Merge branch 'main' into Isabelle_dev

Isabelle_DOF-Example-Extra/CENELEC_50128/mini_odo/ROOT

@@ -1,4 +1,4 @@
-session "mini_odo" = "Isabelle_DOF" +
+session "mini_odo" = "Isabelle_DOF-Ontologies" +
   options [document = pdf, document_output = "output", document_build = dof]
   sessions 
     "Physical_Quantities"

Isabelle_DOF-Example-Extra/CENELEC_50128/mini_odo/mini_odo.thy

@@ -15,7 +15,7 @@
 theory 
   mini_odo
 imports  
-  "Isabelle_DOF.CENELEC_50128" 
+  "Isabelle_DOF-Ontologies.CENELEC_50128" 
   "Isabelle_DOF.technical_report"
   "Physical_Quantities.SI" "Physical_Quantities.SI_Pretty"
 begin
@@ -628,14 +628,14 @@ text\<open>
 \<close>
 
 text\<open>Examples for declaration of typed doc-classes "assumption" (sic!) and "hypothesis" (sic!!),
-     concepts defined in the underlying ontology @{theory "Isabelle_DOF.CENELEC_50128"}. \<close>
+     concepts defined in the underlying ontology @{theory "Isabelle_DOF-Ontologies.CENELEC_50128"}. \<close>
 text*[ass2::assumption, long_name="Some ''assumption one''"] \<open> The subsystem Y is safe. \<close>
 text*[hyp1::hypothesis] \<open> \<open>P \<noteq> NP\<close> \<close>
   
 text\<open>  
-   A real example fragment fsrom a larger project, declaring a text-element as a
+   A real example fragment from a larger project, declaring a text-element as a
    "safety-related application condition", a concept defined in the 
-   @{theory "Isabelle_DOF.CENELEC_50128"} ontology:\<close>  
+   @{theory "Isabelle_DOF-Ontologies.CENELEC_50128"} ontology:\<close>  
 
 text*[hyp2::hypothesis]\<open>Under the assumption @{assumption \<open>ass2\<close>} we establish the following: ... \<close>
 

Isabelle_DOF-Example-Extra/scholarly_paper/ROOTS

@@ -0,0 +1 @@
+2020-iFM-CSP

Isabelle_DOF-Example-Scholarly_Paper/IsaDofApplications.thy

@@ -17,7 +17,7 @@ theory IsaDofApplications
 begin
 
 use_template "lncs"
-use_ontology "scholarly_paper"
+use_ontology "Isabelle_DOF.scholarly_paper"
 
 open_monitor*[this::article] 
 declare[[strict_monitor_checking=false]]

Isabelle_DOF-Example-Scholarly_Paper/ROOT

@@ -1,4 +1,4 @@
-session "2018-cicm-isabelle_dof-applications" = "Isabelle_DOF" + 
+session "Isabelle_DOF-Example-Scholarly_Paper" (AFP) = "Isabelle_DOF" + 
   options [document = pdf, document_output = "output", document_build = dof, quick_and_dirty = true]
   theories
     IsaDofApplications

Isabelle_DOF-Examples-Extra/scholarly_paper/ROOTS

@@ -1,2 +0,0 @@
-2018-cicm-isabelle_dof-applications
-2020-iFM-CSP

Isabelle_DOF-Ontologies/CENELEC_50128/CENELEC_50128.thy

@@ -24,8 +24,10 @@ identifies:
  \<close> 
 
 (*<<*)  
-theory CENELEC_50128
-  imports  "Isabelle_DOF.technical_report"
+theory 
+  CENELEC_50128
+  imports  
+  "document_setup"
 begin
 
 define_ontology "DOF-CENELEC_50128.sty"
@@ -523,9 +525,11 @@ text\<open>Figure 3 in Chapter 5: Illustrative Development Lifecycle 1\<close>
 
 text\<open>Global Overview\<close>
 
+(*
 figure*[fig3::figure, relative_width="100", 
  src="''examples/CENELEC_50128/mini_odo/document/figures/CENELEC-Fig.3-docStructure.png''"]
 \<open>Illustrative Development Lifecycle 1\<close>
+*)
 
 text\<open>Actually, the Figure 4 in Chapter 5: Illustrative Development Lifecycle 2 is more fidele
 to the remaining document: Software Architecture and Design phases are merged, like in 7.3.\<close>
@@ -616,9 +620,10 @@ doc_class cenelec_report = text_element +
    invariant must_be_chapter :: "text_element.level \<sigma> = Some(0)" 
    invariant three_eyes_prcpl:: "  written_by \<sigma> \<noteq> fst_check \<sigma> 
                                  \<and> written_by \<sigma> \<noteq> snd_check \<sigma>"
-   
+  
+(* 
 text\<open>see \<^figure>\<open>fig3\<close> and Fig 4 in Chapter 5: Illustrative Development Lifecycle 2\<close>
-
+*)
 doc_class external_specification =
   phase        :: "phase"  <= "SYSDEV_ext"
 
@@ -1038,7 +1043,7 @@ in  DOF_core.add_ml_invariant binding check_sil thy end)
 \<close>
 
 text\<open>
-A more generic example of check_sil which can be generalized:
+A more generic example of check\_sil which can be generalized:
 it is decoupled from the CENELEC current implementation
 but is much less efficient regarding time computation by relying on Isabelle evaluation mechanism.\<close>
 ML\<open>
@@ -1259,15 +1264,16 @@ doc_class test_documentation =    (* OUTDATED ? *)
 
 
 section\<open>Global Documentation Structure\<close>
-
+(*<<*)
 doc_class global_documentation_structure = text_element +
    level :: "int option" <= "Some(-1::int)"  \<comment> \<open>document must be a chapter\<close>
-   accepts "SYSREQS      ~~                  \<comment> \<open>system_requirements_specification\<close>
-            SYSSREQS     ~~                  \<comment> \<open>system_safety_requirements_specification\<close> 
-            SYSAD        ~~                  \<comment> \<open>system_architecture description\<close>
+   accepts "SYSREQS      ~~                  \<comment> \<open>system requiremens specification\<close>
+            SYSSREQS     ~~                  \<comment> \<open>system safety requirements specification\<close> 
+            SYSAD        ~~                  \<comment> \<open>system architecture description\<close>
             SYSS_pl      ~~                  \<comment> \<open>system safety plan\<close> 
             (SWRS || OSWTS)  "                \<comment> \<open>software requirements specification OR
                                                  overall software test specification\<close> 
+(*>>*)
 (* MORE TO COME : *)
 
 section\<open> META : Testing and Validation \<close>
@@ -1302,4 +1308,4 @@ ML
   Syntax.read_typ                  @{context} "hypothesis"  handle  _ => dummyT;
   Proof_Context.init_global; \<close>
 
-end
+end

Isabelle_DOF-Ontologies/CENELEC_50128/CENELEC_50128_Documentation.thy

@@ -0,0 +1,396 @@
+(*************************************************************************
+ * Copyright (C) 
+ *               2019-2023      The University of Exeter 
+ *               2018-2023 The University of Paris-Saclay
+ *               2018      The University of Sheffield
+ *
+ * License:
+ *   This program can be redistributed and/or modified under the terms
+ *   of the 2-clause BSD-style license.
+ *
+ *   SPDX-License-Identifier: BSD-2-Clause
+ *************************************************************************)
+
+(*<<*)  
+theory 
+  CENELEC_50128_Documentation
+  imports  
+  CENELEC_50128
+           
+begin
+define_shortcut* dof     \<rightleftharpoons> \<open>\dof\<close>
+                 isadof  \<rightleftharpoons> \<open>\isadof{}\<close>
+define_shortcut* TeXLive \<rightleftharpoons> \<open>\TeXLive\<close>
+                 BibTeX  \<rightleftharpoons> \<open>\BibTeX{}\<close> 
+                 LaTeX   \<rightleftharpoons> \<open>\LaTeX{}\<close>
+                 TeX     \<rightleftharpoons> \<open>\TeX{}\<close>
+                 pdf     \<rightleftharpoons> \<open>PDF\<close>
+
+ML\<open>
+
+fun boxed_text_antiquotation name (* redefined in these more abstract terms *) =
+    DOF_lib.gen_text_antiquotation name DOF_lib.report_text
+                           (fn ctxt => DOF_lib.string_2_text_antiquotation ctxt
+                                       #> DOF_lib.enclose_env false ctxt "isarbox")
+
+val neant = K(Latex.text("",\<^here>))
+
+fun boxed_theory_text_antiquotation name (* redefined in these more abstract terms *) =
+    DOF_lib.gen_text_antiquotation name DOF_lib.report_theory_text
+                           (fn ctxt => DOF_lib.string_2_theory_text_antiquotation ctxt
+                                        #> DOF_lib.enclose_env false ctxt "isarbox"
+                                        (* #> neant *)) (*debugging *)
+
+fun boxed_sml_text_antiquotation name  =
+    DOF_lib.gen_text_antiquotation name (K(K()))
+                           (fn ctxt => Input.source_content
+                                        #> Latex.text
+                                        #> DOF_lib.enclose_env true ctxt "sml")
+                           (* the simplest conversion possible *)
+
+fun boxed_pdf_antiquotation name =
+    DOF_lib.gen_text_antiquotation name (K(K()))
+                           (fn ctxt => Input.source_content
+                                        #> Latex.text
+                                        #> DOF_lib.enclose_env true ctxt "out")
+                           (* the simplest conversion possible *)
+
+fun boxed_latex_antiquotation name =
+    DOF_lib.gen_text_antiquotation name (K(K()))
+                           (fn ctxt => Input.source_content
+                                        #> Latex.text
+                                        #> DOF_lib.enclose_env true ctxt "ltx")
+                           (* the simplest conversion possible *)
+
+fun boxed_bash_antiquotation name =
+    DOF_lib.gen_text_antiquotation name (K(K()))
+                           (fn ctxt => Input.source_content
+                                        #> Latex.text
+                                        #> DOF_lib.enclose_env true ctxt "bash")
+                           (* the simplest conversion possible *)
+\<close>
+
+setup\<open>(* std_text_antiquotation        \<^binding>\<open>my_text\<close> #> *)
+      boxed_text_antiquotation         \<^binding>\<open>boxed_text\<close> #>
+      (* std_text_antiquotation        \<^binding>\<open>my_cartouche\<close> #> *)
+      boxed_text_antiquotation         \<^binding>\<open>boxed_cartouche\<close> #>
+      (* std_theory_text_antiquotation \<^binding>\<open>my_theory_text\<close>#> *)
+      boxed_theory_text_antiquotation  \<^binding>\<open>boxed_theory_text\<close> #>
+
+      boxed_sml_text_antiquotation     \<^binding>\<open>boxed_sml\<close> #>
+      boxed_pdf_antiquotation          \<^binding>\<open>boxed_pdf\<close> #>
+      boxed_latex_antiquotation        \<^binding>\<open>boxed_latex\<close>#>
+      boxed_bash_antiquotation         \<^binding>\<open>boxed_bash\<close>
+     \<close>
+
+
+
+(*>>*)  
+
+section*[cenelec_onto::example]\<open>Writing Certification Documents \<^boxed_theory_text>\<open>CENELEC_50128\<close>\<close>
+subsection\<open>The CENELEC 50128 Example\<close>
+text\<open> 
+  The ontology \<^verbatim>\<open>CENELEC_50128\<close>\index{ontology!CENELEC\_50128} is a small ontology modeling 
+  documents for a certification following CENELEC 50128~@{cite "boulanger:cenelec-50128:2015"}.
+  The \<^isadof> distribution contains a small example  using the ontology ``CENELEC\_50128'' in 
+  the directory \nolinkurl{examples/CENELEC_50128/mini_odo/}. You can inspect/edit the 
+  integrated source example by either 
+  \<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the 
+    Isabelle-Icon provided by the Isabelle installation) and loading the file 
+    \nolinkurl{examples/CENELEC_50128/mini_odo/mini_odo.thy}.
+  \<^item> starting Isabelle/jEdit from the command line by calling:
+
+@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë 
+  isabelle jedit examples/CENELEC_50128/mini_odo/mini_odo.thy \<close>}
+\<close>
+text\<open>\<^noindent> Finally, you
+  \<^item>   can build the \<^pdf>-document by calling:
+@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë isabelle build mini_odo \<close>}
+\<close>
+ 
+subsection\<open>Modeling CENELEC 50128\<close>
+
+text\<open>
+  Documents to be provided in formal certifications (such as CENELEC 
+  50128~@{cite "boulanger:cenelec-50128:2015"} or Common Criteria~@{cite "cc:cc-part3:2006"}) can 
+  much profit from the control of ontological consistency:  a substantial amount of the work
+  of evaluators in formal certification processes consists in  tracing down the links from 
+  requirements over assumptions down to elements of evidence, be it in form of semi-formal 
+  documentation, models, code, or tests.  In a certification process, traceability becomes a major 
+  concern; and providing mechanisms to ensure complete traceability already at the development of 
+  the integrated source can in our view increase the speed and reduce the risk certification 
+  processes. Making the link-structure machine-checkable, be it between requirements, assumptions, 
+  their implementation and their discharge by evidence (be it tests, proofs, or authoritative 
+  arguments), has the potential in our view to decrease the cost of software developments 
+  targeting certifications. 
+
+  As in many other cases, formal certification documents come with an own terminology and pragmatics
+  of what has to be demonstrated and where, and how the traceability of requirements through 
+  design-models over code to system environment assumptions has to be assured.  
+
+  In the sequel, we present a simplified version of an ontological model used in a 
+  case-study~@{cite "bezzecchi.ea:making:2018"}. We start with an introduction of the concept of 
+  requirement:
+
+@{boxed_theory_text [display]\<open>
+doc_class requirement = long_name :: "string option"
+
+doc_class hypothesis = requirement +
+      hyp_type :: hyp_type <= physical  (* default *)
+  
+datatype ass_kind = informal | semiformal | formal
+  
+doc_class assumption = requirement +
+     assumption_kind :: ass_kind <= informal 
+\<close>}
+
+Such ontologies can be enriched by larger explanations and examples, which may help
+the team of engineers substantially when developing the central document for a certification, 
+like an explication of what is precisely the difference between an \<^typ>\<open>hypothesis\<close> and an 
+\<^typ>\<open>assumption\<close> in the context of the evaluation standard. Since the PIDE makes for each 
+document class its definition available by a simple mouse-click, this kind on meta-knowledge 
+can be made far more accessible during the document evolution.
+
+For example, the term of category \<^typ>\<open>assumption\<close> is used for domain-specific assumptions. 
+It has \<^const>\<open>formal\<close>, \<^const>\<open>semiformal\<close> and \<^const>\<open>informal\<close> sub-categories. They have to be 
+tracked and discharged by appropriate validation procedures within a 
+certification process, be it by test or proof. It is different from a \<^typ>\<open>hypothesis\<close>, which is
+globally assumed and accepted.
+
+In the sequel, the category \<^typ>\<open>exported_constraint\<close> (or \<^typ>\<open>EC\<close> for short)
+is used for formal assumptions, that arise during the analysis,
+design or implementation and have to be tracked till the final
+evaluation target, and discharged by appropriate validation procedures 
+within the certification process, be it by test or proof.  A particular class of interest 
+is the category \<^typ>\<open>safety_related_application_condition\<close> (or \<^typ>\<open>SRAC\<close> 
+for short) which is used for \<^typ>\<open>EC\<close>'s that establish safety properties
+of the evaluation target. Their traceability throughout the certification
+is therefore particularly critical. This is naturally modeled as follows:
+@{boxed_theory_text [display]\<open>  
+doc_class EC = assumption  +
+     assumption_kind :: ass_kind <= (*default *) formal
+                        
+doc_class SRAC = EC  +
+     assumption_kind :: ass_kind <= (*default *) formal
+\<close>}
+
+We now can, \<^eg>, write 
+
+@{boxed_theory_text [display]\<open>
+text*[ass123::SRAC]\<open> 
+  The overall sampling frequence of the odometer subsystem is therefore 
+  14 khz, which includes sampling, computing and result communication 
+  times \ldots
+\<close>
+\<close>}
+
+This will be shown in the \<^pdf> as follows:
+\<close>
+text*[ass123::SRAC] \<open> The overall sampling frequency of the odometer
+subsystem is therefore 14 khz, which includes sampling, computing and
+result communication times \ldots \<close>
+
+text\<open>Note that this \<^pdf>-output is the result of a specific setup for \<^typ>\<open>SRAC\<close>s.\<close>
+
+subsection*[ontopide::technical]\<open>Editing Support for CENELEC 50128\<close>  
+figure*[figfig3::figure,relative_width="95",src="''figures/antiquotations-PIDE''"]
+\<open> Standard antiquotations referring to theory elements.\<close>
+text\<open> The corresponding view in @{docitem  \<open>figfig3\<close>} shows core part of a document 
+conforming to the \<^verbatim>\<open>CENELEC_50128\<close> ontology. The first sample shows standard Isabelle antiquotations 
+@{cite "wenzel:isabelle-isar:2020"} into formal entities of a theory. This way, the informal parts 
+of a document get ``formal content'' and become more robust under change.\<close>
+
+figure*[figfig5::figure, relative_width="95", src="''figures/srac-definition''"]
+        \<open> Defining a \<^typ>\<open>SRAC\<close> in the integrated source ... \<close>
+
+figure*[figfig7::figure, relative_width="95", src="''figures/srac-as-es-application''"]
+        \<open> Using a \<^typ>\<open>SRAC\<close> as \<^typ>\<open>EC\<close> document element. \<close>
+text\<open> The subsequent sample in @{figure \<open>figfig5\<close>} shows the definition of a
+\<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which 
+has the consequence that a certain calculation must be executed sufficiently fast on an embedded 
+device. This condition can not be established inside the formal theory but has to be 
+checked by system integration tests. Now we reference in @{figure  \<open>figfig7\<close>} this 
+safety-related condition; however, this happens in a context where general \<^emph>\<open>exported constraints\<close> 
+are listed. \<^isadof>'s checks and establishes that this is legal in the given ontology. 
+\<close>    
+
+text\<open>
+\<^item> \<^theory_text>\<open>@{term_ \<open>term\<close> }\<close> parses and type-checks \<open>term\<close> with term antiquotations,
+  for instance \<^theory_text>\<open>@{term_ \<open>@{cenelec-term \<open>FT\<close>}\<close>}\<close> will parse and check
+  that \<open>FT\<close> is indeed an instance of the class \<^typ>\<open>cenelec_term\<close>,
+\<close>
+
+subsection\<open>A Domain-Specific Ontology: \<^verbatim>\<open>CENELEC_50128\<close>\<close>
+(*<*)
+ML\<open>val toLaTeX = String.translate (fn c => if c = #"_" then "\\_" else String.implode[c])\<close>     
+ML\<open>writeln (DOF_core.print_doc_class_tree 
+                 @{context} (fn (n,l) =>  true (*     String.isPrefix "technical_report" l 
+                                         orelse String.isPrefix "Isa_COL" l *)) 
+                 toLaTeX)\<close>
+(*>*)
+text\<open> The \<^verbatim>\<open>CENELEC_50128\<close> ontology in \<^theory>\<open>Isabelle_DOF-Ontologies.CENELEC_50128\<close>
+is an example of a domain-specific ontology.
+It is based on  \<^verbatim>\<open>technical_report\<close> since we assume that this kind of format will be most
+appropriate for this type of long-and-tedious documents,
+
+%
+\begin{center}
+\begin{minipage}{.9\textwidth}\footnotesize
+\dirtree{%
+.0 .
+.1 CENELEC\_50128.judgement\DTcomment{...}.
+.1 CENELEC\_50128.test\_item\DTcomment{...}.
+.2 CENELEC\_50128.test\_case\DTcomment{...}.
+.2 CENELEC\_50128.test\_tool\DTcomment{...}.
+.2 CENELEC\_50128.test\_result\DTcomment{...}.
+.2 CENELEC\_50128.test\_adm\_role\DTcomment{...}.
+.2 CENELEC\_50128.test\_environment\DTcomment{...}.
+.2 CENELEC\_50128.test\_requirement\DTcomment{...}.
+.2 CENELEC\_50128.test\_specification\DTcomment{...}.
+.1 CENELEC\_50128.objectives\DTcomment{...}.
+.1 CENELEC\_50128.design\_item\DTcomment{...}.
+.2 CENELEC\_50128.interface\DTcomment{...}.
+.1 CENELEC\_50128.sub\_requirement\DTcomment{...}.
+.1 CENELEC\_50128.test\_documentation\DTcomment{...}.
+.1 Isa\_COL.text\_element\DTcomment{...}.
+.2 CENELEC\_50128.requirement\DTcomment{...}.
+.3 CENELEC\_50128.TC\DTcomment{...}.
+.3 CENELEC\_50128.FnI\DTcomment{...}.
+.3 CENELEC\_50128.SIR\DTcomment{...}.
+.3 CENELEC\_50128.CoAS\DTcomment{...}.
+.3 CENELEC\_50128.HtbC\DTcomment{...}.
+.3 CENELEC\_50128.SILA\DTcomment{...}.
+.3 CENELEC\_50128.assumption\DTcomment{...}.
+.4 CENELEC\_50128.AC\DTcomment{...}.
+.5 CENELEC\_50128.EC\DTcomment{...}.
+.6 CENELEC\_50128.SRAC\DTcomment{...}.
+.3 CENELEC\_50128.hypothesis\DTcomment{...}.
+.4 CENELEC\_50128.security\_hyp\DTcomment{...}.
+.3 CENELEC\_50128.safety\_requirement\DTcomment{...}.
+.2 CENELEC\_50128.cenelec\_text\DTcomment{...}.
+.3 CENELEC\_50128.SWAS\DTcomment{...}.
+.3 [...].
+.2 scholarly\_paper.text\_section\DTcomment{...}.
+.3 scholarly\_paper.technical\DTcomment{...}.
+.4 scholarly\_paper.math\_content\DTcomment{...}.
+.5 CENELEC\_50128.semi\_formal\_content\DTcomment{...}.
+.1 ...
+}
+\end{minipage}
+\end{center}
+\<close>
+
+(* TODO : Rearrange ontology hierarchies. *)
+
+subsubsection\<open>Examples\<close>
+
+text\<open>
+The category ``exported constraint (EC)'' is, in the file 
+\<^file>\<open>CENELEC_50128.thy\<close> defined as follows:
+
+@{boxed_theory_text [display]\<open>
+doc_class requirement = text_element +
+   long_name    :: "string option"
+   is_concerned :: "role set"
+doc_class assumption = requirement +
+     assumption_kind :: ass_kind <= informal 
+doc_class AC = assumption +
+   is_concerned :: "role set" <= "UNIV"
+doc_class EC = AC  +
+     assumption_kind :: ass_kind <= (*default *) formal
+\<close>}
+\<close>
+text\<open>
+We now define the document representations, in the file 
+\<^file>\<open>DOF-CENELEC_50128.sty\<close>. Let us assume that we want to 
+register the definition of EC's in a dedicated table of contents (\<^boxed_latex>\<open>tos\<close>) 
+and use an earlier defined environment \inlineltx|\begin{EC}...\end{EC}| for their graphical 
+representation. Note that the \inlineltx|\newisadof{}[]{}|-command requires the 
+full-qualified names, \<^eg>, \<^boxed_theory_text>\<open>text.CENELEC_50128.EC\<close> for the document class and 
+\<^boxed_theory_text>\<open>CENELEC_50128.requirement.long_name\<close> for the  attribute \<^const>\<open>long_name\<close>, 
+inherited from the document class \<^typ>\<open>requirement\<close>. The representation of \<^typ>\<open>EC\<close>'s
+can now be defined as follows:
+% TODO:
+% Explain the text qualifier of the long_name text.CENELEC_50128.EC
+
+\begin{ltx}
+\newisadof{text.CENELEC_50128.EC}%
+[label=,type=%
+,Isa_COL.text_element.level=%
+,Isa_COL.text_element.referentiable=%
+,Isa_COL.text_element.variants=%
+,CENELEC_50128.requirement.is_concerned=%
+,CENELEC_50128.requirement.long_name=%
+,CENELEC_50128.EC.assumption_kind=][1]{%
+\begin{isamarkuptext}%
+   \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
+      % If long_name is not defined, we only create an entry in the table tos
+      % using the auto-generated number of the EC 
+      \begin{EC}%
+          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
+    }{%
+      % If long_name is defined, we use the long_name as title in the 
+      % layout of the EC, in the table "tos" and as index entry. .
+      \begin{EC}[\commandkey{CENELEC_50128.requirement.long_name}]%
+        \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: %
+              \commandkey{CENELEC_50128.requirement.long_name}}%
+        \DOFindex{EC}{\commandkey{CENELEC_50128.requirement.long_name}}%
+    }%
+    \label{\commandkey{label}}% we use the label attribute as anchor 
+    #1% The main text of the EC
+  \end{EC}
+\end{isamarkuptext}%
+}
+\end{ltx}
+\<close>
+text\<open>
+  For example, the @{docitem "ass123"} from page \pageref{ass123} is mapped to
+
+@{boxed_latex [display]
+\<open>\begin{isamarkuptext*}%
+[label = {ass122},type = {CENELEC_50128.SRAC}, 
+ args={label = {ass122}, type = {CENELEC_50128.SRAC}, 
+       CENELEC_50128.EC.assumption_kind = {formal}}
+] The overall sampling frequence of the odometer subsystem is therefore 
+ 14 khz, which includes sampling, computing and result communication 
+ times ...
+\end{isamarkuptext*}\<close>}
+
+This environment is mapped to a plain \<^LaTeX> command via:
+@{boxed_latex [display]
+\<open> \NewEnviron{isamarkuptext*}[1][]{\isaDof[env={text},#1]{\BODY}} \<close>}
+\<close>
+text\<open>
+For the command-based setup, \<^isadof> provides a dispatcher that selects the most specific 
+implementation for a given \<^boxed_theory_text>\<open>doc_class\<close>:
+
+@{boxed_latex [display]
+\<open>%% The Isabelle/DOF dispatcher:
+\newkeycommand+[\|]\isaDof[env={UNKNOWN},label=,type={dummyT},args={}][1]{%
+  \ifcsname isaDof.\commandkey{type}\endcsname%
+      \csname isaDof.\commandkey{type}\endcsname%
+              [label=\commandkey{label},\commandkey{args}]{#1}%
+  \else\relax\fi%
+  \ifcsname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
+      \csname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
+              [label=\commandkey{label},\commandkey{args}]{#1}%
+  \else%
+      \message{Isabelle/DOF: Using default LaTeX representation for concept %
+        "\commandkey{env}.\commandkey{type}".}%
+      \ifcsname isaDof.\commandkey{env}\endcsname%
+         \csname isaDof.\commandkey{env}\endcsname%
+                [label=\commandkey{label}]{#1}%
+      \else%
+      \errmessage{Isabelle/DOF: No LaTeX representation for concept %
+        "\commandkey{env}.\commandkey{type}" defined and no default %
+        definition for "\commandkey{env}" available either.}%
+      \fi%
+  \fi%
+}\<close>}
+\<close>
+
+
+
+(*<<*)  
+end 
+(*>>*)  

Isabelle_DOF-Ontologies/ROOT

@@ -4,11 +4,13 @@ session "Isabelle_DOF-Ontologies" = "Isabelle_DOF" +
     "CC_v3_1_R5"
     "Conceptual"
     "small_math"
+    "CENELEC_50128"
   theories
     "document_setup"
     "CC_v3_1_R5/CC_v3_1_R5"
     "CC_v3_1_R5/CC_terminology"  
     "Conceptual/Conceptual"
     "small_math/small_math"
+    "CENELEC_50128/CENELEC_50128"
   document_files
     ".empty"

Isabelle_DOF/ROOT

@@ -6,14 +6,12 @@ session "Isabelle_DOF" (AFP) = "Functional-Automata" +
     "thys"
     "thys/manual"
     "ontologies"
-    "ontologies/CENELEC_50128"
     "ontologies/scholarly_paper"
     "ontologies/technical_report"
   theories [document = false]
     "ontologies/ontologies"
     "ontologies/technical_report/technical_report"
     "ontologies/scholarly_paper/scholarly_paper"
-    "ontologies/CENELEC_50128/CENELEC_50128"
     "thys/RegExpInterface"
     "thys/Isa_DOF"
     "thys/Isa_COL"

Isabelle_DOF/document/preamble.tex

@@ -36,8 +36,8 @@
 \title{<TITLE>}
 \author{<AUTHOR>}
 
-\renewcommand{\listofSRACs}{\relax}
-\renewcommand{\listofECs}{\relax}
+%\renewcommand{\listofSRACs}{\relax}
+%\renewcommand{\listofECs}{\relax}
 \pagestyle{headings}
 
 \uppertitleback{
@@ -116,5 +116,15 @@ France, and therefore granted with public funds of the Program ``Investissements
   \end{minipage}
 \end{minipage}
 }
+% Index setup
+\usepackage{index}
+\makeindex
+\AtEndDocument{\printindex}
+
+\newcommand{\DOFindex}[2]{%
+  \marginnote{\normalfont\textbf{#1}: #2}%
+  \expandafter\index\expandafter{\expanded{#2 (#1)}}%
+}%
+
 
 \AtBeginDocument{\isabellestyle{literal}\newcommand{\lstnumberautorefname}{Line}}

Isabelle_DOF/ontologies/ontologies.thy

@@ -14,7 +14,6 @@
 theory 
   ontologies
 imports
-  "CENELEC_50128/CENELEC_50128"
   "scholarly_paper/scholarly_paper"
   "technical_report/technical_report"
 begin

Isabelle_DOF/scala/dof_document_build.scala

@@ -69,15 +69,17 @@ object DOF_Document_Build
 
       val isabelle_dof_dir = context.session_context.sessions_structure(DOF.session).dir
 
+       val ltx_ontologies = split_lines(the_document_entry(context, "dof/use_ontology").text)
+
       // LaTeX styles from Isabelle/DOF directory
-      List(Path.explode("latex/styles"), Path.explode("ontologies"))
+      (List(Path.explode("latex/styles"), Path.explode("ontologies")):::(ltx_ontologies.map(name => 
+              context.session_context.sessions_structure((Long_Name.qualifier(name)).mkString).dir)))
         .flatMap(dir => File.find_files((isabelle_dof_dir + dir).file, _.getName.endsWith(".sty")))
         .foreach(sty => Isabelle_System.copy_file(sty, directory.doc_dir.file))
 
       // ontologies.tex from session exports
       File.write(directory.doc_dir + Path.explode("ontologies.tex"),
-        split_lines(the_document_entry(context, "dof/use_ontology").text)
-          .map(name => "\\usepackage{DOF-" + name + "}\n").mkString)
+           ltx_ontologies.map(name => "\\usepackage{DOF-" + Long_Name.base_name(name) + "}\n").mkString)
 
       // root.tex from session exports
       File.write(directory.doc_dir + Path.explode("root.tex"),

Isabelle_DOF/thys/Isa_DOF.thy

@@ -3105,8 +3105,9 @@ fun use_template context arg =
 
 fun use_ontology context args =
   let
-    val xml = args
-      |> map (check_ontology context #> fst #> Long_Name.base_name)
+    val xml = args                                       
+     (* |> map (check_ontology context #> fst #> Long_Name.base_name) *)
+      |> map (check_ontology context #> fst )
       |> cat_lines |> XML.string;
   in Export.export (Context.theory_of context) \<^path_binding>\<open>dof/use_ontology\<close> xml end;
 

Isabelle_DOF/thys/manual/00_Frontmatter.thy

@@ -15,11 +15,10 @@
 theory "00_Frontmatter"
   imports 
     "Isabelle_DOF.technical_report"
-    "Isabelle_DOF.CENELEC_50128"
 begin
  
 use_template "scrreprt-modern"
-use_ontology "technical_report" and "CENELEC_50128"
+use_ontology "technical_report"
 
 
 

Isabelle_DOF/thys/manual/03_GuidedTour.thy

@@ -532,132 +532,6 @@ on the level of generated \<^verbatim>\<open>.aux\<close>-files, which are not n
 error-message and compiling a with a consistent bibtex usually makes disappear this behavior. 
 \<close>
 
-section*[cenelec_onto::example]\<open>Writing Certification Documents \<^boxed_theory_text>\<open>CENELEC_50128\<close>\<close>
-subsection\<open>The CENELEC 50128 Example\<close>
-text\<open> 
-  The ontology \<^verbatim>\<open>CENELEC_50128\<close>\index{ontology!CENELEC\_50128} is a small ontology modeling 
-  documents for a certification following CENELEC 50128~@{cite "boulanger:cenelec-50128:2015"}.
-  The \<^isadof> distribution contains a small example  using the ontology ``CENELEC\_50128'' in 
-  the directory \nolinkurl{examples/CENELEC_50128/mini_odo/}. You can inspect/edit the 
-  integrated source example by either 
-  \<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the 
-    Isabelle-Icon provided by the Isabelle installation) and loading the file 
-    \nolinkurl{examples/CENELEC_50128/mini_odo/mini_odo.thy}.
-  \<^item> starting Isabelle/jEdit from the command line by calling:
-
-@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë 
-  isabelle jedit examples/CENELEC_50128/mini_odo/mini_odo.thy \<close>}
-\<close>
-text\<open>\<^noindent> Finally, you
-  \<^item>   can build the \<^pdf>-document by calling:
-@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë isabelle build mini_odo \<close>}
-\<close>
- 
-subsection\<open>Modeling CENELEC 50128\<close>
-
-text\<open>
-  Documents to be provided in formal certifications (such as CENELEC 
-  50128~@{cite "boulanger:cenelec-50128:2015"} or Common Criteria~@{cite "cc:cc-part3:2006"}) can 
-  much profit from the control of ontological consistency:  a substantial amount of the work
-  of evaluators in formal certification processes consists in  tracing down the links from 
-  requirements over assumptions down to elements of evidence, be it in form of semi-formal 
-  documentation, models, code, or tests.  In a certification process, traceability becomes a major 
-  concern; and providing mechanisms to ensure complete traceability already at the development of 
-  the integrated source can in our view increase the speed and reduce the risk certification 
-  processes. Making the link-structure machine-checkable, be it between requirements, assumptions, 
-  their implementation and their discharge by evidence (be it tests, proofs, or authoritative 
-  arguments), has the potential in our view to decrease the cost of software developments 
-  targeting certifications. 
-
-  As in many other cases, formal certification documents come with an own terminology and pragmatics
-  of what has to be demonstrated and where, and how the traceability of requirements through 
-  design-models over code to system environment assumptions has to be assured.  
-
-  In the sequel, we present a simplified version of an ontological model used in a 
-  case-study~@{cite "bezzecchi.ea:making:2018"}. We start with an introduction of the concept of 
-  requirement:
-
-@{boxed_theory_text [display]\<open>
-doc_class requirement = long_name :: "string option"
-
-doc_class hypothesis = requirement +
-      hyp_type :: hyp_type <= physical  (* default *)
-  
-datatype ass_kind = informal | semiformal | formal
-  
-doc_class assumption = requirement +
-     assumption_kind :: ass_kind <= informal 
-\<close>}
-
-Such ontologies can be enriched by larger explanations and examples, which may help
-the team of engineers substantially when developing the central document for a certification, 
-like an explication of what is precisely the difference between an \<^typ>\<open>hypothesis\<close> and an 
-\<^typ>\<open>assumption\<close> in the context of the evaluation standard. Since the PIDE makes for each 
-document class its definition available by a simple mouse-click, this kind on meta-knowledge 
-can be made far more accessible during the document evolution.
-
-For example, the term of category \<^typ>\<open>assumption\<close> is used for domain-specific assumptions. 
-It has \<^const>\<open>formal\<close>, \<^const>\<open>semiformal\<close> and \<^const>\<open>informal\<close> sub-categories. They have to be 
-tracked and discharged by appropriate validation procedures within a 
-certification process, be it by test or proof. It is different from a \<^typ>\<open>hypothesis\<close>, which is
-globally assumed and accepted.
-
-In the sequel, the category \<^typ>\<open>exported_constraint\<close> (or \<^typ>\<open>EC\<close> for short)
-is used for formal assumptions, that arise during the analysis,
-design or implementation and have to be tracked till the final
-evaluation target, and discharged by appropriate validation procedures 
-within the certification process, be it by test or proof.  A particular class of interest 
-is the category \<^typ>\<open>safety_related_application_condition\<close> (or \<^typ>\<open>SRAC\<close> 
-for short) which is used for \<^typ>\<open>EC\<close>'s that establish safety properties
-of the evaluation target. Their traceability throughout the certification
-is therefore particularly critical. This is naturally modeled as follows:
-@{boxed_theory_text [display]\<open>  
-doc_class EC = assumption  +
-     assumption_kind :: ass_kind <= (*default *) formal
-                        
-doc_class SRAC = EC  +
-     assumption_kind :: ass_kind <= (*default *) formal
-\<close>}
-
-We now can, \<^eg>, write 
-
-@{boxed_theory_text [display]\<open>
-text*[ass123::SRAC]\<open> 
-  The overall sampling frequence of the odometer subsystem is therefore 
-  14 khz, which includes sampling, computing and result communication 
-  times \ldots
-\<close>
-\<close>}
-
-This will be shown in the \<^pdf> as follows:
-\<close>
-text*[ass123::SRAC] \<open> The overall sampling frequency of the odometer
-subsystem is therefore 14 khz, which includes sampling, computing and
-result communication times \ldots \<close>
-
-text\<open>Note that this \<^pdf>-output is the result of a specific setup for \<^typ>\<open>SRAC\<close>s.\<close>
-
-subsection*[ontopide::technical]\<open>Editing Support for CENELEC 50128\<close>  
-figure*[figfig3::figure,relative_width="95",src="''figures/antiquotations-PIDE''"]
-\<open> Standard antiquotations referring to theory elements.\<close>
-text\<open> The corresponding view in @{docitem  \<open>figfig3\<close>} shows core part of a document 
-conforming to the \<^verbatim>\<open>CENELEC_50128\<close> ontology. The first sample shows standard Isabelle antiquotations 
-@{cite "wenzel:isabelle-isar:2020"} into formal entities of a theory. This way, the informal parts 
-of a document get ``formal content'' and become more robust under change.\<close>
-
-figure*[figfig5::figure, relative_width="95", src="''figures/srac-definition''"]
-        \<open> Defining a \<^typ>\<open>SRAC\<close> in the integrated source ... \<close>
-
-figure*[figfig7::figure, relative_width="95", src="''figures/srac-as-es-application''"]
-        \<open> Using a \<^typ>\<open>SRAC\<close> as \<^typ>\<open>EC\<close> document element. \<close>
-text\<open> The subsequent sample in @{figure \<open>figfig5\<close>} shows the definition of a
-\<^emph>\<open>safety-related application condition\<close>, a side-condition of a theorem which 
-has the consequence that a certain calculation must be executed sufficiently fast on an embedded 
-device. This condition can not be established inside the formal theory but has to be 
-checked by system integration tests. Now we reference in @{figure  \<open>figfig7\<close>} this 
-safety-related condition; however, this happens in a context where general \<^emph>\<open>exported constraints\<close> 
-are listed. \<^isadof>'s checks and establishes that this is legal in the given ontology. 
-\<close>    
 
 
 section*[tech_onto::example]\<open>Writing Technical Reports in \<^boxed_theory_text>\<open>technical_report\<close>\<close>  
@@ -693,9 +567,6 @@ motivate authors to choose the aforementioned freeform-style.
 
 Additionally, documents antiquotations were added to check and evaluate terms with
 term antiquotations:
-\<^item> \<^theory_text>\<open>@{term_ \<open>term\<close> }\<close> parses and type-checks \<open>term\<close> with term antiquotations,
-  for instance \<^theory_text>\<open>@{term_ \<open>@{cenelec-term \<open>FT\<close>}\<close>}\<close> will parse and check
-  that \<open>FT\<close> is indeed an instance of the class \<^typ>\<open>cenelec_term\<close>,
 \<^item> \<^theory_text>\<open>@{value_ \<open>term\<close> }\<close> performs the evaluation of \<open>term\<close> with term antiquotations,
   for instance \<^theory_text>\<open>@{value_ \<open>mcc @{cenelec-term \<open>FT\<close>}\<close>}\<close>
   will print the value of the \<^const>\<open>mcc\<close> attribute of the instance \<open>FT\<close>.

Isabelle_DOF/thys/manual/04_RefMan.thy

@@ -403,9 +403,6 @@ in the context of the SML toplevel of the Isabelle system as in the correspondin
 \<^theory_text>\<open>ML\<open> \<dots> SML-code \<dots> \<close>\<close>-command.
 Additionally, ML antiquotations were added to check and evaluate terms with
 term antiquotations:
-\<^item> \<^theory_text>\<open>@{term_ \<open>term\<close> }\<close> parses and type-checks \<open>term\<close> with term antiquotations,
-  for instance \<^theory_text>\<open>@{term_ \<open>@{cenelec-term \<open>FT\<close>}\<close>}\<close> will parse and check
-  that \<open>FT\<close> is indeed an instance of the class \<^typ>\<open>cenelec_term\<close>,
 \<^item> \<^theory_text>\<open>@{value_ \<open>term\<close> }\<close> performs the evaluation of \<open>term\<close> with term antiquotations,
   for instance \<^theory_text>\<open>@{value_ \<open>mcc @{cenelec-term \<open>FT\<close>}\<close>}\<close>
   will print the value of the \<^const>\<open>mcc\<close> attribute of the instance \<open>FT\<close>.
@@ -789,128 +786,6 @@ high-level arranged at root-class level,
 \<close>
 
 
-subsection\<open>A Domain-Specific Ontology: \<^verbatim>\<open>CENELEC_50128\<close>\<close>
-(*<*)
-ML\<open>val toLaTeX = String.translate (fn c => if c = #"_" then "\\_" else String.implode[c])\<close>     
-ML\<open>writeln (DOF_core.print_doc_class_tree 
-                 @{context} (fn (n,l) =>  true (*     String.isPrefix "technical_report" l 
-                                         orelse String.isPrefix "Isa_COL" l *)) 
-                 toLaTeX)\<close>
-(*>*)
-text\<open> The \<^verbatim>\<open>CENELEC_50128\<close> ontology in \<^theory>\<open>Isabelle_DOF.CENELEC_50128\<close>
-is an example of a domain-specific ontology.
-It is based on  \<^verbatim>\<open>technical_report\<close> since we assume that this kind of format will be most
-appropriate for this type of long-and-tedious documents,
-
-%
-\begin{center}
-\begin{minipage}{.9\textwidth}\footnotesize
-\dirtree{%
-.0 .
-.1 CENELEC\_50128.judgement\DTcomment{...}.
-.1 CENELEC\_50128.test\_item\DTcomment{...}.
-.2 CENELEC\_50128.test\_case\DTcomment{...}.
-.2 CENELEC\_50128.test\_tool\DTcomment{...}.
-.2 CENELEC\_50128.test\_result\DTcomment{...}.
-.2 CENELEC\_50128.test\_adm\_role\DTcomment{...}.
-.2 CENELEC\_50128.test\_environment\DTcomment{...}.
-.2 CENELEC\_50128.test\_requirement\DTcomment{...}.
-.2 CENELEC\_50128.test\_specification\DTcomment{...}.
-.1 CENELEC\_50128.objectives\DTcomment{...}.
-.1 CENELEC\_50128.design\_item\DTcomment{...}.
-.2 CENELEC\_50128.interface\DTcomment{...}.
-.1 CENELEC\_50128.sub\_requirement\DTcomment{...}.
-.1 CENELEC\_50128.test\_documentation\DTcomment{...}.
-.1 Isa\_COL.text\_element\DTcomment{...}.
-.2 CENELEC\_50128.requirement\DTcomment{...}.
-.3 CENELEC\_50128.TC\DTcomment{...}.
-.3 CENELEC\_50128.FnI\DTcomment{...}.
-.3 CENELEC\_50128.SIR\DTcomment{...}.
-.3 CENELEC\_50128.CoAS\DTcomment{...}.
-.3 CENELEC\_50128.HtbC\DTcomment{...}.
-.3 CENELEC\_50128.SILA\DTcomment{...}.
-.3 CENELEC\_50128.assumption\DTcomment{...}.
-.4 CENELEC\_50128.AC\DTcomment{...}.
-.5 CENELEC\_50128.EC\DTcomment{...}.
-.6 CENELEC\_50128.SRAC\DTcomment{...}.
-.3 CENELEC\_50128.hypothesis\DTcomment{...}.
-.4 CENELEC\_50128.security\_hyp\DTcomment{...}.
-.3 CENELEC\_50128.safety\_requirement\DTcomment{...}.
-.2 CENELEC\_50128.cenelec\_text\DTcomment{...}.
-.3 CENELEC\_50128.SWAS\DTcomment{...}.
-.3 [...].
-.2 scholarly\_paper.text\_section\DTcomment{...}.
-.3 scholarly\_paper.technical\DTcomment{...}.
-.4 scholarly\_paper.math\_content\DTcomment{...}.
-.5 CENELEC\_50128.semi\_formal\_content\DTcomment{...}.
-.1 ...
-}
-\end{minipage}
-\end{center}
-\<close>
-
-(* TODO : Rearrange ontology hierarchies. *)
-
-subsubsection\<open>Examples\<close>
-text\<open>
-The category ``exported constraint (EC)'' is, in the file 
-\<^file>\<open>../../ontologies/CENELEC_50128/CENELEC_50128.thy\<close> defined as follows:
-
-@{boxed_theory_text [display]\<open>
-doc_class requirement = text_element +
-   long_name    :: "string option"
-   is_concerned :: "role set"
-doc_class assumption = requirement +
-     assumption_kind :: ass_kind <= informal 
-doc_class AC = assumption +
-   is_concerned :: "role set" <= "UNIV"
-doc_class EC = AC  +
-     assumption_kind :: ass_kind <= (*default *) formal
-\<close>}
-
-We now define the document representations, in the file 
-\<^file>\<open>../../ontologies/CENELEC_50128/DOF-CENELEC_50128.sty\<close>. Let us assume that we want to 
-register the definition of EC's in a dedicated table of contents (\<^boxed_latex>\<open>tos\<close>) 
-and use an earlier defined environment \inlineltx|\begin{EC}...\end{EC}| for their graphical 
-representation. Note that the \inlineltx|\newisadof{}[]{}|-command requires the 
-full-qualified names, \<^eg>, \<^boxed_theory_text>\<open>text.CENELEC_50128.EC\<close> for the document class and 
-\<^boxed_theory_text>\<open>CENELEC_50128.requirement.long_name\<close> for the  attribute \<^const>\<open>long_name\<close>, 
-inherited from the document class \<^typ>\<open>requirement\<close>. The representation of \<^typ>\<open>EC\<close>'s
-can now be defined as follows:
-% TODO:
-% Explain the text qualifier of the long_name text.CENELEC_50128.EC
-
-\begin{ltx}
-\newisadof{text.CENELEC_50128.EC}%
-[label=,type=%
-,Isa_COL.text_element.level=%
-,Isa_COL.text_element.referentiable=%
-,Isa_COL.text_element.variants=%
-,CENELEC_50128.requirement.is_concerned=%
-,CENELEC_50128.requirement.long_name=%
-,CENELEC_50128.EC.assumption_kind=][1]{%
-\begin{isamarkuptext}%
-   \ifthenelse{\equal{\commandkey{CENELEC_50128.requirement.long_name}}{}}{%
-      % If long_name is not defined, we only create an entry in the table tos
-      % using the auto-generated number of the EC 
-      \begin{EC}%
-          \addxcontentsline{tos}{chapter}[]{\autoref{\commandkey{label}}}%
-    }{%
-      % If long_name is defined, we use the long_name as title in the 
-      % layout of the EC, in the table "tos" and as index entry. .
-      \begin{EC}[\commandkey{CENELEC_50128.requirement.long_name}]%
-        \addxcontentsline{toe}{chapter}[]{\autoref{\commandkey{label}}: %
-              \commandkey{CENELEC_50128.requirement.long_name}}%
-        \DOFindex{EC}{\commandkey{CENELEC_50128.requirement.long_name}}%
-    }%
-    \label{\commandkey{label}}% we use the label attribute as anchor 
-    #1% The main text of the EC
-  \end{EC}
-\end{isamarkuptext}%
-}
-\end{ltx}
-\<close>
-
 
 
 subsubsection\<open>For Isabelle Hackers: Defining New Top-Level Commands\<close>
@@ -1475,9 +1350,9 @@ text\<open>
   requires a solid understanding of \<^LaTeX>'s expansion mechanism. In this context, the recently 
   introduced \inlineltx|\expanded{}|-primitive 
   (see \<^url>\<open>https://www.texdev.net/2018/12/06/a-new-primitive-expanded\<close>) is particularly useful. 
-  Examples of its use can be found, \<^eg>, in the ontology-styles 
-  \<^file>\<open>../../ontologies/scholarly_paper/DOF-scholarly_paper.sty\<close> or 
-  \<^file>\<open>../../ontologies/CENELEC_50128/DOF-CENELEC_50128.sty\<close>.  For details about the expansion mechanism 
+  Examples of its use can be found, \<^eg>, in the ontology-style 
+  \<^file>\<open>../../ontologies/scholarly_paper/DOF-scholarly_paper.sty\<close>.
+  For details about the expansion mechanism
   in general, we refer the reader to the \<^LaTeX> literature (\<^eg>,~@{cite "knuth:texbook:1986"
   and "mittelbach.ea:latex:1999" and "eijkhout:latex-cs:2012"}).  
 \<close>

Isabelle_DOF/thys/manual/05_Implementation.thy

@@ -225,50 +225,8 @@ text\<open>
   The \<^LaTeX>-generator of \<^isadof> maps each \<^boxed_theory_text>\<open>doc_item\<close> to an \<^LaTeX>-environment (recall
   @{docitem "text-elements"}). As generic \<^boxed_theory_text>\<open>doc_item\<close>s are derived from the text element, 
   the environment \inlineltx|isamarkuptext*| builds the core of \<^isadof>'s \<^LaTeX> implementation. 
-  For example, the @{docitem "ass123"} from page \pageref{ass123} is mapped to
 
-@{boxed_latex [display]
-\<open>\begin{isamarkuptext*}%
-[label = {ass122},type = {CENELEC_50128.SRAC}, 
- args={label = {ass122}, type = {CENELEC_50128.SRAC}, 
-       CENELEC_50128.EC.assumption_kind = {formal}}
-] The overall sampling frequence of the odometer subsystem is therefore 
- 14 khz, which includes sampling, computing and result communication 
- times ...
-\end{isamarkuptext*}\<close>}
-
-This environment is mapped to a plain \<^LaTeX> command via (again, recall @{docitem "text-elements"}):
-@{boxed_latex [display]
-\<open> \NewEnviron{isamarkuptext*}[1][]{\isaDof[env={text},#1]{\BODY}} \<close>}
-
-For the command-based setup, \<^isadof> provides a dispatcher that selects the most specific 
-implementation for a given \<^boxed_theory_text>\<open>doc_class\<close>:
-
-@{boxed_latex [display]
-\<open>%% The Isabelle/DOF dispatcher:
-\newkeycommand+[\|]\isaDof[env={UNKNOWN},label=,type={dummyT},args={}][1]{%
-  \ifcsname isaDof.\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{type}\endcsname%
-              [label=\commandkey{label},\commandkey{args}]{#1}%
-  \else\relax\fi%
-  \ifcsname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
-      \csname isaDof.\commandkey{env}.\commandkey{type}\endcsname%
-              [label=\commandkey{label},\commandkey{args}]{#1}%
-  \else%
-      \message{Isabelle/DOF: Using default LaTeX representation for concept %
-        "\commandkey{env}.\commandkey{type}".}%
-      \ifcsname isaDof.\commandkey{env}\endcsname%
-         \csname isaDof.\commandkey{env}\endcsname%
-                [label=\commandkey{label}]{#1}%
-      \else%
-      \errmessage{Isabelle/DOF: No LaTeX representation for concept %
-        "\commandkey{env}.\commandkey{type}" defined and no default %
-        definition for "\commandkey{env}" available either.}%
-      \fi%
-  \fi%
-}\<close>}
 \<close>
-
 (*<*)
 end
 (*>*)

ROOTS

@@ -2,4 +2,5 @@ Isabelle_DOF
 Isabelle_DOF-Proofs
 Isabelle_DOF-Ontologies
 Isabelle_DOF-Unit-Tests
-Isabelle_DOF-Examples-Extra
+Isabelle_DOF-Example-Extra
+Isabelle_DOF-Example-Scholarly_Paper