initial commit after deleting history

.gitignore

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+*~lock*
+*~
+*.pyc
+.idea/*
+tests/example/example_project/*
+tools/fop/*
+sessions/*
+editors/metadata/bower_components/*
+plugins/import/omp/settings.json

.gitmodules

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+[submodule "tools/meTypeset"]
+	path = tools/meTypeset
+	url = https://github.com/UB-Heidelberg/meTypeset.git
+[submodule "tools/saxon-he"]
+	path = tools/saxon-he
+	url = https://github.com/pressbooks/saxon-he

README.md

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+![Heidelberg Monograph Publication  Tool (heiMPT)](https://raw.githubusercontent.com/withanage/heimpt/master/static/images/heiMPT.jpg)
+
+**Heidelberg Monograph Publication Tool (heiMPT)** is a stand-alone platform, as well as a plug-in application for OMP, developed by staff of **Heidelberg University Library** in cooperation with external partners, with  fundings of  German Research Foundation ([DFG](http://www.dfg.de/)). It enables a high degree of automation in the digital publication process.
+The platform consists of 4  modules: (1) typesetting (meTypeset), (2) xml-processor,  (3) an output generation engine and (4) a WYSIWYG editor.
+
+
+(1) To covert from a Microsoft Word .docx format to NLM/JATS-XML for scholarly/scientific article typesetting, we utilize meTypeset, which we developed in collaboration with Dr. Martin Eve and the Public Knowledge Project (PKP). meTypeset is an extension/wrapper of OxGarage and uses TEI as an intermediary format to facilitate interchange. meTypeset allows for intelligent size processing of input documents and section grouping algorithms. It automatically detects figure and table lists, footnotes, heading structure, bibliographies, and metadata.
+
+(2)  A Set of utilities to process the  XML files  and functions to manipulate the content. Some of the functions are numbering, sorting references, deleting unreferenced references etc.
+
+(3) XML documents are converted to desired output formats that can then be offered to users, including HTML, PDF, and ePub.
+
+(4)  The WYSIWYG editor, provides an interactive interface to confirm the information detected by meTypeset and to generate a suitable layout for the desired output format. The editor is written in both HTML and JavaScript, and handles data in XML format, so that each monograph is efficiently standardized and can be re-used. The editor is designed in a WYSIWYG (what you see is what you get) format that enables users to work with both text and images as they envision them.
+
+![doc2pdf Pipeline](https://raw.githubusercontent.com/withanage/heimpt/master/images/mpt.png)
+
+## Presentations
+* PKP Conference, 2017 [Paper](https://pkp.sfu.ca/pkp2017/paper/view/565) [Slides](https://pkp.sfu.ca/pkp2017/paper/download/565/402) [:movie_camera: Video](https://www.youtube.com/watch?v=yOH1DS2EUck)
+
+
+## Documentation
+https://withanage.github.io/heimpt
+
+
+## heiMPT Installation
+
+Check if you have persmissions  to intall in the BUILD_DIR
+
+ ```
+ BUILD_DIR=/usr/local
+ git clone https://github.com/withanage/heimpt.git $BUILD_DIR/heimpt 
+ cd $BUILD_DIR/heimpt
+ git submodule update --init --recursive
+ pip install -r requirements.txt
+ java -version 
+ ```
+ Optionally required
+  ```
+ cd editors/metadata/
+ bower install 
+ 
+ ```
+
+### FO Processors 
+Only needed if you generate PDF files.
+
+* Apache FOP (free): Download from [Apache FOP processor](https://xmlgraphics.apache.org/fop/download.html) (Binary version) into  $BUILD_DIR/heimpt/tools
+  ```
+  cd $BUILD_DIR/heimpt/tools
+  tar -xvzf fop-2.2-bin.tar.gz;
+  mv fop-2.2 fop
+  chmod u+x fop/fop/fop
+  ```
+  If you changed the default $BUILD_DIR in the installation step, set the path in fop.print.xml and fop.electronic.xml in tools/configurations/fop/conf/ folder.
+
+* Antenna- House(Commercial) : See the [distributor's](https://www.antennahouse.com) instructions
+
+
+### Test your  Installation
+If your `$BUILD_DIR` differs from the previous path, change project path in `example.json`
+
+```
+python $BUILD_DIR//heimmpt.py  $BUILD_DIR/configurations/example.json --debug
+```
+## Tests
+```
+pip install  -U pytest pytest-xdist pytest-json
+
+```
+
+
+## Credits
+
+The lead developer is Dulip Withanage,  Heidelberg  University Library
+
+Additional contributions were made, in (alphabetical order) by:
+
+* Frank Krabbes, Heidelberg  University Library 
+* Mayumi Ohta (Jun.2014 - Feb.2015), Cluster of Excellence,  University Heidelberg
+* Katharina Wäschle (Nov.2015- Oct.2016), Heidelberg  University Library 
+* Nils Weiher, Heidelberg  University Library
+
+

cmos2jats_citations.py

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+import re
+import sys
+from lxml import etree
+
+
+cmos1 = 'Heilman, James M., and Andrew G. West "Wikipedia and Medicine: Quantifying Readership, Editors, and the Significance of Natural Language." Journal of Medical Internet Research 17 no. 3 (2015) e62 doi:10.2196/jmir.4069'
+cmos2 = 'Knaller, Susanne. 2012. &#8220;The Ambiguousness of the Authentic:          Authenticity Between Reference, Fictionality, and Fake in Modern and Contemporary         Art.&#8221; In <italic>Authenticity: Contemporary Perspectives on a Critical            Concept</italic>, edited by Julia Straub, 51&#8211;75. Bielefeld:          transcript.'
+cmos3 = 'Susanne Knaller studied Romance and German Philology at the University of Graz. 2002 Habilitation (Romance Philology and General and Comparative Literature) at Johann-Wolfgang-Goethe-University Frankfurt. In 1999/2000 Fellow and in 2002/2003 Visiting Professor at Columbia University. Since 2002 Associate Professor at the University of Graz. Founder and Speaker of the Research Department General and Comparative Literature in Graz. Since 2013 Director of the Center of Cultural Studies at the University of Graz. A selection of recent publications includes: <italic>Ein Wort aus der Fremde. Geschichte und Theorie des Begriffs Authentizit&#228;t</italic> (2007); <italic>Realit&#228;tsbegriffe in der Moderne. Beitr&#228;ge zu Literatur, Kunst, Philosophie und Wissenschaft</italic>. (2011), edited with Harro M&#252;ller; <italic>Literaturwissenschaft heute &#8211; Gegenstand, Positionen, Relevanz </italic>(2013), edited with Doris Pichler; <italic>Realit&#228;t und Wirklichkeit in der Moderne. Texte zu Literatur, Kunst, Film und Fotografie </italic>(2013); and <italic>Die Realit&#228;t der Kunst. Programme und Theorien zu Literatur, Kunst und Fotografie seit 1700</italic> (2015); <italic>&#196;sthetische Emotion. Formen und Figurationen zur Zeit des Umbruchs der Medien und Gattungen (1880 &#8211; 1939)</italic> (2016), edited with Rita Rieger.'
+
+
+#article_title = re.findall('<italic>(.*)</italic>',cmos2)
+#journal_title = re.findall('\"(.*)\"',cmos1)
+#person_group = re.split('^(\D+)',cmos2)
+
+def clean(s):
+    return s.strip().replace('\n', ' ').replace('\r', '') if s else s
+
+
+def cre(s):
+    return etree.Element(s)
+
+
+def set_element_citations(t):
+    rl = t.findall('.//mixed-citation')
+    for r in rl:
+        r.tag = 'element-citation'
+        r.attrib['publication-type'] = "book"
+        pr = clean(r.text)
+        r.text = ''
+        athrs = re.split('^(\D+)', pr) if pr else []
+        pg = cre('person-group')
+        pg.attrib['person-group-type'] = "author"
+        n = cre("name")
+        g = cre('given-names')
+        s = cre('surname')
+        n.append(g)
+        n.append(s)
+        pg.append(n)
+        r.append(pg)
+
+        for i in r.findall('.//italic'):
+            i.tag = 'article-title'
+            tl = clean(i.tail)
+            i.tail = ''
+            s = cre('source')
+
+            s.text = tl
+            r.append(s)
+
+            # print etree.tostring(r)
+
+
+t = etree.parse(sys.argv[1])
+
+
+def convert_citation2reference(t):
+    bd = t.find('.//body')
+    sc = etree.Element('sec')
+    ttl = etree.Element('title')
+    ttl.text = 'References'
+    sc.append(ttl)
+    mc = t.findall('.//mixed-citation')
+    if len(mc) > 0:
+        for r in mc:
+            r.tag = 'p'
+            sc.append(r)
+        bd.append(sc)
+        rlst = t.find('.//ref-list')
+        rlst.getparent().remove(rlst)
+        bck = t.find('.//back')
+        bck.append(etree.Element('ref-list'))
+
+
+convert_citation2reference(t)
+
+
+t.write('output.xml', pretty_print=True,
+        xml_declaration=True,   encoding="utf-8")

configurations/01_wintz.bits.json

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+{
+  "projects": [
+    {
+      "active": true,
+      "chain": true,
+      "files": {
+        "1": "Wintz_01_Remerciements.docx",
+        "2": "Wintz_02_Introduction.docx",
+        "3": "Wintz_03_Chapitre_1.docx",
+        "4": "Wintz_04_Chapitre_2.docx",
+        "5": "Wintz_05_Chapitre_3.docx",
+        "6": "Wintz_06_Conclusion.docx",
+        "7": "Wintz_07_Bibliographie.docx"
+      },
+      "name": "Processed_Data",
+      "path": "/home/wit/Arbeit/OMP/Heiup/Wintz",
+      "typesetters": {
+        "1": {
+          "arguments": {
+            "1": "--create-dir"
+          },
+          "name": "metypeset",
+          "out_type": "xml",
+          "process": true
+        },
+        "2": {
+          "arguments": {
+            "1": "--create-dir"
+          },
+          "name": "xmlprocess",
+          "out_type": "xml",
+          "process": true
+        },
+        "3": {
+          "arguments": {
+            "1": "--create-dir",
+            "2": "bits",
+            "3": "--metadata book-meta.bits2",
+            "4": "--set-numbering-tags=disp-quote,tr,sec,title,p"
+          },
+          "name": "xmlmerge",
+          "out_type": "xml",
+          "out_file": "fullFile.xml",
+          "merge": true
+        },
+        "4": {
+          "name": "xml2fo",
+          "out_type": "fo",
+          "expand": true,
+          "arguments": {
+            "1": "--create-dir"
+          }
+        },
+        "5": {
+          "name": "fo2pdf",
+          "out_type": "pdf",
+          "expand": true,
+          "arguments": {
+            "1": "--create-dir"
+          }
+        }
+      }
+    }
+  ],
+  "typesetters": {
+    "metypeset": {
+      "arguments": {
+        "1": "docx",
+        "2": "--debug",
+        "3": "--nogit",
+        "4": "--noimageprocessing"
+
+      },
+      "executable": "/home/wit/projects/heimpt/meTypeset/bin/meTypeset.py"
+    },
+    "xmlprocess": {
+      "arguments": {
+        "1": "--metadata book-part-meta.bits2",
+        "2": "--set-uuids=fn,ref",
+        "3": "--set-numbering-values=xref,ref-type,fn",
+        "4": "--clean-references"
+      },
+      "executable": "/home/wit/projects/heimpt/prepare.py"
+    },
+    "xmlmerge": {
+      "arguments": {
+      },
+      "executable": "/home/wit/projects/heimpt/merge.py"
+    },
+    "xml2fo": {
+      "arguments": {
+        "1": "--xsl=/formatter.xsl",
+        "2": "--medium=electronic,print",
+        "3": "--formatter=AH",
+        "4": "--out-type=FO"
+      },
+      "executable": "/home/wit/projects/heimpt/disseminate.py"
+    },
+    "fo2pdf": {
+      "arguments": {
+        "1": "--medium=electronic,print",
+        "2": "--formatter=AH",
+        "3": "--out-type=PDF"
+      },
+      "executable": "/home/wit/projects/heimpt/disseminate.py"
+    }
+  }
+}

configurations/01_wintz.jats.json

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+{
+  "projects": [
+    {
+      "active": true,
+      "chain": true,
+      "files": {
+        "1": "Wintz_01_Remerciements.xml",
+        "2": "Wintz_02_Introduction.xml",
+        "3": "Wintz_03_Chapitre_1.xml",
+        "4": "Wintz_04_Chapitre_2.xml",
+        "5": "Wintz_05_Chapitre_3.xml",
+        "6": "Wintz_06_Conclusion.xml",
+        "7": "Wintz_07_Bibliographie.xml"
+      },
+      "name": "wintz_xml",
+      "path": "/home/wit/Arbeit/OMP/wintz/wintz-jats/",
+      "typesetters": {
+        "1": {
+          "arguments": {
+            "1": "--create-dir",
+            "2": "--stand-alone"
+          },
+          "name": "xmlprepare",
+          "out_type": "xml",
+          "process": true
+        }
+
+
+      }
+    }
+  ],
+  "typesetters": {
+    "xmlprepare": {
+      "arguments": {
+        "1": "--metadata book-part-meta.jats",
+        "2": "--set-uuids=fn,ref",
+        "3": "--set-numbering-values=xref,ref-type,fn",
+        "4": "--citations-to-references"
+      },
+      "executable": "/home/wit/projects/heimpt/prepare.py"
+    },
+    "xmlmerge": {
+      "arguments": {
+      },
+      "executable": "/home/wit/projects/heimpt/merge.py"
+    }
+  }
+}