{"action":"created","issue":{"url":"https://api.github.com/repos/jbs1/tract2/issues/183","repository_url":"https://api.github.com/repos/jbs1/tract2","labels_url":"https://api.github.com/repos/jbs1/tract2/issues/183/labels{/name}","comments_url":"https://api.github.com/repos/jbs1/tract2/issues/183/comments","events_url":"https://api.github.com/repos/jbs1/tract2/issues/183/events","html_url":"https://github.com/jbs1/tract2/issues/183","id":162220174,"number":183,"title":"Beilstein feedback on SVN revision 2210-2213","user":{"login":"jbs1","id":6561806,"avatar_url":"https://avatars.githubusercontent.com/u/6561806?v=3","gravatar_id":"","url":"https://api.github.com/users/jbs1","html_url":"https://github.com/jbs1","followers_url":"https://api.github.com/users/jbs1/followers","following_url":"https://api.github.com/users/jbs1/following{/other_user}","gists_url":"https://api.github.com/users/jbs1/gists{/gist_id}","starred_url":"https://api.github.com/users/jbs1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbs1/subscriptions","organizations_url":"https://api.github.com/users/jbs1/orgs","repos_url":"https://api.github.com/users/jbs1/repos","events_url":"https://api.github.com/users/jbs1/events{/privacy}","received_events_url":"https://api.github.com/users/jbs1/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"jbs1","id":6561806,"avatar_url":"https://avatars.githubusercontent.com/u/6561806?v=3","gravatar_id":"","url":"https://api.github.com/users/jbs1","html_url":"https://github.com/jbs1","followers_url":"https://api.github.com/users/jbs1/followers","following_url":"https://api.github.com/users/jbs1/following{/other_user}","gists_url":"https://api.github.com/users/jbs1/gists{/gist_id}","starred_url":"https://api.github.com/users/jbs1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbs1/subscriptions","organizations_url":"https://api.github.com/users/jbs1/orgs","repos_url":"https://api.github.com/users/jbs1/repos","events_url":"https://api.github.com/users/jbs1/events{/privacy}","received_events_url":"https://api.github.com/users/jbs1/received_events","type":"User","site_admin":false},"assignees":[{"login":"jbs1","id":6561806,"avatar_url":"https://avatars.githubusercontent.com/u/6561806?v=3","gravatar_id":"","url":"https://api.github.com/users/jbs1","html_url":"https://github.com/jbs1","followers_url":"https://api.github.com/users/jbs1/followers","following_url":"https://api.github.com/users/jbs1/following{/other_user}","gists_url":"https://api.github.com/users/jbs1/gists{/gist_id}","starred_url":"https://api.github.com/users/jbs1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbs1/subscriptions","organizations_url":"https://api.github.com/users/jbs1/orgs","repos_url":"https://api.github.com/users/jbs1/repos","events_url":"https://api.github.com/users/jbs1/events{/privacy}","received_events_url":"https://api.github.com/users/jbs1/received_events","type":"User","site_admin":false}],"milestone":null,"comments":6,"created_at":"2016-06-24T19:59:26Z","updated_at":"2016-06-24T19:59:31Z","closed_at":"2016-06-24T19:59:27Z","body":"_migrated from Trac, where originally posted by **beilstein** on 6-Sep-2013 2:18pm_\n\nMany of the manuscripts in the repository were converted without errors. Thanks for the great work. However, some errors occured (very few, but at repeated instances), and they are reported here.\n\nA few general remarks at the beginning. For the sake of consistency, all tex sources were consistently renamed to the scheme mXXXXXX.tex for processing. Some of these sources needed to be modified and were subsequently re-comitted to the repository. Hence, the SVN revision is meanwhile 2213. If you need to reproduce the errors, please use the mXXXXXXX.tex sources in each directory.\n\nInstead of going through each manuscript separately, I decided to sort the errors by type and to give the respective manuscript numbers. If possible, I also try to point out, where the problem might be found.\n\n1. Two manuscripts failed conversion to .beil. Unfortunately, I could not find out where the problem was from reading the log files. However, a copy of the log files are in the respective directory with a bracketed (Beilstein) in the file name. \n\nm2926664 m3592508\n\n\n2. The attribute value \"\" of type ID in the element <reference> is empty. This happens, when there is a line break in a string in the \\bib-item-argument. A \"%\" is inserted, which presumably causes the problem. For instance in *m1081239*:\n```\n\\setboolean{nobreakdashused}{false}\\bibitem[Ehrhart(1991)]{landolt_three_twent%\nyfive}\nEhrhart,~P. Atomic Defects in Metals. In \\emph{Landolt-B\\\"ornstein: Numerical\n  data and functional relationships in science and technology}; Ullmaier,~H.,\n  Madelung,~O., Hellwege,~K.-H., Eds.;\n\\newblock Group III, Condensed Matter, Vol. 25;\n\\newblock Springer-Verlag: Heidelberg, Germany, 1991.\n```\nis converted to\n```\n <reference type=\"unknown\" id=\"\">\n      <comment>\n         <paragraph>\n            <chunk> Ehrhart, P. Atomic Defects in Metals. In </chunk>\n            <chunk italic=\"yes\">Landolt-Börnstein: Numerical data and functional relationships in science and technology</chunk>\n            <chunk>; Ullmaier, H., Madelung, O., Hellwege, K.-H., Eds.; </chunk>\n            <chunk>Group III, Condensed Matter, Vol. 25; </chunk>\n            <chunk>Springer-Verlag: Heidelberg, Germany, 1991. </chunk>\n         </paragraph>\n      </comment>\n   </reference>\n```\n\nm1081239 m1472120 m1475912 m1541500 m1698334 m1715028 m1872174  m1952193 m2027014 m2081680 m2525915 m2960319 m3184105 m3332599 m3539697 m3566801 m3577250\n\n2. The LTXML tags <p role=\"background\">,  <p role=\"results\"> and <p role=\"conclusion\"> are not converted into XML appropriately. Hence, the bold faced expressions \"Background:\", \"Results:\" and \"Conclusion:\" are missing in the abstract section. See \n\nhttps://trac.kwarc.info/arXMLiv/ticket/1529#comment:6\n\nm1124044 m1140600 m1242256 m1473569 m1698392 m2336656 m2390089 m2445518 m2591962 m3121575 m3479303 \n\n3. In *m1473569*, the citation to Equation 3 is not converted. \n```\nfull polaron transformed compound (Equation \\ref{HPMTpol}). Then[…]\n```\nis converted to\n```\n<chunk>To derive an equation of motion for the combined dynamics of charge and phonon degrees of freedom, one starts from a Liouville–von Neumann equation for the full polaron transformed compound (Equation </chunk>            <!--Elided element ref --><chunk>). Then […]\n```\n\n```\nwhere all expectation values are calculated with the full Hamiltonian (Equation \\ref{HPMTpol})\n```\nis converted to\n```\n<chunk>where all expectation values are calculated with the full Hamiltonian (Equation </chunk>\n            <!--Elided element ref --><chunk>). Of course, for </chunk>\n```\n\n```\nthe model (Equation \\ref{HPMTpol}) can \n```\nis converted to\n```\n<chunk>, the model (Equation </chunk>            <!--Elided element ref --><chunk>) can</chunk>\n```\n\n4. In *m1664701*, Figure 1 is converted into a <float-target> with an empty attribute \"id\".[[BR]]\nLaTeX:\n```\nConsider a flux of electrons travelling through an elastic medium. Intuitively, we expect\nthe flux to preferentially emit phonons with momentum parallel to the electron flow.\nThis becomes evident, when we consider the setup in figure 1.\n\n\\begin{figure}\n\\begin{center}\n\\includegraphics{m1664701-1}\n\\caption{An electrode--junction--electrode system, in the Landauer picture.\nThe details are discussed in the text.}\n\\end{center}\n\\end{figure}\n```\n\nXML:\n```\n<chunk>Consider a flux of electrons travelling through an elastic medium. Intuitively, we expect the flux to preferentially emit phonons with momentum parallel to the electron flow. This becomes evident, when we consider the setup in figure 1.</chunk>\n         </paragraph>\n         <float target=\"\"/>\n```\n\n\n5. Author affiliations are not transformed correctly. For instance, in *m1670316*:\n\nLaTeX:\n```\n\\author{F. May}\n\\affiliation{Institut f\\\"ur Theoretische Physik, Johann Wolfgang Goethe-Universit\\\"at, 60438 Frankfurt/Main, Germany}\n\\affiliation{Max Planck Institute for Polymer Research, 55128 Mainz, Germany}\n\n\\author*{M. R. Wegewijs}{m.r.wegewijs@fz-juelich.de}\n\\affiliation{Institut f\\\"ur Theorie der Statistischen Physik, RWTH Aachen, 52056 Aachen,  Germany}\n\\affiliation{Peter Gr{\\\"u}nberg Institut and JARA - Fundamentals of Information Technology, Forschungszentrum J{\\\"u}lich, 52425 J{\\\"u}lich,  Germany }\n\\author[1,2]{W. Hofstetter}\n```\n\nLTXML:\n```\n<creator role=\"author\">\n    <contact role=\"name\">F. May</contact>\n    <contact mark=\"1\" role=\"affiliation\">Institut für Theoretische Physik, Johann Wolfgang Goethe-Universität, 60438 Frankfurt/Main, Germany</contact>\n    <contact mark=\"2\" role=\"affiliation\">Max Planck Institute for Polymer Research, 55128 Mainz, Germany</contact>\n  </creator>\n  <creator role=\"corresponding-author\">\n    <contact role=\"name\">M. R. Wegewijs</contact>\n    <contact role=\"address\">m.r.wegewijs@fz-juelich.de</contact>\n    <contact mark=\"3\" role=\"affiliation\">Institut für Theorie der Statistischen Physik, RWTH Aachen, 52056 Aachen,  Germany</contact>\n    <contact mark=\"4\" role=\"affiliation\">Peter Grünberg Institut and JARA - Fundamentals of Information Technology, Forschungszentrum Jülich, 52425 Jülich,  Germany </contact>\n  </creator>\n  <creator role=\"author\">\n    <contact role=\"name\">W. Hofstetter</contact>\n    <contact mark=\"1,2\" role=\"affiliation\"/>\n  </creator>\n```\n\nXML:\n```\n  <author given-names=\"\" last-name=\"F. May\" email=\"\" affiliations=\"a1 a2\"/>\n   <author given-names=\"\" last-name=\"M. R. Wegewijs\" email=\"m.r.wegewijs@fz-juelich.de\"\n           corresponding-author=\"yes\"\n           affiliations=\"a3 a4\"/>\n   <author given-names=\"\" last-name=\"W. Hofstetter\" email=\"\" affiliations=\"a5\"/>\n   <affiliation id=\"a1\">Institut für Theoretische Physik, Johann Wolfgang Goethe-Universität, 60438 Frankfurt/Main, Germany</affiliation>\n   <affiliation id=\"a2\">Max Planck Institute for Polymer Research, 55128 Mainz, Germany</affiliation>\n   <affiliation id=\"a3\">Institut für Theorie der Statistischen Physik, RWTH Aachen, 52056 Aachen,  Germany</affiliation>\n   <affiliation id=\"a4\">Peter Grünberg Institut and JARA - Fundamentals of Information Technology, Forschungszentrum Jülich, 52425 Jülich,  Germany </affiliation>\n   <affiliation id=\"a5\"/>\n```\n\nm1670316 m2018234 m2458960 m2806550 m3121575 m3539471 m3764443\n\n\n6. In *m1771034*, the table footnotes are not converted in footnotes. (In Beilstein-XML, table footnotes are supposed to be chunks in the element <table-footer>, see page 25 ff. of Creating_Beilstein_XMLFile_20130607.pdf)\n\n\n7. Also in *m1771034*, the BBL-code\n```\n\\setboolean{nobreakdashused}{false}\\bibitem[exp()]{exp_butane_homo}\n \\url{http://webbook.nist.gov/cgi/cbook.cgi?ID=C106978&Units=SI&Mask=20#Ion-En%ergetics} (accessed Aug 16, 2011).\n```\ngives a wrongly formatted reference (again due to a \"%\"):\n\nXML\n```\n <reference type=\"unknown\" id=\"r55\">\n      <comment>\n         <paragraph>\n            <chunk> </chunk>\n            <chunk>http://webbook.nist.gov/cgi/cbook.cgi?ID=C106978&amp;Units=SI&amp;Mask=20#Ion-En%Ωergetics</chunk>\n            <chunk> (accessed Aug 16, 2011). </chunk>\n         </paragraph>\n      </comment>\n      <external-link type=\"uri\"\n                     public-id=\"http://webbook.nist.gov/cgi/cbook.cgi?ID=C106978&amp;Units=SI&amp;Mask=20#Ion-En%ergetics\"/>\n   </reference>\n```\n\n\n8. In *m1941364*, the unexpected atrribute 'class' (value=ltx_centering) appears in the element <math>. Hence, validation failed. For instance:\n```\n<inline-math id=\"im33\" fragid=\"S2.SS1.m15\" tex=\"-v_{y}[\\upmu\\rm{m/s}](theor.)\">\n         <m:math  xmlns:m=\"http://www.w3.org/1998/Math/MathML\"\n                 alttext=\"-v_{y}[\\upmu\\rm{m/s}](theor.)\"\n                 class=\"ltx_centering\"\n                 display=\"inline\">\n            <m:mrow>\n               <m:mo>-</m:mo>\n               <m:msub>\n                  <m:mi>v</m:mi>\n                  <m:mi>y</m:mi>\n               </m:msub>\n               <m:mrow>\n                  <m:mo>[</m:mo>\n                  <m:mi mathvariant=\"normal\">μ</m:mi>\n                  <m:mi mathvariant=\"normal\">m</m:mi>\n                  <m:mo>/</m:mo>\n                  <m:mi mathvariant=\"normal\">s</m:mi>\n                  <m:mo>]</m:mo>\n               </m:mrow>\n               <m:mrow>\n                  <m:mo>(</m:mo>\n                  <m:mi>theor</m:mi>\n                  <m:mo>.</m:mo>\n                  <m:mo>)</m:mo>\n               </m:mrow>\n            </m:mrow>\n         </m:math>\n      </inline-math>\n```\n\n9. In *m2018234*, the references to Supporting Information Files are not converted.\n\nLaTeX:\n```\nand the scripts are available in \\ref{si:Sader} and \\ref{si:Matrix}, respectively\n```\n\nXML:\n```\n <chunk>, and the scripts are available in </chunk>\n            <!--Elided element ref --><chunk> and </chunk>\n            <!--Elided element ref --><chunk>, respectively\n```\n\nThe text should read:  \"and the scripts are available in Supporting Information File 1 and Supporting Information File 2, respectively\"\n\n\n10. In the converted DOIs, there are strange characters between \"doi:\" and the number. These characters are either something like a \"non-breaking space\" or a \"capital greek letter omega\". Since these characters are not present in the LaTeX-PDF, they should removed from the XML as well.\n"},"comment":{"url":"https://api.github.com/repos/jbs1/tract2/issues/comments/228447710","html_url":"https://github.com/jbs1/tract2/issues/183#issuecomment-228447710","issue_url":"https://api.github.com/repos/jbs1/tract2/issues/183","id":228447710,"user":{"login":"jbs1","id":6561806,"avatar_url":"https://avatars.githubusercontent.com/u/6561806?v=3","gravatar_id":"","url":"https://api.github.com/users/jbs1","html_url":"https://github.com/jbs1","followers_url":"https://api.github.com/users/jbs1/followers","following_url":"https://api.github.com/users/jbs1/following{/other_user}","gists_url":"https://api.github.com/users/jbs1/gists{/gist_id}","starred_url":"https://api.github.com/users/jbs1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jbs1/subscriptions","organizations_url":"https://api.github.com/users/jbs1/orgs","repos_url":"https://api.github.com/users/jbs1/repos","events_url":"https://api.github.com/users/jbs1/events{/privacy}","received_events_url":"https://api.github.com/users/jbs1/received_events","type":"User","site_admin":false},"created_at":"2016-06-24T19:59:30Z","updated_at":"2016-06-24T19:59:30Z","body":"_migrated from Trac, where originally posted by **lkohlhase** on 17-Sep-2013 4:18pm_\n\nFor 3. I think I fixed the issue. \nI had mixed up the ids I was using internally. In my current model I am assuming that math is always referred to by its label.\n\nFor 4. I fixed this. Here I wrongly assumed that every figure would have a label ( <==> I was assuming that every figure was being referred to). However this was not the case for this figure. I fixed it by referring to the xml:id attribute every time that we are not in a reference. "}}
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