Updated for use with geosteering.no

script is not updated

.idea/vcs.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file

geosteering-out.html

+\ecvitem{\highlight{Publications}}{Journal Articles}
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Wilson A. </td></tr> 
+ <tr>     <td>Title</td><td> New Geosteering Work Flow Integrates Real-Time Measurements With Geomodels </td></tr>  
+<tr>      <td>Source</td>         <td> Journal of Petroleum Technology </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="https://www.spe.org/en/jpt/jpt-article-detail/?art=4530">https://www.spe.org/en/jpt/jpt-article-detail/?art=4530</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Jakobsen M., and Tveit S. </td></tr> 
+ <tr>     <td>Title</td><td> Distorted Born iterative T-matrix method for inversion of CSEM data in anisotropic media </td></tr>  
+<tr>      <td>Source</td>         <td> Geophysical Journal International </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.1093/gji/ggy197">http://dx.doi.org/10.1093/gji/ggy197</a> </td>   </tr>   
+</table> </center> 
+ 
+\ecvitem{\highlight{Other publications}}{}
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Sergey Alyaev, Erich Suter, Reidar Bratvold, Aojie Hong, and Xiaodong Luo </td></tr> 
+ <tr>     <td>Title</td><td> A Decision Support System for Multi-target Geosteering </td></tr>  
+<tr>      <td>Source</td>         <td>  </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2019 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="https://arxiv.org/abs/1903.03933">https://arxiv.org/abs/1903.03933</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Suter E., Kårstad T., Escalona A., A. Friis H., Vefring E., and Alyaev S. </td></tr> 
+ <tr>     <td>Title</td><td> A Methodology for Effective Earth Model Management while Geosteering </td></tr>  
+<tr>      <td>Source</td>         <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803215">http://dx.doi.org/10.3997/2214-4609.201803215</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Sommer M., and Jakobsen M. </td></tr> 
+ <tr>     <td>Title</td><td> Towards a Fast Integral Equation Method for Inversion of Electromagnetic Data </td></tr>  
+<tr>      <td>Source</td>         <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803216">http://dx.doi.org/10.3997/2214-4609.201803216</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Alyaev S., Bratvold R.B., Luo X., Suter E., Vefring E.H., and others </td></tr> 
+ <tr>     <td>Title</td><td> An Interactive Decision Support System for Geosteering Operations </td></tr>  
+<tr>      <td>Source</td>         <td> in SPE Norway One Day Seminar </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.2118/191337-MS">http://dx.doi.org/10.2118/191337-MS</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Alyaev S., Suter E., Bratvold R., Vefring E., and Jahani N. </td></tr> 
+ <tr>     <td>Title</td><td> Ensemble-based decision-support workflow for operational geosteering </td></tr>  
+<tr>      <td>Source</td>         <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803140">http://dx.doi.org/10.3997/2214-4609.201803140</a> </td>   </tr>   
+</table> </center> 
+ 
+<center> <table class="submit-table" id="deadlines"> 
+ <tr>     <td>Authors</td><td> Alyaev S., Hong A., and B Bratvold R. </td></tr> 
+ <tr>     <td>Title</td><td> Are you myopic, naive or farsighted about your geosteering decisions? </td></tr>  
+<tr>      <td>Source</td>         <td> Second EAGE/SPE Geosteering and Well Placement Workshop </td>   </tr>   
+<tr>      <td>Publication Date</td>         <td> 2018 </td>   </tr>   
+<tr>      <td>URL</td>         <td> <a href="http://dx.doi.org/10.3997/2214-4609.201803217">http://dx.doi.org/10.3997/2214-4609.201803217</a> </td>   </tr>   
+</table> </center> 
+ 

geosteering.bib

+@article{jakobsen2018distorted,
+  title={Distorted Born iterative T-matrix method for inversion of CSEM data in anisotropic media},
+  author={Jakobsen, Morten and Tveit, Svenn},
+  journal={Geophysical Journal International},
+  volume={214},
+  number={3},
+  pages={1524--1537},
+  year={2018},
+  publisher={Oxford University Press},
+  doi = {10.1093/gji/ggy197}
+}
+@article{wilson2018new,
+  title={New Geosteering Work Flow Integrates Real-Time Measurements With Geomodels},
+  author={Wilson, Adam},
+  journal={Journal of Petroleum Technology},
+  volume={70},
+  number={09},
+  pages={102--105},
+  year={2018},
+  publisher={Society of Petroleum Engineers},
+  url = {https://www.spe.org/en/jpt/jpt-article-detail/?art=4530}
+}
+@inproceedings{sommer2018eage,
+  title={Towards a Fast Integral Equation Method for Inversion of Electromagnetic Data},
+  author={Sommer, M. and Jakobsen, M.},
+  journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+  year={2018},
+  publisher={SPE, EAGE},
+  doi = {10.3997/2214-4609.201803216}
+}
+@inproceedings{suter2018eage,
+  title={A Methodology for Effective Earth Model Management while Geosteering},
+  author={Suter, E. and Kårstad, T. and Escalona, A. and A. Friis, H. and Vefring, E. and Alyaev, S.},
+  journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+  year={2018},
+  publisher={SPE, EAGE},
+  doi = {10.3997/2214-4609.201803215}
+}
+@inproceedings{alyaev2018eage,
+  title={Are you myopic, naive or farsighted about your geosteering decisions?},
+  author={Alyaev, S. and Hong, A and B Bratvold, R.},
+  journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+  year={2018},
+  publisher={SPE, EAGE},
+  doi = {10.3997/2214-4609.201803217}
+}
+@inproceedings{alyaev2018eageposter,
+  title={Ensemble-based decision-support workflow for operational geosteering},
+  author={Alyaev, S. and Suter, E and Bratvold, R. and Vefring, E. and Jahani, N.},
+  journal={Second EAGE/SPE Geosteering and Well Placement Workshop },
+  year={2018},
+  publisher={SPE, EAGE},
+  doi = {10.3997/2214-4609.201803140}
+}
+@misc{alyaev2019decision,
+    title={A Decision Support System for Multi-target Geosteering},
+    author={Sergey Alyaev and Erich Suter and Reidar Bratvold and Aojie Hong and Xiaodong Luo},
+    year={2019},
+    eprint={1903.03933},
+    archivePrefix={arXiv},
+    primaryClass={cs.CE},
+    url={https://arxiv.org/abs/1903.03933}
+}
+@inproceedings{alyaev2018interactive,
+  title={An Interactive Decision Support System for Geosteering Operations},
+  author={Alyaev, Sergey and Bratvold, Reidar Brumer and Luo, Xiaodong and Suter, Erich and Vefring, Erlend H and others},
+  booktitle={SPE Norway One Day Seminar},
+  year={2018},
+  organization={Society of Petroleum Engineers},
+  doi={10.2118/191337-MS}
+}

parser.py

+__author__ = 'Sergey Alyaev'
+
+"""Collect command-line options in a dictionary"""
+
+
+def getopts(argv):
+    opts = {}  # Empty dictionary to store key-value pairs.
+    while argv:  # While there are arguments left to parse...
+        if argv[0][0] == '-':  # Found a "-name value" pair.
+            opts[argv[0]] = argv[1]  # Add key and value to the dictionary.
+        argv = argv[1:]  # Reduce the argument list by copying it starting from index 1.
+    return opts
+
+
+
+class bibentry(object):
+
+    #staic
+    label_to_abbrev = dict()
+    abbreviations = set()
+
+    def __init__(self, entry_type, entry_label = None):
+        self.entry_type = entry_type
+        self.entry_label = entry_label
+        self.fields = dict()
+        self.abbr = None
+
+    def __str__(self):
+        return self.entry_label + ":[" + self.entry_type + "]"
+
+    def __repr__(self):
+        return self.__str__()
+
+    def strip_author_name(self, author_name, abbreviate=True, ceparator_space=' '):
+        """
+        Makes name to desired format
+        :param author_name:
+        :param abbreviate:
+        :return:
+        """
+        if abbreviate:
+            name_parts = author_name.split(',')
+            out = name_parts[0].strip()
+            if len(name_parts)>1:
+                out += ceparator_space
+                name_parts = name_parts[1].split(' ')
+                for i in range(len(name_parts)):
+                    if len(name_parts[i].strip())>0:
+                        out += name_parts[i].strip()[0]+'.'
+            return out
+        else:
+            return author_name.strip()
+
+
+
+
+    def get_authors(self, max_authors=3, abbreviate=True, ceparator_space=' '):
+        """
+
+        :param max_authors:
+        :return:
+        """
+        out = ""
+        if 'author' in self.fields:
+            authors = self.fields['author'].split(' and ')
+            total_len = len(authors)
+            if total_len <= 1:
+                out += self.strip_author_name(authors[0], abbreviate)
+            elif (total_len > max_authors+1):
+                for i in range(max_authors-1):
+                    out += self.strip_author_name(authors[i], abbreviate)+", "
+                out += self.strip_author_name(authors[max_authors-1], abbreviate)+" et" + ceparator_space +"al."
+            else:
+                for i in range(total_len-1):
+                    out += self.strip_author_name(authors[i], abbreviate)+", "
+                out += "and " + self.strip_author_name(authors[total_len-1], abbreviate)
+        else:
+            out = 'x'
+        return out
+
+
+    def get_year(self):
+        """
+
+        :return:
+        """
+        out = ''
+        if 'year' in self.fields:
+            out += (self.fields['year'].strip())
+        return out
+
+    def get_title(self):
+        """
+
+        :return:
+        """
+        out = ''
+        if 'title' in self.fields:
+            out += (self.fields['title'].strip())
+        return out
+
+    url_prefix = 'URL '
+    doi_prefix = 'http://dx.doi.org/'
+
+    def get_url_html(self, prefer_doi = True):
+        """
+
+        :return:
+        """
+        out = ''
+        added = False
+        if 'url' in self.fields:
+            out = self.fields['url']
+            added = True
+        if 'doi' in self.fields:
+            if (not added) or prefer_doi:
+                out = self.doi_prefix+self.fields['doi']
+        return out
+
+    def get_url(self, url_enviorment, prefer_doi = True):
+        """
+
+        :return:
+        """
+        out = ''
+        added = False
+        if 'url' in self.fields:
+            out = self.url_prefix + url_enviorment+'{'+ self.fields['url']+'}'
+            added = True
+        if 'doi' in self.fields:
+            if (not added) or prefer_doi:
+                out = self.url_prefix + url_enviorment+'{'+self.doi_prefix+self.fields['doi'] +'}'
+        return out
+
+
+    def get_publisher(self, always_with_publisher=False):
+        """
+        gets the publisher e.g. journal
+        :return:
+        """
+        out = ''
+        if self.entry_type.lower().find('mastersthesis')>=0:
+            out += 'Master\'s thesis. '
+            if 'school' in self.fields:
+                out += self.fields['school']
+        elif self.entry_type.lower().find('phdthesis')>=0:
+            out += 'PhD thesis. '
+            if 'school' in self.fields:
+                out += self.fields['school']
+        elif self.entry_type.lower().find('techreport')>=0:
+            out += 'Technical report. '
+            if 'institution' in self.fields:
+                out += self.fields['institution']
+        elif 'journal' in self.fields:
+            if self.entry_type.lower() == 'unpublished':
+                out += "submitted to "
+            out += self.fields['journal']
+        elif 'booktitle' in self.fields:
+            out += 'in '+ self.fields['booktitle']
+        elif 'note' in self.fields:
+            out += self.fields['note']
+
+        if always_with_publisher or len(out)==0:
+            if 'publisher' in self.fields:
+                out += ' (' + self.fields['publisher']+')'
+            elif 'organization' in self.fields:
+                out += ' (' + self.fields['organization']+')'
+            #elif 'institution' in self.fields:
+            #    out += ' (' + self.fields['institution']+')'
+
+        if (len(out)>0):
+            return out
+        else:
+            return ''
+
+    def get_abbreviation(self):
+        """
+        :return abbreviation
+        """
+        #TODO test for multiple of the same to work correctly
+        if self.label_to_abbrev.has_key(self.entry_label):
+            return self.label_to_abbrev[self.entry_label]
+        abbr = ''
+        if 'author' in self.fields:
+            authors = self.fields['author'].split(' and ')
+            for a in authors:
+                abbr += a[0]
+        else:
+            abbr = 'x'
+        if 'year' in self.fields:
+            abbr += self.fields['year']
+        if abbr in self.abbreviations:
+            abbr += 'a'
+        while abbr in self.abbreviations:
+            abbr[len(abbr)] = chr(int(abbr[len(abbr)])+1)
+        self.label_to_abbrev[self.entry_label] = abbr
+        self.abbreviations.add(abbr)
+        return abbr
+
+
+
+
+
+
+def find_first_outer_brackets(st):
+    """
+    :param st:
+    :return: finds closing "{}" paranthesis non-matching
+    """
+    opened = 0
+    open_b = -1
+    index = 0
+    while index < len(st):
+        c = st[index]
+        if (c == '{'):
+            opened +=1
+            if open_b == -1:
+                open_b = index
+        if (c == '}'):
+            opened -=1
+            if opened == 0:
+                close_b = index
+                return open_b, close_b
+        if (c == '\\'):
+            index += 1
+        if opened < 0:
+            print("Incorrect parenthesis in ", st)
+            return -1, -1
+        index+=1
+    print("No bracket pairs found ", st)
+    return -1, -1
+
+def populate_entry(entry, st):
+    clean = st.strip()
+    comma_pos = clean.find(',')
+    entry.entry_label = clean[0:comma_pos]
+    while True:
+        clean = clean[comma_pos+1:].strip()
+        p_in, p_out = find_first_outer_brackets(clean)
+        if (p_in<0 or p_out<0):
+            break
+        eq_ind = clean.find('=', 0, p_in)
+        key = clean[0:eq_ind].strip()
+        value = clean[p_in+1:p_out].strip()
+        entry.fields[key] = value
+        comma_pos = clean.find(',', p_out)
+        if comma_pos < 0:
+            break
+
+
+def check_person(entry, person):
+    """
+    checks if the person is the author of the entry
+    :param entry:
+    :param person:
+    :return:
+    """
+    if person == None:
+        return True
+    if 'author' in entry.fields:
+        if entry.fields['author'].find(person) >= 0:
+            return True
+    return False
+
+
+def find_entries(st, person_name = None):
+    entries = []
+    while True:
+        index = st.find('@')
+        if index==-1:
+            break
+        st = st[index:]
+        b_in, b_out = find_first_outer_brackets(st)
+
+        #print(st[b_in+1:b_out  ])
+        entry = bibentry(st[1:b_in])
+        populate_entry(entry, st[b_in+1:b_out])
+        if check_person(entry, person_name):
+            entries.append(entry)
+        st = st[b_out+1:]
+
+    return  entries
+
+
+def parse_bib_file(filename, person_name):
+    file = open(filename, 'r')
+    lines = file.readlines()
+    st = ''
+    for line in lines:
+        st += line
+    file.close()
+    return find_entries(st, person_name)
+
+
+def get_sorting(entry):
+    """
+
+    :param entry: bib entry
+    :return: gets 'year'
+    """
+    if 'year' in entry.fields:
+        if 'author' in entry.fields:
+            return entry.fields['year'], entry.fields['author']
+        else:
+            return entry.fields['year'], "ZZZ"
+    else:
+        return '0000', "ZZZ"
+
+def get_year(entry):
+    """
+
+    :param entry: bib entry
+    :return: gets 'year'
+    """
+    if 'year' in entry.fields:
+        return entry.fields['year']
+    else:
+        return '0000'
+
+
+
+
+# "\\providecommand{\\url}[1]{\\texttt{#1}}\n" \
+file_prefix =               "\\providecommand{\\urlprefix}{URL }\n"
+file_suffix = "\n"
+
+def entry_to_tex(entry):
+    """
+
+    :param entry:
+    :return:
+    """
+    s ="<center> <table class=\"submit-table\" id=\"deadlines\"> \n " \
+       "<tr> " \
+       "    <td>Authors</td>" \
+       "<td> {0} </td>" \
+       "</tr> \n " \
+       "<tr> " \
+       "    <td>Title</td>" \
+       "<td> {4} </td>" \
+       "</tr>  \n" \
+       "<tr>  " \
+       "    <td>Source</td>     " \
+       "    <td> {1} </td>   " \
+       "</tr>   \n" \
+       "<tr>  " \
+       "    <td>Publication Date</td>     " \
+       "    <td> {2} </td>   " \
+       "</tr>   \n" \
+       "<tr>  " \
+       "    <td>URL</td>     " \
+       "    <td> <a href=\"{3}\">{3}</a> </td>   " \
+       "</tr>   \n" \
+       "</table> </center> \n \n".format(entry.get_authors(max_authors=100),
+                                   entry.get_publisher(False),
+                                   entry.get_year(),
+                                   entry.get_url_html(prefer_doi=True),
+                                   entry.get_title())
+    # s = '\\paperecvitem{'
+    # s += "\\label{" + entry.entry_label + "}"
+    # s += entry.get_authors()
+    # s += " ("+entry.get_year()+")"
+    # s += "}"
+    # s += "{"
+    # s += "\\highlight{"
+    # s += entry.get_title()
+    # s += ",} "
+    # s += entry.get_publisher(False) +' '
+    # s += entry.get_url(url_enviorment='\\url',prefer_doi=True)
+    # s += "}\n"
+    #+"}{"+"}"
+    return s
+
+
+def default_entry_filter(entry):
+    """
+    returns True
+    :param entry:
+    :return:
+    """
+    return True
+
+
+def compare_entry_filter_type(entry, type=''):
+    """
+
+    :param entry:
+    :param type:
+    :return:
+    """
+    if entry.entry_type.lower() == type.lower():
+        return True
+    return False
+
+
+def write_file_default(file, entries, entry_filter=default_entry_filter,
+                       prefix='', suffix='', written=set()):
+    """
+
+    :param filename: name of a file
+    :param entries: collection of bibentries
+    :return: returns set of written items
+    """
+
+    #check if there is at lest one entry
+    count = 0
+    for entry in entries:
+        if entry_filter(entry) and (not entry in written):
+            count += 1
+    if count == 0:
+        return written
+
+    file.write(prefix)
+    #write entries
+    for entry in entries:
+        if entry_filter(entry) and (not entry in written):
+            file.write(entry_to_tex(entry))
+            written.add(entry)
+    #write suffix
+    file.write(suffix)
+
+    return written
+
+
+
+
+
+if __name__ == '__main__':
+    from sys import argv
+
+    my_args = getopts(argv)
+    if '-f' in my_args:  # Example usage.
+        filename = my_args['-f']
+        print("Processing file: ", filename)
+        print(my_args)
+    else:
+        print("Usage ... -f filename -o output_file_name -p author_family_name")
+        exit()
+
+    person_name = None
+    if '-p' in my_args:
+        person_name = my_args['-p']
+        print("Filtering person: ", person_name)
+
+    entries = parse_bib_file(filename, person_name)
+    sorted_entries = sorted(entries, key=get_sorting, reverse=True)
+    #sorted_entries contain all the input
+    for entry in sorted_entries:
+        print(entry)
+
+    output_file_name = 'publications.tex'
+    if '-o' in my_args:
+        output_file_name = my_args['-o']
+        print("Outputting to: ", output_file_name)
+
+
+    file = open(output_file_name, 'w')
+    #write prefix
+
+    # file.write(file_prefix)
+    #writting out articles
+    def filter_articles(entry):
+        return compare_entry_filter_type(entry, type='article')
+
+
+    #initializing a set of written items
+    written = set()
+
+    written = write_file_default(file, sorted_entries,
+                                 entry_filter=filter_articles,
+                                 prefix='\\ecvitem{\\highlight{Publications}}{Journal Articles}\n',
+                                 written=written)
+
+    #writting out articles
+    def filter_exclude_reports(entry):
+        return not compare_entry_filter_type(entry, type='TechReport')
+
+    write_file_default(file, sorted_entries,
+                       entry_filter=filter_exclude_reports,
+                       prefix='\\ecvitem{\\highlight{Other publications}}{}\n',
+                       written=written)
+
+    #writting out articles
+    def filter_reports(entry):
+        return compare_entry_filter_type(entry, type='TechReport')
+
+    write_file_default(file, sorted_entries,
+                       entry_filter=filter_reports,
+                       prefix='\\ecvitem{\\highlight{Technical Reports}}{}\n',
+                       written=written)
+
+
+    # file.write(file_suffix)
+    file.close()
+
+
+

run_parser.sh

+
+python parser.py -f fromScholar.bib -p Alyaev
+python parser.py -f reports.bib -p Alyaev -o reports.tex
\ No newline at end of file