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>e11b9a2bb8</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.</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 Communication</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 tools to provide published record and citation.</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>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</example_published_documents_url>
</papertype>
<papertype>
<name>Forum Paper</name>
<good_for>Forum Paper</good_for>
<description>Publication meant to initiate 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>Taxonomic Paper</name>
<good_for>Taxonomic Paper</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.</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>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</example_published_documents_url>
</papertype>
<papertype>
<name>Single Taxon Treatment</name>
<good_for>Single Taxon Treatment
</good_for>
<description>Publication of a single new taxon, new synonym, change in taxonomic status, re-description, biological / ecological observations on a single species, and others.</description>
<schema_url>https://arpha.pensoft.net/dev/xsd/single_taxon_treatment</schema_url>
<example_documents_url>https://arpha.pensoft.net/dev/example/single_taxon_treatment</example_documents_url>
<example_published_documents_url>/examples.php?id=71 </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 species group. Contains a link to an openly accessible described online key.</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>http://bdj.pensoft.net/browse_journal_articles.php?journal_name=bdj&form_name=filter_articles&sortby=0&journal_id=1&section_type%5B%5D=9</example_published_documents_url>
</papertype>
<papertype>
<name>Data Paper (Biosciences)</name>
<good_for>Data Paper (Biosciences)</good_for>
<description>Description of large datasets. Should contain a link to openly accessible described data. Alternatively, datasets can be uploaded and published as supplementary files.</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>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</example_published_documents_url>
</papertype>
<papertype>
<name>OMIC Data Paper</name>
<good_for>OMICS Data Paper</good_for>
<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.</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 the experiments and their rationale used for a research outcome to be concluded and verified.</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 concluding significant new and original information.</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 exported to the Global Invasive Species Database (GISD).</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. Does not include original data.</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>