Began storage of wiki forms and templates.

svn path=/; revision=107

diff --git a/preecej/semantic_wiki/PS_TransformForImport.pl b/preecej/semantic_wiki/PS_TransformForImport.pl
index 1a219b09ba1d661e73d890ca771fe5b51de66f15..ac74a486bc2de117e85349e9459b2baba59977c2 100644 (file)
--- a/preecej/semantic_wiki/PS_TransformForImport.pl
+++ b/preecej/semantic_wiki/PS_TransformForImport.pl
@@ -306,7 +306,7 @@ sub write_xml
             }
         }
         if (!(defined $curr_accession_id)) {
-            die "Error: No Accession ID available\n";
+            die "Error: No Accession ID available. Ending program.\n";
         }
         
         # iterate through the annotation data and assign to <Field> elements

diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki
new file mode 100644 (file)
index 0000000..464eb3a
--- /dev/null
+++ b/preecej/semantic_wiki/forms/Annotation.wiki
@@ -0,0 +1,145 @@
+<noinclude>
+This is the "Annotation" form.
+To create a page with this form, enter the page name below;
+if a page with that name already exists, you will be sent to a form to edit that page.
+{{#forminput:form=Annotation}}
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Annotation:<unique number;start=1>}}}
+__NOTOC__
+{{#ifexist: {{PAGENAME}}
+    |<font size=6>'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')'''</font>
+    |
+}}
+
+= Annotation =
+
+{{{for template|Annotation}}}
+
+{| class="formtable"
+! Accession ID:
+| {{{field|Accession ID}}}
+|-
+! Species Name:
+| {{{field|Species Name}}}
+|-
+! Species ID:
+| {{{field|Species ID}}}
+|-
+! Gene Symbol:
+|   {{#if:
+        {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]]
+            [[Is Associated With Field::Gene Symbol]]
+            [[Is Associated With Template::Annotation]]
+            |?is_Provenance
+        }}
+        |{{{field|Gene Symbol|restricted}}}
+        |{{{field|Gene Symbol}}}
+    }}
+|-
+! Gene Name:
+| {{{field|Gene Name}}}
+|-
+! Gene Synonyms:
+| synonym code here...
+|-
+! Gene Type:
+| {{{field|Gene Type}}}
+|-
+! EC Number(s):
+| {{{field|EC Numbers|list|delimiter=,}}}
+|-
+! Chromosome:
+|   {{#if:
+        {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]]
+            [[Is Associated With Field::Chromosome]]
+            [[Is Associated With Template::Annotation]]
+            |?is_Provenance
+        }}
+        |{{{field|Chromosome|restricted}}}
+        |{{{field|Chromosome}}}
+    }}
+|-
+! Has Phenotype:
+| {{{field|Has Phenotype}}}
+|-
+! Description:
+| {{{field|Annotation Description}}}
+|}
+
+{{{end template}}}
+
+= External References =
+
+{{#ifexist: {{PAGENAME}}
+    | {{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+        | Add, edit, or remove external reference data {{#formlink:form=External_References|link text=here|target={{PAGENAME}}/External_References }}.
+        {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References* ]]
+            | mainlabel=-
+            |? from_External_Source
+            |? has_External_Accession_ID
+        }}
+        | Add external references for this annotation.<br>{{#formlink:form=External_References|link text=Add|link type=button|query string=External_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }}
+      }}
+    | To add external references, first save your basic annotation information on the "Annotation" tab.
+}}
+
+= Ontologies =
+
+{{#ifexist: {{PAGENAME}}
+    | {{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+        | Add, edit, or remove ontology references {{#formlink:form=Ontological_References|link text=here|target={{PAGENAME}}/Ontologies }}.
+        {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies*]]
+            | mainlabel=-
+            |? has_Term_ID
+            |? has_Term_Name
+            |? has_Aspect
+        }}
+        | Add ontological associations for this annotation.<br>{{#formlink:form=Ontological_References|link text=Add|link type=button|query string=Ontological_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }}
+      }}
+    | To add ontological references, first save your basic annotation information on the "Annotation" tab.
+}}
+
+= Sequences =
+
+{{#ifexist: {{PAGENAME}}
+    | {{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+        | Add, edit, or remove sequence references {{#formlink:form=Sequences|link text=here|target={{PAGENAME}}/Sequences }}.
+        {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences*]]
+            | mainlabel=-
+            |? has_Sequence_Type
+            |? has_Sequence_Source
+            |? has_External_Accession_ID
+        }}
+        | Add sequence references for this annotation.<br>{{#formlink:form=Sequences|link text=Add|link type=button|query string=Sequences[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }}
+      }}
+    | To add sequence references, first save your basic annotation information on the "Annotation" tab.
+}}
+
+= Literature =
+
+{{#ifexist: {{PAGENAME}}
+    | Add a reference to a publication listed with PubMed or the DOI registry {{#formlink:form=Reference_Publication|link text=here|link type=|query string=Reference_Publication[New Annotation Reference]={{PAGENAME}} }}.<br>
+
+Need to add a reference to a publication without a PubMed ID or DOI (Digital Object Identifier)?<br>
+{{#formlink:form=Publication|link text=Add a new publication reference|link type=|query string=Publication[New Annotation Reference]={{PAGENAME}} }}
+    
+    {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }}
+      | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]]
+          |? has First Author
+          |? has Publication ID
+        }}
+      |
+    }}
+    | To add publication references, first save your basic annotation information on the "Annotation" tab.
+}}
+<headertabs/>
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+    
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki
new file mode 100644 (file)
index 0000000..4e4e8b5
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Annotation.wiki
@@ -0,0 +1,115 @@
+<noinclude>
+This is the "Annotation" template.
+It should be called in the following format:
+<pre>
+{{Annotation
+|Accession ID=
+|Species Name=
+|Species ID=
+|Gene Symbol=
+|Gene Name=
+|Gene Type=
+|EC Number(s)=
+|Chromosome=
+|Has Phenotype=
+|Annotation Description=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+
+__NOTOC__
+<font size=6>'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')'''</font>
+
+= Annotation =
+
+{| class="wikitable"
+! Accession ID
+| [[Has Accession ID::{{{Accession ID|}}}]]
+|-
+! Species Name
+| [[Has Species Name::{{{Species Name|}}}]]
+|-
+! Species ID
+| [[Has Species ID::{{{Species ID|}}}]]
+|-
+! Gene Symbol
+| [[Has Gene Symbol::{{{Gene Symbol|}}}]]
+|-
+! Gene Name
+| [[Has Gene Name::{{{Gene Name|}}}]]
+|-
+! Gene Synonyms
+| coming soon...
+|-
+! Gene Type
+| [[Has Gene Type::{{{Gene Type|}}}]]
+|-
+! EC number(s)
+| {{#arraymap:{{{EC Numbers|}}}|,|x|[[Has EC Numbers::x]]}}
+|-
+! Chromosome
+| [[Exists On Chromosome Number::{{{Chromosome|}}}]]
+|-
+! Has Phenotype?
+| [[Has Phenotype::{{{Has Phenotype|}}}]]
+|}
+
+{| class="wikitable"
+! Description
+| [[Has Annotation Description::{{{Annotation Description|}}}]]
+|}
+
+{{#ifexist: {{PAGENAME}}/Provenance
+    | To review the provenance of this data, click [[{{PAGENAME}}/Provenance|here]].
+    |
+}}
+
+= External References =
+
+{{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+    | {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References]]
+        | mainlabel=-
+        |? from_External_Source
+        |? has_External_Accession_ID
+    }}
+    | There are no external references available for this annotation.
+}}
+
+= Ontologies =
+
+{{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+    | {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies]]
+        | mainlabel=-
+        |? has_Term_ID
+        |? has_Term_Name
+        |? has_Aspect
+    }}
+    | There are no ontological associations available for this gene annotation.
+}}
+
+= Sequences =
+
+{{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+    | {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences]]
+        | mainlabel=-
+        |? has_Sequence_Type
+        |? has_Sequence_Source
+        |? has_External_Accession_ID
+    }}
+    | There is no sequence data available for this gene annotation.
+}}
+
+= Literature =
+
+{{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }}
+    | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]]
+        |? has First Author
+        |? has Publication ID
+      }}
+    | There are no publications associated with this annotation.
+}}
+<headertabs/>
+[[Category:Annotations]]
+</includeonly>
+