From b655687fe7f3e1795979f4d019e3097d35d390b9 Mon Sep 17 00:00:00 2001 From: Marcello Perathoner Date: Mon, 18 Sep 2023 15:47:11 +0200 Subject: [PATCH] Update docs. --- doc_src/_static/my_theme.css | 23 ++ doc_src/_static/super-collator-phase1.html | 13 + doc_src/_static/super-collator-phase2.html | 13 + doc_src/_static/super-collator-result.html | 4 + doc_src/conf.py | 2 +- doc_src/overviews/collation_tool.rst | 197 ++++++++++---- docs/.buildinfo | 2 +- .../_sources/overviews/collation_tool.rst.txt | 197 ++++++++++---- docs/_static/my_theme.css | 23 ++ docs/_static/super-collator-phase1.html | 13 + docs/_static/super-collator-phase2.html | 13 + docs/_static/super-collator-result.html | 4 + docs/doctrees/environment.pickle | Bin 392486 -> 395827 bytes .../doctrees/overviews/collation_tool.doctree | Bin 17188 -> 71355 bytes .../wordpress/plugins/dynamic-menu.doctree | Bin 39504 -> 39504 bytes .../wordpress/plugins/meta-search.doctree | Bin 149726 -> 149849 bytes .../vm/apache/wordpress/theme/main.doctree | Bin 248684 -> 248684 bytes docs/genindex.html | 7 +- docs/http-routingtable.html | 7 +- docs/index.html | 12 +- docs/maintenance.html | 2 +- docs/maintenance/logfiles.html | 2 +- docs/maintenance/wordpress.html | 2 +- docs/overviews.html | 12 +- docs/overviews/collation_tool.html | 256 ++++++++++++------ docs/overviews/collections.html | 2 +- docs/overviews/html_generation.html | 2 +- docs/overviews/meta_search.html | 2 +- docs/php-modindex.html | 7 +- docs/py-modindex.html | 7 +- docs/search.html | 7 +- docs/searchindex.js | 2 +- docs/troubleshooting.html | 2 +- docs/troubleshooting/collation_tool.html | 2 +- docs/vm.html | 2 +- docs/vm/apache.html | 2 +- docs/vm/apache/database.html | 2 +- docs/vm/apache/wordpress-custom.html | 2 +- docs/vm/apache/wordpress.html | 2 +- docs/vm/apache/wordpress/developer.html | 2 +- docs/vm/apache/wordpress/plugins.html | 2 +- .../wordpress/plugins/collation-tool.html | 2 +- .../wordpress/plugins/dynamic-menu.html | 2 +- .../wordpress/plugins/file-includer.html | 2 +- docs/vm/apache/wordpress/plugins/lib.html | 2 +- .../apache/wordpress/plugins/meta-search.html | 8 +- .../wordpress/plugins/page-generator.html | 2 +- docs/vm/apache/wordpress/theme.html | 2 +- docs/vm/apache/wordpress/theme/main.html | 2 +- docs/vm/apache/wordpress/theme/widgets.html | 2 +- docs/vm/app_server.html | 2 +- docs/vm/backup.html | 2 +- docs/vm/database.html | 2 +- docs/vm/intro.html | 2 +- docs/vm/transformations.html | 2 +- docs/vm/user.html | 2 +- 56 files changed, 659 insertions(+), 228 deletions(-) create mode 100644 doc_src/_static/super-collator-phase1.html create mode 100644 doc_src/_static/super-collator-phase2.html create mode 100644 doc_src/_static/super-collator-result.html create mode 100644 docs/_static/super-collator-phase1.html create mode 100644 docs/_static/super-collator-phase2.html create mode 100644 docs/_static/super-collator-result.html diff --git a/doc_src/_static/my_theme.css b/doc_src/_static/my_theme.css index 27f7efff..1f3cb655 100644 --- a/doc_src/_static/my_theme.css +++ b/doc_src/_static/my_theme.css @@ -24,3 +24,26 @@ padding: 0.2em; text-align: left; } + +table.super-collator { border-collapse: collapse } +table.super-collator th, +table.super-collator td.outer { border: 1px solid black } +table.super-collator td.inner { width: 50%; padding: 0 0.5ex; text-align: right } +table.super-collator td.prefilled { background-color: #eee } +table.super-collator td.em { font-weight: bold } +table.super-collator th { padding: 0 0.5ex; text-align: right } +table.super-collator table { width: 100% } +table.super-collator-result td { border: 1px solid black; padding: 0 1ex } + +table.super-collator { + margin-bottom: 1em; +} + +#super-collator-phase2 td.outer.bt { + background-color: #fefece; + border: 1.5pt solid #a80136; +} + +#super-collator-phase2 td.outer.bt .arrow { + color: #a80136; +} diff --git a/doc_src/_static/super-collator-phase1.html b/doc_src/_static/super-collator-phase1.html new file mode 100644 index 00000000..546ed9c4 --- /dev/null +++ b/doc_src/_static/super-collator-phase1.html @@ -0,0 +1,13 @@ + + + + + + + + + + + +
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+ diff --git a/doc_src/_static/super-collator-result.html b/doc_src/_static/super-collator-result.html new file mode 100644 index 00000000..070559f5 --- /dev/null +++ b/doc_src/_static/super-collator-result.html @@ -0,0 +1,4 @@ + + +
thequickbrownfoxjumpsoverthelazydog
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+ diff --git a/doc_src/conf.py b/doc_src/conf.py index 6fdfd385..1470e831 100644 --- a/doc_src/conf.py +++ b/doc_src/conf.py @@ -150,7 +150,7 @@ # General information about the project. project = 'Capitularia' -copyright = '2018-22 CCeH - Licensed under the GNU GPL v3 or later' +copyright = '2018-23 CCeH - Licensed under the GNU GPL v3 or later' author = 'Marcello Perathoner' # The version info for the project you're documenting, acts as replacement for diff --git a/doc_src/overviews/collation_tool.rst b/doc_src/overviews/collation_tool.rst index 1648e11d..268b567e 100644 --- a/doc_src/overviews/collation_tool.rst +++ b/doc_src/overviews/collation_tool.rst @@ -1,22 +1,23 @@ .. _collation-tool-overview: +.. default-role:: math Overview of the Collation Tool ============================== -Description of the collation tool and the pre-processing of the TEI files. +This overview describes the `collation tool `_ +and the pre-processing of the TEI files. Pre-Processing of the TEI files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -We extract every chapter of every capitular from all manuscripts and store them -in separate records in the Postgres database on the application Server. The -text stored in the database is normalized. +We extract every chapter of every capitular from all manuscripts and store them in the +Postgres database. The text stored in the database is already normalized. -If a manuscript contains more than one copy of a chapter, all copies are -extracted. If a corrector hand was active in the chapter, both an original and -a corrected version are extracted. +If a manuscript contains more than one copy of a chapter, all copies are extracted. If +one or more correcting hands were active in the chapter, the original and each corrected +version are extracted. The online collation tool knows about all versions and offers them to the user. @@ -27,18 +28,15 @@ The online collation tool knows about all versions and offers them to the user. skinparam DefaultTextAlignment center skinparam componentStyle uml2 - database "Manuscript files\n(XML+TEI)" as tei + database "Manuscript files\n(XML+TEI)" as tei note left of tei: publ/mss/*.xml - - cloud "VM" { - component "Cron" as cron - component "Makefile" as make - component "mss-extract-chapters.xsl" as saxon - database "Chapter files\n(plain text)" as chapters - note left of chapters: publ/cache/extracted/*/*.txt - component "import.py" as import - database "Database\n(Postgres)" as db - } + component "Cron" as cron + component "Makefile" as make + component "mss-extract-chapters-txt.xsl" as saxon + database "Preprocessed files\n(XML)" as chapters + note left of chapters: publ/cache/collation/*.xml + component "import.py" as import + database "Database\n(Postgres)" as db tei --> saxon saxon --> chapters @@ -49,25 +47,27 @@ The online collation tool knows about all versions and offers them to the user. make .> saxon make .> import -The Makefile is run by cron on the Capitularia VM at regular intervals. - The Makefile knows all the dependencies between the files and runs the appropriate tools to keep the database up-to-date with the manuscript files. -All intermediate files can be found in the cache/extracted directory. One -directory per manuscript, and one file per chapter, copy, and hand. The -intermediate files are normalized, eg. have V replaced by U. +The Makefile is run by cron at regular intervals. + +All preprocessed files can be found in the :file:`publ/cache/collation` directory. The +preprocessed files are normalized, eg. have the letter *V* replaced by *U*. + +The :program:`import.py` script imports the preprocessed text files into the database. -The import.py script imports the intermediate text files into the database. +Collation Tool +~~~~~~~~~~~~~~ -Collation -~~~~~~~~~ +The collation tool consists of two parts: one frontend written in JavaScript and using +the Vue.js library, and one backend application server written in Python and using the +`super-collator `_ library. -The collation tool is divided in two parts, one frontend written in JavaScript and the -Vue.js library, and one backend application server written in Python. The application -server retrieves the chapters to collate from the database and collates them. The -results are sent to the frontend that does the formatting for display. +The application server retrieves the chapters from the database and collates them. The +results of the collation are sent in json to the frontend that does the formatting for +display. .. pic:: uml :caption: Data flow during collation @@ -76,14 +76,16 @@ results are sent to the frontend that does the formatting for display. skinparam DefaultTextAlignment center skinparam componentStyle uml2 - cloud "VM" { - database "Database\n(Postgres)" as db - component "API Server\n(Python)" as api + cloud "Backend" { + database "Database\n(Postgres)" as db + component "API Server\n(Python)" as api + component "Super-Collator\n(Python library)" as lib } component "Frontend\n(Javascript)" as client - db --> api - api --> client + db --> api + api --> client + lib <-> api The collation unit is the chapter, so that only short texts need to be collated, @@ -93,20 +95,111 @@ The Wordpress collation plugin delivers the Javascript client to the user. After that, all communication happens directly between the client and the application server. -The application server uses an enhacement of the Needleman-Wunsch algorithm by Gotoh. -[Gotoh1982]_ + +Collation Algorithm +~~~~~~~~~~~~~~~~~~~ + +The application server uses an enhancement of the Needleman-Wunsch algorithm by Gotoh +[Gotoh1982]_. This section provides a very high level overview of the algorithm. + + +Phase 1 - Build Table +--------------------- + +In phase 1 the algorithm builds a table. For example this is the table built for the +two strings: *the quick brown fox jumps over the lazy dog* and *sick fox is crazy.* + +.. raw:: html + :file: ../_static/super-collator-phase1.html + +Every cell in the table contains three values, referred to as `D`, `P`, and `Q` in +Gotoh's paper, and an arrow, like this: + +.. raw:: html + :align: center + + + + +
+ + + +
DP
Q↖
+
+ +The grayed cells in the first row and first column are initialized using the *gap start* +and *gap extension* penalties. The numbers for each remaining cell are calculated using +only values from the three cells, to the top-left, the top, and the left, of the current +cell: + +.. math:: + + D = \max(D_↖, P_↖, Q_↖) + \mbox{similarity}(word_←, word_↑) + +.. math:: + + P = \max(D_↑ + openingpenalty, P_↑ + extensionpenalty) + +.. math:: + + Q = \max(D_← + openingpenalty, Q_← + extensionpenalty) + +Finally the arrow in the current cell is set to point to that cell which yielded the +highest of the current cell's `D`, `P`, and `Q` values. + + +Phase 2 - Backtrack +------------------- + +When the table is thus completed, two empty sequences are created. Then the algorithm +starts backtracking from the last (bottom-right) cell following the arrows until it +reaches the first (top-left) cell. If the arrow points: + +↑ + the word in the row header is added to the first sequence, a hyphen is added to the + second sequence, +↖ + the word in the row header is added to the first sequence, the word in the column + header is added to the second sequence, +← + a hyphen is added to the first sequence, the word in the column header is added to the + second sequence. + +.. raw:: html + :file: ../_static/super-collator-phase2.html + +Finally the two sequences are reversed and printed. + +.. raw:: html + :file: ../_static/super-collator-result.html + + +Parameters +---------- + +The algorithm can be customized by setting: + +- a word comparison (similarity) function, +- the starting gap penalty, +- the gap opening penalty, +- and the gap extension penalty. Word Comparison Function ------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~ + +The word comparison function returns a similarity value between 0 and 1, 0 being totally +different and 1 being completely equal. The chosen function is not critical to the +functioning of the aligner. The similarity should increase with the desirability of the +alignment, but otherwise there are no fixed rules. -The word comparison function returns a similarity value between 0 and 1. The -similarity is calculated as follows: +In the current implementation the similarity is calculated as follows: -All words in the input texts are split into sets of trigrams. The trigrams are -obtained by first prefixing and suffixing the word with two spaces respectively, -then cutting the resulting string into all possible strings of length 3. This -means that all trigrams partially overlap each other. +All words in the input texts are split into sets of trigrams (sometimes called +3-shingles). The trigrams are obtained by first prefixing and suffixing the word with +two spaces respectively, then cutting the resulting string into all possible strings of +length 3. This means that all trigrams partially overlap each other. To calculate the similarity between two words three sets are built: the set of trigrams in word a, the set of trigrams in word b, and the set of trigrams @@ -114,9 +207,12 @@ common to both words. The similarity is then given by the formula: .. math:: - \mbox{similarity}(a,b)= \frac{2\times |set_{ab}|}{|set_a| + |set_b|} + \mbox{similarity}(a,b)= \frac{2|set_{a} \cap set_{b}|}{|set_a| + |set_b|} -The factor 2 was added to bring the similarity of identical words to 1. +The factor of 2 was added to bring the similarity of identical words to 1. + +This is sometimes called the +`Sørensen–Dice coefficient `_. An example calculation follows: @@ -124,10 +220,10 @@ An example calculation follows: :caption: Calculating similarity using trigrams The similarity based on trigrams was chosen because its calculation can be done in -:math:`\mathcal{O}(n)` time whereas a similarity based on Levenshtein distance needs -:math:`\mathcal{O}(n^2)` time. The sets of trigrams for each input word are calculated +`\mathcal{O}(n)` time whereas a similarity based on Levenshtein distance needs +`\mathcal{O}(n^2)` time. The sets of trigrams for each input word are calculated only once and if you presort the trigrams in these sets (to be implemented), the common -set can be found in :math:`\mathcal{O}(n)` time. +set can be found in `\mathcal{O}(n)` time. Optimizations yet to be implemented: in a first step gather all trigrams in all input texts, give each one an integer id, and later operate on the ids only. @@ -135,6 +231,9 @@ Maybe hash each trigram onto a value 0..63 and build a bitmask for each word, later operate on the masks only. +References +~~~~~~~~~~ + .. [Gotoh1982] Gotoh, O. 1982, *An Improved Algorithm for Matching Biological Sequences,* J. Mol. Biol. 162, 705-708 http://jaligner.sourceforge.net/references/gotoh1982.pdf diff --git a/docs/.buildinfo b/docs/.buildinfo index be759de2..5b3220c8 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: ced4ca6551f202d99d0e5bff9d03d412 +config: b8f291bbba787294fe6294c1c942e659 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_sources/overviews/collation_tool.rst.txt b/docs/_sources/overviews/collation_tool.rst.txt index 1648e11d..268b567e 100644 --- a/docs/_sources/overviews/collation_tool.rst.txt +++ b/docs/_sources/overviews/collation_tool.rst.txt @@ -1,22 +1,23 @@ .. _collation-tool-overview: +.. default-role:: math Overview of the Collation Tool ============================== -Description of the collation tool and the pre-processing of the TEI files. +This overview describes the `collation tool `_ +and the pre-processing of the TEI files. Pre-Processing of the TEI files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -We extract every chapter of every capitular from all manuscripts and store them -in separate records in the Postgres database on the application Server. The -text stored in the database is normalized. +We extract every chapter of every capitular from all manuscripts and store them in the +Postgres database. The text stored in the database is already normalized. -If a manuscript contains more than one copy of a chapter, all copies are -extracted. If a corrector hand was active in the chapter, both an original and -a corrected version are extracted. +If a manuscript contains more than one copy of a chapter, all copies are extracted. If +one or more correcting hands were active in the chapter, the original and each corrected +version are extracted. The online collation tool knows about all versions and offers them to the user. @@ -27,18 +28,15 @@ The online collation tool knows about all versions and offers them to the user. skinparam DefaultTextAlignment center skinparam componentStyle uml2 - database "Manuscript files\n(XML+TEI)" as tei + database "Manuscript files\n(XML+TEI)" as tei note left of tei: publ/mss/*.xml - - cloud "VM" { - component "Cron" as cron - component "Makefile" as make - component "mss-extract-chapters.xsl" as saxon - database "Chapter files\n(plain text)" as chapters - note left of chapters: publ/cache/extracted/*/*.txt - component "import.py" as import - database "Database\n(Postgres)" as db - } + component "Cron" as cron + component "Makefile" as make + component "mss-extract-chapters-txt.xsl" as saxon + database "Preprocessed files\n(XML)" as chapters + note left of chapters: publ/cache/collation/*.xml + component "import.py" as import + database "Database\n(Postgres)" as db tei --> saxon saxon --> chapters @@ -49,25 +47,27 @@ The online collation tool knows about all versions and offers them to the user. make .> saxon make .> import -The Makefile is run by cron on the Capitularia VM at regular intervals. - The Makefile knows all the dependencies between the files and runs the appropriate tools to keep the database up-to-date with the manuscript files. -All intermediate files can be found in the cache/extracted directory. One -directory per manuscript, and one file per chapter, copy, and hand. The -intermediate files are normalized, eg. have V replaced by U. +The Makefile is run by cron at regular intervals. + +All preprocessed files can be found in the :file:`publ/cache/collation` directory. The +preprocessed files are normalized, eg. have the letter *V* replaced by *U*. + +The :program:`import.py` script imports the preprocessed text files into the database. -The import.py script imports the intermediate text files into the database. +Collation Tool +~~~~~~~~~~~~~~ -Collation -~~~~~~~~~ +The collation tool consists of two parts: one frontend written in JavaScript and using +the Vue.js library, and one backend application server written in Python and using the +`super-collator `_ library. -The collation tool is divided in two parts, one frontend written in JavaScript and the -Vue.js library, and one backend application server written in Python. The application -server retrieves the chapters to collate from the database and collates them. The -results are sent to the frontend that does the formatting for display. +The application server retrieves the chapters from the database and collates them. The +results of the collation are sent in json to the frontend that does the formatting for +display. .. pic:: uml :caption: Data flow during collation @@ -76,14 +76,16 @@ results are sent to the frontend that does the formatting for display. skinparam DefaultTextAlignment center skinparam componentStyle uml2 - cloud "VM" { - database "Database\n(Postgres)" as db - component "API Server\n(Python)" as api + cloud "Backend" { + database "Database\n(Postgres)" as db + component "API Server\n(Python)" as api + component "Super-Collator\n(Python library)" as lib } component "Frontend\n(Javascript)" as client - db --> api - api --> client + db --> api + api --> client + lib <-> api The collation unit is the chapter, so that only short texts need to be collated, @@ -93,20 +95,111 @@ The Wordpress collation plugin delivers the Javascript client to the user. After that, all communication happens directly between the client and the application server. -The application server uses an enhacement of the Needleman-Wunsch algorithm by Gotoh. -[Gotoh1982]_ + +Collation Algorithm +~~~~~~~~~~~~~~~~~~~ + +The application server uses an enhancement of the Needleman-Wunsch algorithm by Gotoh +[Gotoh1982]_. This section provides a very high level overview of the algorithm. + + +Phase 1 - Build Table +--------------------- + +In phase 1 the algorithm builds a table. For example this is the table built for the +two strings: *the quick brown fox jumps over the lazy dog* and *sick fox is crazy.* + +.. raw:: html + :file: ../_static/super-collator-phase1.html + +Every cell in the table contains three values, referred to as `D`, `P`, and `Q` in +Gotoh's paper, and an arrow, like this: + +.. raw:: html + :align: center + + + + +
+ + + +
DP
Q↖
+
+ +The grayed cells in the first row and first column are initialized using the *gap start* +and *gap extension* penalties. The numbers for each remaining cell are calculated using +only values from the three cells, to the top-left, the top, and the left, of the current +cell: + +.. math:: + + D = \max(D_↖, P_↖, Q_↖) + \mbox{similarity}(word_←, word_↑) + +.. math:: + + P = \max(D_↑ + openingpenalty, P_↑ + extensionpenalty) + +.. math:: + + Q = \max(D_← + openingpenalty, Q_← + extensionpenalty) + +Finally the arrow in the current cell is set to point to that cell which yielded the +highest of the current cell's `D`, `P`, and `Q` values. + + +Phase 2 - Backtrack +------------------- + +When the table is thus completed, two empty sequences are created. Then the algorithm +starts backtracking from the last (bottom-right) cell following the arrows until it +reaches the first (top-left) cell. If the arrow points: + +↑ + the word in the row header is added to the first sequence, a hyphen is added to the + second sequence, +↖ + the word in the row header is added to the first sequence, the word in the column + header is added to the second sequence, +← + a hyphen is added to the first sequence, the word in the column header is added to the + second sequence. + +.. raw:: html + :file: ../_static/super-collator-phase2.html + +Finally the two sequences are reversed and printed. + +.. raw:: html + :file: ../_static/super-collator-result.html + + +Parameters +---------- + +The algorithm can be customized by setting: + +- a word comparison (similarity) function, +- the starting gap penalty, +- the gap opening penalty, +- and the gap extension penalty. Word Comparison Function ------------------------- +~~~~~~~~~~~~~~~~~~~~~~~~ + +The word comparison function returns a similarity value between 0 and 1, 0 being totally +different and 1 being completely equal. The chosen function is not critical to the +functioning of the aligner. The similarity should increase with the desirability of the +alignment, but otherwise there are no fixed rules. -The word comparison function returns a similarity value between 0 and 1. The -similarity is calculated as follows: +In the current implementation the similarity is calculated as follows: -All words in the input texts are split into sets of trigrams. The trigrams are -obtained by first prefixing and suffixing the word with two spaces respectively, -then cutting the resulting string into all possible strings of length 3. This -means that all trigrams partially overlap each other. +All words in the input texts are split into sets of trigrams (sometimes called +3-shingles). The trigrams are obtained by first prefixing and suffixing the word with +two spaces respectively, then cutting the resulting string into all possible strings of +length 3. This means that all trigrams partially overlap each other. To calculate the similarity between two words three sets are built: the set of trigrams in word a, the set of trigrams in word b, and the set of trigrams @@ -114,9 +207,12 @@ common to both words. The similarity is then given by the formula: .. math:: - \mbox{similarity}(a,b)= \frac{2\times |set_{ab}|}{|set_a| + |set_b|} + \mbox{similarity}(a,b)= \frac{2|set_{a} \cap set_{b}|}{|set_a| + |set_b|} -The factor 2 was added to bring the similarity of identical words to 1. +The factor of 2 was added to bring the similarity of identical words to 1. + +This is sometimes called the +`Sørensen–Dice coefficient `_. An example calculation follows: @@ -124,10 +220,10 @@ An example calculation follows: :caption: Calculating similarity using trigrams The similarity based on trigrams was chosen because its calculation can be done in -:math:`\mathcal{O}(n)` time whereas a similarity based on Levenshtein distance needs -:math:`\mathcal{O}(n^2)` time. The sets of trigrams for each input word are calculated +`\mathcal{O}(n)` time whereas a similarity based on Levenshtein distance needs +`\mathcal{O}(n^2)` time. The sets of trigrams for each input word are calculated only once and if you presort the trigrams in these sets (to be implemented), the common -set can be found in :math:`\mathcal{O}(n)` time. +set can be found in `\mathcal{O}(n)` time. Optimizations yet to be implemented: in a first step gather all trigrams in all input texts, give each one an integer id, and later operate on the ids only. @@ -135,6 +231,9 @@ Maybe hash each trigram onto a value 0..63 and build a bitmask for each word, later operate on the masks only. +References +~~~~~~~~~~ + .. [Gotoh1982] Gotoh, O. 1982, *An Improved Algorithm for Matching Biological Sequences,* J. Mol. 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a/docs/genindex.html +++ b/docs/genindex.html @@ -52,7 +52,10 @@
  • Overview of the Collation Tool
  • Meta Search
      @@ -1815,7 +1818,7 @@

      X

      -

      © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

      +

      © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

      Built with Sphinx using a diff --git a/docs/http-routingtable.html b/docs/http-routingtable.html index 0f98f358..43a7d70d 100644 --- a/docs/http-routingtable.html +++ b/docs/http-routingtable.html @@ -59,7 +59,10 @@
    • Overview of the Collation Tool
    • Meta Search
        @@ -219,7 +222,7 @@

        HTTP Routing Table

        -

        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

        +

        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

        Built with Sphinx using a diff --git a/docs/index.html b/docs/index.html index f4a7576d..afe9a7d5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -54,7 +54,10 @@
      • Overview of the Collation Tool
      • Meta Search
          @@ -169,7 +172,10 @@

          Developer ManualOverview of the Collation Tool
        • Meta Search
            @@ -267,7 +273,7 @@

            Indices and tables -

            © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

            +

            © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

            Built with             Sphinx using a diff --git a/docs/maintenance.html b/docs/maintenance.html index 0083459a..61d557fd 100644 --- a/docs/maintenance.html +++ b/docs/maintenance.html @@ -185,7 +185,7 @@
            -

            © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

            +

            © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

            Built with Sphinx using a diff --git a/docs/maintenance/logfiles.html b/docs/maintenance/logfiles.html index 597d01b3..e2c61e20 100644 --- a/docs/maintenance/logfiles.html +++ b/docs/maintenance/logfiles.html @@ -185,7 +185,7 @@

            Python Import Script
            -

            © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

            +

            © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

            Built with             Sphinx using a diff --git a/docs/maintenance/wordpress.html b/docs/maintenance/wordpress.html index a7234240..f4b26d15 100644 --- a/docs/maintenance/wordpress.html +++ b/docs/maintenance/wordpress.html @@ -212,7 +212,7 @@

            qtranslate-xt -

            © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

            +

            © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

            Built with             Sphinx using a diff --git a/docs/overviews.html b/docs/overviews.html index 5e0a9931..be24667f 100644 --- a/docs/overviews.html +++ b/docs/overviews.html @@ -55,7 +55,10 @@
          • Overview of the Collation Tool
          • Meta Search
              @@ -167,7 +170,10 @@
            • Overview of the Collation Tool
            • Meta Search
                @@ -196,7 +202,7 @@
                -

                © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                +

                © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                Built with Sphinx using a diff --git a/docs/overviews/collation_tool.html b/docs/overviews/collation_tool.html index 277cecbc..3bc7b292 100644 --- a/docs/overviews/collation_tool.html +++ b/docs/overviews/collation_tool.html @@ -56,7 +56,10 @@
              • Overview of the Collation Tool
              • Meta Search
                  @@ -160,34 +163,33 @@

                  Overview of the Collation Tool

                  -

                  Description of the collation tool and the pre-processing of the TEI files.

                  +

                  This overview describes the collation tool +and the pre-processing of the TEI files.

                  Pre-Processing of the TEI files

                  -

                  We extract every chapter of every capitular from all manuscripts and store them -in separate records in the Postgres database on the application Server. The -text stored in the database is normalized.

                  -

                  If a manuscript contains more than one copy of a chapter, all copies are -extracted. If a corrector hand was active in the chapter, both an original and -a corrected version are extracted.

                  +

                  We extract every chapter of every capitular from all manuscripts and store them in the +Postgres database. The text stored in the database is already normalized.

                  +

                  If a manuscript contains more than one copy of a chapter, all copies are extracted. If +one or more correcting hands were active in the chapter, the original and each corrected +version are extracted.

                  The online collation tool knows about all versions and offers them to the user.

                  -
                  +
                  -VMCronMakefilemss-extract-chapters.xslChapter files(plain text)publ/cache/extracted/*/*.txtimport.pyDatabase(Postgres)Manuscript files(XML+TEI)publ/mss/*.xmlManuscript files(XML+TEI)publ/mss/*.xmlCronMakefilemss-extract-chapters-txt.xslPreprocessed files(XML)publ/cache/collation/*.xmlimport.pyDatabase(Postgres)
                  -

                  Data flow during pre-processing

                  +

                  Data flow during pre-processing

                  -

                  The Makefile is run by cron on the Capitularia VM at regular intervals.

                  The Makefile knows all the dependencies between the files and runs the appropriate tools to keep the database up-to-date with the manuscript files.

                  -

                  All intermediate files can be found in the cache/extracted directory. One -directory per manuscript, and one file per chapter, copy, and hand. The -intermediate files are normalized, eg. have V replaced by U.

                  -

                  The import.py script imports the intermediate text files into the database.

                  +

                  The Makefile is run by cron at regular intervals.

                  +

                  All preprocessed files can be found in the publ/cache/collation directory. The +preprocessed files are normalized, eg. have the letter V replaced by U.

                  +

                  The import.py script imports the preprocessed text files into the database.

                  -
                  -

                  Collation

                  -

                  The collation tool is divided in two parts, one frontend written in JavaScript and the -Vue.js library, and one backend application server written in Python. The application -server retrieves the chapters to collate from the database and collates them. The -results are sent to the frontend that does the formatting for display.

                  -
                  +
                  +

                  Collation Tool

                  +

                  The collation tool consists of two parts: one frontend written in JavaScript and using +the Vue.js library, and one backend application server written in Python and using the +super-collator library.

                  +

                  The application server retrieves the chapters from the database and collates them. The +results of the collation are sent in json to the frontend that does the formatting for +display.

                  +
                  -VMDatabase(Postgres)API Server(Python)Frontend(Javascript)BackendDatabase(Postgres)API Server(Python)Super-Collator(Python library)Frontend(Javascript)
                  -

                  Data flow during collation

                  +

                  Data flow during collation

                  The collation unit is the chapter, so that only short texts need to be collated, @@ -299,24 +303,118 @@

                  Collation[Gotoh1982]

                  +

                  +
                  +

                  Collation Algorithm

                  +

                  The application server uses an enhancement of the Needleman-Wunsch algorithm by Gotoh +[Gotoh1982]. This section provides a very high level overview of the algorithm.

                  +
                  +

                  Phase 1 - Build Table

                  +

                  In phase 1 the algorithm builds a table. For example this is the table built for the +two strings: the quick brown fox jumps over the lazy dog and sick fox is crazy.

                  + + + + + + + + + + + +
                  sickfoxiscrazy
                  0.000.00
                  0.00⏹
                  -0.50-0.50
                  -0.50←
                  -0.70-0.70
                  -0.70←
                  -0.90-0.90
                  -0.90←
                  -1.10-1.10
                  -1.10←
                  the
                  -0.50-0.50
                  -0.50↑
                  0.00-0.70
                  -0.70↖
                  -0.50-0.90
                  -0.50←
                  -0.70-1.10
                  -0.70←
                  -0.90-1.30
                  -0.90←
                  quick
                  -0.70-0.70
                  -0.70↑
                  -0.04-0.50
                  -0.90↖
                  0.00-1.00
                  -0.54↖
                  -0.50-1.20
                  -0.50←
                  -0.70-1.40
                  -0.70←
                  brown
                  -0.90-0.90
                  -0.90↑
                  -0.70-0.54
                  -1.10↑
                  -0.04-0.50
                  -1.04↖
                  0.00-1.00
                  -0.54↖
                  -0.50-1.20
                  -0.50←
                  fox
                  -1.10-1.10
                  -1.10↑
                  -0.90-0.74
                  -1.30↑
                  0.46-0.54
                  -1.24↖
                  -0.04-0.50
                  -0.04←
                  0.00-1.00
                  -0.24↖
                  jumps
                  -1.30-1.30
                  -1.30↑
                  -1.10-0.94
                  -1.50↑
                  -0.74-0.04
                  -1.44↑
                  0.64-0.54
                  -0.54↖
                  -0.04-0.50
                  0.14←
                  over
                  -1.50-1.50
                  -1.50↑
                  -1.30-1.14
                  -1.70↑
                  -0.94-0.24
                  -1.64↑
                  -0.040.14
                  -0.74↑
                  0.64-0.36
                  -0.36↖
                  the
                  -1.70-1.70
                  -1.70↑
                  -1.50-1.34
                  -1.90↑
                  -1.14-0.44
                  -1.84↑
                  -0.24-0.06
                  -0.94↑
                  0.140.14
                  -0.56↑
                  lazy
                  -1.90-1.90
                  -1.90↑
                  -1.70-1.54
                  -2.10↑
                  -1.34-0.64
                  -2.04↑
                  -0.44-0.26
                  -1.14↑
                  0.40-0.06
                  -0.76↖
                  dog
                  -2.10-2.10
                  -2.10↑
                  -1.90-1.74
                  -2.30↑
                  -1.54-0.84
                  -2.24↑
                  -0.64-0.46
                  -1.34↑
                  -0.26-0.10
                  -0.96↑
                  + +

                  Every cell in the table contains three values, referred to as \(D\), \(P\), and \(Q\) in +Gotoh’s paper, and an arrow, like this:

                  + + + +
                  + + + +
                  DP
                  Q↖
                  +

                  The grayed cells in the first row and first column are initialized using the gap start +and gap extension penalties. The numbers for each remaining cell are calculated using +only values from the three cells, to the top-left, the top, and the left, of the current +cell:

                  +
                  +\[D = \max(D_↖, P_↖, Q_↖) + \mbox{similarity}(word_←, word_↑)\]
                  +
                  +\[P = \max(D_↑ + openingpenalty, P_↑ + extensionpenalty)\]
                  +
                  +\[Q = \max(D_← + openingpenalty, Q_← + extensionpenalty)\]
                  +

                  Finally the arrow in the current cell is set to point to that cell which yielded the +highest of the current cell’s \(D\), \(P\), and \(Q\) values.

                  +
                  +
                  +

                  Phase 2 - Backtrack

                  +

                  When the table is thus completed, two empty sequences are created. Then the algorithm +starts backtracking from the last (bottom-right) cell following the arrows until it +reaches the first (top-left) cell. If the arrow points:

                  +
                  +
                  ↑

                  the word in the row header is added to the first sequence, a hyphen is added to the +second sequence,

                  +
                  +
                  ↖

                  the word in the row header is added to the first sequence, the word in the column +header is added to the second sequence,

                  +
                  +
                  ←

                  a hyphen is added to the first sequence, the word in the column header is added to the +second sequence.

                  +
                  +
                  + + + + + + + + + + + +
                  sickfoxiscrazy
                  0.000.00
                  0.00⏹
                  -0.50-0.50
                  -0.50←
                  -0.70-0.70
                  -0.70←
                  -0.90-0.90
                  -0.90←
                  -1.10-1.10
                  -1.10←
                  the
                  -0.50-0.50
                  -0.50↑
                  0.00-0.70
                  -0.70↖
                  -0.50-0.90
                  -0.50←
                  -0.70-1.10
                  -0.70←
                  -0.90-1.30
                  -0.90←
                  quick
                  -0.70-0.70
                  -0.70↑
                  -0.04-0.50
                  -0.90↖
                  0.00-1.00
                  -0.54↖
                  -0.50-1.20
                  -0.50←
                  -0.70-1.40
                  -0.70←
                  brown
                  -0.90-0.90
                  -0.90↑
                  -0.70-0.54
                  -1.10↑
                  -0.04-0.50
                  -1.04↖
                  0.00-1.00
                  -0.54↖
                  -0.50-1.20
                  -0.50←
                  fox
                  -1.10-1.10
                  -1.10↑
                  -0.90-0.74
                  -1.30↑
                  0.46-0.54
                  -1.24↖
                  -0.04-0.50
                  -0.04←
                  0.00-1.00
                  -0.24↖
                  jumps
                  -1.30-1.30
                  -1.30↑
                  -1.10-0.94
                  -1.50↑
                  -0.74-0.04
                  -1.44↑
                  0.64-0.54
                  -0.54↖
                  -0.04-0.50
                  0.14←
                  over
                  -1.50-1.50
                  -1.50↑
                  -1.30-1.14
                  -1.70↑
                  -0.94-0.24
                  -1.64↑
                  -0.040.14
                  -0.74↑
                  0.64-0.36
                  -0.36↖
                  the
                  -1.70-1.70
                  -1.70↑
                  -1.50-1.34
                  -1.90↑
                  -1.14-0.44
                  -1.84↑
                  -0.24-0.06
                  -0.94↑
                  0.140.14
                  -0.56↑
                  lazy
                  -1.90-1.90
                  -1.90↑
                  -1.70-1.54
                  -2.10↑
                  -1.34-0.64
                  -2.04↑
                  -0.44-0.26
                  -1.14↑
                  0.40-0.06
                  -0.76↖
                  dog
                  -2.10-2.10
                  -2.10↑
                  -1.90-1.74
                  -2.30↑
                  -1.54-0.84
                  -2.24↑
                  -0.64-0.46
                  -1.34↑
                  -0.26-0.10
                  -0.96↑
                  + +

                  Finally the two sequences are reversed and printed.

                  + + +
                  thequickbrownfoxjumpsoverthelazydog
                  -sick-foxis--crazy-
                  + +
                  +
                  +

                  Parameters

                  +

                  The algorithm can be customized by setting:

                  +
                    +

                  • a word comparison (similarity) function,

                    • +

                  • the starting gap penalty,

                    • +

                  • the gap opening penalty,

                    • +

                  • and the gap extension penalty.

                    • +
                  +
                  +
                  -

                  Word Comparison Function

                  -

                  The word comparison function returns a similarity value between 0 and 1. The -similarity is calculated as follows:

                  -

                  All words in the input texts are split into sets of trigrams. The trigrams are -obtained by first prefixing and suffixing the word with two spaces respectively, -then cutting the resulting string into all possible strings of length 3. This -means that all trigrams partially overlap each other.

                  +

                  Word Comparison Function

                  +

                  The word comparison function returns a similarity value between 0 and 1, 0 being totally +different and 1 being completely equal. The chosen function is not critical to the +functioning of the aligner. The similarity should increase with the desirability of the +alignment, but otherwise there are no fixed rules.

                  +

                  In the current implementation the similarity is calculated as follows:

                  +

                  All words in the input texts are split into sets of trigrams (sometimes called +3-shingles). The trigrams are obtained by first prefixing and suffixing the word with +two spaces respectively, then cutting the resulting string into all possible strings of +length 3. This means that all trigrams partially overlap each other.

                  To calculate the similarity between two words three sets are built: the set of trigrams in word a, the set of trigrams in word b, and the set of trigrams common to both words. The similarity is then given by the formula:

                  -\[\mbox{similarity}(a,b)= \frac{2\times |set_{ab}|}{|set_a| + |set_b|}\]
                  -

                  The factor 2 was added to bring the similarity of identical words to 1.

                  +\[\mbox{similarity}(a,b)= \frac{2|set_{a} \cap set_{b}|}{|set_a| + |set_b|}\] +

                  The factor of 2 was added to bring the similarity of identical words to 1.

                  +

                  This is sometimes called the +Sørensen–Dice coefficient.

                  An example calculation follows:

                  -
                  +
                  @@ -435,7 +533,7 @@

                  Word Comparison FunctionCalculating similarity using trigrams

                  +

                  Calculating similarity using trigrams

                  The similarity based on trigrams was chosen because its calculation can be done in @@ -447,16 +545,18 @@

                  Word Comparison Function +

                  References

                  -[Gotoh1982] +[Gotoh1982]

                  Gotoh, O. 1982, An Improved Algorithm for Matching Biological Sequences, J. Mol. Biol. 162, 705-708 http://jaligner.sourceforge.net/references/gotoh1982.pdf

                  -
                  @@ -470,7 +570,7 @@

                  Word Comparison Function -

                  © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                  +

                  © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                  Built with                   Sphinx using a diff --git a/docs/overviews/collections.html b/docs/overviews/collections.html index 24b963c9..0b262148 100644 --- a/docs/overviews/collections.html +++ b/docs/overviews/collections.html @@ -228,7 +228,7 @@

                  Algorithm -

                  © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                  +

                  © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                  Built with                   Sphinx using a diff --git a/docs/overviews/html_generation.html b/docs/overviews/html_generation.html index de58fde0..a1ca6f9f 100644 --- a/docs/overviews/html_generation.html +++ b/docs/overviews/html_generation.html @@ -316,7 +316,7 @@

                  User Delivery -

                  © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                  +

                  © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                  Built with                   Sphinx using a diff --git a/docs/overviews/meta_search.html b/docs/overviews/meta_search.html index d1b4525d..df6a4c8e 100644 --- a/docs/overviews/meta_search.html +++ b/docs/overviews/meta_search.html @@ -333,7 +333,7 @@

                  Search
                  -

                  © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                  +

                  © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                  Built with                   Sphinx using a diff --git a/docs/php-modindex.html b/docs/php-modindex.html index c2f6acc3..59e714eb 100644 --- a/docs/php-modindex.html +++ b/docs/php-modindex.html @@ -55,7 +55,10 @@
                • Overview of the Collation Tool
                • Meta Search
                    @@ -211,7 +214,7 @@

                    PHP Namespace Index

                    -

                    © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                    +

                    © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                    Built with Sphinx using a diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 2457b280..3520deb8 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -55,7 +55,10 @@
                  • Overview of the Collation Tool
                  • Meta Search
                      @@ -473,7 +476,7 @@

                      Python Module Index

                      -

                      © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                      +

                      © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                      Built with Sphinx using a diff --git a/docs/search.html b/docs/search.html index 80f3d429..089dbb22 100644 --- a/docs/search.html +++ b/docs/search.html @@ -55,7 +55,10 @@
                    • Overview of the Collation Tool
                    • Meta Search
                        @@ -175,7 +178,7 @@
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with Sphinx using a diff --git a/docs/searchindex.js b/docs/searchindex.js index 3676ff53..053dd06c 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["index", "maintenance", "maintenance/logfiles", "maintenance/wordpress", "overviews", "overviews/collation_tool", "overviews/collections", "overviews/html_generation", "overviews/meta_search", "troubleshooting", "troubleshooting/collation_tool", "vm", "vm/apache", "vm/apache/database", "vm/apache/wordpress", "vm/apache/wordpress-custom", "vm/apache/wordpress/developer", "vm/apache/wordpress/plugins", "vm/apache/wordpress/plugins/collation-tool", "vm/apache/wordpress/plugins/dynamic-menu", "vm/apache/wordpress/plugins/file-includer", "vm/apache/wordpress/plugins/lib", "vm/apache/wordpress/plugins/meta-search", "vm/apache/wordpress/plugins/page-generator", "vm/apache/wordpress/theme", "vm/apache/wordpress/theme/main", "vm/apache/wordpress/theme/widgets", 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"b": [3, 5, 10, 23, 25, 29], "There": [3, 16, 19, 29, 30], "alreadi": [3, 8, 23, 25, 29], "i": [3, 5, 6, 7, 8, 10, 13, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32], "nightli": [3, 30], "run": [3, 5, 7, 8, 10, 18, 22, 30, 32], "login": [3, 25], "ssh": [3, 10, 32], "cd": [3, 10, 14], "www": [3, 13, 14, 27, 28, 32], "wp": [3, 13, 14, 16, 23, 25], "help": [3, 22, 23, 25, 27], "core": [3, 14, 16, 23], "theme": [3, 12, 14, 15, 16, 21, 30], "plugin": [3, 5, 7, 8, 12, 13, 14, 15, 16, 25, 30], "The": [3, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "need": [3, 5, 16, 17, 20, 22, 23, 26, 30, 32], "manual": [3, 28], "content": [3, 7, 8, 16, 18, 19, 20, 22, 23, 25, 27], "wget": [3, 28], "http": [3, 5, 16, 20, 21, 22, 23, 25, 26, 27, 28, 30], "github": 3, "com": [3, 16, 20, 21, 23, 28], "archiv": [3, 24, 25], "3": [3, 5, 16, 23, 31], "6": [3, 27], "2": [3, 5, 6, 16, 18, 20, 22, 23, 25, 27, 29], "zip": 3, "unzip": 3, "rm": 3, "replac": [3, 5, 18, 19, 22, 23, 26, 28], "latest": [3, 28], "version": [3, 5, 18, 19, 20, 21, 22, 23, 28, 30], "Then": [3, 7, 16, 22, 23], "go": [3, 19, 22, 23], "admin": [3, 17, 19, 20, 21, 22, 23, 25, 26, 32], "deactiv": 3, "old": [3, 17, 19, 20, 21, 22, 23, 25, 26], "activ": [3, 5, 15, 18, 23], "cceh": [3, 16, 19, 20, 21, 22, 23, 25, 32], "issu": 3, "62": 3, "descript": [5, 6, 8, 13, 16, 18, 19, 20, 21, 22, 23, 25, 29], "everi": [5, 8, 19, 21, 25, 30], "chapter": [5, 8, 10, 22, 27, 29, 30], "capitular": [5, 22, 25, 27, 29, 30], "from": [5, 8, 14, 16, 18, 19, 20, 21, 22, 23, 25, 26, 29, 31], "store": [5, 7, 8, 18, 20, 21, 23, 30], "them": [5, 8, 10, 16, 18, 20, 21, 23], "separ": [5, 19, 22, 23, 25], "record": [5, 29], "postgr": [5, 8, 18, 29, 30], "text": [5, 8, 16, 18, 19, 20, 21, 22, 23, 24, 25, 27, 29, 30], "normal": [5, 18, 22, 24, 26, 27], "If": [5, 7, 16, 20, 21, 22, 23, 25, 29], "contain": [5, 6, 8, 10, 16, 18, 20, 21, 22, 23, 25, 26, 27, 29], "more": [5, 6, 7, 19, 20, 21, 23, 29], 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Collation Tool": [[5, "overview-of-the-collation-tool"]], "Pre-Processing of the TEI files": [[5, "pre-processing-of-the-tei-files"]], "Collation Algorithm": [[5, "collation-algorithm"]], "Phase 1 - Build Table": [[5, "phase-1-build-table"]], "Phase 2 - Backtrack": [[5, "phase-2-backtrack"]], "Parameters": [[5, "parameters"]], "Word Comparison Function": [[5, "word-comparison-function"]], "References": [[5, "references"]]}, "indexentries": {}}) \ No newline at end of file diff --git a/docs/troubleshooting.html b/docs/troubleshooting.html index 2b04cbc1..7ac081f9 100644 --- a/docs/troubleshooting.html +++ b/docs/troubleshooting.html @@ -179,7 +179,7 @@
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with Sphinx using a diff --git a/docs/troubleshooting/collation_tool.html b/docs/troubleshooting/collation_tool.html index 6dfbb5f8..f84d6bad 100644 --- a/docs/troubleshooting/collation_tool.html +++ b/docs/troubleshooting/collation_tool.html @@ -185,7 +185,7 @@

                        Manuscripts do not show up -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm.html b/docs/vm.html index 34b29d86..9704a32f 100644 --- a/docs/vm.html +++ b/docs/vm.html @@ -211,7 +211,7 @@
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with Sphinx using a diff --git a/docs/vm/apache.html b/docs/vm/apache.html index 261527b6..1dc69a36 100644 --- a/docs/vm/apache.html +++ b/docs/vm/apache.html @@ -187,7 +187,7 @@
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with Sphinx using a diff --git a/docs/vm/apache/database.html b/docs/vm/apache/database.html index e6bd3bd3..71d38dc7 100644 --- a/docs/vm/apache/database.html +++ b/docs/vm/apache/database.html @@ -187,7 +187,7 @@

                        Metadata -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress-custom.html b/docs/vm/apache/wordpress-custom.html index 5c8a4f64..f364433b 100644 --- a/docs/vm/apache/wordpress-custom.html +++ b/docs/vm/apache/wordpress-custom.html @@ -193,7 +193,7 @@
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with Sphinx using a diff --git a/docs/vm/apache/wordpress.html b/docs/vm/apache/wordpress.html index ede447be..ff430b93 100644 --- a/docs/vm/apache/wordpress.html +++ b/docs/vm/apache/wordpress.html @@ -186,7 +186,7 @@

                        Wordpress Installation
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/developer.html b/docs/vm/apache/wordpress/developer.html index 549f67b9..681962f0 100644 --- a/docs/vm/apache/wordpress/developer.html +++ b/docs/vm/apache/wordpress/developer.html @@ -424,7 +424,7 @@

                        Enqueue Translations
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins.html b/docs/vm/apache/wordpress/plugins.html index 137629e4..5f03c66f 100644 --- a/docs/vm/apache/wordpress/plugins.html +++ b/docs/vm/apache/wordpress/plugins.html @@ -241,7 +241,7 @@

                        Obsolete Plugins -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins/collation-tool.html b/docs/vm/apache/wordpress/plugins/collation-tool.html index befcc709..d58908f6 100644 --- a/docs/vm/apache/wordpress/plugins/collation-tool.html +++ b/docs/vm/apache/wordpress/plugins/collation-tool.html @@ -476,7 +476,7 @@

                        plugins/collation/too
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins/dynamic-menu.html b/docs/vm/apache/wordpress/plugins/dynamic-menu.html index aae648d5..2a4440ed 100644 --- a/docs/vm/apache/wordpress/plugins/dynamic-menu.html +++ b/docs/vm/apache/wordpress/plugins/dynamic-menu.html @@ -296,7 +296,7 @@

                        plugins/dynamic-menu<
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins/file-includer.html b/docs/vm/apache/wordpress/plugins/file-includer.html index 816987c2..2c2f02b9 100644 --- a/docs/vm/apache/wordpress/plugins/file-includer.html +++ b/docs/vm/apache/wordpress/plugins/file-includer.html @@ -913,7 +913,7 @@

                        plugins/cap-file-incl
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins/lib.html b/docs/vm/apache/wordpress/plugins/lib.html index 1e841f54..571ef055 100644 --- a/docs/vm/apache/wordpress/plugins/lib.html +++ b/docs/vm/apache/wordpress/plugins/lib.html @@ -790,7 +790,7 @@

                        plugins/lib
                        -

                        © Copyright 2018-22 CCeH - Licensed under the GNU GPL v3 or later.

                        +

                        © Copyright 2018-23 CCeH - Licensed under the GNU GPL v3 or later.

                        Built with                         Sphinx using a diff --git a/docs/vm/apache/wordpress/plugins/meta-search.html b/docs/vm/apache/wordpress/plugins/meta-search.html index 9eb6b968..53df945f 100644 --- a/docs/vm/apache/wordpress/plugins/meta-search.html +++ b/docs/vm/apache/wordpress/plugins/meta-search.html @@ -320,7 +320,7 @@

                        plugins/cap-meta-sear
                        on_the_content(content)

                        Highlight the search terms in the post.

                        -

                        Highlight the full post if it we came through the search page. We use +

                        Highlight the full post if we came through the search page. We use the query string in the HTTP referrer to highlight the content.

                        The naive approach:

                        @@ -744,8 +744,8 @@

                        plugins/cap-meta-sear

                        Get the permalink for the search result

                        -

                        Return a link that will go to the post and highlight the search terms -if followed.

                        +

                        Called from the search results page of the Capitularia theme. Return a link that +will go to the post and highlight the search terms if followed.

                        Parameters: