Merge branch 'Eric_new_Python_API' of
git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API Conflicts: python/obitools3/obidms/_obidms.pxd python/obitools3/obidms/_obidms.pyx python/obitools3/obidms/_obidmscolumn_bool.pyx python/obitools3/obidms/_obidmscolumn_str.pyx python/obitools3/obidms/_obiseq.pxd python/obitools3/obidms/_obiseq.pyx python/obitools3/obidms/_obitaxo.pxd python/obitools3/obidms/_obitaxo.pyx python/obitools3/obidms/_obiview.pxd python/obitools3/obidms/_obiview.pyx python/obitools3/obidms/_obiview_nuc_seq.pxd python/obitools3/obidms/_obiview_nuc_seq.pyx python/obitools3/obidms/_obiview_nuc_seq_qual.pxd python/obitools3/obidms/_obiview_nuc_seq_qual.pyx python/obitools3/obidms/capi/obialign.pxd python/obitools3/obidms/capi/obidmscolumn.pxd python/obitools3/obidms/capi/obitaxonomy.pxd python/obitools3/obidms/capi/obiview.pxd
This commit is contained in:
Celine Mercier
@ -36,7 +36,7 @@ extensions = [
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'sphinx.ext.pngmath',
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'sphinx.ext.ifconfig',
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'sphinx.ext.viewcode',
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# 'breathe',
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'breathe',
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]
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# Add any paths that contain templates here, relative to this directory.
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@ -295,4 +295,6 @@ texinfo_documents = [
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sys.path.append( "breathe/" )
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breathe_projects = { "OBITools3": "doxygen/xml/" }
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breathe_default_project = "OBITools3"
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#breathe_projects_source = {
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# "auto" : ( "../src", ["obidms.h", "obiavl.h"] )
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# }
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@ -11,7 +11,7 @@ OBITools3 documentation
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Programming guidelines <guidelines>
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Data structures <data>
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Code documentation <code_doc/codedoc>
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Indices and tables
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------------------
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@ -4,6 +4,7 @@ OBITypes
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.. image:: ./UML/OBITypes_UML.png
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:download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
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@ -1 +1 @@
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build/lib.macosx-10.6-intel-3.5
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build/lib.macosx-10.6-intel-3.4
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BIN
python/obitools3/__init__.pyc
Normal file
BIN
python/obitools3/__init__.pyc
Normal file
Binary file not shown.
96
python/obitools3/commands/uniq.pyx
Normal file
96
python/obitools3/commands/uniq.pyx
Normal file
@ -0,0 +1,96 @@
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection # TODO cimport doesn't work
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from functools import reduce
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import time
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__title__="Grep view lines that match the given predicates"
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default_config = { 'inputview' : None,
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'outputview' : None
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}
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def addOptions(parser):
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# TODO put this common group somewhere else but I don't know where
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group=parser.add_argument_group('DMS and view options')
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group.add_argument('--default-dms','-d',
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action="store", dest="obi:defaultdms",
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metavar='<DMS NAME>',
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default=None,
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type=str,
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help="Name of the default DMS for reading and writing data.")
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group.add_argument('--input-view','-i',
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action="store", dest="obi:inputview",
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metavar='<INPUT VIEW NAME>',
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default=None,
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type=str,
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help="Name of the input view, either raw if the view is in the default DMS,"
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" or in the form 'dms:view' if it is in another DMS.")
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group.add_argument('--output-view','-o',
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action="store", dest="obi:outputview",
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metavar='<OUTPUT VIEW NAME>',
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default=None,
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type=str,
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help="Name of the output view, either raw if the view is in the default DMS,"
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" or in the form 'dms:view' if it is in another DMS.")
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group=parser.add_argument_group('obi grep specific options')
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group.add_argument('--predicate','-p',
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action="append", dest="grep:predicates",
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metavar='<PREDICATE>',
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default=None,
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type=str,
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help="Grep lines that match the given python expression on <line> or <sequence>.")
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def run(config):
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# Open DMS
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d = OBIDMS(config['obi']['defaultdms'])
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# Open input view 1
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iview = d.open_view(config['obi']['inputview'])
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# Initialize the progress bar
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pb = ProgressBar(len(iview), config, seconde=5)
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# Apply filter
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selection = OBIView_line_selection(iview)
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for i in range(len(iview)) :
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pb(i)
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line = iview[i]
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loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
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good = (reduce(lambda bint x, bint y: x and y,
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(bool(eval(p, loc_env, line))
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for p in config['grep']['predicates']), True))
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if good :
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selection.append(i)
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# Create output view with the line selection
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oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
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#print("\n")
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#print(repr(oview))
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iview.close()
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oview.close()
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d.close()
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2
python/obitools3/dms/__init__.py
Normal file
2
python/obitools3/dms/__init__.py
Normal file
@ -0,0 +1,2 @@
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from .dms import DMS # @UnresolvedImport
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0
python/obitools3/dms/capi/__init__.py
Normal file
0
python/obitools3/dms/capi/__init__.py
Normal file
41
python/obitools3/dms/capi/obialign.pxd
Normal file
41
python/obitools3/dms/capi/obialign.pxd
Normal file
@ -0,0 +1,41 @@
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#cython: language_level=3
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from obitools3.obidms.capi.obidms cimport OBIDMS_p
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from obitools3.obidms.capi.obitypes cimport const_char_p
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cdef extern from "obi_align.h" nogil:
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int obi_lcs_align_one_column(OBIDMS_p dms,
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const_char_p seq_view_name,
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const_char_p seq_column_name,
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const_char_p seq_elt_name,
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const_char_p id_column_name,
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const_char_p output_view_name,
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const_char_p output_view_comments,
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bint print_seq,
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bint print_count,
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double threshold,
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bint normalize,
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int reference,
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bint similarity_mode,
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int thread_count)
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int obi_lcs_align_two_columns(OBIDMS_p dms,
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const_char_p seq1_view_name,
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const_char_p seq2_view_name,
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const_char_p seq1_column_name,
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const_char_p seq2_column_name,
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const_char_p seq1_elt_name,
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const_char_p seq2_elt_name,
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||||
const_char_p id1_column_name,
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const_char_p id2_column_name,
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||||
const_char_p output_view_name,
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||||
const_char_p output_view_comments,
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bint print_seq,
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bint print_count,
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||||
double threshold,
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||||
bint normalize,
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||||
int reference,
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||||
bint similarity_mode)
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16
python/obitools3/dms/capi/obidms.pxd
Normal file
16
python/obitools3/dms/capi/obidms.pxd
Normal file
@ -0,0 +1,16 @@
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||||
#cython: language_level=3
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||||
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||||
from .obitypes cimport const_char_p
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cdef extern from "obidms.h" nogil:
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struct OBIDMS_t:
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const_char_p dms_name
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ctypedef OBIDMS_t* OBIDMS_p
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OBIDMS_p obi_dms(const_char_p dms_name)
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int obi_close_dms(OBIDMS_p dms)
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char* obi_dms_get_dms_path(OBIDMS_p dms)
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char* obi_dms_get_full_path(OBIDMS_p dms, const_char_p path_name)
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227
python/obitools3/dms/capi/obidmscolumn.pxd
Normal file
227
python/obitools3/dms/capi/obidmscolumn.pxd
Normal file
@ -0,0 +1,227 @@
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||||
#cython: language_level=3
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||||
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||||
from ..capi.obidms cimport OBIDMS_p
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from ..capi.obitypes cimport const_char_p, \
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OBIType_t, \
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obiversion_t, \
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obiint_t, \
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obibool_t, \
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obichar_t, \
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obifloat_t, \
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index_t, \
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time_t
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from libc.stdint cimport uint8_t
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cdef extern from "obidmscolumn.h" nogil:
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struct Column_reference_t :
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const_char_p column_name
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obiversion_t version
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ctypedef Column_reference_t* Column_reference_p
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struct OBIDMS_column_header_t:
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size_t header_size
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size_t data_size
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index_t line_count
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index_t lines_used
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index_t nb_elements_per_line
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const_char_p elements_names
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OBIType_t returned_data_type
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OBIType_t stored_data_type
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time_t creation_date
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obiversion_t version
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obiversion_t cloned_from
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const_char_p name
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const_char_p indexer_name
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Column_reference_t associated_column
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const_char_p comments
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ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
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struct OBIDMS_column_t:
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OBIDMS_p dms
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OBIDMS_column_header_p header
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bint writable
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ctypedef OBIDMS_column_t* OBIDMS_column_p
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int obi_close_column(OBIDMS_column_p column)
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obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
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const_char_p column_name)
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OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms,
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const_char_p column_name,
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obiversion_t version_number)
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int obi_close_header(OBIDMS_column_header_p header)
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char* obi_get_elements_names(OBIDMS_column_p column)
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cdef extern from "obidmscolumn_int.h" nogil:
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int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
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index_t line_nb,
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const_char_p element_name,
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obiint_t value)
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int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column,
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index_t line_nb,
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index_t element_idx,
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obiint_t value)
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obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column,
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index_t line_nb,
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||||
const_char_p element_name)
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obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column,
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index_t line_nb,
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index_t element_idx)
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||||
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cdef extern from "obidmscolumn_bool.h" nogil:
|
||||
|
||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
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||||
const_char_p element_name,
|
||||
obibool_t value)
|
||||
|
||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obibool_t value)
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_char.h" nogil:
|
||||
|
||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obichar_t value)
|
||||
|
||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obichar_t value)
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_float.h" nogil:
|
||||
|
||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obifloat_t value)
|
||||
|
||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obifloat_t value)
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_str.h" nogil:
|
||||
|
||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
cdef extern from "obidmscolumn_seq.h" nogil:
|
||||
|
||||
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
cdef extern from "obidmscolumn_qual.h" nogil:
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
int* value_length)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
int* value_length)
|
||||
|
||||
5
python/obitools3/dms/capi/obierrno.pxd
Normal file
5
python/obitools3/dms/capi/obierrno.pxd
Normal file
@ -0,0 +1,5 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
cdef extern from "obierrno.h":
|
||||
int obi_errno
|
||||
65
python/obitools3/dms/capi/obitaxonomy.pxd
Normal file
65
python/obitools3/dms/capi/obitaxonomy.pxd
Normal file
@ -0,0 +1,65 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .obitypes cimport const_char_p
|
||||
from .obidms cimport OBIDMS_p
|
||||
from libc.stdint cimport int32_t
|
||||
|
||||
|
||||
cdef extern from "obidms_taxonomy.h" nogil:
|
||||
|
||||
struct ecotxnode :
|
||||
int32_t taxid
|
||||
int32_t rank
|
||||
int32_t farest
|
||||
ecotxnode* parent
|
||||
char* name
|
||||
char* preferred_name
|
||||
|
||||
ctypedef ecotxnode ecotx_t
|
||||
|
||||
|
||||
struct ecotxidx_t :
|
||||
int32_t count
|
||||
int32_t max_taxid
|
||||
int32_t buffer_size
|
||||
ecotx_t* taxon
|
||||
|
||||
|
||||
struct OBIDMS_taxonomy_t :
|
||||
# ecorankidx_t* ranks
|
||||
# econameidx_t* names
|
||||
ecotxidx_t* taxa
|
||||
|
||||
ctypedef OBIDMS_taxonomy_t* OBIDMS_taxonomy_p
|
||||
|
||||
|
||||
OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const_char_p taxonomy_name, bint read_alternative_names)
|
||||
|
||||
OBIDMS_taxonomy_p obi_read_taxdump(const_char_p taxdump)
|
||||
|
||||
int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const_char_p tax_name)
|
||||
|
||||
int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx)
|
||||
|
||||
ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid)
|
||||
|
||||
bint obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid)
|
||||
|
||||
ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy)
|
||||
|
||||
int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid)
|
||||
|
||||
int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name)
|
||||
|
||||
int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name)
|
||||
|
||||
56
python/obitools3/dms/capi/obitypes.pxd
Normal file
56
python/obitools3/dms/capi/obitypes.pxd
Normal file
@ -0,0 +1,56 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
from libc.stdint cimport int32_t, int64_t, uint8_t
|
||||
|
||||
from posix.types cimport time_t
|
||||
|
||||
|
||||
cdef extern from *:
|
||||
ctypedef char* const_char_p "const char*"
|
||||
|
||||
|
||||
cdef extern from "encode.h" nogil:
|
||||
bint only_ATGC(const_char_p seq)
|
||||
|
||||
|
||||
cdef extern from "obitypes.h" nogil:
|
||||
|
||||
enum OBIType:
|
||||
OBI_VOID,
|
||||
OBI_INT,
|
||||
OBI_FLOAT,
|
||||
OBI_BOOL,
|
||||
OBI_CHAR,
|
||||
OBI_QUAL,
|
||||
OBI_STR,
|
||||
OBI_SEQ,
|
||||
OBI_IDX
|
||||
|
||||
|
||||
ctypedef OBIType OBIType_t
|
||||
|
||||
enum OBIBool:
|
||||
pass
|
||||
|
||||
ctypedef OBIBool obibool_t
|
||||
ctypedef int32_t obiint_t
|
||||
ctypedef double obifloat_t
|
||||
ctypedef char obichar_t
|
||||
ctypedef int64_t index_t
|
||||
|
||||
ctypedef int32_t obiversion_t
|
||||
|
||||
extern obiint_t OBIInt_NA
|
||||
extern index_t OBIIdx_NA
|
||||
extern obifloat_t OBIFloat_NA
|
||||
extern obichar_t OBIChar_NA
|
||||
extern obibool_t OBIBool_NA
|
||||
extern const_char_p OBISeq_NA
|
||||
extern const_char_p OBIStr_NA
|
||||
extern const_char_p OBIQual_char_NA
|
||||
extern uint8_t* OBIQual_int_NA
|
||||
|
||||
const_char_p name_data_type(int data_type)
|
||||
|
||||
ctypedef OBIType_t obitype_t
|
||||
12
python/obitools3/dms/capi/obiutils.pxd
Normal file
12
python/obitools3/dms/capi/obiutils.pxd
Normal file
@ -0,0 +1,12 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
from posix.types cimport time_t
|
||||
|
||||
from ..capi.obitypes cimport const_char_p
|
||||
|
||||
|
||||
cdef extern from "utils.h" nogil:
|
||||
|
||||
const_char_p obi_format_date(time_t date)
|
||||
|
||||
294
python/obitools3/dms/capi/obiview.pxd
Normal file
294
python/obitools3/dms/capi/obiview.pxd
Normal file
@ -0,0 +1,294 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .obitypes cimport const_char_p, \
|
||||
OBIType_t, \
|
||||
obiversion_t, \
|
||||
obiint_t, \
|
||||
obibool_t, \
|
||||
obichar_t, \
|
||||
obifloat_t, \
|
||||
index_t, \
|
||||
time_t
|
||||
from ..capi.obidms cimport OBIDMS_p
|
||||
from ..capi.obidmscolumn cimport OBIDMS_column_p, \
|
||||
Column_reference_t, \
|
||||
Column_reference_p
|
||||
|
||||
from libc.stdint cimport uint8_t
|
||||
|
||||
|
||||
cdef extern from "obiview.h" nogil:
|
||||
|
||||
extern const_char_p VIEW_TYPE_NUC_SEQS
|
||||
extern const_char_p NUC_SEQUENCE_COLUMN
|
||||
extern const_char_p ID_COLUMN
|
||||
extern const_char_p DEFINITION_COLUMN
|
||||
extern const_char_p QUALITY_COLUMN
|
||||
|
||||
|
||||
struct Alias_column_pair_t :
|
||||
Column_reference_t column_refs
|
||||
const_char_p alias
|
||||
|
||||
ctypedef Alias_column_pair_t* Alias_column_pair_p
|
||||
|
||||
|
||||
struct Obiview_infos_t :
|
||||
time_t creation_date
|
||||
const_char_p name
|
||||
const_char_p created_from
|
||||
const_char_p view_type
|
||||
bint all_lines
|
||||
Column_reference_t line_selection
|
||||
index_t line_count
|
||||
int column_count
|
||||
Alias_column_pair_p column_references
|
||||
const_char_p comments
|
||||
|
||||
ctypedef Obiview_infos_t* Obiview_infos_p
|
||||
|
||||
|
||||
struct Obiview_t :
|
||||
Obiview_infos_p infos
|
||||
OBIDMS_p dms
|
||||
bint read_only
|
||||
OBIDMS_column_p line_selection
|
||||
OBIDMS_column_p columns
|
||||
int nb_predicates
|
||||
# TODO declarations for column dictionary and predicate function array?
|
||||
|
||||
ctypedef Obiview_t* Obiview_p
|
||||
|
||||
|
||||
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments, bint quality_column)
|
||||
|
||||
Obiview_p obi_new_view(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
|
||||
|
||||
Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
|
||||
|
||||
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments, bint quality_column)
|
||||
|
||||
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name, bint finished)
|
||||
|
||||
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
|
||||
|
||||
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
|
||||
|
||||
int obi_view_add_column(Obiview_p view,
|
||||
const_char_p column_name,
|
||||
obiversion_t version_number,
|
||||
const_char_p alias,
|
||||
OBIType_t data_type,
|
||||
index_t nb_lines,
|
||||
index_t nb_elements_per_line,
|
||||
char* elements_names,
|
||||
const_char_p indexer_name,
|
||||
const_char_p associated_column_name,
|
||||
obiversion_t associated_column_version,
|
||||
const_char_p comments,
|
||||
bint create)
|
||||
|
||||
int obi_view_delete_column(Obiview_p view, const_char_p column_name)
|
||||
|
||||
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
|
||||
|
||||
OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const_char_p column_name)
|
||||
|
||||
int obi_view_create_column_alias(Obiview_p view, const_char_p current_name, const_char_p alias)
|
||||
|
||||
int obi_save_and_close_view(Obiview_p view)
|
||||
|
||||
|
||||
# OBI_INT
|
||||
int obi_set_int_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obiint_t value)
|
||||
|
||||
int obi_set_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obiint_t value)
|
||||
|
||||
obiint_t obi_get_int_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obiint_t obi_get_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
# OBI_BOOL
|
||||
int obi_set_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obibool_t value)
|
||||
|
||||
int obi_set_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obibool_t value)
|
||||
|
||||
obibool_t obi_get_bool_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obibool_t obi_get_bool_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
# OBI_CHAR
|
||||
int obi_set_char_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obichar_t value)
|
||||
|
||||
int obi_set_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obichar_t value)
|
||||
|
||||
obichar_t obi_get_char_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obichar_t obi_get_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
# OBI_FLOAT
|
||||
int obi_set_float_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
obifloat_t value)
|
||||
|
||||
int obi_set_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
obifloat_t value)
|
||||
|
||||
obifloat_t obi_get_float_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
obifloat_t obi_get_float_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
# OBI_QUAL
|
||||
int obi_set_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const char* value)
|
||||
|
||||
int obi_set_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_get_qual_char_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
const uint8_t* obi_get_qual_int_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
int* value_length)
|
||||
|
||||
int obi_set_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
const char* value)
|
||||
|
||||
int obi_set_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_get_qual_char_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const char* element_name)
|
||||
|
||||
const uint8_t* obi_get_qual_int_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
int* value_length)
|
||||
|
||||
|
||||
# OBI_STR
|
||||
int obi_set_str_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_set_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
const_char_p obi_get_str_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
const_char_p obi_get_str_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
# OBI_SEQ
|
||||
int obi_set_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_set_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
char* obi_get_seq_with_elt_name_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
char* obi_get_seq_with_elt_idx_and_col_p_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column_p,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
25
python/obitools3/dms/column.pxd
Normal file
25
python/obitools3/dms/column.pxd
Normal file
@ -0,0 +1,25 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport index_t, \
|
||||
obitype_t
|
||||
from .capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
from .view cimport View
|
||||
|
||||
cdef class Column:
|
||||
|
||||
cdef OBIDMS_column_p* _pointer
|
||||
cdef View _view
|
||||
|
||||
cpdef close(self)
|
||||
|
||||
cdef class Column_line:
|
||||
|
||||
cdef Column _column
|
||||
cdef index_t _index
|
||||
|
||||
cpdef update(self, data)
|
||||
|
||||
cdef register_column_class(obitype_t obitype,
|
||||
type classe,
|
||||
type python)
|
||||
180
python/obitools3/dms/column.pyx
Normal file
180
python/obitools3/dms/column.pyx
Normal file
@ -0,0 +1,180 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport name_data_type
|
||||
|
||||
from .capi.obidmscolumn cimport OBIDMS_column_header_p, \
|
||||
obi_close_column, \
|
||||
obi_column_prepare_to_get_value
|
||||
|
||||
from .capi.obiutils cimport obi_format_date
|
||||
|
||||
from .dms cimport __OBIDMS_COLUMN_CLASS__
|
||||
|
||||
from obitools3.utils cimport bytes2str
|
||||
|
||||
|
||||
cdef class Column :
|
||||
"""
|
||||
The obitools3.dms.column.Column class wraps a C instance of a column in the context of a View
|
||||
"""
|
||||
|
||||
# Note: should only be initialized through a subclass
|
||||
def __init__(self,
|
||||
View view,
|
||||
int __internalCall__):
|
||||
'''
|
||||
Creates a new OBDMS column objected referring to a already created column
|
||||
in the context of a view.
|
||||
|
||||
This constructor is normally only called by subclass constructor.
|
||||
|
||||
@param view: The view object containing the column.
|
||||
@type view: OBIView
|
||||
'''
|
||||
|
||||
cdef OBIDMS_column_p* column_pp
|
||||
|
||||
if __internalCall__!=987654:
|
||||
raise RuntimeError('OBIView constructor cannot be called directly')
|
||||
|
||||
# Check that the class is only created as a subclass instance
|
||||
if type(self)==Column or not isinstance(self, Column):
|
||||
raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
|
||||
|
||||
# Fill structure
|
||||
self._pointer = NULL
|
||||
self._view = view
|
||||
|
||||
def __len__(self):
|
||||
'''
|
||||
Implements the len() function for the Column class
|
||||
|
||||
@rtype: `int`
|
||||
'''
|
||||
return self.lines_used
|
||||
|
||||
def __sizeof__(self):
|
||||
'''
|
||||
returns the size of the C object wrapped by the Column instance
|
||||
'''
|
||||
cdef OBIDMS_column_header_p header = self._pointer[0].header
|
||||
return header.header_size + header.data_size
|
||||
|
||||
def __iter__(self):
|
||||
cdef index_t line_nb
|
||||
|
||||
for line_nb in range(self.lines_used):
|
||||
yield self[line_nb]
|
||||
|
||||
def __str__(self) :
|
||||
cdef str to_print
|
||||
to_print = ''
|
||||
for line in self :
|
||||
to_print = to_print + str(line) + "\n"
|
||||
return to_print
|
||||
|
||||
def __repr__(self) :
|
||||
return b"%s, original name: %s, version %d, data type: %d" % (
|
||||
self._alias,
|
||||
self.original_name,
|
||||
self.version,
|
||||
self.data_type
|
||||
)
|
||||
|
||||
cpdef close(self):
|
||||
if self._pointer != NULL:
|
||||
if obi_close_column(self._pointer[0]) < 0 :
|
||||
raise Exception("Problem closing column %s" % bytes2str(self.name))
|
||||
|
||||
# Column alias property getter and setter
|
||||
@property
|
||||
def name(self):
|
||||
return self._alias
|
||||
@name.setter
|
||||
def name(self, new_alias): # @DuplicatedSignature
|
||||
self._view.change_column_alias(self._alias, new_alias)
|
||||
|
||||
# elements_names property getter
|
||||
@property
|
||||
def elements_names(self):
|
||||
return (((self._pointer)[0].header).elements_names).split(b';')
|
||||
|
||||
# nb_elements_per_line property getter
|
||||
@property
|
||||
def nb_elements_per_line(self):
|
||||
return ((self._pointer)[0].header).nb_elements_per_line
|
||||
|
||||
# data_type property getter
|
||||
@property
|
||||
def data_type(self):
|
||||
return name_data_type(((self._pointer)[0].header).returned_data_type)
|
||||
|
||||
# original_name property getter
|
||||
@property
|
||||
def original_name(self):
|
||||
return ((self._pointer)[0].header).name
|
||||
|
||||
# version property getter
|
||||
@property
|
||||
def version(self):
|
||||
return ((self._pointer)[0].header).version
|
||||
|
||||
# lines_used property getter
|
||||
@property
|
||||
def lines_used(self):
|
||||
return (self._pointer)[0].header.lines_used
|
||||
|
||||
# comments property getter
|
||||
@property
|
||||
def comments(self):
|
||||
return (self._pointer)[0].header.comments
|
||||
|
||||
# creation_date property getter
|
||||
@property
|
||||
def creation_date(self):
|
||||
return obi_format_date((self._pointer)[0].header.creation_date)
|
||||
|
||||
|
||||
######################################################################################################
|
||||
|
||||
|
||||
cdef class Column_line :
|
||||
|
||||
def __init__(self, Column column, index_t line_nb) :
|
||||
self._index = line_nb
|
||||
self._column = column
|
||||
|
||||
if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
|
||||
raise IndexError("Cannot access to the line %d" % line_nb)
|
||||
|
||||
|
||||
def __contains__(self, str element_name):
|
||||
pass
|
||||
#return (element_name in self._column.elements_names)
|
||||
|
||||
def __repr__(self) :
|
||||
return str(self._column.get_line(self._index))
|
||||
|
||||
cpdef update(self, data):
|
||||
if isinstance(data, dict):
|
||||
data=data.items()
|
||||
for key,value in data:
|
||||
if key in self:
|
||||
self[key]=value
|
||||
|
||||
|
||||
######################################################################################################
|
||||
|
||||
|
||||
cdef register_column_class(obitype_t obitype,
|
||||
type classe,
|
||||
type python):
|
||||
"""
|
||||
Each sub class of `OBIDMS_column` needs to be registered after its declaration
|
||||
to declare its relationship with an `OBIType_t`
|
||||
"""
|
||||
global __OBIDMS_COLUMN_CLASS__
|
||||
|
||||
assert issubclass(classe,Column)
|
||||
|
||||
__OBIDMS_COLUMN_CLASS__[obitype]=(classe,python)
|
||||
1
python/obitools3/dms/column/__init__.py
Normal file
1
python/obitools3/dms/column/__init__.py
Normal file
@ -0,0 +1 @@
|
||||
from .column import column # @UnresolvedImport
|
||||
56
python/obitools3/dms/column/bool.pxd
Normal file
56
python/obitools3/dms/column/bool.pxd
Normal file
@ -0,0 +1,56 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from cpython.bool cimport bool, PyBool_FromLong
|
||||
|
||||
from ..capi.obitypes cimport index_t, \
|
||||
const_char_p, \
|
||||
OBIType_t, \
|
||||
obibool_t, \
|
||||
OBI_BOOL, \
|
||||
OBIBool_NA
|
||||
|
||||
from ..capi.obiview cimport obi_get_bool_with_elt_name_and_col_p_in_view, \
|
||||
obi_get_bool_with_elt_idx_and_col_p_in_view, \
|
||||
obi_set_bool_with_elt_name_and_col_p_in_view, \
|
||||
obi_set_bool_with_elt_idx_and_col_p_in_view
|
||||
|
||||
from ..capi.obidmscolumn cimport obi_column_get_obibool_with_elt_name, \
|
||||
obi_column_get_obibool_with_elt_idx, \
|
||||
obi_column_set_obibool_with_elt_name, \
|
||||
obi_column_set_obibool_with_elt_idx, \
|
||||
OBIDMS_column_p
|
||||
|
||||
from ..capi.obierrno cimport obi_errno
|
||||
|
||||
from .column cimport Column, \
|
||||
Column_line, \
|
||||
register_column_class
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
cdef class Column_line_bool(OBIDMS_column_line) :
|
||||
|
||||
@staticmethod
|
||||
cdef bool obibool_t2bool(obibool_t value)
|
||||
|
||||
@staticmethod
|
||||
cdef bool2obibool_t(bool value)
|
||||
|
||||
cpdef bool get_bool_item_by_name(self,bytes element_name)
|
||||
cpdef bool get_bool_item_by_idx(self,index_t index)
|
||||
cpdef set_bool_item_by_name(self,bytes element_name,bool value)
|
||||
cpdef set_bool_item_by_idx(self,index_t index,bool value)
|
||||
|
||||
|
||||
# cdef obibool_t [:] _data_view
|
||||
|
||||
cdef class Column_bool(OBIDMS_column):
|
||||
cdef Column _new(OBIView view,
|
||||
bytes column_name,
|
||||
index_t nb_elements_per_line=1,
|
||||
object elements_names=None,
|
||||
bytes comments=b""):
|
||||
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
|
||||
294
python/obitools3/dms/column/bool.pyx
Normal file
294
python/obitools3/dms/column/bool.pyx
Normal file
@ -0,0 +1,294 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
cdef class OBIDMS_column_line_bool(OBIDMS_column_line) :
|
||||
|
||||
cdef update_pointer(self):
|
||||
"""
|
||||
Checks if the obicolumn address changed since the last call and update
|
||||
if need the `_column_p` and `_data_view` data structure fields.
|
||||
"""
|
||||
cdef OBIDMS_column_p column_p = self._column_pp[0]
|
||||
|
||||
if column_p != self._column_p:
|
||||
self._column_p = column_p
|
||||
# self._data_view = (<obibool_t*> (column_p.data)) + \
|
||||
# self._index * column_p.header.nb_elements_per_line
|
||||
|
||||
@staticmethod
|
||||
cdef bool obibool_t2bool(obibool_t value):
|
||||
cdef bool result
|
||||
|
||||
if value == OBIBool_NA :
|
||||
result = None
|
||||
else :
|
||||
result = PyBool_FromLong(value)
|
||||
|
||||
return result
|
||||
|
||||
@staticmethod
|
||||
cdef bool2obibool_t(bool value):
|
||||
cdef obibool_t result
|
||||
|
||||
if value is None:
|
||||
result=OBIBool_NA
|
||||
else:
|
||||
result= <obibool_t> <int> value
|
||||
|
||||
return result
|
||||
|
||||
|
||||
def __init__(self, OBIDMS_column column, index_t line_nb) :
|
||||
"""
|
||||
Creates a new `OBIDMS_column_line_bool`
|
||||
|
||||
@param column: an OBIDMS_column instance
|
||||
@param line_nb: the line in the column
|
||||
"""
|
||||
|
||||
OBIDMS_column_line.__init__(self,column,line_nb)
|
||||
self.update_pointer()
|
||||
|
||||
|
||||
|
||||
cpdef bool get_bool_item_by_name(self,bytes element_name):
|
||||
"""
|
||||
Returns the value associated to the name `element_name` of the current line
|
||||
|
||||
@param element_name: a `bytes` instance containing the name of the element
|
||||
|
||||
@return: the `bool` value corresponding to the name
|
||||
"""
|
||||
cdef char* cname = element_name
|
||||
cdef obibool_t value
|
||||
global obi_errno
|
||||
|
||||
self.update_pointer()
|
||||
|
||||
value = obi_column_get_obibool_with_elt_name(self._column_p,
|
||||
self._index,
|
||||
cname)
|
||||
|
||||
if obi_errno > 0 :
|
||||
obi_errno = 0
|
||||
raise KeyError("Cannot access to key %s" % bytes2str(element_name))
|
||||
|
||||
return OBIDMS_column_line_bool.obibool_t2bool(value)
|
||||
|
||||
cpdef bool get_bool_item_by_idx(self,index_t index):
|
||||
"""
|
||||
Returns the value associated to the name `element_name` of the current line
|
||||
|
||||
@param index: a `int` instance containing the index of the element
|
||||
|
||||
@return: the `bool` value corresponding to the name
|
||||
"""
|
||||
cdef obibool_t value # @DuplicatedSignature
|
||||
global obi_errno
|
||||
|
||||
|
||||
self.update_pointer()
|
||||
|
||||
value = obi_column_get_obibool_with_elt_idx(self._column_p,
|
||||
self._index,
|
||||
index)
|
||||
|
||||
if obi_errno > 0 :
|
||||
obi_errno = 0
|
||||
raise IndexError("Cannot access to element %d" % index)
|
||||
|
||||
return OBIDMS_column_line_bool.obibool_t2bool(value)
|
||||
|
||||
|
||||
def __getitem__(self, object element_name) :
|
||||
cdef bytes name
|
||||
cdef int cindex
|
||||
cdef obibool_t value
|
||||
cdef type typearg = type(element_name)
|
||||
cdef bool result
|
||||
|
||||
|
||||
if typearg == int:
|
||||
cindex=element_name
|
||||
if cindex < 0:
|
||||
cindex = self._len - cindex
|
||||
result=self.get_bool_item_by_idx(cindex)
|
||||
elif typearg == bytes:
|
||||
result=self.get_bool_item_by_name(element_name)
|
||||
elif typearg == str:
|
||||
name = str2bytes(element_name)
|
||||
result=self.get_bool_item_by_name(name)
|
||||
|
||||
return result
|
||||
|
||||
cpdef set_bool_item_by_name(self,bytes element_name,bool value):
|
||||
"""
|
||||
Sets the value associated to the name `element_name` of the current line
|
||||
|
||||
@param element_name: a `bytes` instance containing the name of the element
|
||||
@param value: a `bool` instance of the new value
|
||||
|
||||
@return: the `bool` value corresponding to the name
|
||||
"""
|
||||
cdef char* cname = element_name
|
||||
cdef obibool_t cvalue
|
||||
|
||||
self.update_pointer()
|
||||
cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
|
||||
|
||||
if ( obi_column_set_obibool_with_elt_name(self._column_p,
|
||||
self._index,
|
||||
cname,
|
||||
cvalue) < 0 ):
|
||||
raise KeyError("Cannot access to key %s" % bytes2str(element_name))
|
||||
|
||||
cpdef set_bool_item_by_idx(self,index_t index,bool value):
|
||||
"""
|
||||
Sets the value associated to the name `element_name` of the current line
|
||||
|
||||
@param index: a `int` instance containing the index of the element
|
||||
@param value: a `bool` instance of the new value
|
||||
|
||||
@return: the `bool` value corresponding to the name
|
||||
"""
|
||||
cdef obibool_t cvalue # @DuplicatedSignature
|
||||
|
||||
self.update_pointer()
|
||||
cvalue = OBIDMS_column_line_bool.bool2obibool_t(value)
|
||||
|
||||
if ( obi_column_set_obibool_with_elt_idx(self._column_p,
|
||||
self._index,
|
||||
index,
|
||||
cvalue) < 0 ):
|
||||
raise IndexError("Cannot access to item index %d" % index)
|
||||
|
||||
|
||||
|
||||
def __setitem__(self, object element_name, object value):
|
||||
cdef bytes name
|
||||
cdef int cindex
|
||||
cdef type typearg = type(element_name)
|
||||
cdef bool result
|
||||
|
||||
|
||||
if typearg == int:
|
||||
cindex=element_name
|
||||
if cindex < 0:
|
||||
cindex = self._len - cindex
|
||||
self.set_bool_item_by_idx(cindex,value)
|
||||
elif typearg == bytes:
|
||||
self.set_bool_item_by_name(element_name,value)
|
||||
elif typearg == str:
|
||||
name = str2bytes(element_name)
|
||||
self.set_bool_item_by_name(name,value)
|
||||
|
||||
def __repr__(self) :
|
||||
return str(self._column.get_line(self._index))
|
||||
|
||||
def __len__(self):
|
||||
return self._len
|
||||
|
||||
|
||||
|
||||
cdef class Column_bool(Column):
|
||||
|
||||
@staticmethod
|
||||
def new(OBIView view,
|
||||
object column_name,
|
||||
index_t nb_elements_per_line=1,
|
||||
object elements_names=None,
|
||||
object comments=b""):
|
||||
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
cdef bytes comments_b
|
||||
cdef bytes elements_names_b
|
||||
cdef char* elements_names_p
|
||||
cdef OBIDMS_column new_column
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
if elements_names is not None:
|
||||
elements_names_b = b''.join([tobytes(x) for x in elements_names])
|
||||
elements_names_p = elements_names_b
|
||||
else:
|
||||
elements_names_p = NULL
|
||||
|
||||
if (obi_view_add_column(view = view._pointer,
|
||||
column_name = column_name_b,
|
||||
version_number = -1,
|
||||
alias = NULL,
|
||||
data_type = OBI_BOOL,
|
||||
nb_lines = len(view),
|
||||
nb_elements_per_line = nb_elements_per_line,
|
||||
elements_names = elements_names_p,
|
||||
indexer_name = NULL,
|
||||
associated_column_name = NULL,
|
||||
associated_column_version = -1,
|
||||
comments = comments_b,
|
||||
create = True)<0):
|
||||
raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name),
|
||||
bytes2str(view.name)))
|
||||
|
||||
view.__init_columns__()
|
||||
new_column = self._columns[column_name]
|
||||
|
||||
return new_column
|
||||
|
||||
def add_to_view(self,
|
||||
OBIView view,
|
||||
object column_name=None,
|
||||
object comments=b""):
|
||||
|
||||
cdef OBIDMS_column_p column_p = self._column_pp[0]
|
||||
cdef bytes alias
|
||||
|
||||
if (column_name is None):
|
||||
alias = self._alias
|
||||
else:
|
||||
alias = tobytes(column_name)
|
||||
|
||||
if (obi_view_add_column(view = view._ponter,
|
||||
column_name = column_p.header.name,
|
||||
version_number = column_p.header.version,
|
||||
alias = alias,
|
||||
data_type = OBI_BOOL,
|
||||
nb_lines = column_p.header.lines_used,
|
||||
nb_elements_per_line = column_p.header.nb_elements_per_line,
|
||||
elements_names = column_p.header.elements_names,
|
||||
indexer_name = NULL,
|
||||
associated_column_name = NULL,
|
||||
associated_column_version = NULL,
|
||||
comments = tobytes(comments),
|
||||
create = False) < 0):
|
||||
raise RuntimeError("Cannot insert column %s (%s@%d) into view %s" %
|
||||
( bytes2str(alias),
|
||||
bytes2str(column_p.header.name),
|
||||
column_p.header.version,
|
||||
bytes2str(view.name)
|
||||
))
|
||||
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obibool_t value
|
||||
cdef object result
|
||||
global obi_errno
|
||||
|
||||
value = obi_get_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIBool_NA :
|
||||
result = None
|
||||
else :
|
||||
result = PyBool_FromLong(value)
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
value = OBIBool_NA
|
||||
if obi_set_bool_with_elt_idx_and_col_p_in_view(self._view._pointer, (self._pointer)[0], line_nb, 0, <obibool_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
register_column_class(OBI_BOOL,Column_bool,bool)
|
||||
26
python/obitools3/dms/column/column.pxd
Normal file
26
python/obitools3/dms/column/column.pxd
Normal file
@ -0,0 +1,26 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..capi.obitypes cimport index_t, \
|
||||
obitype_t
|
||||
from ..capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
from ..view cimport View
|
||||
|
||||
cdef class Column:
|
||||
|
||||
cdef OBIDMS_column_p* _pointer
|
||||
cdef View _view
|
||||
|
||||
cpdef close(self)
|
||||
|
||||
cdef class Column_line:
|
||||
|
||||
cdef Column _column
|
||||
cdef index_t _index
|
||||
|
||||
cpdef update(self, data)
|
||||
|
||||
cdef register_column_class(obitype_t obitype,
|
||||
type classe,
|
||||
type matrix,
|
||||
type python)
|
||||
225
python/obitools3/dms/column/column.pyx
Normal file
225
python/obitools3/dms/column/column.pyx
Normal file
@ -0,0 +1,225 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport name_data_type
|
||||
|
||||
from .capi.obidmscolumn cimport OBIDMS_column_header_p, \
|
||||
obi_close_column, \
|
||||
obi_column_prepare_to_get_value
|
||||
|
||||
from .capi.obiutils cimport obi_format_date
|
||||
|
||||
from .dms cimport __OBIDMS_COLUMN_CLASS__
|
||||
|
||||
from obitools3.utils cimport bytes2str
|
||||
|
||||
|
||||
cdef class Column :
|
||||
"""
|
||||
The obitools3.dms.column.Column class wraps a c instance of a column in the context of a View
|
||||
"""
|
||||
|
||||
# Note: should only be initialized through a subclass
|
||||
def __init__(self,
|
||||
View view,
|
||||
int __internalCall__):
|
||||
'''
|
||||
Create a new OBDMS column objected referring to a already created column
|
||||
in the context of a view.
|
||||
|
||||
This constructor is normally only called by subclass constructor.
|
||||
|
||||
@param view: The view object containing the column.
|
||||
@type view: OBIView
|
||||
'''
|
||||
|
||||
cdef OBIDMS_column_p* column_pp
|
||||
|
||||
if __internalCall__!=987654:
|
||||
raise RuntimeError('OBIView constructor cannot be called directly')
|
||||
|
||||
# Check that the class is only created as a subclass instance
|
||||
if type(self)==Column or not isinstance(self, Column):
|
||||
raise RuntimeError('OBIDMS.Column constructor cannot be called directly')
|
||||
|
||||
# Fill structure
|
||||
self._pointer = NULL
|
||||
self._view = view
|
||||
|
||||
@staticmethod
|
||||
def new(OBIView view,
|
||||
object column_name,
|
||||
index_t nb_elements_per_line=1,
|
||||
object elements_names=None,
|
||||
object comments=b""):
|
||||
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
cdef bytes comments_b
|
||||
cdef bytes elements_names_b
|
||||
cdef char* elements_names_p
|
||||
cdef OBIDMS_column new_column
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
if elements_names is not None:
|
||||
elements_names_b = b''.join([tobytes(x) for x in elements_names])
|
||||
elements_names_p = elements_names_b
|
||||
else:
|
||||
elements_names_p = NULL
|
||||
|
||||
if (obi_view_add_column(view = view._pointer,
|
||||
column_name = column_name_b,
|
||||
version_number = -1,
|
||||
alias = NULL,
|
||||
data_type = self.pointer.header.returned_data_type,
|
||||
nb_lines = len(view),
|
||||
nb_elements_per_line = nb_elements_per_line,
|
||||
elements_names = elements_names_p,
|
||||
indexer_name = NULL,
|
||||
associated_column_name = NULL,
|
||||
associated_column_version = -1,
|
||||
comments = comments_b,
|
||||
create = True)<0):
|
||||
raise RuntimeError("Cannot create column %s in view %s" % (bytes2str(column_name),
|
||||
bytes2str(view.name)))
|
||||
|
||||
view.__init_columns__()
|
||||
new_column = self._columns[column_name]
|
||||
|
||||
return new_column
|
||||
|
||||
def __len__(self):
|
||||
'''
|
||||
implements the len() function for the Column class
|
||||
|
||||
@rtype: `int`
|
||||
'''
|
||||
return self.lines_used
|
||||
|
||||
def __sizeof__(self):
|
||||
'''
|
||||
returns the size of the C object wrapped by the Column instance
|
||||
'''
|
||||
cdef OBIDMS_column_header_p header = self._pointer[0].header
|
||||
return header.header_size + header.data_size
|
||||
|
||||
def __iter__(self):
|
||||
cdef index_t line_nb
|
||||
|
||||
for line_nb in range(self.lines_used):
|
||||
yield self[line_nb]
|
||||
|
||||
def __str__(self) :
|
||||
cdef str to_print
|
||||
to_print = ''
|
||||
for line in self :
|
||||
to_print = to_print + str(line) + "\n"
|
||||
return to_print
|
||||
|
||||
def __repr__(self) :
|
||||
return b"%s, original name: %s, version %d, data type: %d" % (
|
||||
self._alias,
|
||||
self.original_name,
|
||||
self.version,
|
||||
self.data_type
|
||||
)
|
||||
|
||||
cpdef close(self):
|
||||
if self._pointer != NULL:
|
||||
if obi_close_column(self._pointer[0]) < 0 :
|
||||
raise Exception("Problem closing column %s" % bytes2str(self.name))
|
||||
|
||||
# Column alias property getter and setter
|
||||
@property
|
||||
def name(self):
|
||||
return self._alias
|
||||
@name.setter
|
||||
def name(self, new_alias): # @DuplicatedSignature
|
||||
self._view.change_column_alias(self._alias, new_alias)
|
||||
|
||||
# elements_names property getter
|
||||
@property
|
||||
def elements_names(self):
|
||||
return (((self._pointer)[0].header).elements_names).split(b';')
|
||||
|
||||
# nb_elements_per_line property getter
|
||||
@property
|
||||
def nb_elements_per_line(self):
|
||||
return ((self._pointer)[0].header).nb_elements_per_line
|
||||
|
||||
# data_type property getter
|
||||
@property
|
||||
def data_type(self):
|
||||
return name_data_type(((self._pointer)[0].header).returned_data_type)
|
||||
|
||||
# original_name property getter
|
||||
@property
|
||||
def original_name(self):
|
||||
return ((self._pointer)[0].header).name
|
||||
|
||||
# version property getter
|
||||
@property
|
||||
def version(self):
|
||||
return ((self._pointer)[0].header).version
|
||||
|
||||
# lines_used property getter
|
||||
@property
|
||||
def lines_used(self):
|
||||
return (self._pointer)[0].header.lines_used
|
||||
|
||||
# comments property getter
|
||||
@property
|
||||
def comments(self):
|
||||
return (self._pointer)[0].header.comments
|
||||
|
||||
# creation_date property getter
|
||||
@property
|
||||
def creation_date(self):
|
||||
return obi_format_date((self._pointer)[0].header.creation_date)
|
||||
|
||||
|
||||
######################################################################################################
|
||||
|
||||
|
||||
cdef class Column_line :
|
||||
|
||||
def __init__(self, Column column, index_t line_nb) :
|
||||
self._index = line_nb
|
||||
self._column = column
|
||||
|
||||
if obi_column_prepare_to_get_value(self._column._pointer[0],line_nb) < 0:
|
||||
raise IndexError("Cannot access to the line %d" % line_nb)
|
||||
|
||||
|
||||
def __contains__(self, str element_name):
|
||||
pass
|
||||
#return (element_name in self._column.elements_names)
|
||||
|
||||
def __repr__(self) :
|
||||
return str(self._column.get_line(self._index))
|
||||
|
||||
cpdef update(self, data):
|
||||
if isinstance(data, dict):
|
||||
data=data.items()
|
||||
for key,value in data:
|
||||
if key in self:
|
||||
self[key]=value
|
||||
|
||||
|
||||
######################################################################################################
|
||||
|
||||
|
||||
cdef register_column_class(obitype_t obitype,
|
||||
type classe,
|
||||
type python):
|
||||
"""
|
||||
Each sub class of `OBIDMS_column` needs to be registered after its declaration
|
||||
to declare its relationship with an `OBIType_t`
|
||||
"""
|
||||
global __OBIDMS_COLUMN_CLASS__
|
||||
|
||||
assert issubclass(classe,Column)
|
||||
|
||||
__OBIDMS_COLUMN_CLASS__[obitype]=(classe,python)
|
||||
32
python/obitools3/dms/dms.cfiles
Normal file
32
python/obitools3/dms/dms.cfiles
Normal file
@ -0,0 +1,32 @@
|
||||
../../../src/bloom.c
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/crc64.c
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/hashtable.c
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiblob.c
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.c
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obierrno.c
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/upperband.c
|
||||
../../../src/utils.c
|
||||
25
python/obitools3/dms/dms.pxd
Normal file
25
python/obitools3/dms/dms.pxd
Normal file
@ -0,0 +1,25 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obidms cimport OBIDMS_p
|
||||
from .capi.obitypes cimport obiversion_t, \
|
||||
obitype_t, \
|
||||
index_t
|
||||
|
||||
from .object cimport OBIObject
|
||||
|
||||
cdef dict __OBIDMS_COLUMN_CLASS__
|
||||
cdef dict __OBIDMS_VIEW_CLASS__
|
||||
|
||||
cdef class DMS(OBIObject):
|
||||
|
||||
cdef OBIDMS_p _pointer
|
||||
|
||||
@staticmethod
|
||||
cdef type get_column_class(obitype_t obitype)
|
||||
|
||||
@staticmethod
|
||||
cdef type get_python_type(obitype_t obitype)
|
||||
|
||||
cpdef close(self)
|
||||
cpdef int view_count(self)
|
||||
|
||||
152
python/obitools3/dms/dms.pyx
Normal file
152
python/obitools3/dms/dms.pyx
Normal file
@ -0,0 +1,152 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from libc.stdlib cimport free
|
||||
from cpython.list cimport PyList_Size
|
||||
|
||||
from .capi.obidms cimport obi_dms, \
|
||||
obi_close_dms, \
|
||||
obi_dms_get_full_path
|
||||
|
||||
from .capi.obitypes cimport const_char_p
|
||||
|
||||
from obitools3.utils cimport bytes2str, \
|
||||
str2bytes, \
|
||||
tobytes, \
|
||||
tostr
|
||||
|
||||
from .object cimport OBIObjectClosedInstance
|
||||
|
||||
from pathlib import Path
|
||||
|
||||
|
||||
__OBIDMS_COLUMN_CLASS__ = {}
|
||||
__OBIDMS_VIEW_CLASS__= {}
|
||||
|
||||
|
||||
cdef class DMS(OBIObject):
|
||||
|
||||
@staticmethod
|
||||
cdef type get_column_class(obitype_t obitype):
|
||||
"""
|
||||
Internal function returning the python class representing
|
||||
a column for a given obitype.
|
||||
"""
|
||||
return __OBIDMS_COLUMN_CLASS__[obitype][0]
|
||||
|
||||
@staticmethod
|
||||
cdef type get_python_type(obitype_t obitype):
|
||||
"""
|
||||
Internal function returning the python type representing
|
||||
an instance for a given obitype.
|
||||
"""
|
||||
return __OBIDMS_COLUMN_CLASS__[obitype][1]
|
||||
|
||||
@staticmethod
|
||||
cdef type get_view_class(bytes viewtype):
|
||||
return __OBIDMS_VIEW_CLASS__[viewtype]
|
||||
|
||||
|
||||
def __init__(self, object dms_name) :
|
||||
'''
|
||||
Constructor of a obitools3.dms.DMS instance.
|
||||
|
||||
@param dms_name: The name of the DMS
|
||||
@type dms_name: a `str` or a `bytes` instance
|
||||
'''
|
||||
|
||||
OBIObject.__init__(self)
|
||||
|
||||
# Declarations
|
||||
cdef bytes dms_name_b = tobytes(dms_name)
|
||||
|
||||
# Fill structure and create or open the DMS
|
||||
self._pointer = obi_dms(<const_char_p> dms_name_b)
|
||||
|
||||
if self._pointer == NULL :
|
||||
raise Exception("Failed opening or creating an OBIDMS")
|
||||
|
||||
# name property getter
|
||||
@property
|
||||
def name(self):
|
||||
"""
|
||||
Returns the name of the DMS instance
|
||||
|
||||
@rtype: bytes
|
||||
"""
|
||||
return <bytes> self._pointer.dms_name
|
||||
|
||||
def close(self) :
|
||||
"""
|
||||
Closes the DNS instance and free the associated memory
|
||||
|
||||
the `close` method is automatically called by the object destructor.
|
||||
"""
|
||||
cdef OBIDMS_p pointer = self._pointer
|
||||
|
||||
OBIObject.close(self)
|
||||
self._pointer=NULL
|
||||
|
||||
if pointer!=NULL:
|
||||
if (obi_close_dms(pointer)) < 0 :
|
||||
raise Exception("Problem closing an OBIDMS")
|
||||
else:
|
||||
raise OBIObjectClosedInstance()
|
||||
|
||||
def keys(self):
|
||||
cdef const_char_p path = obi_dms_get_full_path(self._pointer,
|
||||
b"VIEWS"
|
||||
)
|
||||
|
||||
if path==NULL:
|
||||
raise RuntimeError("Cannot retreive the Dataabase path")
|
||||
|
||||
p = Path(bytes2str(path))
|
||||
|
||||
free(path)
|
||||
|
||||
for v in p.glob("*.obiview"):
|
||||
yield str2bytes(v.stem)
|
||||
|
||||
def values(self):
|
||||
cdef bytes view_name
|
||||
|
||||
for view_name in self.keys():
|
||||
yield self.get_view(view_name)
|
||||
|
||||
def items(self):
|
||||
cdef bytes view_name
|
||||
|
||||
for view_name in self.keys():
|
||||
yield (view_name,self.get_view(view_name))
|
||||
|
||||
def __contains__(self,key):
|
||||
cdef str key_s = tostr(key)
|
||||
cdef const_char_p path = obi_dms_get_full_path(self._pointer,
|
||||
b"VIEWS"
|
||||
)
|
||||
p = Path(bytes2str(path),key_s)
|
||||
|
||||
free(path)
|
||||
|
||||
return p.with_suffix(".obiview").is_file()
|
||||
|
||||
cpdef int view_count(self):
|
||||
return PyList_Size(list(self.keys()))
|
||||
|
||||
def get_view(self):
|
||||
raise NotImplemented
|
||||
|
||||
def __len__(self):
|
||||
return self.view_count()
|
||||
|
||||
def __getitem__(self, object view_name):
|
||||
return self.get_view(view_name)
|
||||
|
||||
def __iter__(self):
|
||||
return self.keys()
|
||||
|
||||
cpdef bint is_view_writable(self, object view_name):
|
||||
raise NotImplemented
|
||||
|
||||
|
||||
|
||||
13
python/obitools3/dms/object.pxd
Normal file
13
python/obitools3/dms/object.pxd
Normal file
@ -0,0 +1,13 @@
|
||||
#cython: language_level=3
|
||||
|
||||
cdef class OBIObject:
|
||||
|
||||
cdef dict _dependent_object
|
||||
|
||||
cpdef register(self, OBIObject object)
|
||||
cpdef unregister(self, OBIObject object)
|
||||
cpdef close(self)
|
||||
|
||||
|
||||
cdef class OBIObjectClosedInstance(Exception):
|
||||
pass
|
||||
39
python/obitools3/dms/object.pyx
Normal file
39
python/obitools3/dms/object.pyx
Normal file
@ -0,0 +1,39 @@
|
||||
#cython: language_level=3
|
||||
|
||||
cdef class OBIObject:
|
||||
|
||||
cpdef register(self, OBIObject object):
|
||||
self._dependent_object[id(object)]=object
|
||||
|
||||
|
||||
cpdef unregister(self, OBIObject object):
|
||||
del self._dependent_object[id(object)]
|
||||
|
||||
|
||||
def close(self):
|
||||
cdef OBIObject object
|
||||
cdef list toclose = list(self._dependent_object.values())
|
||||
|
||||
for object in toclose:
|
||||
object.close()
|
||||
|
||||
assert len(dependent_object.values)==0
|
||||
|
||||
|
||||
def __init__(self):
|
||||
self._dependent_object={}
|
||||
|
||||
|
||||
def __dealloc__(self):
|
||||
"""
|
||||
Destructor of any OBI instance.
|
||||
|
||||
The destructor automatically calls the `close` method and
|
||||
therefore frees all the associated memory.
|
||||
"""
|
||||
|
||||
self.close()
|
||||
|
||||
|
||||
cdef class OBIObjectClosedInstance(Exception):
|
||||
pass
|
||||
60
python/obitools3/dms/view.pxd
Normal file
60
python/obitools3/dms/view.pxd
Normal file
@ -0,0 +1,60 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obiview cimport Obiview_p
|
||||
from .capi.obitypes cimport index_t, \
|
||||
obitype_t
|
||||
|
||||
from .dms cimport DMS
|
||||
from .column cimport Column
|
||||
|
||||
|
||||
|
||||
cdef class View:
|
||||
|
||||
cdef DMS _dms
|
||||
cdef Obiview_p _pointer
|
||||
|
||||
cpdef View clone(self,
|
||||
object view_name,
|
||||
object comments=*)
|
||||
|
||||
@staticmethod
|
||||
cdef View _new(DMS dms,
|
||||
bytes view_name,
|
||||
bytes comments=*)
|
||||
|
||||
@staticmethod
|
||||
cdef View _open(DMS dms,
|
||||
bytes view_name)
|
||||
|
||||
cpdef close(self)
|
||||
|
||||
cpdef get_column(self,
|
||||
object column_name)
|
||||
|
||||
cpdef delete_column(self,
|
||||
object column_name)
|
||||
|
||||
cpdef rename_column(self,
|
||||
object current_name,
|
||||
object new_name)
|
||||
|
||||
cpdef View_line_selection new_selection(self,
|
||||
list lines=*)
|
||||
|
||||
cdef class View_line_selection(list):
|
||||
|
||||
cdef View _view
|
||||
|
||||
cdef index_t* __build_binary_list__(self)
|
||||
|
||||
cpdef View materialize(self,
|
||||
object view_name,
|
||||
object comments=*)
|
||||
|
||||
cdef class View_line :
|
||||
|
||||
cdef index_t _index
|
||||
cdef View _view
|
||||
|
||||
|
||||
417
python/obitools3/dms/view.pyx
Normal file
417
python/obitools3/dms/view.pyx
Normal file
@ -0,0 +1,417 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from libc.stdlib cimport malloc
|
||||
|
||||
from .capi.obiview cimport obi_new_view, \
|
||||
obi_open_view, \
|
||||
obi_save_and_close_view, \
|
||||
obi_view_get_pointer_on_column_in_view, \
|
||||
obi_view_delete_column, \
|
||||
obi_view_create_column_alias
|
||||
|
||||
from .capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
from obitools3.utils cimport tobytes, \
|
||||
bytes2str
|
||||
|
||||
|
||||
cdef class View :
|
||||
|
||||
|
||||
def __init__(self,dms,int __internalCall__):
|
||||
|
||||
if __internalCall__!=987654:
|
||||
raise RuntimeError('OBIView constructor cannot be called directly')
|
||||
|
||||
self._dms = dms
|
||||
self._pointer = NULL
|
||||
|
||||
cpdef View clone(self,
|
||||
object view_name,
|
||||
object comments=None):
|
||||
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
cdef bytes comments_b
|
||||
cdef View view = View(self._dms,
|
||||
987654)
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
view._pointer = obi_new_view(self._pointer.dms,
|
||||
view_name_b,
|
||||
self._pointer,
|
||||
NULL,
|
||||
comments_b)
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||
% (str(self.name),
|
||||
bytes2str(view_name_b))
|
||||
)
|
||||
|
||||
return view
|
||||
|
||||
@staticmethod
|
||||
cdef View _new(DMS dms,
|
||||
bytes view_name,
|
||||
bytes comments=b""):
|
||||
|
||||
cdef View view = View(dms,
|
||||
987654) # @DuplicatedSignature
|
||||
|
||||
view._pointer = obi_new_view(dms._pointer,
|
||||
view_name,
|
||||
NULL,
|
||||
NULL,
|
||||
comments)
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot create view %s" % view_name)
|
||||
|
||||
return view
|
||||
|
||||
@staticmethod
|
||||
def new(DMS dms,
|
||||
object view_name,
|
||||
object comments=None):
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
cdef bytes comments_b
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
|
||||
return View._new(dms,
|
||||
view_name_b,
|
||||
comments_b)
|
||||
|
||||
|
||||
@staticmethod
|
||||
cdef View _open(DMS dms,
|
||||
bytes view_name):
|
||||
|
||||
cdef View view = View(dms,
|
||||
987654) # @DuplicatedSignature
|
||||
|
||||
view._pointer = obi_open_view(dms._pointer,
|
||||
view_name)
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name))
|
||||
|
||||
return view
|
||||
|
||||
@staticmethod
|
||||
def open(DMS dms, # @ReservedAssignment
|
||||
object view_name):
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
|
||||
return View._open(dms,view_name_b)
|
||||
|
||||
cpdef close(self):
|
||||
if (obi_save_and_close_view(self._pointer) < 0) :
|
||||
raise Exception("Problem closing view %s" %
|
||||
bytes2str(self.name))
|
||||
|
||||
def __dealloc__(self):
|
||||
self.close()
|
||||
|
||||
def __repr__(self) :
|
||||
cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
|
||||
comments = str(self.comments),
|
||||
line_count = self.line_count)
|
||||
|
||||
#for column_name in self._columns :
|
||||
# s = s + repr(self._columns[column_name]) + '\n'
|
||||
|
||||
return s
|
||||
|
||||
cpdef get_column(self,
|
||||
object column_name):
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
cdef OBIDMS_column_p* column_pp
|
||||
cdef OBIDMS_column_p column_p
|
||||
cdef Column column
|
||||
cdef obitype_t column_type
|
||||
|
||||
column_pp = obi_view_get_pointer_on_column_in_view(self._pointer,
|
||||
column_name_b)
|
||||
|
||||
if column_pp == NULL:
|
||||
raise KeyError("Cannot access to column %s in view %s" % (
|
||||
bytes2str(column_name_b),
|
||||
bytes2str(self.name)
|
||||
))
|
||||
|
||||
column_p = column_pp[0]
|
||||
column_type = column_p.header.returned_data_type
|
||||
|
||||
column = DMS.get_column_class(column_type)(self)
|
||||
column._pointer = column_pp
|
||||
|
||||
return column
|
||||
|
||||
cpdef delete_column(self,
|
||||
object column_name) :
|
||||
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
|
||||
if obi_view_delete_column(self._pointer, column_name_b) < 0 :
|
||||
raise Exception("Problem deleting column %s from a view",
|
||||
bytes2str(column_name_b))
|
||||
|
||||
|
||||
|
||||
cpdef rename_column(self,
|
||||
object current_name,
|
||||
object new_name):
|
||||
|
||||
cdef Column column
|
||||
cdef bytes current_name_b = tobytes(current_name)
|
||||
cdef bytes new_name_b = tobytes(new_name)
|
||||
|
||||
if (obi_view_create_column_alias(self._pointer,
|
||||
tobytes(current_name_b),
|
||||
tobytes(new_name_b)) < 0) :
|
||||
raise Exception("Problem in renaming column %s to %s" % (
|
||||
bytes2str(current_name_b),
|
||||
bytes2str(new_name_b)))
|
||||
|
||||
|
||||
cpdef View_line_selection new_selection(self,list lines=None):
|
||||
return View_line_selection(self,lines)
|
||||
|
||||
def __iter__(self):
|
||||
# Iteration on each line of all columns
|
||||
|
||||
# Declarations
|
||||
cdef index_t line_nb
|
||||
cdef View_line line
|
||||
|
||||
# Yield each line
|
||||
for line_nb in range(self.line_count) :
|
||||
line = self[line_nb]
|
||||
yield line
|
||||
|
||||
|
||||
def __getitem__(self, object item) :
|
||||
if type(item) == str :
|
||||
return (self._columns)[item]
|
||||
elif type(item) == int :
|
||||
return View_line(self, item)
|
||||
|
||||
|
||||
def __contains__(self, str column_name):
|
||||
return (column_name in self._columns)
|
||||
|
||||
|
||||
def __len__(self):
|
||||
return(self.line_count)
|
||||
|
||||
|
||||
def __str__(self) :
|
||||
cdef View_line line
|
||||
cdef str to_print
|
||||
to_print = ""
|
||||
for line in self :
|
||||
to_print = to_print + str(line) + "\n"
|
||||
return to_print
|
||||
|
||||
|
||||
@property
|
||||
def dms(self):
|
||||
return self._dms
|
||||
|
||||
# line_count property getter
|
||||
@property
|
||||
def line_count(self):
|
||||
return self._pointer.infos.line_count
|
||||
|
||||
# name property getter
|
||||
@property
|
||||
def name(self):
|
||||
return <bytes> self._pointer.infos.name
|
||||
|
||||
# view type property getter
|
||||
@property
|
||||
def type(self): # @ReservedAssignment
|
||||
return bytes2str(self._pointer.infos.view_type)
|
||||
|
||||
# comments property getter
|
||||
@property
|
||||
def comments(self):
|
||||
return <bytes> self._pointer.infos.comments
|
||||
# TODO setter that concatenates new comments?
|
||||
|
||||
|
||||
cdef class View_line_selection(list):
|
||||
|
||||
def __init__(self, View view, lines=None) :
|
||||
if view._pointer == NULL:
|
||||
raise Exception("Error: trying to create a line selection with an invalidated view")
|
||||
self._view = view
|
||||
self._view_name = view.name
|
||||
|
||||
if lines is not None:
|
||||
self.extend(lines)
|
||||
|
||||
def extend(self, iterable):
|
||||
cdef index_t i
|
||||
cdef index_t max_i = self._view.line_count
|
||||
|
||||
for i in iterable:
|
||||
if i > max_i:
|
||||
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||
(i,
|
||||
max_i,
|
||||
self._view_name)
|
||||
)
|
||||
list.append(self,i)
|
||||
|
||||
def append(self, index_t idx) :
|
||||
if idx >= self._view.line_count :
|
||||
raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||
(idx,
|
||||
self._view.line_count,
|
||||
bytes2str(self.name))
|
||||
)
|
||||
list.append(self,idx)
|
||||
|
||||
cdef index_t* __build_binary_list__(self):
|
||||
cdef index_t* line_selection_p = NULL
|
||||
cdef int i
|
||||
cdef size_t l_selection = len(self)
|
||||
|
||||
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
|
||||
for i in range(l_selection) :
|
||||
line_selection_p[i] = self[i]
|
||||
line_selection_p[l_selection] = -1 # flagging the end of the array
|
||||
|
||||
return line_selection_p
|
||||
|
||||
cpdef View materialize(self,
|
||||
object view_name,
|
||||
object comments=""):
|
||||
|
||||
cdef View view = View(987654)
|
||||
cdef bytes view_name_b=tobytes(view_name)
|
||||
|
||||
view._pointer = obi_new_view(self._view._pointer.dms,
|
||||
view_name_b,
|
||||
self._view._pointer,
|
||||
self.__build_binary_list__(),
|
||||
tobytes(comments))
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||
% (str(self.name),
|
||||
view_name)
|
||||
)
|
||||
|
||||
return view
|
||||
|
||||
|
||||
cdef class View_line :
|
||||
|
||||
def __init__(self, View view, index_t line_nb) :
|
||||
self._index = line_nb
|
||||
self._view = view
|
||||
|
||||
def __getitem__(self, str column_name) :
|
||||
return ((self._view)._columns)[column_name][self._index]
|
||||
|
||||
# def __setitem__(self, str column_name, object value):
|
||||
# # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
|
||||
# # TODO OBI_QUAL ?
|
||||
# cdef type value_type
|
||||
# cdef str value_obitype
|
||||
# cdef bytes value_b
|
||||
#
|
||||
# if column_name not in self._view :
|
||||
# if value == None :
|
||||
# raise Exception("Trying to create a column from a None value (can't guess type)")
|
||||
# value_type = type(value)
|
||||
# if value_type == int :
|
||||
# value_obitype = 'OBI_INT'
|
||||
# elif value_type == float :
|
||||
# value_obitype = 'OBI_FLOAT'
|
||||
# elif value_type == bool :
|
||||
# value_obitype = 'OBI_BOOL'
|
||||
# elif value_type == str or value_type == bytes :
|
||||
# if value_type == str :
|
||||
# value_b = str2bytes(value)
|
||||
# else :
|
||||
# value_b = value
|
||||
# if only_ATGC(value_b) : # TODO detect IUPAC
|
||||
# value_obitype = 'OBI_SEQ'
|
||||
# elif len(value) == 1 :
|
||||
# value_obitype = 'OBI_CHAR'
|
||||
# elif (len(value) > 1) :
|
||||
# value_obitype = 'OBI_STR'
|
||||
# else :
|
||||
# raise Exception("Could not guess the type of a value to create a new column")
|
||||
# self._view.add_column(column_name, type=value_obitype)
|
||||
#
|
||||
# (((self._view)._columns)[column_name]).set_line(self._index, value)
|
||||
#
|
||||
# def __iter__(self):
|
||||
# for column_name in ((self._view)._columns) :
|
||||
# yield column_name
|
||||
#
|
||||
# def __contains__(self, str column_name):
|
||||
# return (column_name in self._view._columns)
|
||||
|
||||
def __repr__(self):
|
||||
cdef dict line
|
||||
cdef str column_name
|
||||
line = {}
|
||||
# for column_name in self._view._columns :
|
||||
# line[column_name] = self[column_name]
|
||||
return str(line)
|
||||
|
||||
|
||||
# cpdef dict get_view_infos(self, str view_name) :
|
||||
#
|
||||
# cdef Obiview_infos_p view_infos_p
|
||||
# cdef dict view_infos_d
|
||||
# cdef Alias_column_pair_p column_refs
|
||||
# cdef int i, j
|
||||
# cdef str column_name
|
||||
#
|
||||
# view_infos_p = obi_view_map_file(self._pointer,
|
||||
# tobytes(view_name))
|
||||
# view_infos_d = {}
|
||||
# view_infos_d["name"] = bytes2str(view_infos_p.name)
|
||||
# view_infos_d["comments"] = bytes2str(view_infos_p.comments)
|
||||
# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
|
||||
# view_infos_d["column_count"] = <int> view_infos_p.column_count
|
||||
# view_infos_d["line_count"] = <int> view_infos_p.line_count
|
||||
# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
|
||||
# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
|
||||
# if (view_infos_p.all_lines) :
|
||||
# view_infos_d["line_selection"] = None
|
||||
# else :
|
||||
# view_infos_d["line_selection"] = {}
|
||||
# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
|
||||
# view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
|
||||
# view_infos_d["column_references"] = {}
|
||||
# column_references = view_infos_p.column_references
|
||||
# for j in range(view_infos_d["column_count"]) :
|
||||
# column_name = bytes2str((column_references[j]).alias)
|
||||
# view_infos_d["column_references"][column_name] = {}
|
||||
# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
|
||||
# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
|
||||
#
|
||||
# obi_view_unmap_file(self._pointer, view_infos_p)
|
||||
#
|
||||
# return view_infos_d
|
||||
|
||||
|
||||
3
python/obitools3/dms/view/__init__.py
Normal file
3
python/obitools3/dms/view/__init__.py
Normal file
@ -0,0 +1,3 @@
|
||||
from .view import View # @UnresolvedImport
|
||||
from .view import Line_selection # @UnresolvedImport
|
||||
from .view import Line # @UnresolvedImport
|
||||
44
python/obitools3/dms/view/view.pxd
Normal file
44
python/obitools3/dms/view/view.pxd
Normal file
@ -0,0 +1,44 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..capi.obiview cimport Obiview_p
|
||||
from ..capi.obitypes cimport index_t, \
|
||||
obitype_t
|
||||
|
||||
from ..object cimport OBIObject
|
||||
from ..dms cimport DMS
|
||||
|
||||
from ..column.column cimport Column
|
||||
|
||||
|
||||
|
||||
cdef class View(OBIObject):
|
||||
|
||||
cdef DMS _dms
|
||||
cdef Obiview_p _pointer
|
||||
|
||||
cpdef delete_column(self,
|
||||
object column_name)
|
||||
|
||||
cpdef rename_column(self,
|
||||
object current_name,
|
||||
object new_name)
|
||||
|
||||
cpdef View_line_selection new_selection(self,
|
||||
list lines=*)
|
||||
|
||||
cdef class Line_selection(list):
|
||||
|
||||
cdef View _view
|
||||
|
||||
cdef index_t* __build_binary_list__(self)
|
||||
|
||||
cpdef View materialize(self,
|
||||
object view_name,
|
||||
object comments=*)
|
||||
|
||||
cdef class Line :
|
||||
|
||||
cdef index_t _index
|
||||
cdef View _view
|
||||
|
||||
|
||||
443
python/obitools3/dms/view/view.pyx
Normal file
443
python/obitools3/dms/view/view.pyx
Normal file
@ -0,0 +1,443 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from libc.stdlib cimport malloc
|
||||
|
||||
from ..capi.obiview cimport Alias_column_pair_p, \
|
||||
obi_new_view, \
|
||||
obi_open_view, \
|
||||
obi_save_and_close_view, \
|
||||
obi_view_get_pointer_on_column_in_view, \
|
||||
obi_view_delete_column, \
|
||||
obi_view_create_column_alias
|
||||
|
||||
from ..capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
from .dms cimport __OBIDMS_VIEW_CLASS__
|
||||
|
||||
from obitools3.utils cimport tobytes, \
|
||||
bytes2str
|
||||
|
||||
from ..object cimport OBIObjectClosedInstance
|
||||
|
||||
|
||||
cdef class View(OBIObject) :
|
||||
|
||||
|
||||
def __init__(self,dms,int __internalCall__):
|
||||
|
||||
OBIObject.__init__(self)
|
||||
|
||||
if __internalCall__!=987654:
|
||||
raise RuntimeError('OBIView constructor cannot be called directly')
|
||||
|
||||
self._dms = dms
|
||||
self._pointer = NULL
|
||||
|
||||
def clone(self,
|
||||
object view_name,
|
||||
object comments=None):
|
||||
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
cdef bytes comments_b
|
||||
cdef View view = View(self._dms,
|
||||
987654)
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
view._pointer = obi_new_view(self._pointer.dms,
|
||||
view_name_b,
|
||||
self._pointer,
|
||||
NULL,
|
||||
comments_b)
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||
% (str(self.name),
|
||||
bytes2str(view_name_b))
|
||||
)
|
||||
|
||||
self._dms.register(view)
|
||||
|
||||
return view
|
||||
|
||||
@staticmethod
|
||||
def new(DMS dms,
|
||||
object view_name,
|
||||
object comments=None):
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
cdef bytes comments_b
|
||||
cdef str message
|
||||
|
||||
cdef View view = View(dms,
|
||||
987654) # @DuplicatedSignature
|
||||
|
||||
if comments is not None:
|
||||
comments_b = tobytes(comments)
|
||||
else:
|
||||
comments_b = b''
|
||||
|
||||
view._pointer = obi_new_view(dms._pointer,
|
||||
view_name_b,
|
||||
NULL,
|
||||
NULL,
|
||||
comments_b)
|
||||
|
||||
if view._pointer == NULL :
|
||||
message = "Error : Cannot create view %s" % bytes2str(view_name_b)
|
||||
raise RuntimeError(message)
|
||||
|
||||
dms.register(view)
|
||||
|
||||
return view
|
||||
|
||||
@staticmethod
|
||||
def open(DMS dms, # @ReservedAssignment
|
||||
object view_name):
|
||||
|
||||
cdef bytes view_name_b = tobytes(view_name)
|
||||
cdef View view = View(dms,
|
||||
987654) # @DuplicatedSignature
|
||||
|
||||
view._pointer = obi_open_view(dms._pointer,
|
||||
view_name_b)
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot open view %s" % bytes2str(view_name_b))
|
||||
|
||||
dms.register(view)
|
||||
|
||||
return view
|
||||
|
||||
def close(self):
|
||||
cdef Obiview_p pointer = self._pointer
|
||||
|
||||
if (pointer != NULL):
|
||||
self._dms.unregister(self)
|
||||
OBIObject.close(self)
|
||||
|
||||
self._pointer = NULL
|
||||
|
||||
if obi_save_and_close_view(self._pointer) < 0 :
|
||||
raise Exception("Problem closing view %s" %
|
||||
bytes2str(self.name))
|
||||
else:
|
||||
raise OBIObjectClosedInstance()
|
||||
|
||||
|
||||
def __repr__(self) :
|
||||
cdef str s = "{name:s}\n{comments:s}\n{line_count:d} lines\n".format(name = str(self.name),
|
||||
comments = str(self.comments),
|
||||
line_count = self.line_count)
|
||||
|
||||
#for column_name in self._columns :
|
||||
# s = s + repr(self._columns[column_name]) + '\n'
|
||||
|
||||
return s
|
||||
|
||||
def keys(self):
|
||||
cdef int i
|
||||
cdef int nb_column = self._pointer.infos.column_count
|
||||
cdef Alias_column_pair_p column_p = self._pointer.infos.column_references
|
||||
|
||||
for i in range(nb_column) :
|
||||
col_alias = bytes2str(self._pointer.infos.column_references[i].alias)
|
||||
yield col_alias
|
||||
|
||||
def get_column(self,
|
||||
object column_name):
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
cdef OBIDMS_column_p* column_pp
|
||||
cdef OBIDMS_column_p column_p
|
||||
cdef Column column
|
||||
cdef obitype_t column_type
|
||||
|
||||
column_pp = obi_view_get_pointer_on_column_in_view(self._pointer,
|
||||
column_name_b)
|
||||
|
||||
if column_pp == NULL:
|
||||
raise KeyError("Cannot access to column %s in view %s" % (
|
||||
bytes2str(column_name_b),
|
||||
bytes2str(self.name)
|
||||
))
|
||||
|
||||
column_p = column_pp[0]
|
||||
column_type = column_p.header.returned_data_type
|
||||
|
||||
column = DMS.get_column_class(column_type)(self)
|
||||
column._pointer = column_pp
|
||||
|
||||
return column
|
||||
|
||||
cpdef delete_column(self,
|
||||
object column_name) :
|
||||
|
||||
cdef bytes column_name_b = tobytes(column_name)
|
||||
|
||||
if obi_view_delete_column(self._pointer, column_name_b) < 0 :
|
||||
raise Exception("Problem deleting column %s from a view",
|
||||
bytes2str(column_name_b))
|
||||
|
||||
|
||||
|
||||
cpdef rename_column(self,
|
||||
object current_name,
|
||||
object new_name):
|
||||
|
||||
cdef Column column
|
||||
cdef bytes current_name_b = tobytes(current_name)
|
||||
cdef bytes new_name_b = tobytes(new_name)
|
||||
|
||||
if (obi_view_create_column_alias(self._pointer,
|
||||
tobytes(current_name_b),
|
||||
tobytes(new_name_b)) < 0) :
|
||||
raise Exception("Problem in renaming column %s to %s" % (
|
||||
bytes2str(current_name_b),
|
||||
bytes2str(new_name_b)))
|
||||
|
||||
|
||||
cpdef View_line_selection new_selection(self,list lines=None):
|
||||
return View_line_selection(self,lines)
|
||||
|
||||
def __iter__(self):
|
||||
# Iteration on each line of all columns
|
||||
|
||||
# Declarations
|
||||
cdef index_t line_nb
|
||||
cdef View_line line
|
||||
|
||||
# Yield each line
|
||||
for line_nb in range(self.line_count) :
|
||||
line = self[line_nb]
|
||||
yield line
|
||||
|
||||
|
||||
def __getitem__(self, object item) :
|
||||
if type(item) == str :
|
||||
return (self._columns)[item]
|
||||
elif type(item) == int :
|
||||
return View_line(self, item)
|
||||
|
||||
|
||||
def __contains__(self, str column_name):
|
||||
return (column_name in self._columns)
|
||||
|
||||
|
||||
def __len__(self):
|
||||
return(self.line_count)
|
||||
|
||||
|
||||
def __str__(self) :
|
||||
cdef View_line line
|
||||
cdef str to_print
|
||||
to_print = ""
|
||||
for line in self :
|
||||
to_print = to_print + str(line) + "\n"
|
||||
return to_print
|
||||
|
||||
|
||||
@property
|
||||
def dms(self):
|
||||
return self._dms
|
||||
|
||||
# line_count property getter
|
||||
@property
|
||||
def line_count(self):
|
||||
return self._pointer.infos.line_count
|
||||
|
||||
# name property getter
|
||||
@property
|
||||
def name(self):
|
||||
return <bytes> self._pointer.infos.name
|
||||
|
||||
# view type property getter
|
||||
@property
|
||||
def type(self): # @ReservedAssignment
|
||||
return <bytes> self._pointer.infos.view_type
|
||||
|
||||
# comments property getter
|
||||
@property
|
||||
def comments(self):
|
||||
return <bytes> self._pointer.infos.comments
|
||||
# TODO setter that concatenates new comments?
|
||||
|
||||
|
||||
cdef class Line_selection(list):
|
||||
|
||||
def __init__(self, View view, lines=None) :
|
||||
if view._pointer == NULL:
|
||||
raise Exception("Error: trying to create a line selection with an invalidated view")
|
||||
self._view = view
|
||||
self._view_name = view.name
|
||||
|
||||
if lines is not None:
|
||||
self.extend(lines)
|
||||
|
||||
def extend(self, iterable):
|
||||
cdef index_t i
|
||||
cdef index_t max_i = self._view.line_count
|
||||
|
||||
for i in iterable:
|
||||
if i > max_i:
|
||||
raise RuntimeError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||
(i,
|
||||
max_i,
|
||||
self._view_name)
|
||||
)
|
||||
list.append(self,i)
|
||||
|
||||
def append(self, index_t idx) :
|
||||
if idx >= self._view.line_count :
|
||||
raise IndexError("Error: trying to select line %d beyond the line count %d of view %s" %
|
||||
(idx,
|
||||
self._view.line_count,
|
||||
bytes2str(self.name))
|
||||
)
|
||||
list.append(self,idx)
|
||||
|
||||
cdef index_t* __build_binary_list__(self):
|
||||
cdef index_t* line_selection_p = NULL
|
||||
cdef int i
|
||||
cdef size_t l_selection = len(self)
|
||||
|
||||
line_selection_p = <index_t*> malloc((l_selection + 1) * sizeof(index_t)) # +1 for the -1 flagging the end of the array
|
||||
for i in range(l_selection) :
|
||||
line_selection_p[i] = self[i]
|
||||
line_selection_p[l_selection] = -1 # flagging the end of the array
|
||||
|
||||
return line_selection_p
|
||||
|
||||
cpdef View materialize(self,
|
||||
object view_name,
|
||||
object comments=""):
|
||||
|
||||
cdef View view = View(987654)
|
||||
cdef bytes view_name_b=tobytes(view_name)
|
||||
|
||||
view._pointer = obi_new_view(self._view._pointer.dms,
|
||||
view_name_b,
|
||||
self._view._pointer,
|
||||
self.__build_binary_list__(),
|
||||
tobytes(comments))
|
||||
|
||||
if view._pointer == NULL :
|
||||
raise RuntimeError("Error : Cannot clone view %s into view %s"
|
||||
% (str(self.name),
|
||||
view_name)
|
||||
)
|
||||
|
||||
return view
|
||||
|
||||
|
||||
cdef class Line :
|
||||
|
||||
def __init__(self, View view, index_t line_nb) :
|
||||
self._index = line_nb
|
||||
self._view = view
|
||||
|
||||
def __getitem__(self, str column_name) :
|
||||
return ((self._view)._columns)[column_name][self._index]
|
||||
|
||||
# def __setitem__(self, str column_name, object value):
|
||||
# # TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
|
||||
# # TODO OBI_QUAL ?
|
||||
# cdef type value_type
|
||||
# cdef str value_obitype
|
||||
# cdef bytes value_b
|
||||
#
|
||||
# if column_name not in self._view :
|
||||
# if value == None :
|
||||
# raise Exception("Trying to create a column from a None value (can't guess type)")
|
||||
# value_type = type(value)
|
||||
# if value_type == int :
|
||||
# value_obitype = 'OBI_INT'
|
||||
# elif value_type == float :
|
||||
# value_obitype = 'OBI_FLOAT'
|
||||
# elif value_type == bool :
|
||||
# value_obitype = 'OBI_BOOL'
|
||||
# elif value_type == str or value_type == bytes :
|
||||
# if value_type == str :
|
||||
# value_b = str2bytes(value)
|
||||
# else :
|
||||
# value_b = value
|
||||
# if only_ATGC(value_b) : # TODO detect IUPAC
|
||||
# value_obitype = 'OBI_SEQ'
|
||||
# elif len(value) == 1 :
|
||||
# value_obitype = 'OBI_CHAR'
|
||||
# elif (len(value) > 1) :
|
||||
# value_obitype = 'OBI_STR'
|
||||
# else :
|
||||
# raise Exception("Could not guess the type of a value to create a new column")
|
||||
# self._view.add_column(column_name, type=value_obitype)
|
||||
#
|
||||
# (((self._view)._columns)[column_name]).set_line(self._index, value)
|
||||
#
|
||||
# def __iter__(self):
|
||||
# for column_name in ((self._view)._columns) :
|
||||
# yield column_name
|
||||
#
|
||||
# def __contains__(self, str column_name):
|
||||
# return (column_name in self._view._columns)
|
||||
|
||||
def __repr__(self):
|
||||
cdef dict line
|
||||
cdef str column_name
|
||||
line = {}
|
||||
# for column_name in self._view._columns :
|
||||
# line[column_name] = self[column_name]
|
||||
return str(line)
|
||||
|
||||
|
||||
# cpdef dict get_view_infos(self, str view_name) :
|
||||
#
|
||||
# cdef Obiview_infos_p view_infos_p
|
||||
# cdef dict view_infos_d
|
||||
# cdef Alias_column_pair_p column_refs
|
||||
# cdef int i, j
|
||||
# cdef str column_name
|
||||
#
|
||||
# view_infos_p = obi_view_map_file(self._pointer,
|
||||
# tobytes(view_name))
|
||||
# view_infos_d = {}
|
||||
# view_infos_d["name"] = bytes2str(view_infos_p.name)
|
||||
# view_infos_d["comments"] = bytes2str(view_infos_p.comments)
|
||||
# view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
|
||||
# view_infos_d["column_count"] = <int> view_infos_p.column_count
|
||||
# view_infos_d["line_count"] = <int> view_infos_p.line_count
|
||||
# view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
|
||||
# view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
|
||||
# if (view_infos_p.all_lines) :
|
||||
# view_infos_d["line_selection"] = None
|
||||
# else :
|
||||
# view_infos_d["line_selection"] = {}
|
||||
# view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
|
||||
# view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
|
||||
# view_infos_d["column_references"] = {}
|
||||
# column_references = view_infos_p.column_references
|
||||
# for j in range(view_infos_d["column_count"]) :
|
||||
# column_name = bytes2str((column_references[j]).alias)
|
||||
# view_infos_d["column_references"][column_name] = {}
|
||||
# view_infos_d["column_references"][column_name]["original_name"] = bytes2str((column_references[j]).column_refs.column_name)
|
||||
# view_infos_d["column_references"][column_name]["version"] = (column_references[j]).column_refs.version
|
||||
#
|
||||
# obi_view_unmap_file(self._pointer, view_infos_p)
|
||||
#
|
||||
# return view_infos_d
|
||||
|
||||
|
||||
cdef register_view_class(bytes viewtype,
|
||||
type classe):
|
||||
"""
|
||||
Each sub class of `dms.View` needs to be registered after its declaration
|
||||
to declare its relationship with an `OBIType_t`
|
||||
"""
|
||||
global __OBIDMS_VIEW_CLASS__
|
||||
|
||||
assert issubclass(classe,View)
|
||||
|
||||
__OBIDMS_VIEW_CLASS__[viewtype]=classe
|
||||
|
||||
@ -6,8 +6,12 @@ Created on 30 mars 2016
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
#from obitools3.dms._obiseq cimport OBI_Seq
|
||||
|
||||
def fastaIterator(lineiterator, int buffersize=100000000):
|
||||
|
||||
def fastaIterator(lineiterator,
|
||||
int buffersize=100000000
|
||||
):
|
||||
cdef LineBuffer lb
|
||||
cdef str ident
|
||||
cdef str definition
|
||||
@ -15,6 +19,7 @@ def fastaIterator(lineiterator, int buffersize=100000000):
|
||||
cdef list s
|
||||
cdef bytes sequence
|
||||
cdef bytes quality
|
||||
# cdef OBI_Seq seq
|
||||
|
||||
if isinstance(lineiterator,(str,bytes)):
|
||||
lineiterator=uopen(lineiterator)
|
||||
@ -41,7 +46,60 @@ def fastaIterator(lineiterator, int buffersize=100000000):
|
||||
|
||||
sequence = b"".join(s)
|
||||
quality = None
|
||||
|
||||
|
||||
|
||||
# seq = OBI_Seq(id,
|
||||
# sequence,
|
||||
# definition,
|
||||
# tags=tags,
|
||||
# )
|
||||
yield { "id" : ident,
|
||||
"definition" : definition,
|
||||
"sequence" : sequence,
|
||||
"quality" : quality,
|
||||
"tags" : tags,
|
||||
"annotation" : {}
|
||||
}
|
||||
|
||||
|
||||
def fastaNucIterator(lineiterator, int buffersize=100000000):
|
||||
cdef LineBuffer lb
|
||||
cdef str ident
|
||||
cdef str definition
|
||||
cdef dict tags
|
||||
cdef list s
|
||||
cdef bytes sequence
|
||||
cdef bytes quality
|
||||
# cdef OBI_Seq seq
|
||||
|
||||
if isinstance(lineiterator,(str,bytes)):
|
||||
lineiterator=uopen(lineiterator)
|
||||
|
||||
if isinstance(lineiterator, LineBuffer):
|
||||
lb=lineiterator
|
||||
else:
|
||||
lb=LineBuffer(lineiterator,buffersize)
|
||||
|
||||
i = iter(lb)
|
||||
line = next(i)
|
||||
|
||||
while True:
|
||||
ident,tags,definition = parseHeader(line)
|
||||
s = []
|
||||
line = next(i)
|
||||
|
||||
try:
|
||||
while line[0]!='>':
|
||||
s.append(str2bytes(line)[0:-1])
|
||||
line = next(i)
|
||||
except StopIteration:
|
||||
pass
|
||||
|
||||
sequence = b"".join(s)
|
||||
quality = None
|
||||
|
||||
|
||||
# seq =
|
||||
yield { "id" : ident,
|
||||
"definition" : definition,
|
||||
"sequence" : sequence,
|
||||
|
||||
@ -2,5 +2,6 @@
|
||||
|
||||
|
||||
cdef bytes str2bytes(str string)
|
||||
|
||||
cdef str bytes2str(bytes string)
|
||||
cdef str bytes2str(bytes string)
|
||||
cdef bytes tobytes(object string)
|
||||
cdef str tostr(object string)
|
||||
@ -1,6 +1,5 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
cdef bytes str2bytes(str string):
|
||||
"""
|
||||
Short cut to convert ascii encoded python string (str) to bytes
|
||||
@ -24,3 +23,32 @@ cdef str bytes2str(bytes string):
|
||||
"""
|
||||
return string.decode('ascii')
|
||||
|
||||
cdef bytes tobytes(object string):
|
||||
"""
|
||||
Short cut to convert ascii encoded string (str or bytes) to bytes
|
||||
which can be easily converted to C-strings.
|
||||
|
||||
@param string: the python string to be converted.
|
||||
@type string: bytes or str
|
||||
@return a transcoded string
|
||||
@rtype: bytes
|
||||
"""
|
||||
if isinstance(string, bytes):
|
||||
return string
|
||||
return str2bytes(string)
|
||||
|
||||
|
||||
cdef str tostr(object string):
|
||||
"""
|
||||
Short cut to convert ascii encoded string (str or bytes) to bytes
|
||||
which can be easily converted to C-strings.
|
||||
|
||||
@param string: the python string to be converted.
|
||||
@type string: bytes or str
|
||||
@return a transcoded string
|
||||
@rtype: bytes
|
||||
"""
|
||||
if isinstance(string, str):
|
||||
return string
|
||||
return bytes2str(string)
|
||||
|
||||
|
||||
BIN
python/obitools3/version.pyc
Normal file
BIN
python/obitools3/version.pyc
Normal file
Binary file not shown.
@ -865,7 +865,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
obidebug(1, "\nCan't create column because of empty column name");
|
||||
return NULL;
|
||||
}
|
||||
if ((data_type < 1) || (data_type > 8)) // TODO check in more robust way
|
||||
if ((data_type < 1) || (data_type > 8)) // TODO check in more robust way and use macro define somewhere
|
||||
{
|
||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nCan't create column because of invalid data type");
|
||||
@ -891,7 +891,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
// Build the indexer name if needed
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
|
||||
{
|
||||
if ((indexer_name == NULL) || (strcmp(indexer_name, "") == 0))
|
||||
if ((indexer_name == NULL) || (*indexer_name == 0))
|
||||
{
|
||||
final_indexer_name = obi_build_indexer_name(column_name, version_number);
|
||||
if (final_indexer_name == NULL)
|
||||
|
||||
@ -112,18 +112,22 @@ typedef struct OBIDMS_column_header {
|
||||
* creating, opening or cloning an OBIDMS column.
|
||||
*/
|
||||
typedef struct OBIDMS_column {
|
||||
OBIDMS_p dms; /**< A pointer to the OBIDMS structure to which the column belongs.
|
||||
OBIDMS_p dms; /**< A pointer to the OBIDMS structure to
|
||||
* which the column belongs.
|
||||
*/
|
||||
OBIDMS_column_directory_p column_directory; /**< A pointer to the OBIDMS column directory structure to which the column belongs.
|
||||
OBIDMS_column_directory_p column_directory; /**< A pointer to the OBIDMS column directory
|
||||
* structure to which the column belongs.
|
||||
*/
|
||||
OBIDMS_column_header_p header; /**< A pointer to the header of the column.
|
||||
*/
|
||||
Obi_indexer_p indexer; /**< A pointer to the blob indexer associated with the column if there is one.
|
||||
Obi_indexer_p indexer; /**< A pointer to the blob indexer associated
|
||||
* with the column if there is one.
|
||||
*/
|
||||
void* data; /**< A `void` pointer to the beginning of the data.
|
||||
*
|
||||
* @warning Never use this member directly outside of the code of the
|
||||
* low level functions of the OBIDMS.
|
||||
* @warning Never use this member directly outside
|
||||
* of the code of the low level functions
|
||||
* of the OBIDMS.
|
||||
*/
|
||||
bool writable; /**< Indicates if the column is writable or not.
|
||||
* - `true` the column is writable
|
||||
@ -132,7 +136,8 @@ typedef struct OBIDMS_column {
|
||||
* A column is writable only by its creator
|
||||
* until it closes it.
|
||||
*/
|
||||
size_t counter; /**< Indicates by how many threads/programs (TODO) the column is used.
|
||||
size_t counter; /**< Indicates by how many threads/programs
|
||||
* (TODO) the column is used.
|
||||
*/
|
||||
} OBIDMS_column_t, *OBIDMS_column_p;
|
||||
|
||||
|
||||
@ -12,6 +12,7 @@
|
||||
#include "obilittlebigman.h"
|
||||
|
||||
|
||||
// TODO this function does not seem to work properly
|
||||
bool obi_is_little_endian() {
|
||||
union { int entier;
|
||||
char caractere[4] ;
|
||||
|
||||
Reference in New Issue
Block a user