<commit_before><?xml version="1.0" ?>
<!--
  #%L
  SurveyorCore
  %%
  Copyright (C) 2013 - 2014 University of Oxford
  %%
  Redistribution and use in source and binary forms, with or without modification,
  are permitted provided that the following conditions are met:
  
  1. Redistributions of source code must retain the above copyright notice, this
     list of conditions and the following disclaimer.
  
  2. Redistributions in binary form must reproduce the above copyright notice,
     this list of conditions and the following disclaimer in the documentation
     and/or other materials provided with the distribution.
  
  3. Neither the name of the University of Oxford nor the names of its contributors
     may be used to endorse or promote products derived from this software without
     specific prior written permission.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
  BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
  LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
  OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
  OF THE POSSIBILITY OF SUCH DAMAGE.
  #L%
  -->


<surveyor>
    <!--
   A sample data source, default might be the standard JSON data source
    -->
    <datasource type="LocalClientSideDataProvider">
        <property name="fileLocation" value="data/publications.json"/>
        <schema>
            <field name="CLON" type="CoordinateLon"/> <!-- type would be controlled vocabulary containing: Coordinate, Date, String, Integer-->
            <field name="CLAT" type="CoordinateLat"/>
            <field name="PY" type="Date"/>
            <field name="URL" type="String"/>
            <field name="PTN" type="String"/>
            <field name="DCN" type="String"/>
            <field name="DN" type="String"/>
            <field name="STN" type="String"/>
            <field name="OTN" type="String"/>
            <field name="QI" type="String"/>
            <field name="FA" type="String"/>
            <field name="TTL" type="String"/>
            <field name="PUB" type="String"/>
            <field name="CN" type="String"/>
            <field name="FR" type="Integer"/>
            <field name="DSN" type="String"/>
            <field name="PID" type="Integer"/>
        </schema>
    </datasource>

    <views>
        <map name="Medicine Quality Map" maxZoomOutLevel="2" range="World"> <!-- alternative type may be tabular data -->
            <!-- Assuming the range is a enumerated list of places, like World, Asia, Africa, Europe etc-->
            <filter>
                <field name="type" value="Molecular"/>
            </filter>
            <marker>
                <lonField fieldName="CLON"/>
                <latField fieldName="CLAT"/>
            </marker>
            <label>

            </label>
        </map>
        <table name="Report table">
            <columns>
                <column fieldName="FA" fieldTitle="1st Author"/>
                <column fieldName="PY" fieldTitle="Year"/>
                <column fieldName="TTL" fieldTitle="Title" hyperlinkField="URL"/>
                <column fieldName="PUB" fieldTitle="Publication"/>
                <column fieldName="CN" fieldTitle="Countries"/>
            </columns>
            <label>

            </label>
        </table>
    </views>

    <filters>
        <label>
            <![CDATA[
            Select filters:
            <br/>
            Use the filters below to selected publications or survey rows,
            <br/> according to Medicine, Report type, Sampling type, Medicine source,
            <br/> and Quality issue.
            ]]>
        </label>

        <filter field="DCN" name="Medicines">
            <!-- We can infers how to display the filter, based on the of the field,
            or we could have an additional tag to describe this. So for a string field assumed that multiselect field is used-->
            <label>
                Allows the user to select the medicines, based on International Nonproprietary Names (INN)
                or categories of medicines. Medicines are classified in three categories Artemisinin derivatives
                (including all the artemisinin derivative monotherapies), Artemisinin based Combination Therapies (ACTs)
                and Non-artemisinins. These categories are mutually exclusive and individual drugs or combinations are
                listed below. The selection of all publications that contain information on each individual medicine or
                medicine categories can be obtained by filtering.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="All">All drugs and combination therapies</filterLabel>
                <filterLabel fieldValue="ACT">Artemisinin Combination Therapies</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="PTN" name="Report type" >
            <label>
                Lists the different types of publication found describing antimalarial drug quality.
                Papers on techniques, drug legislation, reviews, and other reports usually
                do not contain location information and therefore will not appear in the map.
                They can however be found in the report table.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="All">Any type of report</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="STN" name="Collection type">
            <label>
                Lists the type of sampling methodology used in each report.
                Only studies with evidence describing how randomisation was performed have been included as 'Random Survey'
            </label>
            <filterValueLabelMap>
            </filterValueLabelMap>

        </filter>
        <filter field="QI" name="Quality classification">
            <label>
                We use, unless otherwise specified in the report, the term 'falsified' as a synonym for
                counterfeit or spurious, referring to a medical
                product produced with criminal intent to mislead, without reference to intellectual
                property concerns. If authors did not examine packaging
                we class samples that failed chemical assays, but without detected
                wrong active ingredients, as poor quality and not falsified/counterfeit.
                Samples that did not fail chemical assays and/or a packaging tests are considered as good quality.
                Samples are only classified as 'Good Quality' if all samples collected were good quality.
                Samples classified as poor quality, falsified or substandard may contain good quality medicines.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="Falsified">Samples with fake packaging + right amount of API or wrong or none or incorrect API. Also those samples with no genuine packaging to check + wrong or no Active Pharmaceutical Ingredient</filterLabel>
                <filterLabel fieldValue="Substandard">Samples with genuine packaging + incorrect quantity of correct API</filterLabel>
                <filterLabel fieldValue="Poor Quality">‘Samples without reference packaging available for comparison, containing incorrect quantities (>zero %) of the correct API or failure to comply with other quality specifications (e.g. dissolution tests, contents of impurity, sterility etc)</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="OTN" name="Medicine Source">
            <label>
                Lists the type of outlet where the collection of samples was
                performed. Reports that do not provide clear information about the drug provider
                will be classified as unknown.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="Unknown">Studies where the source of samples is unknown</filterLabel>
                <filterLabel fieldValue="Private pharmacy">Samples collected only in private sector pharmacies</filterLabel>
                <filterLabel fieldValue="Distributor/ agent/ trader/ wholesale pharmacies">Samples provided from distributor, agent, trader or wholesale pharmacies</filterLabel>
                <filterLabel fieldValue="Govt &amp; Private outlets">Samples collected from private and public sectors</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filterByDateRange field="PY" name="Filter by year" startDate="1975" endDate="currentYear"><commit_msg>fixing label to match data.<commit_after><?xml version="1.0" ?>
<!--
  #%L
  SurveyorCore
  %%
  Copyright (C) 2013 - 2014 University of Oxford
  %%
  Redistribution and use in source and binary forms, with or without modification,
  are permitted provided that the following conditions are met:
  
  1. Redistributions of source code must retain the above copyright notice, this
     list of conditions and the following disclaimer.
  
  2. Redistributions in binary form must reproduce the above copyright notice,
     this list of conditions and the following disclaimer in the documentation
     and/or other materials provided with the distribution.
  
  3. Neither the name of the University of Oxford nor the names of its contributors
     may be used to endorse or promote products derived from this software without
     specific prior written permission.
  
  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
  BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
  LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
  OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
  OF THE POSSIBILITY OF SUCH DAMAGE.
  #L%
  -->


<surveyor>
    <!--
   A sample data source, default might be the standard JSON data source
    -->
    <datasource type="LocalClientSideDataProvider">
        <property name="fileLocation" value="data/publications.json"/>
        <schema>
            <field name="CLON" type="CoordinateLon"/> <!-- type would be controlled vocabulary containing: Coordinate, Date, String, Integer-->
            <field name="CLAT" type="CoordinateLat"/>
            <field name="PY" type="Date"/>
            <field name="URL" type="String"/>
            <field name="PTN" type="String"/>
            <field name="DCN" type="String"/>
            <field name="DN" type="String"/>
            <field name="STN" type="String"/>
            <field name="OTN" type="String"/>
            <field name="QI" type="String"/>
            <field name="FA" type="String"/>
            <field name="TTL" type="String"/>
            <field name="PUB" type="String"/>
            <field name="CN" type="String"/>
            <field name="FR" type="Integer"/>
            <field name="DSN" type="String"/>
            <field name="PID" type="Integer"/>
        </schema>
    </datasource>

    <views>
        <map name="Medicine Quality Map" maxZoomOutLevel="2" range="World"> <!-- alternative type may be tabular data -->
            <!-- Assuming the range is a enumerated list of places, like World, Asia, Africa, Europe etc-->
            <filter>
                <field name="type" value="Molecular"/>
            </filter>
            <marker>
                <lonField fieldName="CLON"/>
                <latField fieldName="CLAT"/>
            </marker>
            <label>

            </label>
        </map>
        <table name="Report table">
            <columns>
                <column fieldName="FA" fieldTitle="1st Author"/>
                <column fieldName="PY" fieldTitle="Year"/>
                <column fieldName="TTL" fieldTitle="Title" hyperlinkField="URL"/>
                <column fieldName="PUB" fieldTitle="Publication"/>
                <column fieldName="CN" fieldTitle="Countries"/>
            </columns>
            <label>

            </label>
        </table>
    </views>

    <filters>
        <label>
            <![CDATA[
            Select filters:
            <br/>
            Use the filters below to selected publications or survey rows,
            <br/> according to Medicine, Report type, Sampling type, Medicine source,
            <br/> and Quality issue.
            ]]>
        </label>

        <filter field="DCN" name="Medicines">
            <!-- We can infers how to display the filter, based on the of the field,
            or we could have an additional tag to describe this. So for a string field assumed that multiselect field is used-->
            <label>
                Allows the user to select the medicines, based on International Nonproprietary Names (INN)
                or categories of medicines. Medicines are classified in three categories Artemisinin derivatives
                (including all the artemisinin derivative monotherapies), Artemisinin based Combination Therapies (ACTs)
                and Non-artemisinins. These categories are mutually exclusive and individual drugs or combinations are
                listed below. The selection of all publications that contain information on each individual medicine or
                medicine categories can be obtained by filtering.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="All">All drugs and combination therapies</filterLabel>
                <filterLabel fieldValue="ACT">Artemisinin Combination Therapies</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="PTN" name="Report type" >
            <label>
                Lists the different types of publication found describing antimalarial drug quality.
                Papers on techniques, drug legislation, reviews, and other reports usually
                do not contain location information and therefore will not appear in the map.
                They can however be found in the report table.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="All">Any type of report</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="STN" name="Collection type">
            <label>
                Lists the type of sampling methodology used in each report.
                Only studies with evidence describing how randomisation was performed have been included as 'Random Survey'
            </label>
            <filterValueLabelMap>
            </filterValueLabelMap>

        </filter>
        <filter field="QI" name="Quality classification">
            <label>
                We use, unless otherwise specified in the report, the term 'falsified' as a synonym for
                counterfeit or spurious, referring to a medical
                product produced with criminal intent to mislead, without reference to intellectual
                property concerns. If authors did not examine packaging
                we class samples that failed chemical assays, but without detected
                wrong active ingredients, as poor quality and not falsified/counterfeit.
                Samples that did not fail chemical assays and/or a packaging tests are considered as good quality.
                Samples are only classified as 'Good Quality' if all samples collected were good quality.
                Samples classified as poor quality, falsified or substandard may contain good quality medicines.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="Falsified">Samples with fake packaging + right amount of API or wrong or none or incorrect API. Also those samples with no genuine packaging to check + wrong or no Active Pharmaceutical Ingredient</filterLabel>
                <filterLabel fieldValue="Substandard">Samples with genuine packaging + incorrect quantity of correct API</filterLabel>
                <filterLabel fieldValue="Poor Quality">‘Samples without reference packaging available for comparison, containing incorrect quantities (>zero %) of the correct API or failure to comply with other quality specifications (e.g. dissolution tests, contents of impurity, sterility etc)</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filter field="OTN" name="Medicine Source">
            <label>
                Lists the type of outlet where the collection of samples was
                performed. Reports that do not provide clear information about the drug provider
                will be classified as unknown.
            </label>
            <filterValueLabelMap>
                <filterLabel fieldValue="Unknown">Studies where the source of samples is unknown</filterLabel>
                <filterLabel fieldValue="Private pharmacy">Samples collected only in private sector pharmacies</filterLabel>
                <filterLabel fieldValue="Distributor/agent/trader/wholesale pharmacies">Samples provided from distributor, agent, trader or wholesale pharmacies</filterLabel>
                <filterLabel fieldValue="Govt &amp; Private outlets">Samples collected from private and public sectors</filterLabel>
            </filterValueLabelMap>
        </filter>
        <filterByDateRange field="PY" name="Filter by year" startDate="1975" endDate="currentYear">
{'fraction_non_alphanumeric': 0.07746979388770434, 'fraction_numerical': 0.002077524465584167, 'mean_word_length': 2.4107775498787993, 'pattern_counts': {'":': 0, '<': 227, '<?xml version=': 2, '>': 229, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5399177', 'n_tokens_mistral': 4380, 'n_tokens_neox': 4047, 'n_words': 1796}