Merge branch 'feat-classes' into develop

.pit/pit-956ed1a521100b3b

@@ -1,7 +1,7 @@
 [header]
 title = citekey support
 id = 956ed1a521100b3b0bb0638f61b3b5a03204ffa6
-status = open
+status = closed
 type = feature
 author = Fabien Benureau
 mail = fabien.benureau+git@gmail.com
@@ -9,6 +9,7 @@ date = 2012-10-05 at 15:00 UCT
 
 [eventlog]
 opened[0] = opened the 2012-10-05 at 15:00 UCT by Fabien Benureau
+closed[1] = closed the 2012-10-11 at 17:57(UCT) by Fabien Benureau
 
 [discussion]
 desc = # enter your description here

.pit/pit-ac8c05c020d251c6

@@ -0,0 +1,16 @@
+[header]
+title = remove configparser for internal mapping
+id = ac8c05c020d251c6fa9ac5fc239038837b636b3b
+status = closed
+type = bug
+author = Fabien Benureau
+mail = fabien.benureau+git@gmail.com
+date = 2012-10-11 at 07:25 UCT
+
+[eventlog]
+opened[0] = opened the 2012-10-11 at 07:25 UCT by Fabien Benureau
+closed[1] = closed the 2012-10-11 at 17:57(UCT) by Fabien Benureau
+
+[discussion]
+desc = # enter your description here
+

papers/commands/add_cmd.py

@@ -7,6 +7,7 @@ except ImportError:
 from .. import color
 from .. import files
 from .. import pretty
+from .. import repo
 
 
 def parser(subparsers, config):
@@ -20,41 +21,5 @@ def command(config, pdffile, bibfile):
     :param pdffilepath  path (no url yet) to a pdf or ps file
     :param bibtex       bibtex file (in .bib, .bibml or .yaml format.
     """
-    papersdir = files.find_papersdir()
+    rp = repo.Repository()
-
+    rp.add_paper(pdffile, bibfile)
-    fullpdfpath = os.path.abspath(pdffile)
-    fullbibpath = os.path.abspath(bibfile)
-    files.check_file(fullpdfpath)
-    files.check_file(fullbibpath)
-
-    filename, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
-    if ext != '.pdf' and ext != '.ps':
-        print('{}warning{}: extention {}{}{} not recognized{}'.format(
-               color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
-
-    meta = configparser.ConfigParser()
-    meta.add_section('metadata')
-
-    meta.set('metadata', 'filename', filename)
-    meta.set('metadata', 'extension', ext)
-    meta.set('metadata', 'path', os.path.normpath(fullpdfpath))
-
-    meta.add_section('notes')
-
-    if bibfile is not None:
-        bib_data = files.load_externalbibfile(fullbibpath)
-        print('{}bibliographic data present in {}{}{}'.format(
-               color.grey, color.cyan, bibfile, color.end))
-        print(pretty.bib_desc(bib_data))
-        files.write_bibdata(bib_data, filename)
-
-    papers = files.load_papers()
-    count = papers.get('header', 'count')
-    papers.set('header', 'count', int(count) + 1)
-    
-    citekey = pretty.create_citekey(bib_data)
-    papers.set('papers', citekey, filename)
-    papers.set('citekeys', 'ck' + count, citekey)
-
-    files.write_papers(papers)
-    files.write_meta(meta, filename)

papers/commands/init_cmd.py

@@ -26,12 +26,11 @@ def command(config):
         os.makedirs(papersdir+os.sep+'bibdata')
         os.makedirs(papersdir+os.sep+'meta')
         
-        papers = configparser.ConfigParser()
+        papers = {}
-        papers.add_section('header')
+        papers['count'] = 0
-        papers.set('header', 'count', 0)
+        papers['citekeys'] = {}
-        papers.add_section('papers')
+        papers['numbers'] = {}
-        papers.add_section('citekeys')
+        files.save_papers(papers)
-        files.write_papers(papers)
 
     else:
         print('{}error {} : papers already present in {}{}{}'.format(

papers/commands/list_cmd.py

@@ -1,25 +1,22 @@
-from .. import files
-from .. import pretty
-from .. import color
-
 import subprocess
 import tempfile
 
+from .. import pretty
+from .. import color
+from .. import repo
+
 def parser(subparsers, config):
     parser = subparsers.add_parser('list', help="list all papers")
     return parser
 
 def command(config):
-    papers = files.load_papers()
+    rp = repo.Repository()
-
+    
     articles = []
-    for p in papers.options('citekeys'):
+    for n in sorted(rp.numbers.keys()):
-        number = p[2:]
+        paper = rp.paper_from_number(n, fatal = True)
-        citekey = papers.get('citekeys', p)
+        bibdesc = pretty.bib_oneliner(paper.bib_data)
-        filename = papers.get('papers', citekey)
+        articles.append('{:3d} {}{}{}{}   {}'.format(int(paper.number), color.purple, paper.citekey, color.end, (8-len(paper.citekey))*' ', bibdesc))
-        bibdata = files.load_bibdata(filename + '.bibyaml')
-        bibdesc = pretty.bib_oneliner(bibdata)
-        articles.append('{:3d} {}{}{}{}   {}'.format(int(number), color.purple, citekey, color.end, (8-len(citekey))*' ', bibdesc))
 
     with tempfile.NamedTemporaryFile(suffix=".tmp", delete=True) as tmpf:
         tmpf.write('\n'.join(articles))

papers/commands/open_cmd.py

@@ -1,30 +1,26 @@
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
 import subprocess
 
-from .. import files
 from .. import color
+from .. import repo
+from ..paper import NoDocumentFile
 
 def parser(subparsers, config):
-    parser = subparsers.add_parser('open', help="open the paper in a pdf viewer")
+    parser = subparsers.add_parser('open', help='{}open the paper in a pdf viewer{}'.format(color.normal, color.end))
-    parser.add_argument("citekey", help="the paper associated citekey")
+    parser.add_argument('citekey', help='{}the paper associated citekey{}'.format(color.normal, color.end))
     return parser
 
 def command(config, citekey):
-    papers = files.load_papers()
+    rp = repo.Repository()
+    paper = rp.paper_from_any(citekey, fatal = True)
     try:
-        filename = papers.get('papers', str(citekey))
+        if paper.check_file():
-    except configparser.NoOptionError:
+            filepath = paper.get_file_path()
-        try:
+
-            ck = papers.get('citekeys', 'ck'+str(citekey))
+            p = subprocess.Popen(['open', filepath])
-            filename = papers.get('papers', str(ck))
+            print('{}{}{} opened.{}'.format(
-        except configparser.NoOptionError:
+                color.filepath, filepath, color.normal, color.end))
-            print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
+    except NoDocumentFile:
-                color.red, color.grey, color.cyan, citekey, color.grey, color.end))
+        print('{}error{}: No document associated to this entry {}{}{}'.format(
-            exit(-1)
+            color.error, color.normal, color.citekey, citekey, color.end))
-    meta_data = files.load_meta(filename)
+        exit(-1)
-    filepath = meta_data.get('metadata', 'path')
+
-    p = subprocess.Popen(['open', filepath])
-    print('{}{}{} opened.{}'.format(color.cyan, filepath, color.grey, color.end))

papers/files.py

@@ -8,6 +8,8 @@ try:
 except ImportError:
     import configparser
     
+import yaml
+    
 import color
 
 try:
@@ -49,6 +51,13 @@ def find_papersdir():
 
     return _papersdir
 
+def name_from_path(fullpdfpath, verbose = False):
+    name, ext = os.path.splitext(os.path.split(fullpdfpath)[1])
+    if verbose:
+        if ext != '.pdf' and ext != '.ps':
+            print('{}warning{}: extension {}{}{} not recognized{}'.format(
+                   color.yellow, color.grey, color.cyan, ext, color.grey, color.end))
+    return name, ext    
 
 def check_file(filepath):
     if not os.path.exists(filepath):
@@ -59,29 +68,46 @@ def check_file(filepath):
         print '{}error{}: {}{}{} is not a file{}'.format(
                color.red, color.grey, color.cyan, filepath, color.grey, color.end)
         exit(-1)
+        
+# yaml I/O
 
-def write_configfile(config, filepath):
+def write_yamlfile(filepath, datamap):
     try:
         with open(filepath, 'w') as f:
-            config.write(f)
+            yaml.dump(datamap, f)
     except IOError as e:
-        print '{}error{} : impossible to write on file {}{:s}{}'.format(
+        print '{}error{} : impossible to read file {}{:s}{}'.format(
                color.red, color.grey, color.cyan, filepath, color.end)
-        print 'Verify permissions'
         exit(-1)
 
-def read_configfile(filepath):
+def read_yamlfile(filepath):
+    check_file(filepath)
     try:
         with open(filepath, 'r') as f:
-            config = configparser.ConfigParser()
+            return yaml.load(f)
-            config.readfp(f)
-            return config
     except IOError as e:
         print '{}error{} : impossible to read file {}{:s}{}'.format(
-               color.red, color.grey, color.cyan, filepath, color.end)
+               color.red, color.grey, color.cyan, paperdir, color.end)
-        print 'Verify permissions'
         exit(-1)
 
+def save_papers(datamap):
+    paperyaml = find_papersdir() + os.sep + 'papers.yaml'
+    write_yamlfile(paperyaml, datamap)
+
+def load_papers():
+    paperyaml = find_papersdir() + os.sep + 'papers.yaml'
+    return read_yamlfile(paperyaml)
+
+def save_meta(meta_data, filename):
+    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
+    write_yamlfile(filepath, meta_data)
+
+def load_meta(filename):
+    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
+    return read_yamlfile(filepath)
+
+# specific to bibliography data
+
 def load_externalbibfile(fullbibpath):
     check_file(fullbibpath)
 
@@ -102,31 +128,17 @@ def load_externalbibfile(fullbibpath):
 
     return bib_data
 
-
-def write_papers(config):
-    write_configfile(config, find_papersdir() + os.sep + 'papers')
-
-def load_papers():
-    return read_configfile(find_papersdir() + os.sep + 'papers')
-
 def load_bibdata(filename):
-    fullbibpath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename
+    fullbibpath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename + '.bibyaml'
     return load_externalbibfile(fullbibpath)
 
-def write_bibdata(bib_data, filename):
+def save_bibdata(bib_data, filename):
     filepath = find_papersdir() + os.sep + 'bibdata' + os.sep + filename + '.bibyaml'
     with open(filepath, 'w') as f:
         parser = pybtex.database.output.bibyaml.Writer()
         parser.write_stream(bib_data, f)
 
-def write_meta(meta_data, filename):
+# vim input
-    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
-    write_configfile(meta_data, filepath)
-
-def load_meta(filename):
-    filepath = find_papersdir() + os.sep + 'meta' + os.sep + filename + '.meta'
-    return read_configfile(filepath)
-
 
 try:
     EDITOR = os.environ['EDITOR']

papers/paper.py

@@ -0,0 +1,68 @@
+import os
+    
+import files
+import color
+import pretty
+
+class Paper(object):
+    """Paper class. The object is responsible for the integrity of its own data,
+    and for loading and writing it to disc.
+    """
+
+    @classmethod
+    def from_disc(cls, name, citekey = None, number = None):
+        bib_data = files.load_bibdata(name)
+        metadata = files.load_meta(name)
+        p = Paper(name, bib_data = bib_data, metadata = metadata, 
+                        citekey = citekey, number = number)
+        return p
+
+    @classmethod
+    def from_bibpdffiles(cls, pdfpath, bibpath):
+        bib_data = cls.import_bibdata(bibpath)
+        name, meta = cls.create_meta(pdfpath, bib_data)
+        p = Paper(name, bib_data = bib_data, metadata = meta)
+        
+        return p            
+
+    def __init__(self, name, bib_data = None, metadata = None, 
+                       citekey = None, number = None):
+        self.name = name
+        self.bib_data = bib_data
+        self.metadata = metadata
+        self.citekey  = citekey
+        self.number   = number
+                
+    def save_to_disc(self):
+        files.save_bibdata(self.bib_data, self.name)
+        files.save_meta(self.metadata, self.name)
+
+    @classmethod
+    def import_bibdata(cls, bibfile):        
+        """Import bibligraphic data from a .bibyaml, .bib or .bibtex file"""
+        fullbibpath = os.path.abspath(bibfile)
+        
+        bib_data = files.load_externalbibfile(fullbibpath)
+        print('{}bibliographic data present in {}{}{}'.format(
+               color.grey, color.cyan, bibfile, color.end))
+        print(pretty.bib_desc(bib_data))
+        
+        return bib_data
+
+    @classmethod
+    def create_meta(cls, pdfpath, bib_data):
+    
+        fullpdfpath = os.path.abspath(pdfpath)
+        files.check_file(fullpdfpath)
+    
+        name, ext = files.name_from_path(pdfpath)
+    
+        meta = {}
+    
+        meta['name'] = name
+        meta['extension'] = ext
+        meta['path'] = fullpdfpath
+    
+        meta['notes'] = []
+        
+        return name, meta

papers/pretty.py

@@ -26,33 +26,3 @@ def bib_desc(bib_data):
     s += '\n'
     s += '\n'.join('{}: {}'.format(k, v) for k, v in article.fields.items())
     return s
-
-alphabet = 'abcdefghijklmopqrstuvwxyz'
-
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
-import files
-
-def create_citekey(bib_data):
-    """Create a cite key unique to the paper"""
-    article = bib_data.entries[list(bib_data.entries.keys())[0]]
-    first_author = article.persons['author'][0]
-    year = article.fields['year']
-    prefix = '{}{}'.format(first_author.last()[0][:6], year[2:])
-
-    papers = files.load_papers()
-    letter = 0, False
-    citekey = None
-    
-    citekey = prefix
-    while not letter[1]:
-        try:
-            papers.get('papers', citekey)
-            citekey = prefix + alphabet[letter[0]]
-            letter = letter[0]+1, False
-        except configparser.NoOptionError:
-            letter = letter[0], True
-
-    return citekey

papers/repo.py

@@ -0,0 +1,100 @@
+import files
+import color
+from paper import Paper
+
+alphabet = 'abcdefghijklmopqrstuvwxyz'
+
+
+class Repository(object):
+
+    def __init__(self):
+        self.paperdir = files.find_papersdir()
+        self.papers_config = files.load_papers()
+        self.citekeys = self.papers_config['citekeys']
+        self.numbers  = self.papers_config['numbers']
+
+    # loading existing papers
+
+    def paper_from_number(self, number, fatal = True):
+        try:
+            citekey = self.numbers[int(number)]
+            paper = self.paper_from_citekey(citekey)
+            paper.number = int(number)
+            return paper
+        except KeyError:
+            if fatal:
+                print('{}error{}: no paper with number {}{}{}'.format(
+                    color.error, color.normal, color.citekey, citekey, color.end))
+                exit(-1)
+            raise IOError, 'file not found'
+            
+    def paper_from_citekey(self, citekey, fatal = True):
+        """Load a paper by its citekey from disk, if necessary."""
+        try:
+            name = self.citekeys[citekey]
+            paper = Paper.from_disc(name, citekey = citekey)
+            paper.citekey = citekey
+            return paper
+        except KeyError:
+            if fatal:
+                print('{}error{}: no paper with citekey {}{}{}'.format(
+                       color.error, color.normal, color.citekey, citekey, color.end))
+                exit(-1)
+            raise IOError, 'file not found'
+
+    def paper_from_any(self, key, fatal = True):
+        try:
+            return self.paper_from_citekey(key, fatal = False)
+        except IOError:
+            try:
+                return self.paper_from_number(key, fatal = False)
+            except IOError:
+                if fatal:
+                    print('{}error{}: paper with citekey or number {}{}{} not found{}'.format(
+                        color.error, color.normal, color.citekey, key, color.normal, color.end))
+                    exit(-1)
+                raise IOError, 'file not found'
+
+    # creating new papers
+    
+    def add_paper(self, pdfpath, bibpath):
+        
+        p = Paper.from_bibpdffiles(pdfpath, bibpath)        
+
+        # updating papersconfig
+        p.citekey = self.create_citekey(p.bib_data)
+        p.number  = self.create_number()
+
+        self.papers_config['citekeys'][p.citekey] = p.name
+        self.papers_config['numbers'][p.number] = p.citekey
+
+        self.citekeys[p.citekey] = p.name
+        self.numbers[p.number] = p.citekey
+               
+        # writing all to disk
+        files.save_papers(self.papers_config)
+        p.save_to_disc()
+
+        return p
+
+    def create_citekey(self, bib_data, allowed = tuple()):
+        """Create a cite key unique to a given bib_data"""
+        article = bib_data.entries[list(bib_data.entries.keys())[0]]
+        first_author = article.persons['author'][0]
+        year = article.fields['year']
+        prefix = '{}{}'.format(first_author.last()[0][:6], year[2:])
+
+        letter = 0
+        citekey = None
+
+        citekey = prefix
+        while citekey in self.citekeys and citekey not in allowed:
+            citekey = prefix + alphabet[letter]
+            letter += 1
+
+        return citekey
+        
+    def create_number(self):
+        count = int(self.papers_config['count'])
+        self.papers_config['count'] = count + 1
+        return count