The ARPHA Writing Tool provides a RESTful API for automated creation of AWT documents, which processes HTTP requests at https://arpha.pensoft.net/api.php. The API reports in XML format. All Pensoft users can use the API freely.
Tests that the specified user can be successfully authenticated to the system
A successful authentication result should look like this
<result>
<requestId>1a00d71bd1</requestId>
<returnCode>0</returnCode>
<authentication_result>Authentication successful</authentication_result>
</result>
An unsuccessful authentication result should look like this. A description of the error is stored in the errorMsg node
<result>
<requestId>a67870f997</requestId>
<returnCode>1</returnCode>
<errorCount>1</errorCount>
<errorMsg>pwt.api.noSuchUser</errorMsg>
</result>
Returns username and password associated api key
A successful api key request result should look like this. An api key is returned in returnResult node.
<result>
<requestId>1a00d71bd1</requestId>
<returnCode>0</returnCode>
<returnResult>xxx</returnResult>
</result>
An unsuccessful api key request should look like this. A description of the error is stored in the errorMsg node.
<result>
<requestId>a67870f997</requestId>
<returnCode>1</returnCode>
<errorMsg>Wrong credentials</errorMsg>
<fpassLink>[forgotten password link]</fpassLink>
</result>
Lists all the available journals in which documents can be created.
No credentials are required for this method
<result>
<requestId>9ed1b0e546</requestId>
<returnCode>0</returnCode>
<journals>
<journal>
<full_name>Biodiversity Data Journal</full_name>
<name>bdj</name>
</journal>
</journals>
</result>
A list of all the available journals is returned. Each journal has the following fields:
Lists all the available article types for the specified journal.
No credentials are required for this method
<?xml version="1.0" encoding="UTF-8"?>
<result>
<requestId>ab76fac047</requestId>
<returnCode>0</returnCode>
<papertypes>
<papertype>
<name>R Package</name>
<good_for>R Package</good_for>
<description>Description of an R Package including information on its purpose, installation and usage.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=295">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/r_package</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/r_package</example_documents_url>
<example_published_documents_url>/examples.php?id=101</example_published_documents_url>
</papertype>
<papertype>
<name>Short Communication</name>
<good_for>Short Communication</good_for>
<description>Short articles (usually 3-4 pages) addressing preliminary findings of higher interest, unique approaches, controversial opinions, new methods or innovative technologies etc. that demand fast publication.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/Short Communication</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/Short Communication</example_documents_url>
<example_published_documents_url>/examples.php?id=107</example_published_documents_url>
</papertype>
<papertype>
<name>Software Description</name>
<good_for>Software Description</good_for>
<description>Description of software or an online tool or platform that contains a link to the openly accessible code of the described tool.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="http://bdj.pensoft.net/browse_journal_articles.php?journal_name=bdj&form_name=filter_articles&sortby=0&journal_id=1&section_type%5B%5D=14">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/software_description</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/software_description</example_documents_url>
<example_published_documents_url>/examples.php?id=20</example_published_documents_url>
</papertype>
<papertype>
<name>Forum Paper</name>
<good_for>Forum Paper</good_for>
<description>Publication meant to initiate or respond to participate in a discussion on a particular scientific topic.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/forum_paper_(free_text_template)</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/forum_paper_(free_text_template)</example_documents_url>
<example_published_documents_url>/examples.php?id=98</example_published_documents_url>
</papertype>
<papertype>
<name>Taxonomy & Inventories</name>
<good_for>Taxonomy & Inventories</good_for>
<description>An article that contains more comprehensive taxonomic results (e.g., taxonomic review or revision or several nomenclatural and taxonomic novelties). It must contain at least two taxon treatments, and/or checklists, and/or identification keys.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="http://bdj.pensoft.net/browse_journal_articles.php?journal_name=bdj&form_name=filter_articles&sortby=0&journal_id=1&section_type%5B%5D=3">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/taxonomic_paper</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/taxonomic_paper</example_documents_url>
<example_published_documents_url>/examples.php?id=16</example_published_documents_url>
</papertype>
<papertype>
<name>Interactive Key</name>
<good_for>Interactive Key</good_for>
<description>Online interactive identification key of a given higher taxon or а species group that contains a link to the openly accessible online key. <br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=9">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/interactive_key</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/interactive_key</example_documents_url>
<example_published_documents_url>/examples.php?id=18</example_published_documents_url>
</papertype>
<papertype>
<name>Data Paper (Biosciences)</name>
<good_for>Data Paper (Biosciences)</good_for>
<description>Formal paper describing large datasets. The article should contain a link to the openly accessible dataset deposited in an internationally recognised repository (see instructions and list of recommended repositories in the <a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/about#Datapublication">Data Publishing Guidelines</a>).<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="http://bdj.pensoft.net/browse_journal_articles.php?journal_name=bdj&form_name=filter_articles&sortby=0&journal_id=1&section_type%5B%5D=8">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/data_paper</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/data_paper</example_documents_url>
<example_published_documents_url>/examples.php?id=19</example_published_documents_url>
</papertype>
<papertype>
<name>OMIC Data Paper</name>
<good_for>OMICS Data Paper</good_for>
<description>Description of omics data that can include information about the genome ((meta)genomics), transcription products ((meta)transcriptomics), protein products ((meta)proteomics), and metabolic products ((meta)metabolomics). More information can be found <a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/about#OmicsDataPapers">here</a>.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/omic_data_paper</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/omic_data_paper</example_documents_url>
<example_published_documents_url>/examples.php?id=113</example_published_documents_url>
</papertype>
<papertype>
<name>Editorial </name>
<good_for>Editorial </good_for>
<description>Opinion article written by the senior editorial staff.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/editorial</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/editorial</example_documents_url>
<example_published_documents_url>/examples.php?id=37</example_published_documents_url>
</papertype>
<papertype>
<name>Corrigendum</name>
<good_for>Corrigendum</good_for>
<description>A correction of an error or a list of errors discovered in a research after publication.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/corrigendum</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/corrigendum</example_documents_url>
<example_published_documents_url>/examples.php?id=39</example_published_documents_url>
</papertype>
<papertype>
<name>Species Conservation Profiles</name>
<good_for>Species Conservation Profiles</good_for>
<description>A single or multiple IUCN species assessment report(s) imported and edited in an IUCN-compliant species template.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=294">See published papers with this template</a> </description>
<schema_url>https://arpha.pensoft.net/dev/xsd/species_conservation_profiles</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/species_conservation_profiles</example_documents_url>
<example_published_documents_url>/examples.php?id=100</example_published_documents_url>
</papertype>
<papertype>
<name>Methods</name>
<good_for>Methods</good_for>
<description>Description of novel methodologies and methods used in biodiversity research and biodiversity informatics.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=261">See published papers with this template</a> </description>
<schema_url>https://arpha.pensoft.net/dev/xsd/methods_(free_text_template)</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/methods_(free_text_template)</example_documents_url>
<example_published_documents_url>/examples.php?id=65</example_published_documents_url>
</papertype>
<papertype>
<name>Research Article</name>
<good_for>Research Article</good_for>
<description>Publication of a study presenting significant new and original information.<br/><br/>
<b>NOTE</b>: For submissions to the <b>Biodiversity Data Journal</b> containing taxonomic, nomenclatural, faunistic or floristic data, <br/>please use the “Taxonomic paper” template.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/research_article_(free_text_template)</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/research_article_(free_text_template)</example_documents_url>
<example_published_documents_url>/examples.php?id=68</example_published_documents_url>
</papertype>
<papertype>
<name>Alien Species Profile</name>
<good_for>Alien Species Profile</good_for>
<description>Assessment report of alien or invasive species following an IUCN-compliant species template. After publication, the article can be integrated with the Global Invasive Species Database (GISD).<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=435">See published papers with this template</a>
</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/alien_species_profile</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/alien_species_profile</example_documents_url>
<example_published_documents_url>/examples.php?id=89</example_published_documents_url>
</papertype>
<papertype>
<name>Commentary</name>
<good_for>Commentary</good_for>
<description>Short free-text publication meant to draw attention or criticise a previously published work. It does not include original data.<br/><br/><a style="color:#73cdd9; text-decoration: none;" href="https://bdj.pensoft.net/browse_journal_articles.php?form_name=filter_articles&sortby=0&journal_id=1&search_in_=0&section_type%5B%5D=397">See published papers with this template</a></description>
<schema_url>https://arpha.pensoft.net/dev/xsd/commentary_(free_text_template)</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/commentary_(free_text_template)</example_documents_url>
<example_published_documents_url>/examples.php?id=97</example_published_documents_url>
</papertype>
</papertypes>
</result>
A list of all the available article types for the specified journal:
Validates the specified xml document against the schema corresponding to the document's article type
No credentials are required for this method
document/objects/article_metadata/title_and_authors/author/fields/submitting_author/value
<citation id="6">
<citation_type>tables</citation_type>
<object_id>42</object_id>
<object_id>43</object_id>
</citation>
Notes about the format:
<introduction>
<fields>
<introduction>
<value>
<p>
Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed <inline_citation citation_id="6" /> diam nonummy nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod mazim placerat facer possim assum. Typi non habent claritatem insitam; est usus legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt lectores legere me lius quod ii legunt saepius. Claritas est etiam processus dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum.
</p>
</value>
</introduction>
</fields>
</introduction>
A successful validation result should look like this
<result>
<requestId>558c037d61</requestId>
<returnCode>0</returnCode>
<validation_result>Document validated successfully</validation_result>
</result>
An unsuccessful validation result will look like this. A description of the error is stored in the errorMsg node
<result>
<requestId>4b4195735c</requestId>
<returnCode>1</returnCode>
<errorCount>1</errorCount>
<errorMsg>Xml is invalid!Fatal Error 76: Opening and ending tag mismatch: aut1hor line 17 and author on line 57</errorMsg>
</result>
Imports the document in the system. Before importing the document, user authentication and document validation are executed.
If either one fails an error will occur.
N.B. After a successful import only the users added as authors in the document's xml will be able to see the document on their dashboard and edit it (i.e. if the user running the API is not added as author of the document they won't be able to see the document or access the document link returned from the API).
A successful import result should look like this
<result>
<requestId>edbd3be071</requestId>
<returnCode>0</returnCode>
<document_id>123456</document_id>
<document_link>http://arpha.pensoft.net/display_document.php?document_id=123456</document_link>
<document_autologin_link>[auto login link]</document_autologin_link>
</result>
An unsuccessful import result will look like this. A description of the error is stored in the errorMsg node
<result>
<requestId>4b4195735c</requestId>
<returnCode>1</returnCode>
<errorCount>1</errorCount>
<errorMsg>Xml is invalid!Fatal Error 76: Opening and ending tag mismatch: aut1hor line 17 and author on line 57</errorMsg>
</result>