Difference between revisions of "Bioscape Web Resources"

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{{:Bioscape Status}}
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The Bioscape Web resources provide the principal end-user interface to Bioscape as described in the [[Using the Bioscape Web Application|"Using the Bioscape Web Application"]] document. Typically, a user will follow a specific workflow supported by a number of resources described in the application's "site map", found in the <tt>bsweb</tt> package (specifically in the <tt>__init__.py</tt> source file) in the <tt>bsweb</tt> distribution. The following table summarises the source code organisation:
 
The Bioscape Web resources provide the principal end-user interface to Bioscape as described in the [[Using the Bioscape Web Application|"Using the Bioscape Web Application"]] document. Typically, a user will follow a specific workflow supported by a number of resources described in the application's "site map", found in the <tt>bsweb</tt> package (specifically in the <tt>__init__.py</tt> source file) in the <tt>bsweb</tt> distribution. The following table summarises the source code organisation:
  
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! Logic package/module
 
! Logic package/module
 
! Database access package/module
 
! Database access package/module
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! Templates
 
|-
 
|-
 
| home ([[Using the Bioscape Web Application#Searching|search]]), index ([[Using the Bioscape Web Application#Advanced_Search|advanced search]])
 
| home ([[Using the Bioscape Web Application#Searching|search]]), index ([[Using the Bioscape Web Application#Advanced_Search|advanced search]])
 
| <tt>bsweb.pages</tt>
 
| <tt>bsweb.pages</tt>
 
| <tt>bsweb.pages.collections</tt>
 
| <tt>bsweb.pages.collections</tt>
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| <tt>home_template.xhtml</tt>, <tt>index_template.xhtml</tt>
 
|-
 
|-
 
| [[Using the Bioscape Web Application#Search_Disambiguation|gene disambiguation]], [[Using the Bioscape Web Application#Gene_Summaries|gene summary]]
 
| [[Using the Bioscape Web Application#Search_Disambiguation|gene disambiguation]], [[Using the Bioscape Web Application#Gene_Summaries|gene summary]]
 
| <tt>bsweb.genes</tt>
 
| <tt>bsweb.genes</tt>
 
| <tt>bsweb.genes.collections</tt>
 
| <tt>bsweb.genes.collections</tt>
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| <tt>gene_disambiguation_template.xhtml</tt><br><tt>gene_summary_template.xhtml</tt>
 
|-
 
|-
 
| [[Using the Bioscape Web Application#Mention_Sentences|gene and evidence mention summaries]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.viewers</tt>
 
| [[Using the Bioscape Web Application#Mention_Sentences|gene and evidence mention summaries]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.viewers</tt>
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| <tt>text_mentions_template.xhtml</tt><br><tt>text_evidence_mentions_template.xhtml</tt>
 
|-
 
|-
 
| [[Using the Bioscape Web Application#Navigating_Document_Versions|document lists]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.collections</tt>
 
| [[Using the Bioscape Web Application#Navigating_Document_Versions|document lists]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.collections</tt>
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| <tt>text_index_generation_documents_template.xhtml</tt><br><tt>text_search_generation_documents_template.xhtml</tt><br><tt>text_results_generation_documents_template.xhtml</tt><br><tt>text_evidence_generation_documents_template.xhtml</tt>
 
|-
 
|-
 
| [[Using the Bioscape Web Application#Document_Summaries|annotated documents]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.viewers</tt>
 
| [[Using the Bioscape Web Application#Document_Summaries|annotated documents]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.viewers</tt>
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| <tt>text_index_generation_document_template.xhtml</tt><br><tt>text_search_generation_document_template.xhtml</tt><br><tt>text_results_generation_document_template.xhtml</tt><br><tt>text_evidence_generation_document_template.xhtml</tt>
 
|-
 
|-
 
| [[Using the Bioscape Web Application#Scoring_and_Methods|mention scoring summaries]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.collections</tt>
 
| [[Using the Bioscape Web Application#Scoring_and_Methods|mention scoring summaries]] || <tt>bsweb.documents</tt> || <tt>bsweb.documents.collections</tt>
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| <tt>text_scored_bioentity_template.xhtml</tt><br><tt>text_scored_bioentities_template.xhtml</tt>
 
|}
 
|}
  

Latest revision as of 13:47, 14 July 2010

NoteNotePlease note that this documentation covers an unreleased product and is for internal use only.

The Bioscape Web resources provide the principal end-user interface to Bioscape as described in the "Using the Bioscape Web Application" document. Typically, a user will follow a specific workflow supported by a number of resources described in the application's "site map", found in the bsweb package (specifically in the __init__.py source file) in the bsweb distribution. The following table summarises the source code organisation:

Pages Logic package/module Database access package/module Templates
home (search), index (advanced search) bsweb.pages bsweb.pages.collections home_template.xhtml, index_template.xhtml
gene disambiguation, gene summary bsweb.genes bsweb.genes.collections gene_disambiguation_template.xhtml
gene_summary_template.xhtml
gene and evidence mention summaries bsweb.documents bsweb.documents.viewers text_mentions_template.xhtml
text_evidence_mentions_template.xhtml
document lists bsweb.documents bsweb.documents.collections text_index_generation_documents_template.xhtml
text_search_generation_documents_template.xhtml
text_results_generation_documents_template.xhtml
text_evidence_generation_documents_template.xhtml
annotated documents bsweb.documents bsweb.documents.viewers text_index_generation_document_template.xhtml
text_search_generation_document_template.xhtml
text_results_generation_document_template.xhtml
text_evidence_generation_document_template.xhtml
mention scoring summaries bsweb.documents bsweb.documents.collections text_scored_bioentity_template.xhtml
text_scored_bioentities_template.xhtml

To summarise, page functionality typically resides in the top-level of a package, database queries providing lists of results reside in collections modules, and the special database/text index combination supporting annotated documents resides in the viewers module in the bsweb.documents package.