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munging.py

Source:munging.py

1# coding=utf-82"""3Munge original data together to a more cohesive and uniform shape.4You probably want to run bootstrap_braincode_dir (at the end of this file).5This filters and puts together data for our two datasets (CB1 and T1):6  - in the strawlab central repository (images, templates and segmentations),7  - in Florian's HDF5 files (to find which images go into which dataset, CB1 or T1),8  - in Florian's CSV database dumps (linking images to driver lines).9All these also keep the original brainbase database ids for provenance.10"""11from __future__ import print_function, division12import glob13import sys14import os15import os.path as op16import shutil17from collections import namedtuple18from functools import partial19from itertools import product20from textwrap import dedent21import h5py22import nrrd23import numpy as np24import pandas as pd25from py_amira_file_reader.read_amira import read_amira26from braincode.revisions.config import braincode_dir, BRAINCODE_PACKAGE_DIR, STRAWLAB_ROOT27from braincode.revisions.images import VoxelLabels28# We probably should manage to remove these two imports.29# So ultimately we do not depend on Florian's HDF5s and CSVs.30from braincode.CAUTION.copy_florians_data import my_read_csv31from braincode.util import ExpressionDataset, get_all_datasets, get_all_neuropils, ensure_dir32# --- Original files and configurations33# Where original data and brainbase database query dumps are34# Downsample sizes From [T1|CB1]/.../Antennal_lobe_clusterimage.am35# At the moment the HDF5 files are read using braincode.util36_Originals = namedtuple('Originals', ['template',37                                      'amiras',38                                      'test_amira',39                                      'regions',40                                      'downsampled_size'])41_T1_ORIGINALS = _Originals(42    template=op.join(STRAWLAB_ROOT, 'brainwarp', 'T1V2template', 'T1.am'),43    amiras=op.join(STRAWLAB_ROOT, 'bbweb', 'internal', 'Data', 'channelimages'),44    test_amira='TP10100501L33Sum01.am',45    regions=op.join(STRAWLAB_ROOT, 'Laszlo', 'T1_Ito_new'),46    downsampled_size=(154, 154, 41))47_CB1_ORIGINALS = _Originals(48    template=op.join(STRAWLAB_ROOT, 'brainwarp', 'CB1_template', 'latest',49                     'Merged_highcontrast_BCimpr_final_notcompressed.am'),50    amiras=op.join(STRAWLAB_ROOT, 'bbweb', 'internal', 'Data', 'channelimages'),51    test_amira='CB1_GMR_9C12_AE_01_29-fA01b_C100120_20100120125741015_02_warp_m0g80c8e1e-1x26r301.am',52    regions=op.join(STRAWLAB_ROOT, 'Laszlo', 'CB1_Ito', 'ItoCb1Amira'),53    downsampled_size=(341, 171, 73))54_ID2NAME_CSV = op.join(op.dirname(BRAINCODE_PACKAGE_DIR), 'images_id_to_file.csv')55_NAME2DRIVER_CSV = op.join(op.dirname(BRAINCODE_PACKAGE_DIR), 'CAUTION', 'names_drivers.csv')56def dataset2human(dataset):57    return {'CB1': 'Janelia FlyLight', 'T1': 'Vienna Tiles'}[dataset]58# --- Original segmentations of the brains into "neuropils"59#  Format is not uniform between datasets, these functions take care of it.60#  The annotations on the CB1 dataset were inferred by "warping" these in the T1 dataset.61#  Florian knows the details.62_NEUROPILS = {63    # N.B. capitals to match supplemental dir names64    # When relevant, we did the original clusterings in the right hemisphere65    'SEZ': ['GNG', 'PRW', 'SAD', 'AMMC_L', 'AMMC_R'],66    'Mushroom_Body_L': ['MB_CA_L', 'MB_ML_L', 'MB_PED_L', 'MB_VL_L'],67    'Mushroom_Body_R': ['MB_CA_R', 'MB_ML_R', 'MB_PED_R', 'MB_VL_R'],68    'Mushroom_Body': ['MB_CA_L', 'MB_ML_L', 'MB_PED_L', 'MB_VL_L',69                      'MB_CA_R', 'MB_ML_R', 'MB_PED_R', 'MB_VL_R'],70    'Antennal_lobe_L': ['AL_L'],71    'Antennal_lobe_R': ['AL_R'],72    'Antennal_lobe': ['AL_L', 'AL_R'],73    'Optic_Glomeruli_L': ['AOTU_L', 'PVLP_L', 'PLP_L'],74    'Optic_Glomeruli_R': ['AOTU_R', 'PVLP_R', 'PLP_R'],75    'Optic_Glomeruli': ['AOTU_L', 'PVLP_L', 'PLP_L',76                        'AOTU_R', 'PVLP_R', 'PLP_R'],77    'Central_Complex': ['PB', 'EB', 'FB', 'NO']78}79def neuropil2human(neuropil):80    # The original in braincode-web/util.js81    prefix = 'Left ' if neuropil.endswith('L') else 'Right ' if neuropil.endswith('R') else ''82    n2h = {83        'Optic_Glomeruli': 'Optic Glomeruli (oVLNP)',84        'Mushroom_Body': 'Mushroom Body (MB)',85        'Central_Complex': 'Central Complex (CX)',86        'Antennal_lobe': 'Antennal Lobe (AL)',87        'SEZ': 'Subesophageal Zone (SEZ)',88    }89    for np_name, human_name in n2h.items():90        if neuropil.startswith(np_name):91            return prefix + human_name92    raise ValueError('Unknown region "%s"' % neuropil)93_REGIONNAME2ID_EXPECTATIONS = (94    ('GNG', 39),95    ('PRW', 40),96    ('SAD', 8),97    ('AMMC_L', 48),98    ('AMMC_R', 10),99    ('LO_L', 43),100    ('LO_R', 2),101    ('LOP_L', 58),102    ('LOP_R', 20),103    ('AOTU_L', 68),104    ('AOTU_R', 32),105    ('ME_L', 60),106    ('EB', 21),107)108def _parse_brain_region_descriptions(regions_path):109    # Read the region description110    # This has short descriptions for some acronyms111    regionid2description = {}112    with open(regions_path) as reader:113        text = reader.read().strip()114        for line in text.splitlines():115            region_id, _, region = line.partition(' ')116            region = region.strip()117            regionid2description[region_id] = region118    # Extend to Mushroom Body subregions119    regionid2description['MB_CA'] = \120        regionid2description['MB_ML'] = \121        regionid2description['MB_PED'] = \122        regionid2description['MB_VL'] = regionid2description['MB']123    return regionid2description124def check_region2id(name, expectation, region2id):125    if region2id[name] != expectation:126        raise Exception('Expected ID %d for regions %s, got %d' %127                        (expectation, name, region2id[name]))128def _generate_regions_nrrds(dataset, regions, sanity_checks_dir=None):129    """130    This function generates nrrd files to check by experts:131      - One with with all the region assignments.132      - One per neuropil133    These images go out of the release directory.134    """135    print('\tWriting regions nrrds for dataset %s' % dataset)136    if sanity_checks_dir is None:137        sanity_checks_dir = ensure_dir(op.abspath(op.join(braincode_dir(),138                                                          '..',139                                                          'regions-sanity')))140    # Write nrrd with all the assignments141    print('\t\tAll regions...')142    nrrd.write(op.join(sanity_checks_dir, '%s-regions.nrrd' % dataset),143               regions.voxel2labelid)144    # Write a nrrd per neuropil145    for neuropil in regions.labels() + regions.label_group_names():146        print('\t\t%s...' % neuropil)147        mask = regions.mask(neuropil)148        image = np.zeros_like(mask, dtype=np.uint8)149        image[~mask] = 255150        nrrd.write(op.join(sanity_checks_dir, '%s-%s.nrrd' % (dataset, neuropil)), image)151def _t1_regions_munger():152    amira_path = op.expanduser(op.join(_T1_ORIGINALS.regions,153                                       'composition_s2_t128_laszlo_AL_R_andL.am'))154    # Read the region description155    regions_path = op.join(op.dirname(amira_path),156                           'DrosophilaBrainRegions.terms.txt')157    region2description = _parse_brain_region_descriptions(regions_path)158    # Read the amira data file for voxel assignments and regions mappings159    amira_data = read_amira(amira_path)160    assert amira_data['info'] == {'version': '2.0', 'type': 'AmiraMesh', 'is_binary': True}161    data = amira_data['data']162    # Declared shape163    shape = tuple(data[0]['define']['Lattice'])164    assert shape == (768, 768, 165)165    parameters = data[1]['Parameters']166    # Region2id. Here 1 = exterior, 0 = unselected, anything higher means a named selected region (neuropil)167    region2id = {material: mid['Id'] - 1 for material, mid in parameters['Materials'].items()}168    # Sanity checks - Andrew provided these expectations after looking at the actual image169    for name, expected_id in _REGIONNAME2ID_EXPECTATIONS:170        check_region2id(name, expected_id, region2id)171    # We also have BoundingBox, CoordType, Content and Seeds->Slices172    # Plus data types declarations and data for two tensors:173    #   - data: the labels174    #   - probabilities: byte type, probably we do not need this175    # voxel2regionid176    voxel2regionid = data[4]['data']  # Like 768x768x165 array of codes (aka "labels")177    assert voxel2regionid.shape == shape178    # generate a table label -> id179    def LR_region2description(region):180        prefix = 'left ' if region.endswith('_L') else 'right ' if region.endswith('_R') else ''181        key = region if prefix == '' else region[:-2]182        return prefix + region2description.get(key, key)183    regions = [(region, region_id, LR_region2description(region))184               for region, region_id in sorted(region2id.items())]185    regions_df = pd.DataFrame(regions, columns=['name', 'id', 'description'])186    return VoxelLabels(regions_df, voxel2regionid, label_groups=_NEUROPILS)187def _cb1_regions_munger(clean_spurious_voxels=True):188    path = op.expanduser(_CB1_ORIGINALS.regions)189    # Read the region description190    region2description = _parse_brain_region_descriptions(op.join(path, 'DrosophilaBrainRegions.terms.txt'))191    # Read the map region_name -> label192    # Note, this can be found also in the .surf file, which seems the original193    # So maybe we should use that file instead194    params = op.join(path, 'DrosophilaBrainRegions.params.txt')195    def parse_line(line):196        region_name, _, region_id, _, r, g, b = line.strip().split()197        region_id = int(region_id)198        region_color = (float(r), float(g), float(b))199        return region_name, region_id, region_color200    with open(params, 'r') as reader:201        parsed_params = [parse_line(line) for line in reader if 0 < len(line.strip())]202    region2id = {region_name: region_id - 1 for region_name, region_id, _ in parsed_params}203    # N.B. we probably want to keep colors so we are consistent if we ever generate images204    # Sanity checks - Andrew provided these expectations after looking at the actual image205    for name, expected_id in _REGIONNAME2ID_EXPECTATIONS:206        check_region2id(name, expected_id, region2id)207    # Read the masks208    def fn2label(amira):209        return int(op.basename(amira)[len('NeuropilMask'):].split('.')[0])210    amiras = glob.glob(op.join(path, 'NeuropilMask*.am'))211    label2amira = {fn2label(amira) + 1: amira for amira in amiras}212    # N.B. +1 for making it 1-based, as in the parameters file; it seems that the files go that name213    # All this is too speculative, talk to K/L/F214    # Combine all these into one "labels" image215    voxel2region = None216    for region_id, amira in sorted(label2amira.items()):217        if voxel2region is None:218            voxel2region = read_amira(amira)['data'][3]['data']219            voxel2region[voxel2region == 1] = region_id220        else:221            data = read_amira(amira)['data'][3]['data']222            region_voxels = data == 1223            if ((voxel2region != 0) & region_voxels).any():224                raise Exception('Overlapping regions are not supported at the moment')225            voxel2region[region_voxels] = region_id226    voxel2regionid = voxel2region227    # generate a table label -> id228    def LR_region2description(region):229        prefix = 'left ' if region.endswith('_L') else 'right ' if region.endswith('_R') else ''230        key = region if prefix == '' else region[:-2]231        return prefix + region2description.get(key, key)232    regions = [(region, region_id, LR_region2description(region))233               for region, region_id in sorted(region2id.items())]234    regions_df = pd.DataFrame(regions, columns=['name', 'id', 'description'])235    # clean these pesky spurious voxels236    def remove_spurious_voxels_on_the_other_side(voxel2regionid, regions_df):237        """238        Clean spurious voxels on the other side in L/R segmentations.239        This happens apparently only in the right regions of CB1;240        I have just checked it in "AL_R", "Mushroom_Body_R" and "Optic_Glomeruli_R".241        I will assume it might happens in all the left/right regions.242        Note: this can only work in the CB1 dataset (which is centered).243        """244        # midx = int(np.round(voxel2regionid.shape[0] / 2))245        midx = 510  # Inferred as the mean x in segments joining the mean coordinates of L,R pairs in the dataset246        in_right = np.zeros_like(voxel2regionid, dtype=np.bool)247        in_right[midx:] = True  # Remember that left/right is from "fly perspective"248        # Probably we should just compute neuropil center, a histogram of distances and remove outliers249        # Or use properly fitted reflection planes250        for name, region_id in zip(regions_df.name, regions_df.id):251            if name.endswith('_L'):252                in_region = voxel2regionid == region_id253                spurious = in_region & ~in_right254                print('\t\t\t%s removed %d of %d (%.4f%%) voxels in the other side' %255                      (name, spurious.sum(), in_region.sum(), 100 * spurious.sum() / in_region.sum()))256                voxel2regionid[spurious] = 0257            if name.endswith('_R'):258                in_region = voxel2regionid == region_id259                spurious = in_region & in_right260                print('\t\t\t%s removed %d of %d (%.4f%%) voxels in the other side' %261                      (name, spurious.sum(), in_region.sum(), 100 * spurious.sum() / in_region.sum()))262                voxel2regionid[spurious] = 0263        return voxel2regionid264    if clean_spurious_voxels:265        print('\t\tWARNING: removing spurious voxels in the other side...')266        print('\t\tTHIS IS UNTESTED AND PROBABLY BROKEN AT THE MOMENT')267        voxel2regionid = remove_spurious_voxels_on_the_other_side(voxel2regionid, regions_df)268    return VoxelLabels(regions_df, voxel2regionid, label_groups=_NEUROPILS)269# dest_dir = ensure_dir(op.expanduser('~/clean-vs-not'))270# vl = _cb1_regions_munger(clean_spurious_voxels=False)271# vl.to_hdf5(op.join(dest_dir, 'original.h5'))272# _generate_regions_nrrds('CB1', vl, sanity_checks_dir=ensure_dir(op.join(dest_dir, 'original')))273# vl = _cb1_regions_munger(clean_spurious_voxels=True)274# vl.to_hdf5(op.join(dest_dir, 'clean.h5'))275# _generate_regions_nrrds('CB1', vl, sanity_checks_dir=ensure_dir(op.join(dest_dir, 'clean')))276# exit(22)277# --- Templates278def _read_template(amira_path):279    # Read280    amira_data = read_amira(amira_path)281    data = amira_data['data']282    shape = tuple(data[0]['define']['Lattice'])283    coord_type = data[1]['Parameters']['CoordType'][1:-1]284    bounding_box = np.array(data[1]['Parameters']['BoundingBox'])285    template = data[3]['data']286    # Dumbchecking stuff287    assert amira_data['info'] == {'version': '2.0', 'type': 'AmiraMesh', 'is_binary': True}288    assert coord_type == 'uniform'289    assert data[2]['Lattice']['byte'] in {'ScalarField', 'Data'}290    assert template.shape == shape291    return template, bounding_box292# --- Data release logic293def bootstrap_braincode_dir(id2name_csv=_ID2NAME_CSV,294                            name2driver_csv=_NAME2DRIVER_CSV,295                            bootstrap_dir=None,296                            reset=False,297                            ignore_originals=False,298                            clean_spurious_voxels=False,299                            generate_nrdds=False,300                            relative_symlinks=True,301                            log_duplicate_paths=False):302    """303    This function bootstraps "data release" directories for each of the datasets in our analysis.304    Ideally it should directly query the databases.305    At the moment, we use the files provided by Florian to bootstrap these simple, standalone data repositories.306    It generates the following hierarchy and files:307      bootstrap_dir308       |--T1  # dataset309         |--image2driver.csv                 # "master table" of dataset contents;310         |                                   # it links original db_id with file names and driver lines311         |--image2driver.csv.description     # description of the "master table"312         |--template_regions.h5              # the template image and its segmentation in neuropils are here313         |--template_regions.h5.description  # description314         |--original                         # where the original images are symlinked315           |--images                         # images will be stored316             |--TP10100501L33Sum02.am        # files with such names317             |--...318           |--template.am                    # the template image is here319           |--regions                        # region information for the image (e.g. neuropils)320    """321    # --- Database IDs for the images in our analysis322    #  These are needed to later link to actual filenames, and useful to keep provenance.323    #  Unfortunately this is backwards from Florian's hdf5 files ATM324    #  We do not assume all lines are in all neuropils, so iterate all regions.325    #  Maybe these are not all IDs we need; the way to go should be to run the query ourselves.326    db_ids = []327    for expression_dset, neuropil in product(get_all_datasets(), get_all_neuropils()):328        dset = ExpressionDataset.dataset(dset=expression_dset, neuropil=neuropil)329        db_ids.extend(zip(dset.lines(), [expression_dset] * len(dset.lines())))330    dbids_df = pd.DataFrame(data=sorted(set(db_ids)),331                            columns=['db_id', 'dataset'])332    dbids_df = dbids_df.set_index('db_id')333    # --- db_id -> amira file_name334    #  On a second CSV, we are given the link from a db_id to the amira file name335    #  Probably all these could be done with a simple database query336    # Columns are ['id', 'file_path', 'previews']337    id2file_df = pd.read_csv(id2name_csv, sep=';').sort_values('file_path')338    # Check id uniqueness339    assert len(id2file_df.id) == id2file_df.id.nunique()340    # Rename id -> db_id; file_path -> file_name341    id2file_df = id2file_df.rename(columns=lambda col: {'id': 'db_id', 'file_path': 'file_name'}.get(col, col))342    # Set db_id as the index343    id2file_df = id2file_df.set_index('db_id')344    # Files seems duplicated in the database345    # Fortunately, each file is only once in our analysis, so not a big deal346    if log_duplicate_paths:347        duplicated_paths = id2file_df[id2file_df.file_name.duplicated()].file_name.unique()348        print('Images in more than one entry:\n%s' % '\n'.join(duplicated_paths))349    # Merge350    image2driver_df = pd.merge(id2file_df, dbids_df, left_index=True, right_index=True, how='inner')351    assert len(image2driver_df) == 9484352    assert image2driver_df.file_name.nunique() == 9484353    # --- file_name -> driver line354    #  On a third text file, a weirdo DB dump, we link name to driver line and channel355    #  Andrew deals with it in CAUTION/copy_florians_data.py:my_read_csv356    # This funky function gives a dictionary like this:357    #   {name: {channel: (driver, line number in the CSV)}358    # We will just add name, channel and driver to our dataframe359    n2d = my_read_csv(name2driver_csv, verbose=False)360    # "name" can be inferred from the file_name easily (e.g. TP10100501L33Sum02.am -> TP10100501L33Sum)361    image2driver_df['name'] = image2driver_df.file_name.apply(lambda fp: op.splitext(fp)[0][:-2])362    # Add channel and driver to our dataframe, checking for uniqueness and ambiguities363    def name2driver(name):364        try:365            channel2driver = n2d[name]366            if len(channel2driver) == 0:367                raise Exception('No driver line found for name %s' % name)368            if len(channel2driver) > 1:369                raise Exception('Multiple channels/driver lines found for name %s' % name)370            channel, (driver, _) = channel2driver.popitem()371            return pd.Series({'driver': driver, 'channel': channel})372        except KeyError:373            raise Exception('Cannot find driver line for name %s' % name)374    # add name and driver as dataframe columns375    image2driver_df = image2driver_df.merge(image2driver_df.name.apply(name2driver), left_index=True, right_index=True)376    # make db_id a column377    image2driver_df = image2driver_df.reset_index()378    # reorder, drop name and previews379    image2driver_df = image2driver_df[['db_id', 'dataset', 'file_name', 'channel', 'driver']]380    image2driver_description = dedent("""381    The image2driver.csv file contains a table with an image per row and the following columns:382      - db_id: The ID of the image in the in-house database, for provenance tracking.383      - dataset: The dataset this image pertains to (e.g. T1 (Total Brain 1) or CB1 (Central Brain 1)).384      - file_name: The name of the amira file containing the image.385      - channel: The name of the channel in the image, usually indicating what was expressed (e.g. antiGFP).386      - driver: The driver line ID from flybase.387    """).strip()388    # --- Do release on a per-dataset basis389    bootstrap_dir = braincode_dir(bootstrap_dir, create=False)390    ensure_dir(bootstrap_dir)391    print('Bootstrapping braincode data in directory %s' % op.abspath(bootstrap_dir))392    for dataset, dataset_df in image2driver_df.groupby('dataset'):393        print('Releasing data for dataset %s' % dataset)394        dataset_dir = ensure_dir(op.join(bootstrap_dir, dataset))395        template_regions_h5 = op.join(dataset_dir, 'template_regions.h5')396        # Targeted cleanup397        if reset:398            print('\tRemoving directories and files, please wait...')399            shutil.rmtree(op.join(dataset_dir, 'originals'), ignore_errors=True)400            for fn in ['image2driver.csv', 'image2driver.csv.description',401                       'template_regions.h5', 'template_regions.h5.description']:402                try:403                    os.remove(op.join(dataset_dir, fn))404                except OSError:405                    pass406        # Save the image2driver csv file407        print('\tSaving image2driver.csv')408        image2driver_csv = op.join(dataset_dir, 'image2driver.csv')409        dataset_df.to_csv(image2driver_csv, index=False)410        dataset_df = dataset_df.reset_index(drop=True)411        roundtripped = pd.read_csv(image2driver_csv, index_col=False, dtype={'channel': object})412        assert dataset_df.reset_index(drop=True).equals(roundtripped)413        with open(image2driver_csv + '.description', 'w') as writer:414            writer.write(image2driver_description)415        # Get the location of the original files in strawscience416        originals = _T1_ORIGINALS if dataset == 'T1' else _CB1_ORIGINALS417        # Symlink image files418        if not ignore_originals:419            print('\tSymlinking original amiras')420            original_dest = ensure_dir(op.join(dataset_dir, 'originals', 'images'))421            for file_name in dataset_df.file_name:422                original = op.expanduser(op.join(originals.amiras, file_name))423                if not op.isfile(original):424                    print('WARNING: Cannot find image %s' % original)425                    continue426                dest = op.join(original_dest, file_name)427                if relative_symlinks:428                    original = op.relpath(original, original_dest)429                try:430                    os.symlink(original, dest)431                except OSError as err:432                    print('failing on symlink dest %r' % dest, file=sys.stderr)433                    raise434        # Symlink neuropil files435        if not ignore_originals:436            print('\tSymlinking anatomical regions directory')437            original = op.expanduser(originals.regions)438            if not op.isdir(original):439                print('WARNING: Cannot find regions %s' % original)440            original_dest = op.join(dataset_dir, 'originals', 'regions')441            if relative_symlinks:442                original = op.relpath(original, op.dirname(original_dest))443            os.symlink(original, original_dest)444        # Read regions and save to HDF5445        print('\tMunging regions, please wait...')446        regions_munger = (_t1_regions_munger if dataset == 'T1' else447                          partial(_cb1_regions_munger,448                                  clean_spurious_voxels=clean_spurious_voxels))449        regions = regions_munger()450        regions.to_hdf5(template_regions_h5, dataset_path='regions',451                        compression='gzip', compression_opts=5)452        # Generate template nrrds453        if generate_nrdds:454            print('Generating region nrrds')455            _generate_regions_nrrds(dataset, regions)456        # Symlink template457        if not ignore_originals:458            print('\tSymlinking amira template')459            original = op.expanduser(originals.template)460            if not op.isfile(original):461                print('\tWARNING: Cannot find template %s' % original)462            original_dest = op.join(dataset_dir, 'originals', 'template.am')463            if relative_symlinks:464                original = op.relpath(original, op.dirname(original_dest))465            os.symlink(original, original_dest)466        # Read template and save to hdf5 (probably we could just skip this, for completeness)467        print('\tMunging template, please wait...')468        template, bounding_box = _read_template(op.expanduser(originals.template))469        with h5py.File(template_regions_h5, 'a') as h5:470            dset = h5.create_dataset('template', data=template,471                                     compression='gzip', compression_opts=5)472            dset.attrs['bounding_box'] = bounding_box473            dset.attrs['bounding_box_description'] = 'Bounding box is [xmin, xmax, ymin, ymax, zmin, zmax] micrometers'474        # Save the description of the hdf5 file475        template_regions_description = dedent("""476        This hdf5 file contains the registration template and,477        more importantly, its segmentation into regions/neuropils.478        The template is in dataset "template".479        The values are the intensity of the template image.480        It is a (xsize x ysize x zsize) byte array with attributes:481          - bounding_box: [xmin, xmax, ymin, ymax, zmin, zmax]482          - bounding_box_description: includes units (micrometers)483        The regions is in dataset "regions".484        The values are region id.485        It is a (xsize x ysize x zsize) byte array of "region ids" with attributes:486          - name: an array with the name of each region487          - id: an array with a numeric identifier of each region488          - description: an array with a longer description of each region489          - columns: ['name', 'id', 'description']490          - many 'rs=' attributes, that map region set name to region set labels491        If using python, this can be conveniently read using492        `braincode.revisions.hub.VoxelLabels.from_hdf5`.493        """).strip()494        with open(template_regions_h5 + '.description', 'w') as writer:495            writer.write(template_regions_description)496        print('\t%s done' % dataset)497# Uncomment this to keep developing the clean_spurious_voxels filter498# bootstrap_braincode_dir(generate_nrdds=True, clean_spurious_voxels=True, reset=True)499# exit(22)500if __name__ == '__main__':501    import argh...

manager.py

Source:manager.py

1import errno2import json3import os4from galaxy import util5from galaxy.util.odict import odict6from galaxy.util.template import fill_template7from galaxy.tools.data import TabularToolDataTable8from tool_shed.util import common_util9import tool_shed.util.shed_util_common as suc10#set up logger11import logging12log = logging.getLogger( __name__ )13SUPPORTED_DATA_TABLE_TYPES = ( TabularToolDataTable )14VALUE_TRANSLATION_FUNCTIONS = dict( abspath=os.path.abspath )15DEFAULT_VALUE_TRANSLATION_TYPE = 'template'16class DataManagers( object ):17    def __init__( self, app, xml_filename=None ):18        self.app = app19        self.data_managers = odict()20        self.managed_data_tables = odict()21        self.tool_path = None22        self.filename = xml_filename or self.app.config.data_manager_config_file23        for filename in util.listify( self.filename ):24            if not filename:25                continue26            self.load_from_xml( filename )27        if self.app.config.shed_data_manager_config_file:28            self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True )29    def load_from_xml( self, xml_filename, store_tool_path=True, replace_existing=False ):30        try:31            tree = util.parse_xml( xml_filename )32        except Exception, e:33            log.error( 'There was an error parsing your Data Manager config file "%s": %s' % ( xml_filename, e ) )34            return #we are not able to load any data managers35        root = tree.getroot()36        if root.tag != 'data_managers':37            log.error( 'A data managers configuration must have a "data_managers" tag as the root. "%s" is present' % ( root.tag ) )38            return39        if store_tool_path:40            tool_path = root.get( 'tool_path', None )41            if tool_path is None:42                tool_path = self.app.config.tool_path43            if not tool_path:44                tool_path = '.'45            self.tool_path = tool_path46        for data_manager_elem in root.findall( 'data_manager' ):47            self.load_manager_from_elem( data_manager_elem, replace_existing=replace_existing )48    def load_manager_from_elem( self, data_manager_elem, tool_path=None, add_manager=True, replace_existing=False ):49        try:50            data_manager = DataManager( self, data_manager_elem, tool_path=tool_path )51        except Exception, e:52            log.error( "Error loading data_manager '%s':\n%s" % ( e, util.xml_to_string( data_manager_elem ) ) )53            return None54        if add_manager:55            self.add_manager( data_manager, replace_existing=replace_existing )56        log.debug( 'Loaded Data Manager: %s' % ( data_manager.id ) )57        return data_manager58    def add_manager( self, data_manager, replace_existing=False ):59        if not replace_existing:60            assert data_manager.id not in self.data_managers, "A data manager has been defined twice: %s" % ( data_manager.id )61        elif data_manager.id in self.data_managers:62            # Data Manager already exists, remove first one and replace with new one63            log.warning( "A data manager has been defined twice and will be replaced with the last loaded version: %s" % ( data_manager.id ) )64            self.remove_manager( data_manager.id  )65        self.data_managers[ data_manager.id ] = data_manager66        for data_table_name in data_manager.data_tables.keys():67            if data_table_name not in self.managed_data_tables:68                self.managed_data_tables[ data_table_name ] = []69            self.managed_data_tables[ data_table_name ].append( data_manager )70    def get_manager( self, *args, **kwds ):71        return self.data_managers.get( *args, **kwds )72    def remove_manager( self, manager_ids ):73        if not isinstance( manager_ids, list ):74            manager_ids = [ manager_ids ]75        for manager_id in manager_ids:76            data_manager = self.get_manager( manager_id, None )77            if data_manager is not None:78                del self.data_managers[ manager_id ]79                #remove tool from toolbox80                if data_manager.tool:81                    self.app.toolbox.remove_tool_by_id( data_manager.tool.id )82                #determine if any data_tables are no longer tracked83                for data_table_name in data_manager.data_tables.keys():84                    remove_data_table_tracking = True85                    for other_data_manager in self.data_managers.itervalues():86                        if data_table_name in other_data_manager.data_tables:87                            remove_data_table_tracking = False88                            break89                    if remove_data_table_tracking and data_table_name in self.managed_data_tables:90                        del self.managed_data_tables[ data_table_name ]91class DataManager( object ):92    GUID_TYPE = 'data_manager'93    DEFAULT_VERSION = "0.0.1"94    def __init__( self, data_managers, elem=None, tool_path=None ):95        self.data_managers = data_managers96        self.declared_id = None97        self.name = None98        self.description = None99        self.version = self.DEFAULT_VERSION100        self.guid = None101        self.tool = None102        self.data_tables = odict()103        self.output_ref_by_data_table = {}104        self.move_by_data_table_column = {}105        self.value_translation_by_data_table_column = {}106        self.tool_shed_repository_info_dict = None107        self.undeclared_tables = False108        if elem is not None:109            self.load_from_element( elem, tool_path or self.data_managers.tool_path )110    def load_from_element( self, elem, tool_path ):111        assert elem.tag == 'data_manager', 'A data manager configuration must have a "data_manager" tag as the root. "%s" is present' % ( elem.tag )112        self.declared_id = elem.get( 'id', None )113        self.guid = elem.get( 'guid', None )114        path = elem.get( 'tool_file', None )115        self.version = elem.get( 'version', self.version )116        tool_shed_repository_id = None117        tool_guid = None118        if path is None:119            tool_elem = elem.find( 'tool' )120            assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % ( util.xml_to_string( elem ) )121            path = tool_elem.get( "file", None )122            tool_guid = tool_elem.get( "guid", None )123            #need to determine repository info so that dependencies will work correctly124            tool_shed_url = tool_elem.find( 'tool_shed' ).text125            # Handle protocol changes.126            tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )127            # The protocol is not stored in the database.128            tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )129            repository_name = tool_elem.find( 'repository_name' ).text130            repository_owner = tool_elem.find( 'repository_owner' ).text131            installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text132            self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed,133                                                        name=repository_name,134                                                        owner=repository_owner,135                                                        installed_changeset_revision=installed_changeset_revision )136            tool_shed_repository = \137                suc.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.data_managers.app,138                                                                                              tool_shed,139                                                                                              repository_name,140                                                                                              repository_owner,141                                                                                              installed_changeset_revision )142            if tool_shed_repository is None:143                log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )144                #we'll set tool_path manually here from shed_conf_file145                tool_shed_repository_id = None146                try:147                    tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path )148                except Exception, e:149                    log.error( 'Error determining tool_path for Data Manager during testing: %s', e )150            else:151                tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id )152            #use shed_conf_file to determine tool_path153            shed_conf_file = elem.get( "shed_conf_file", None )154            if shed_conf_file:155                shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename( shed_conf_file, None )156                if shed_conf:157                    tool_path = shed_conf.get( "tool_path", tool_path )158        assert path is not None, "A tool file path could not be determined:\n%s" % ( util.xml_to_string( elem ) )159        self.load_tool( os.path.join( tool_path, path ),160                        guid=tool_guid,161                        data_manager_id=self.id,162                        tool_shed_repository_id=tool_shed_repository_id )163        self.name = elem.get( 'name', self.tool.name )164        self.description = elem.get( 'description', self.tool.description )165        self.undeclared_tables = util.asbool( elem.get( 'undeclared_tables', self.undeclared_tables ) )166        for data_table_elem in elem.findall( 'data_table' ):167            data_table_name = data_table_elem.get( "name" )168            assert data_table_name is not None, "A name is required for a data table entry"169            if data_table_name not in self.data_tables:170                self.data_tables[ data_table_name ] = odict()#{}171            output_elem = data_table_elem.find( 'output' )172            if output_elem is not None:173                for column_elem in output_elem.findall( 'column' ):174                    column_name = column_elem.get( 'name', None )175                    assert column_name is not None, "Name is required for column entry"176                    data_table_coumn_name = column_elem.get( 'data_table_name', column_name )177                    self.data_tables[ data_table_name ][ data_table_coumn_name ] = column_name178                    output_ref = column_elem.get( 'output_ref', None )179                    if output_ref is not None:180                        if data_table_name not in self.output_ref_by_data_table:181                            self.output_ref_by_data_table[ data_table_name ] = {}182                        self.output_ref_by_data_table[ data_table_name ][ data_table_coumn_name ] = output_ref183                    value_translation_elems = column_elem.findall( 'value_translation' )184                    if value_translation_elems is not None:185                        for value_translation_elem in value_translation_elems:186                            value_translation = value_translation_elem.text187                            if value_translation is not None:188                                value_translation_type = value_translation_elem.get( 'type', DEFAULT_VALUE_TRANSLATION_TYPE )189                                if data_table_name not in self.value_translation_by_data_table_column:190                                    self.value_translation_by_data_table_column[ data_table_name ] = {}191                                if data_table_coumn_name not in self.value_translation_by_data_table_column[ data_table_name ]:192                                    self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = []193                                if value_translation_type == 'function':194                                    if value_translation in VALUE_TRANSLATION_FUNCTIONS:195                                        value_translation = VALUE_TRANSLATION_FUNCTIONS[ value_translation ]196                                    else:197                                        raise ValueError( "Unsupported value translation function: '%s'" % ( value_translation ) )198                                else:199                                    assert value_translation_type == DEFAULT_VALUE_TRANSLATION_TYPE, ValueError( "Unsupported value translation type: '%s'" % ( value_translation_type ) )200                                self.value_translation_by_data_table_column[ data_table_name ][ data_table_coumn_name ].append( value_translation )201                    for move_elem in column_elem.findall( 'move' ):202                        move_type = move_elem.get( 'type', 'directory' )203                        relativize_symlinks = move_elem.get( 'relativize_symlinks', False ) #TODO: should we instead always relativize links?204                        source_elem = move_elem.find( 'source' )205                        if source_elem is None:206                            source_base = None207                            source_value = ''208                        else:209                            source_base = source_elem.get( 'base', None )210                            source_value = source_elem.text211                        target_elem = move_elem.find( 'target' )212                        if target_elem is None:213                            target_base = None214                            target_value = ''215                        else:216                            target_base = target_elem.get( 'base', None )217                            target_value = target_elem.text218                        if data_table_name not in self.move_by_data_table_column:219                            self.move_by_data_table_column[ data_table_name ] = {}220                        self.move_by_data_table_column[ data_table_name ][ data_table_coumn_name ] = \221                            dict( type=move_type,222                                  source_base=source_base,223                                  source_value=source_value,224                                  target_base=target_base,225                                  target_value=target_value,226                                  relativize_symlinks=relativize_symlinks )227    @property228    def id( self ):229        return self.guid or self.declared_id #if we have a guid, we will use that as the data_manager id230    def load_tool( self, tool_filename, guid=None, data_manager_id=None, tool_shed_repository_id=None ):231        toolbox = self.data_managers.app.toolbox232        tool = toolbox.load_hidden_tool( tool_filename,233                                         guid=guid,234                                         data_manager_id=data_manager_id,235                                         repository_id=tool_shed_repository_id )236        self.data_managers.app.toolbox.data_manager_tools[ tool.id ] = tool237        self.tool = tool238        return tool239    def process_result( self, out_data ):240        data_manager_dicts = {}241        data_manager_dict = {}242        #TODO: fix this merging below243        for output_name, output_dataset in out_data.iteritems():244            try:245                output_dict = json.loads( open( output_dataset.file_name ).read() )246            except Exception, e:247                log.warning( 'Error reading DataManagerTool json for "%s": %s'  % ( output_name, e ) )248                continue249            data_manager_dicts[ output_name ] = output_dict250            for key, value in output_dict.iteritems():251                if key not in data_manager_dict:252                    data_manager_dict[ key ] = {}253                data_manager_dict[ key ].update( value )254            data_manager_dict.update( output_dict )255        data_tables_dict = data_manager_dict.get( 'data_tables', {} )256        for data_table_name, data_table_columns in self.data_tables.iteritems():257            data_table_values = data_tables_dict.pop( data_table_name, None )258            if not data_table_values:259                log.warning( 'No values for data table "%s" were returned by the data manager "%s".' % ( data_table_name, self.id ) )260                continue #next data table261            data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None )262            if data_table is None:263                log.error( 'The data manager "%s" returned an unknown data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, 'tool_data_table_conf.xml' ) )264                continue #next table name265            if not isinstance( data_table, SUPPORTED_DATA_TABLE_TYPES ):266                log.error( 'The data manager "%s" returned an unsupported data table "%s" with type "%s" with new entries "%s". These entries will not be created. Please confirm that the data table is of a supported type (%s).' % ( self.id, data_table_name, type( data_table ), data_table_values, SUPPORTED_DATA_TABLE_TYPES ) )267                continue #next table name268            output_ref_values = {}269            if data_table_name in self.output_ref_by_data_table:270                for data_table_column, output_ref in self.output_ref_by_data_table[ data_table_name ].iteritems():271                    output_ref_dataset = out_data.get( output_ref, None )272                    assert output_ref_dataset is not None, "Referenced output was not found."273                    output_ref_values[ data_table_column ] = output_ref_dataset274            if not isinstance( data_table_values, list ):275                data_table_values = [ data_table_values ]276            for data_table_row in data_table_values:277                data_table_value = dict( **data_table_row ) #keep original values here278                for name, value in data_table_row.iteritems(): #FIXME: need to loop through here based upon order listed in data_manager config279                    if name in output_ref_values:280                        moved = self.process_move( data_table_name, name, output_ref_values[ name ].extra_files_path, **data_table_value )281                        data_table_value[ name ] = self.process_value_translation( data_table_name, name, **data_table_value )282                data_table.add_entry( data_table_value, persist=True, entry_source=self )283        if self.undeclared_tables and data_tables_dict:284            # We handle the data move, by just moving all the data out of the extra files path285            # moving a directory and the target already exists, we move the contents instead286            log.debug( 'Attempting to add entries for undeclared tables: %s.', ', '.join( data_tables_dict.keys() ) )287            for ref_file in out_data.values():288                util.move_merge( ref_file.extra_files_path, self.data_managers.app.config.galaxy_data_manager_data_path )289            path_column_names = [ 'path' ]290            for data_table_name, data_table_values in data_tables_dict.iteritems():291                data_table = self.data_managers.app.tool_data_tables.get( data_table_name, None )292                if not isinstance( data_table_values, list ):293                    data_table_values = [ data_table_values ]294                for data_table_row in data_table_values:295                    data_table_value = dict( **data_table_row ) #keep original values here296                    for name, value in data_table_row.iteritems():297                        if name in path_column_names:298                            data_table_value[ name ] = os.path.abspath( os.path.join( self.data_managers.app.config.galaxy_data_manager_data_path, value ) )299                    data_table.add_entry( data_table_value, persist=True, entry_source=self )300        else:301            for data_table_name, data_table_values in data_tables_dict.iteritems():302                # tool returned extra data table entries, but data table was not declared in data manager303                # do not add these values, but do provide messages304                log.warning( 'The data manager "%s" returned an undeclared data table "%s" with new entries "%s". These entries will not be created. Please confirm that an entry for "%s" exists in your "%s" file.' % ( self.id, data_table_name, data_table_values, data_table_name, self.data_managers.filename ) )305    def process_move( self, data_table_name, column_name, source_base_path, relative_symlinks=False, **kwd ):306        if data_table_name in self.move_by_data_table_column and column_name in self.move_by_data_table_column[ data_table_name ]:307            move_dict = self.move_by_data_table_column[ data_table_name ][ column_name ]308            source = move_dict[ 'source_base' ]309            if source is None:310                source = source_base_path311            else:312                source = fill_template( source, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )313            if move_dict[ 'source_value' ]:314                source = os.path.join( source, fill_template( move_dict[ 'source_value' ], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )  )315            target = move_dict[ 'target_base' ]316            if target is None:317                target = self.data_managers.app.config.galaxy_data_manager_data_path318            else:319                target = fill_template( target, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd )320            if move_dict[ 'target_value' ]:321                target = os.path.join( target, fill_template( move_dict[ 'target_value' ], GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd  ) )322            if move_dict[ 'type' ] == 'file':323                dirs, filename = os.path.split( target )324                try:325                    os.makedirs( dirs )326                except OSError, e:327                    if e.errno != errno.EEXIST:328                        raise e329            #moving a directory and the target already exists, we move the contents instead330            util.move_merge( source, target )331            if move_dict.get( 'relativize_symlinks', False ):332                util.relativize_symlinks( target )333            return True334        return False335    def process_value_translation( self, data_table_name, column_name, **kwd ):336        value = kwd.get( column_name )337        if data_table_name in self.value_translation_by_data_table_column and column_name in self.value_translation_by_data_table_column[ data_table_name ]:338            for value_translation in self.value_translation_by_data_table_column[ data_table_name ][ column_name ]:339                if isinstance( value_translation, basestring ):340                    value = fill_template( value_translation, GALAXY_DATA_MANAGER_DATA_PATH=self.data_managers.app.config.galaxy_data_manager_data_path, **kwd  )341                else:342                    value = value_translation( value )343        return value344    def get_tool_shed_repository_info_dict( self ):...

drbdlinks

Source:drbdlinks

1#!/usr/bin/env python2#3#  Manage a set of links into a DRBD shared directory4#5#  Written by: Sean Reifschneider <jafo@tummy.com>6#  Copyright (c) 2004-2013, tummy.com, ltd.  All Rights Reserved7#  drbdlinks is under the following license: GPLv28import os9import sys10import stat11import syslog12import shutil13import glob14import subprocess15configFile = '/etc/drbdlinks.conf'16configDir = '/etc/drbdlinks.d/*.conf'17cleanConfigsDirectory = '/var/lib/drbdlinks/configs-to-clean'18syslog.openlog('drbdlinks', syslog.LOG_PID)19try:20    import optparse21except ImportError:22    import optik23    optparse = optik24try:25    from subprocess import DEVNULL26except ImportError:27    DEVNULL = open(os.devnull, 'wb')28try:29    execfile30except NameError:31    def execfile(filepath, globals=None, locals=None):32        with open(filepath, 'rb') as file:33            exec(compile(file.read(), filepath, 'exec'), globals, locals)34class lsb:35    class statusRC:36        OK = 037        VAR_PID = 138        VAR_LOCK = 239        STOPPED = 340        UNKNOWN = 441        LSBRESERVED = 542        DISTRESERVED = 10043        APPRESERVED = 15044        RESERVED = 20045    class exitRC:46        OK = 047        GENERIC = 148        EINVAL = 249        ENOTSUPPORTED = 350        EPERM = 451        NOTINSTALLED = 552        NOTCONFIGED = 653        NOTRUNNING = 754        LSBRESERVED = 855        DISTRESERVED = 10056        APPRESERVED = 15057        RESERVED = 20058###########59def log(s):60    sys.stderr.write(s)61    syslog.syslog(s)62##############################################63def multiInitRestart(flavor, initscript_list):64    for initscript in initscript_list:65        if os.path.exists(initscript):66            if initscript.endswith(".service"):67                retcode = os.system(68                    'systemctl restart %s' % initscript.rsplit('/', 1)[1])69            else:70                retcode = os.system('%s restart' % initscript)71            if retcode != 0:72                log('%s restart returned %d, expected 0' % (flavor, retcode))73            return(retcode != 0)74    syslog.syslog(75        'Unable to locate %s init script, not restarting.' % flavor)76    return(0)77##########################78def restartSyslog(config):79    if not config.restartSyslog:80        return(0)81    return multiInitRestart(82        'syslog', ['/etc/init.d/syslog', '/etc/init.d/rsyslog',83                   '/usr/lib/systemd/system/rsyslog.service'])84########################85def restartCron(config):86    if not config.restartCron:87        return(0)88    return multiInitRestart(89        'cron', ['/etc/init.d/crond', '/etc/init.d/cron',90                 '/usr/lib/systemd/system/crond.service'])91#######################92def testConfig(config):93    allUp = True94    for linkLocal, linkDest, useBindLink in config.linkList:95        suffixName = linkLocal + options.suffix96        #  check to see if the link is in place97        if not os.path.exists(suffixName):98            allUp = False99            if options.verbose >= 1:100                print(101                    'testConfig: Original file not present: "%s"' % suffixName)102            continue103    if options.verbose >= 1:104        print('testConfig: Returning %s' % allUp)105    return(allUp)106###############################107def loadConfigFile(configFile):108    class configClass:109        def __init__(self):110            self.mountpoint = None111            self.cleanthisconfig = 0112            self.linkList = []113            self.useSELinux = 0114            self.selinuxenabledPath = None115            self.useBindMount = 0116            self.debug = 0117            self.restartSyslog = 0118            self.restartCron = 0119            self.makeMountpointShared = 0120            #  Locate where the selinuxenabled binary is121            for path in (122                    '/usr/sbin/selinuxenabled',123                    '/sbin/selinuxenabled', ):124                if os.path.exists(path):125                    self.selinuxenabledPath = path126                    break127            #  auto-detect if SELinux is on128            if self.selinuxenabledPath:129                ret = os.system(self.selinuxenabledPath)130                if ret == 0:131                    self.useSELinux = 1132            #  detect what ls(1) supports to show SELinux context133            try:134                subprocess.check_call(135                    ['ls', '--scontext', __file__],136                    stdout=DEVNULL, stderr=DEVNULL)137                self.showContextCommand = 'ls -d --scontext "%s"'138            except subprocess.CalledProcessError:139                self.showContextCommand = 'ls -d -Z -1 "%s"'140        def cmd_cleanthisconfig(self, enabled=1):141            self.cleanthisconfig = enabled142        def cmd_mountpoint(self, arg, shared=0):143            self.mountpoint = arg144            if shared:145                self.makeMountpointShared = 1146        def cmd_link(self, src, dest=None):147            self.linkList.append((src, dest, self.useBindMount))148        def cmd_selinux(self, enabled=1):149            self.useSELinux = enabled150        def cmd_usebindmount(self, enabled=1):151            self.useBindMount = enabled152        def cmd_debug(self, level=1):153            self.debug = level154        def cmd_restartSyslog(self, enabled=1):155            self.restartSyslog = enabled156        def cmd_restartCron(self, enabled=1):157            self.restartCron = enabled158    #  set up config environment159    config = configClass()160    namespace = {161        'mountpoint': config.cmd_mountpoint,162        'link': config.cmd_link,163        'selinux': config.cmd_selinux,164        'debug': config.cmd_debug,165        'usebindmount': config.cmd_usebindmount,166        'restartSyslog': config.cmd_restartSyslog,167        'restartsyslog': config.cmd_restartSyslog,168        'restartCron': config.cmd_restartCron,169        'restartcron': config.cmd_restartCron,170        'cleanthisconfig': config.cmd_cleanthisconfig,171    }172    #  load the files173    for filename in [configFile] + sorted(glob.iglob(configDir)):174        try:175            execfile(filename, {}, namespace)176        except Exception:177            print(178                'ERROR: Loading configuration file "%s" failed.  '179                'See below for details:' % filename)180            print('Environment: %s' % repr(181                ['%s=%s' % i for i in os.environ.items()182                    if i[0].startswith('OCF_')]))183            raise184    #  process the data we got185    if config.mountpoint:186        config.mountpoint = config.mountpoint.rstrip('/')187    for i in range(len(config.linkList)):188        oldList = config.linkList[i]189        if oldList[1]:190            arg2 = oldList[1].rstrip('/')191        else:192            if not config.mountpoint:193                log(194                    'ERROR: Used link() when no mountpoint() was set '195                    'in the config file.\n')196                sys.exit(3)197            arg2 = oldList[0].lstrip('/')198            arg2 = os.path.join(config.mountpoint, arg2).rstrip('/')199        config.linkList[i] = (200            [oldList[0].rstrip('/'), arg2] + list(oldList[2:]))201    #  return the data202    return(config)203def print_metadata():204    print('''205<?xml version="1.0"?>206<!DOCTYPE resource-agent SYSTEM "ra-api-1.dtd">207<!-- Root element: give the name of the Resource agent -->208<resource-agent name="drbdlinks" version="@@@VERSION@@@">209<!-- Version number of the standard this complies with -->210<version>1.0</version>211<!-- List all the instance parameters the RA supports or requires. -->212<parameters>213<!-- Note that parameters flagged with 'unique' must be unique; ie no214    other resource instance of this resource type may have the same set215    of unique parameters.216-->217<parameter name="configfile" unique="1">218<longdesc lang="en">219The full path of the configuration file on disc.  The default is220/etc/drbdlinks.conf, but you may wish to store this on the shared221storage, or have different config files if you have multiple222resource groups.223</longdesc>224<shortdesc lang="en">Configuration Filename</shortdesc>225<content type="string" default="/etc/drbdlinks.conf" />226</parameter>227<parameter name="suffix">228<longdesc lang="en">229The suffix of the files/directories that are moved out of the way on the host230file-system to make room for the symlink.  By default this is ".drbdlinks".231</longdesc>232<shortdesc lang="en">Host Filename Suffix</shortdesc>233<content type="string" default=".drbdlinks" />234</parameter>235</parameters>236<!-- List the actions supported by the RA -->237<actions>238<action name="start"   timeout="1m" />239<action name="stop"    timeout="1m" />240<action name="monitor" depth="0"  timeout="20" interval="10" />241<action name="meta-data"  timeout="5" />242</actions>243</resource-agent>244'''.strip())245    sys.exit(lsb.exitRC.OK)246#  meta-data may happen when configuration is not present.247if 'meta-data' in sys.argv:248    print_metadata()249#  parse arguments250parser = optparse.OptionParser()251parser.add_option(252    '-c', '--config-file', dest='configFile', type='string',253    default=configFile,254    help='Location of the configuration file.')255parser.add_option(256    '-s', '--suffix', dest='suffix', type='string',257    default='.drbdlinks',258    help='Name to append to the local file-system name when the link '259            'is in place.')260parser.add_option(261    '-v', '--verbose', default=0,262    dest='verbose', action='count',263    help='Increase verbosity level by 1 for every "-v".')264parser.set_usage(265    '%prog (start|stop|auto|status|monitor|list|checklinks|\n'266    '        initialize_shared_storage)')267options, args = parser.parse_args()268origConfigFile = configFile269#  if called from OCF, parse the environment270OCFenabled = os.environ.get('OCF_RA_VERSION_MAJOR') is not None271if OCFenabled:272    try:273        options.configFile = os.environ['OCF_RESKEY_configfile']274    except KeyError:275        pass276    try:277        options.suffix = os.environ['OCF_RESKEY_suffix']278    except KeyError:279        pass280configFile = options.configFile281#  figure out what the mode to run in282if len(args) == 1 or (OCFenabled and len(args) > 0):283    #  NOTE: OCF specifies that additional arguments beyond the first should284    #  be ignored.285    if args[0] not in (286            'start', 'stop', 'auto', 'monitor', 'status', 'list',287            'checklinks', 'initialize_shared_storage'):288        parser.error(289            'ERROR: Unknown mode "%s", expecting one of '290            '(start|stop|auto|\n      status|monitor|list|checklinks|'291            'initialize_shared_storage)' % args[0])292        sys.exit(lsb.exitRC.ENOTSUPPORTED)293    mode = args[0]294else:295    parser.error('Expected exactly one argument to specify the mode.')296    sys.exit(lsb.exitRC.EINVAL)297if options.verbose >= 2:298    print('Initial mode: "%s"' % mode)299#  load config file300try:301    config = loadConfigFile(configFile)302except IOError as e:303    if e.errno == 2:304        if mode == 'monitor' or mode == 'status':305            print(306                'WARNING: Config file "%s" not found, assuming drbdlinks '307                'is stopped' % configFile)308            if mode == 'status':309                sys.exit(lsb.statusRC.STOPPED)310            else:311                sys.exit(lsb.exitRC.NOTRUNNING)312        print('ERROR: Unable to open config file "%s":' % configFile)313        print('  %s' % e)314        syslog.syslog('Invalid config file "%s"' % configFile)315        sys.exit(lsb.statusRC.UNKNOWN)316    raise317if not config.mountpoint:318    log('No mountpoint found in config file.  Aborting.\n')319    if mode == 'monitor':320        if config.debug:321            syslog.syslog('Monitor called without mount point')322        sys.exit(lsb.exitRC.EINVAL)323    if config.debug:324        syslog.syslog('No mount point')325    sys.exit(lsb.statusRC.UNKNOWN)326if not os.path.exists(config.mountpoint):327    log('Mountpoint "%s" does not exist.  Aborting.\n' % config.mountpoint)328    if mode == 'monitor':329        if config.debug:330            syslog.syslog('Mount point does not exist, monitor mode')331        sys.exit(lsb.exitRC.EINVAL)332    if config.debug:333        syslog.syslog('Mount point does not exist')334    sys.exit(lsb.statusRC.UNKNOWN)335#  startup log message336if config.debug:337    syslog.syslog(338        'drbdlinks starting: args: "%s", configfile: "%s"'339        % (repr(sys.argv), configFile))340#  if mode is auto, figure out what mode to use341if mode == 'auto':342    if (os.stat(config.mountpoint).st_dev !=343            os.stat(os.path.join(config.mountpoint, '..')).st_dev):344        if options.verbose >= 1:345            print('Detected mounted file-system on "%s"' % config.mountpoint)346        mode = 'start'347    else:348        mode = 'stop'349if options.verbose >= 1:350    print('Mode: "%s"' % mode)351# just display the list of links352if mode == 'list':353    for linkLocal, linkDest, useBindMount in config.linkList:354        print('%s %s %s' % (linkLocal, linkDest, useBindMount))355    sys.exit(0)356#  set up links357anyLinksChanged = 0358if mode == 'start':359    errorCount = 0360    #  set up shared mountpoint361    if config.makeMountpointShared:362        os.system('mount --make-shared  "%s"' % config.mountpoint)363    #  loop over links364    for linkLocal, linkDest, useBindMount in config.linkList:365        suffixName = linkLocal + options.suffix366        #  check to see if the link is in place367        if os.path.exists(suffixName):368            if options.verbose >= 1:369                print(370                    'Skipping, appears to already be linked: "%s"' % linkLocal)371            continue372        #  make the link373        try:374            if options.verbose >= 2:375                print('Renaming "%s" to "%s"' % (linkLocal, suffixName))376            os.rename(linkLocal, suffixName)377            anyLinksChanged = 1378        except (OSError, IOError) as e:379            log(380                'Error renaming "%s" to "%s": %s\n'381                % (suffixName, linkLocal, str(e)))382            errorCount = errorCount + 1383            if options.verbose >= 2:384                print('Linking "%s" to "%s"' % (linkDest, linkLocal))385            anyLinksChanged = 1386        if useBindMount:387            st = os.stat(linkDest)388            if stat.S_ISREG(st.st_mode):389                open(linkLocal, 'w').close()390            else:391                os.mkdir(linkLocal)392            os.system('mount -o bind "%s" "%s"' % (linkDest, linkLocal))393        else:394            try:395                os.symlink(linkDest, linkLocal)396            except (OSError, IOError) as e:397                log(398                    'Error linking "%s" to "%s": %s'399                    % (linkDest, linkLocal, str(e)))400                errorCount = errorCount + 1401        #  set up in SELinux402        if config.useSELinux:403            fp = os.popen(config.showContextCommand % suffixName, 'r')404            line = fp.readline()405            fp.close()406            if line:407                line = line.split(' ')[0]408                seInfo = line.split(':')409                seUser, seRole, seType = seInfo[:3]410                if len(seInfo) >= 4:411                    seRange = seInfo[3]412                    os.system(413                        'chcon -h -u "%s" -r "%s" -t "%s" -l "%s" "%s"'414                        % (seUser, seRole, seType, seRange, linkLocal))415                else:416                    os.system(417                        'chcon -h -u "%s" -r "%s" -t "%s" "%s"'418                        % (seUser, seRole, seType, linkLocal))419    if anyLinksChanged:420        if restartSyslog(config):421            errorCount = errorCount + 1422        if restartCron(config):423            errorCount = errorCount + 1424    if config.cleanthisconfig and origConfigFile != configFile:425        if not os.path.exists(cleanConfigsDirectory):426            if config.debug:427                syslog.syslog(428                    'Config copy directory "%s" does not exist.'429                    % cleanConfigsDirectory)430        else:431            if config.debug:432                syslog.syslog('Preserving a copy of the config file.')433            shutil.copy(configFile, cleanConfigsDirectory)434    if errorCount:435        if config.debug:436            syslog.syslog('Exiting due to %d errors' % errorCount)437        sys.exit(lsb.exitRC.GENERIC)438    if config.debug:439        syslog.syslog('Exiting with no errors')440    sys.exit(lsb.exitRC.OK)441#  remove links442elif mode == 'stop':443    errorCount = 0444    for linkLocal, linkDest, useBindMount in config.linkList:445        suffixName = linkLocal + options.suffix446        #  check to see if the link is in place447        if not os.path.exists(suffixName):448            if options.verbose >= 1:449                print(450                    'Skipping, appears to already be shut down: "%s"'451                    % linkLocal)452            continue453        #  break the link454        try:455            if options.verbose >= 2:456                print('Removing "%s"' % (linkLocal,))457            anyLinksChanged = 1458            if useBindMount:459                os.system('umount "%s"' % linkLocal)460                try:461                    os.remove(linkLocal)462                except Exception:463                    pass464                if os.path.exists(linkLocal):465                    os.rmdir(linkLocal)466            else:467                os.remove(linkLocal)468        except (OSError, IOError) as e:469            log('Error removing "%s": %s\n' % (linkLocal, str(e)))470            errorCount = errorCount + 1471        try:472            if options.verbose >= 2:473                print('Renaming "%s" to "%s"' % (suffixName, linkLocal))474            os.rename(suffixName, linkLocal)475            anyLinksChanged = 1476        except (OSError, IOError) as e:477            log(478                'Error renaming "%s" to "%s": %s\n'479                % (suffixName, linkLocal, str(e)))480            errorCount = errorCount + 1481    if anyLinksChanged:482        restartSyslog(config)483        restartCron(config)484    if errorCount:485        if config.debug:486            syslog.syslog('Exiting due to %d errors' % errorCount)487        sys.exit(lsb.exitRC.GENERIC)488    if config.debug:489        syslog.syslog('Exiting with no errors')490    sys.exit(lsb.exitRC.OK)491#  monitor mode492elif mode == 'monitor':493    if testConfig(config):494        if config.debug:495            syslog.syslog('Monitor mode returning ok')496        sys.exit(lsb.exitRC.OK)497    if config.debug:498        syslog.syslog('Monitor mode returning notrunning')499    sys.exit(lsb.exitRC.NOTRUNNING)500#  status mode501elif mode == 'status':502    if testConfig(config):503        print("info: DRBD Links OK (present)")504        if config.debug:505            syslog.syslog('Status mode returning ok')506        sys.exit(lsb.statusRC.OK)507    print("info: DRBD Links stopped (not set up)")508    if config.debug:509        syslog.syslog('Status mode returning stopped')510    sys.exit(lsb.statusRC.STOPPED)511#  check mode512elif mode == 'checklinks':513    for linkLocal, linkDest, useBindMount in config.linkList:514        if not os.path.exists(linkDest):515            print('Does not exist: %s' % linkDest)516    sys.exit(lsb.exitRC.OK)517#  initialize_shared_storage mode518elif mode == 'initialize_shared_storage':519    def dirs_to_make(src, dest):520        '''Return a list of paths, from top to bottom, that need to be created521        in the destination.  The return value is a list of tuples of522        (src, dest) where the `src` is the corresponding source directory to523        the `dest`.524        '''525        retval = []526        destdirname = os.path.dirname(dest)527        srcdirname = os.path.dirname(src)528        while srcdirname and srcdirname != '/':529            if os.path.exists(destdirname):530                break531            if os.path.basename(destdirname) != os.path.basename(srcdirname):532                break533            retval.append((srcdirname, destdirname))534            srcdirname = os.path.dirname(srcdirname)535            destdirname = os.path.dirname(destdirname)536        return retval[::-1]537    relative_symlinks = []538    for linkLocal, linkDest, useBindMount in config.linkList:539        if os.path.exists(linkDest):540            continue541        for src, dest in dirs_to_make(linkLocal, linkDest):542            print('Making directory "%s"' % dest)543            os.mkdir(dest)544            srcstat = os.stat(src)545            os.chmod(dest, srcstat.st_mode)546            os.chown(dest, srcstat.st_uid, srcstat.st_gid)547        print('Copying "%s" to "%s"' % (linkLocal, linkDest))548        os.system('cp -ar "%s" "%s"' % (linkLocal, linkDest))549        fp = os.popen('find "%s" -type l -lname "[^/].*" -print0' % linkLocal)550        relative_symlinks += [l for l in fp.read().split('\0') if l]551        fp.close()552    if relative_symlinks:553        print(554            '\nWARNING: The following copied files contain relative '555            'symlinks:\n')556        for symlink in relative_symlinks:557            print('   %s -> %s' % (symlink, os.readlink(symlink)))...

build_tools_cli.py

Source:build_tools_cli.py

...246                                                                               args.relative_sh_script,247                                                                               artifact_dir,248                                                                               filename))249        if args.relative_symlinks:250            handlers.append(lambda filename: build_tools.postprocess_relative_symlinks(ctx.logger, artifact_dir,251                                                                                       filename))252        if args.remove_pkgconfig:253            handlers.append(lambda filename: build_tools.postprocess_remove_pkgconfig(254                ctx.logger, filename))255        if args.relative_pkgconfig:256            handlers.append(lambda filename: build_tools.postprocess_relative_pkgconfig(257                ctx.logger, artifact_dir, filename))258        if args.check_relocatable:259            handlers.append(lambda filename: build_tools.check_relocatable(ctx.logger, args.check_ignore,260                                                                            artifact_dir, filename))261        if args.write_protect:262            handlers.append(build_tools.write_protect)263        if args.path is None:264            try:...

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