Richter C, Kienast T, Hinzpeter A, Heinz A, Schaefer M. Levetiracetam for the treatment of alcohol withdrawal syndrome: an open-label pilot trial. J Clin Psychopharmacol. 2006 Jun;26(3):347-9.</citation>

    <PMID>16702910</PMID>

  </reference>

  <verification_date>September 2008</verification_date>

  <lastchanged_date>December 29, 2009</lastchanged_date>

  <firstreceived_date>September 6, 2005</firstreceived_date>

  <responsible_party>

    <name_title>Martin Schaefer, MD</name_title>

    <organization>Charite University, Berlin, Germany</organization>

  </responsible_party>

  <keyword>alcohol withdrawal</keyword>

  <keyword>detoxification</keyword>

  <keyword>Inpatients</keyword>

  <keyword>alcohol dependence according to DSM-IV/ICD-10</keyword>

  <keyword>withdrawal symptoms</keyword>

  <condition_browse>

    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm  -->

    <mesh_term>Syndrome</mesh_term>

    <mesh_term>Substance Withdrawal Syndrome</mesh_term>

  </condition_browse>

  <intervention_browse>

    <!-- CAUTION:  The following MeSH terms are assigned with an imperfect algorithm  -->

    <mesh_term>Ethanol</mesh_term>

    <mesh_term>Diazepam</mesh_term>

    <mesh_term>Etiracetam</mesh_term>

    <mesh_term>Piracetam</mesh_term>

  </intervention_browse>

  <!-- Results have not yet been posted for this study                                -->

</clinical_study>

So they all use the same tags and i need a few of them like:

• overall_official


• lead_sponsor


• official_title


• results_reference


• overall_status

So far i tried with the following code:

    @echo off

setlocal enabledelayedexpansion

for %%a in (*.xml) do (

call :XMLExtract "%%a" "<results_reference>" location

echo.!location!,%%~na

)

exit /b



:XMLExtract file keystart location

@echo off & setlocal

for /f "tokens=3 delims=<>" %%a in ('Findstr /i /c:%2 "%~1"') do (

   set "loc=%%a" & goto :endloop

)

:endLoop

ENDLOCAL & IF "%~3" NEQ "" (SET %~3=%loc%) ELSE echo.%loc%

exit /b

I ran the batch in the command line as: bat >> output.txt or output.csv and it worked perfectly for the overall_status, but with all of the other tags there are problems e.g.:

• overall_offical: It stops after like 10 of them


• other tags: The file names are listed (as always), but with no information behind it.

I would really appreciate any help on how this can be fixed or another way to efficiently solve this task. I only have a small, basic understanding of programming, but i am sure to be able to work myself into any easy solutions. The best help would be a way to optimize the batch code to fit this. If there is some information missing i am sorry and i will provide it.

@ECHO Off

SETLOCAL

SET "sourcedir=U:sourcedir"

SET "destdir=U:destdir"

:: SET "tags=overall_official lead_sponsor official_title results_reference overall_status"

SET "tags=%*"



FOR /f "tokens=1delims=" %%a IN (

 'dir /b /a-d "%sourcedir%*.xml" '

 ) DO (

 REM Clear detected-tags flags for each file "%%a"

 FOR %%t IN (%tags% malformed) DO SET "%%t="

 REM remove "rem" from following line to delete any existing result file

 REM del "%destdir%%%~na.txt" >nul 2>nul

 REM Read each line to %%L - usebackq to allow "quoted filenames"

 FOR /f "usebackqdelims=" %%L IN ("%sourcedir%%%a") DO (

  REM remove leading spaces from %%L into %%P

  FOR /f "tokens=*" %%P IN ("%%L") DO (

   REM tokenise on "<>"

   FOR /f "tokens=1-3*delims=<>" %%w IN ("%%P") DO (

    IF "%%z" neq "" SET "malformed=%%z"

    FOR %%t IN (%tags%) DO IF "%%w"=="%%t" (SET "%%t=Y") else IF "%%w"=="/%%t" (SET "%%t=") 

    SET "report="

    FOR %%t IN (%tags%) DO IF DEFINED %%t SET "report=Y"

    REM (1 of 2) un-rem this to deposit in individual filenames

    REM (

    IF DEFINED report (

     REM we may have 1,2 or 3 tokens

     REM if 3, output token 2

     REM if 2, output token 1 if token 2 starts "/", token 2 otherwise

     REM if only 1, output entire line unless it is a target token

     IF "%%y" equ "" (

      IF "%%x" equ "" (

       REM only one token

       FOR %%t IN (%tags%) DO IF "%%w"=="%%t" (SET "report=") else IF "%%w"=="/%%t" (SET "report=") 

       IF DEFINED report ECHO %%L

      ) ELSE (

       REM two tokens

       ECHO %%x|FINDSTR /b "/">NUL 2>NUL

       IF ERRORLEVEL 1 (ECHO %%x) ELSE (ECHO %%w)

      )

     ) ELSE (ECHO %%x)

    )

    REM (2 of 2) un-rem this to deposit in individual filenames

    REM )>>"%destdir%%%~na.txt"

    FOR %%t IN (%tags%) DO IF "%%y"=="/%%t" (SET "%%t=") 

    FOR %%t IN (%tags%) DO IF "%%x"=="/%%t" (SET "%%t=") 

   )

  REM pause

  )

 )

)



GOTO :EOF

You would need to change the settings of sourcedir and destdir to suit your circumstances.

This may give you some ideas. You haven't provided an output sample, so perhaps you'd want to prefix each output line with the source filename (in %%~na) in the appropriate echos

Expected syntax to run:

thisbatchname tag tag tag

My approach is to have %%a contain the filename to be processed, %%L the raw line data from the file and %%P the raw line data with leading spaces stripped.

Tokenising %%P using the delimiters yields %%W to %%z as each line contains 1-3 possible elements - tags or data. If there is a fourth, then there's something wrong (the flag malformed is set for the file, although I didn't do anything with it - it will contain the text where the problem lies[could also have been set to %%P for the entire line...])

So, using the required-tags as variable names, simply set those varnames to nothing or something and use if defined to interpret their state - which operates on their run-time status as the data changes line-by-line.

Note that as the entire operational part of the code is one gargantuan code-block, rem and not :: must be used for helpful remarks.

Also note that

(

 commands

)>file

will redirect the output of commands according to the redirector specified (if required)

try with xpath.bat:

for /f "tokens=* delims=" %%# in ('xpath.bat "study.xml" "//reference/citation"') do set "reference_citation=%%#"

echo %reference_citation%



for /f "tokens=* delims=" %%# in ('xpath.bat "study.xml" "//official_title"') do set "official_title=%%#"

echo %official_title%



for /f "tokens=* delims=" %%# in ('xpath.bat "study.xml" "//lead_sponsor/agency"') do set "lead_sponsor=%%#"

echo %lead_sponsor%



for /f "tokens=* delims=" %%# in ('xpath.bat "study.xml"  "//overall_official"') do set  "overall_official=%%#"

echo %overall_official%