port to BIODOCS.yaml

gensoft/Makefile

+NAM=biodocs2mongo
+PREFIX=/local/gensoft2/adm
+BIN=$(PREFIX)/bin
+PYMODULEDIR=$(PREFIX)/share/gensoft/pymodules
+DAT=$(PREFIX)/share/gensoft/$(NAM)
+
+build:
+	sed -i -e 's,^\#!.*python,\#! /local/gensoft2/adm/bin/python,' *.py
+	sed -e 's|^DAT=.*|DAT="$(DAT)"|' \
+		-e 's|^PYMODULEDIR=.*|PYMODULEDIR="$(PYMODULEDIR)"|' $(NAM).py > $(NAM)
+
+
+install: build
+	test -d $(DAT) || mkdir -p $(DAT)
+	install -m 0775 $(NAM) $(BIN)
+	install -m 0664 config.cfg $(DAT)
+	$(MAKE) clean
+
+clean:
+	rm -f $(NAM)
+	rm -f *.pyc
+
+uninstall: 
+	rm -f $(BIN)/$(NAM) $(DAT)/*
+	rm -rf $(DAT)

gensoft/biodocs2mongo.py

-#!/usr/bin/env python2.7
+#! /local/gensoft2/adm/bin/python
+
+from __future__ import print_function
 
 import argparse
-import arrow  # date manipulation made easy.
-import collections
+import ConfigParser
+import os
 import pymongo
 import re
-import os
-import string
 import ssl
+import string
 import sys
 
 
-import BiodocParser
-import mobyledefs
-
-# tweak modulecmd in order to use 3.3.a updated (not yet released)
-os.environ['PY_MODULECMD'] = '/local/gensoft2/adm/Modules/3.3.a/bin/modulecmd'
-import module as M
-
-#from biowebmongo import *
-#from pymongo.errors import BulkWriteError
-
-
-#--------------------------------------------------
-#                SOME GLOBALS
-#--------------------------------------------------
-
-LOGFH= sys.stdout
-ERRFH= sys.stderr
-
-FATAL= 1
-WARN= 0
-
-VERBOSE= 1
-
-MTRUE = True  # "true" value to insert in mongodb
-MFALSE = False # "false" value to insert in mongodb
+from pprint import pprint
 
-ID_SEPARATOR = '@'
+#### TODO !!!!!
+# 
+# add config entry for use module.
+# if set => check program listing from biodocs versus program listing from modules
 
-MOBYLEURL = 'http://mobyle.pasteur.fr'
 
-HOST='bioweb-prod.web.pasteur.fr'
-PORT=27017
 
-JOURNALING=True # implies w=1
-WRITECONCERN=1
-DB_DEF='bioweb'
-COL_DEF='catalog'
+#---- import homebrew modules
 
-known_ops = ['install', 'remove', 'setdefault', 'unsetdefault', 'update']
+PYMODULEDIR="/local/gensoft2/adm/share/gensoft/pymodules"
+sys.path.insert(0, PYMODULEDIR)
+import BiodocParser
 
-mapper = {}
+#---- some hugly global variables
 
-#--------------------------------------------------
-#                INTERNAL USE
-#--------------------------------------------------
+DAT='.'
+ERRFH = sys.stderr
+LOGFH = sys.stdout
+FATAL  = 1
+WARN   = 0
 
-def error(exit_val, *msg):
+def err(exit_val, *msg):
     head=['Warning', 'Error']
-    print >> ERRFH, "%s: %s" % (head[exit_val], " - ".join(map(str, msg)))
+    print ("%s: %s" % (head[exit_val], " - ".join(map(str, msg))), file=ERRFH)
     if exit_val:
         sys.exit(exit_val)
     return None
 
 def log(*msg):
     if VERBOSE:
-        print >> LOGFH, "%s" %(' '.join(map(str, msg)))
+        print ("%s" %(' '.join(map(str, msg))), file=LOGFH)
         LOGFH.flush()
 
-def get_DB(host, port, db_name=DB_DEF, j=JOURNALING, w=WRITECONCERN ):
-
-    log('connect to', host, 'on port:', port)
-    try:
-        client = pymongo.MongoClient(host, port, j=JOURNALING, ssl=True, ssl_cert_reqs=ssl.CERT_NONE)
-    except pymongo.errors.ConnectionFailure as err:
-        error(FATAL, "mongodb %s/%s" %(host, port), err)
-    return  client[db_name]
 
-def getmodule_infos(package):
-    '''
-    returns programs provided by a package//module
-            htmldocs  provided by a package//module
-            pack dependencies
-    information is more uptodate on programs than the
-    one provided by BIODOCS.
-    information may vary given the pack version, while
-    BIDOCS only document default version
-    returns a list of names.
-    '''
-    m = M.Module()
-    def get_progs(info):
-        '''
-        get programs provided by installed module version
-        returns a list of program_names as str
-        '''
-        progs = []
-        keep = False
-        for elem in infos:
-            elem = elem.strip()
-            if not elem:
-                continue
-            if keep:
-                progs.append(elem)
-            if elem == "package provides following commands:":
-                keep = True
-        return progs
+def _id_generator(*arg):
+    return ID_SEPARATOR.join(arg)
 
-    def get_docs(info):
-        '''
-        get local documentation available for given package
-        returns a tuple (htmldocs, txtdocs) of list as str
-        '''
-        htmldocs = []
-        txtdocs = []
-        keep = False
-        for elem in infos:
-            elem = elem.strip()
-            if not elem:
-                continue
-            if elem == "local documentation available:":
-                keep = True
-                continue
-            elif elem == "package provides following commands:":
-                break
-            if keep:
-                if 'bioweb2' in elem:
-                    htmldocs.append(elem)
-                else:
-                    txtdocs.append(elem)
-        return htmldocs, txtdocs
-
-    def get_dependencies(info):
-        '''
-        get the package/version that a given module depends or relies on.
-        returns a list of packages_names
-        '''
-        deps = []
-        for elem in infos:
-            elem = elem.strip()
-            if not elem:
-                continue
-            if 'WARNING' in elem:
-                deps = elem[elem.find('<')+1:elem.find('>')]
-                fields = deps.split()
-                # remove extraneous and or tokens
-                deps = list(set(fields))
-                try:
-                    deps.remove('or')
-                    deps.remove('and')
-                except ValueError as err:
-                    pass
-                break
-        return [item for item in deps if item]
-
-    if testmodule:
-        package = 'test/%s' %(package)
-    print ">>>>>>>>>", package
-    try:
-        infos=m.help(package)
-    except M.ModuleError as err:
-        raise M.ModuleError("no modulefile %s" %(package))
-    garbage = infos.find('*****')
-    if garbage != -1:
-        infos = infos[:garbage]
-    infos = infos.split('\n')
-    ret = {}
-    ret['progs'] = get_progs(infos)
-    ret['htmldocs'], ret['docs']  = get_docs(infos)
-    ret['depends'] = get_dependencies(infos)
-
-    return ret
-
-def format_references(ref_lst):
-    '''
-    format reference information as a dictionary
-    suitable to be embeded in mongo package document
-    '''
-
-    def extract_doi(item):
-        '''
-        extract publication unique id (doi, pmid or pmcid) if
-        available on the reference description from BIODOCS.
-        return a tuble:
-            citation curated from uinique id
-            name of unique identifier ressource or None
-            unique id or None
-        '''
+def check_missing_biodocs(biodocs_lst):
     ret = []
-    for ref in ref_lst:
-        if not ref:
-            continue
-        ret.append({ 'ID': ref['ID']
-                   , 'IDtype': ref['idType']
-                   , 'citation' : ref['title']
-                   })
-    return ret
-
-def version_extract(version):
-    '''
-    extract version from BIODOCS version name
-    returns a tuple.
-        version
-        boolean if default version
-    '''
-
-    default=False
-    if '(default)' in version:
-            version, default = version.split('(')
-    default = MTRUE if default else MFALSE
-    return version, default
-
-def history_maker(history_info):
-    '''
-    format history in a mongo compatible way
-    returns list of dict
-    { 'date' : datetime.datetime object
-    , 'operation' : keyword from 'install', 'remove', 'setdefault', 'unsetdefault', 'update
-    , 'message' : free text as str }
-    '''
-    for info in history_info:
-        if not info:
-            continue
-        try:
-            info['date'] = arrow.get(info['date'], 'YYYY/MM/DD').naive
-        except arrow.parser.ParserError as msg:
-            error(FATAL, date, msg)
-    return history_info
-
-def merge_htmldocs (biodocs_lst, module_lst):
-    '''
-    merge BIODOCS documentation with the one provided by module
-    WARNING: currently discard BIODOCS info
-    '''
-    return module_lst
-
-
-def getMapping(fileName):
-    mapper = {}
-    with open(fileName, 'r') as fh:
-        for line in fh:
-            line = line.strip()
-            if line.startswith('#'): 
+    for biodoc in biodocs_lst:
+        if not os.path.isfile(biodoc):
+            err(WARN, biodoc, 'no such file')
             continue
-            old, new = line.split()
-            mapper[old] = new
-    return mapper
-
-
-def updateCategories(lst, mapper=mapper):
-    ret = []
-    for elem in lst:
-        if elem in mapper:
-            ret.append(mapper[elem])
-        elif elem in EDAM_READY:
-            ret.append(elem)
-        else:
-            error(WARN, elem, "non matching edam operationn or topic")
-
+        ret.append(biodoc)
     return ret
 
-def getOrigin(pack):
-    return pack['ORIGIN'].split()
-
-#--------------------------------------------------
-#                DO THE JOB
-#--------------------------------------------------
-
-def pack2mongo(pack):
-    '''
-    format mongo package document from BIODOCS package informations
-    returns a mongo package document
-    '''
-    #---- get infos from BIODOCS parsed holder
-    pack_name = pack['name']
-    pack_authors = [auth.strip() for auth in pack['authors'] if auth]
-    pack_refs = format_references(pack['references'])
-    pack_library = MTRUE if pack['library'] else MFALSE
-    pack_private = MTRUE if pack['private'] else MFALSE
-    hist = history_maker(pack['history'])
-    if hist is None:
-        error(WARN, pack_name, "invalid history")
-        hist = []
-    pack_history = hist
-    pack_id = "pack%s%s" %(ID_SEPARATOR, pack_name)
-    pack_collections = [pack['origin']]
-
-    #---- map gensoft Categories to edam relevant operation and topic terms
-#    categories = updateCategories(pack['categories'])
-
-    mongopack = { '_id': pack_id
-                , 'type': 'package'
-                , 'name' : pack_name
-                , 'description' : pack['description'] #pack_description
-                , 'home' : pack['home']
-                , 'source' : pack['sources']
-                , 'categories' : pack['operations'] + pack['topics']
-                , 'authors' : pack_authors
-                , 'references' : pack_refs
-                , 'library' : pack_library
-                , 'private' : pack_private
-                , 'history' : pack_history
-                , 'collections' : pack_collections
+def get_biodocs(packdir):
+    # filter to keep only pack_version 
+    pack_name = os.path.basename(packdir)
+    pack_version_lst = [ os.path.join(packdir, d) for d in os.listdir(packdir) if d.startswith(pack_name) ]
+    biodocs_lst = [ os.path.join(d, 'BIODOCS.yaml') for d in pack_version_lst ]
+    return check_missing_biodocs(biodocs_lst)
+
+def citation_key_translate(refs_col):
+    # mapping = {key in yaml : key expected in mongo  }
+    mapping = {'ID': 'ID'
+              ,'idType' : 'IDtype'
+              ,'title': 'citation'
+              }
+    for ref in refs_col:
+        for k, v in mapping.items():
+            ref[v] = ref.pop(k)
+    return refs_col
+
+
+def info2package(info):
+    pack_name =  info['name']
+    pack_id = _id_generator('pack', pack_name)
+    pack_doc = {
+         '_id': pack_id
+       , 'type' : 'package'
+       , 'name' : info['name']
+       , 'description' : info['description']
+       , 'home' : info['home']
+       , 'source' : info['sources']
+       , 'authors' : info['authors']
+       , 'categories' : info['operations'] + info['topics']
+       , 'topics' : info['topics']
+       , 'operations': info['operations']
+       , 'collections' : [info['origin']]
+       , 'history' : info['history']
+       , 'library' : info['library']
+       , 'private' : info['private']
+       , 'references' : citation_key_translate(info['references'])
     }
+    return pack_doc
    
-    return mongopack
 
-def packversion2mongo(pack, version, module_info):
-    '''
-    format mongo package document from BIODOCS package informations
-    returns a mongo package document
-    '''
-    #---- get infos from BIODOCS parsed holder
-    pack_name = pack['name']
-    pack_version, pack_default= version_extract(version)
-    pack_id = "pack%s%s%s%s" %(ID_SEPARATOR, pack_name, ID_SEPARATOR,  pack_version)
-    pack_htmldocs = pack['htmldocs']
-    pack_manpages = pack['manpages']
-
-    #---- complement with module info
-    pack_htmldocs = merge_htmldocs(pack_htmldocs, module_info['htmldocs'])
-    pack_docs = module_info['docs']
-    pack_depends = module_info['depends']
-    pack_id = "pack%s%s" %(ID_SEPARATOR, pack_name)
-    version_id = "pack%s%s%s%s" %(ID_SEPARATOR, pack_name, ID_SEPARATOR,  pack_version)
-
-
-    versionpack = { '_id': version_id
+def info2pack_version(info): 
+    pack_name =  info['name']
+    pack_id = _id_generator("pack", pack_name)
+    pack_version = info['version']
+    pack_version_id = _id_generator("pack", pack_name, pack_version)
+    pack_version_doc = {
+        '_id' : pack_version_id
       , 'type' : 'packageVersion'
-                , 'package': pack_id
-                , 'version' : pack_version
-                , 'default' : pack_default
-                , 'doc' : { 'html': pack_htmldocs
-                          , 'docs': pack_docs
-                          , 'man' : pack_manpages
+      , 'package' : pack_id
+      , 'default' : info['default']
+      , 'version' : info['version']
+      , 'depends' : info['depends']
+      , 'doc'     : {'docs' : []
+                   , 'html' : info['htmldocs']
+                   , 'man'  : []
                    }
-                , 'depends' : pack_depends
       }
+    return pack_version_doc
 
-    return versionpack
 
+def info2progs(info):
+    progs = []
+    pack_name =  info['name']
+    pack_version = info['version']
+ 
+    for elem in info['programs']:
+        new = {}
+        new['_id'] = _id_generator("prog", pack_name, pack_version, elem['name'])
+        new['type'] = 'program'
+        new['name'] = elem['name']
+        new['description'] = elem['description'] if elem['description'] else ''
+        new['packageVersion'] = _id_generator("pack", pack_name, pack_version)
+        new['categories'] = []
+        new['doc'] = {'html': [], 'man': [elem['manpages']]}
+        progs.append(new)
+    return progs
 
-def progs2mongo(pack_name, pack_version, prg_lst, module_info):
-    '''
-    format mongo program document from BIODOCS program informations
-    returns a list of programs mongo documents
-    '''
-    def mongoprog_creator(prog_id, pack_id, name, htmldocs=[], manpages=[],categories=[], description=''):
-        mongoprog= { '_id' : prog_id
-                   , 'type' : 'program'
-                   , 'packageVersion' : pack_id
-                   , 'name' : prog_name
-                   , 'doc' : { 'html': htmldocs
-                             , 'man' : manpages
-                             }
-                   , 'categories' : categories
-                   , 'description' : description
-                   }
-        return mongoprog
-
-    ret = []
-    #---- generate corresponding module name to get uptodate program version
-    #---- only default version package are documented, when they are ;-(
-    pack_version, _ = version_extract(pack_version)
-
-    provided_prgs = [prg.lower() for prg in module_info['progs'] if prg]
-    pack_id = "pack%s%s%s%s" %(ID_SEPARATOR, pack_name, ID_SEPARATOR,  pack_version)
-    #---- because BIDOCS only document one version, we need to perform 2 operations:
-    #---- 1:  remove programs documented in BIODOCS not available in module definitions
-    #---- 2:  add programs in module definitions not documented in BIODOCS
-
-    for prog in prg_lst:
-        prog_name = prog['name']
-        # avoid typo documentation
-        if prog_name.lower() not in provided_prgs:
-            error(WARN,  prog_name, 'not in module', "%s/%s" %(pack_name, pack_version))
-            continue
-        provided_prgs.remove(prog_name.lower())
-        prog_id = "prog%s%s%s%s%s%s" %(ID_SEPARATOR, pack_name, ID_SEPARATOR, pack_version, ID_SEPARATOR, prog_name)
-        prog_description = prog['description'] if prog['description'] else ''
-        mongoprog = mongoprog_creator(prog_id, pack_id, prog_name, prog['HTMLDOCS'], prog['MANPAGES'], prog['CATEGORIES'], prog_description)
-        ret.append(mongoprog)
-    #---- insert non documented programs in BIODOCS if some
-    remaining = []
-
-    for prg in provided_prgs:
-        for prog_name in module_info['progs']:
-            if prog_name.lower() != prg:
-                continue
-            remaining.append(prog_name)
-
-    for prog_name in remaining:
-        prog_id = "prog%s%s%s%s%s%s" %(ID_SEPARATOR, pack_name, ID_SEPARATOR, pack_version, ID_SEPARATOR, prog_name)
-        mongoprog = mongoprog_creator(prog_id, pack_id, prog_name)
-        ret.append(mongoprog)
 
-    return ret
+def info2mobyle(info):
+    # import mobyledefs
+    ##---- should no longer used with Biodocs.yaml
+    # is the version used by mobyle ?
+    # if "%s/%s" %(pack_name, pack_version) not in mobyledefs.pack_info:
+    #     return mobyle
 
-def getweb(web_info):
+    mobyle = []
+    pack_name =  info['name']
+    pack_version = info['version']
     pattern= '(?P<name>[\w-]+)\s*\[(?P<desc>.*)\]'
     auto = re.compile(pattern)
-    match = auto.match(web_info)
-    if match is None:
-        error(WARN, 'invalib web description', web_info)
-    interface_name = match.group('name')
-    description = match.group('desc')
 
-    mobyle_url = "%s#forms::%s" % (MOBYLEURL, interface_name)
-    return interface_name, mobyle_url, description
-
-def mobyle2mongo(pack_name, pack_version, prg_lst, module_info):
-    '''
-    format mongo mobyle document from BIODOCS program informations
-    returns a list of mobyle mongo documents
-    '''
-
-    ret = []
-    #---- filter progs with WEB interface.
-    prg_lst = filter(lambda n: 'WEB' in n, prg_lst)
-    if not prg_lst:
-        return ret
-
-    pack_version, _ = version_extract(pack_version)
-
-    interfaces = collections.defaultdict(list)
-
-    for prog in prg_lst:
-        prog_name=prog['NAME']
-        # one program may hold multiple interfaces
-        for interface in prog['WEB']:
-            if not interface :
+    for prg in info['programs']:
+        prog_name = prg['name']
+        # something to document ?
+        web = prg.get('web', False)
+        if not web:
             continue
-            mobyle_interface_name, mobyle_url, mobyle_desc = getweb(interface)
-            interfaces[mobyle_interface_name].append((prog_name, mobyle_url, mobyle_desc))
-
-    #--- reduce and consistency check
-    for interface in interfaces:
-        programs = []
-        urls = set()
-        descs = []
-        for prg, url, desc in interfaces[interface]:
-            programs.append(prg)
-            urls.add(url)
-            descs.append(desc)
-        if len(urls) != 1:
-            error(FATAL, pack_name, pack_version, "PROG.WEB conflict")
-        interfaces[interface] = (list(urls), programs, descs)
-
-    for interface_name in interfaces:
-        url, prog_names, desc = interfaces[interface_name]
-        url =  url[0]
-        mobyle_desc = ' '.join(desc).strip()
-
-        mobyle_id = "mobyle%s%s%s%s%s%s" % \
-            (ID_SEPARATOR, pack_name, ID_SEPARATOR, pack_version, ID_SEPARATOR, interface_name)
-        pack_id = "pack%s%s%s%s" % \
-            (ID_SEPARATOR, pack_name, ID_SEPARATOR, pack_version)
-        prog_ids = []
-        for prog_name in prog_names:
-            prog_id = "prog%s%s%s%s%s%s" % \
-                (ID_SEPARATOR, pack_name, ID_SEPARATOR, pack_version, ID_SEPARATOR, prog_name)
-            prog_ids.append(prog_id)
-        mongomobyle= { '_id' : mobyle_id
-                     , 'type' : 'mobyle'
-                     , 'programs' : prog_ids
-                     , 'package' : pack_id
-                     , 'name' : interface_name
-                     , 'url' : url
-                     , 'description' : mobyle_desc
-                     }
-
-        ret.append(mongomobyle)
-    return ret
-
-def biodocs2mongo(biodocs_pack_info, biodocs_progs_info, mobyle_progs_info):
-    versions_lst = [biodocs_pack_info['version']]