| Previous changeset 9:2adc3aa47d15 (2019-07-29) Next changeset 11:6c42ea4ab169 (2020-04-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f" |
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modified:
README.rst create_account.py create_features_from_gff3.py create_or_update_organism.py delete_features.py delete_features.xml delete_organism.py export.py fetch_organism_jbrowse.py list_organisms.py macros.xml webapollo.py |
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added:
test-data/arrow.yml test-data/create_org/output.json test-data/create_org/output2.json test-data/dataset_1.dat test-data/dataset_1_files/data/.htaccess test-data/dataset_1_files/data/names/02b/9.json test-data/dataset_1_files/data/names/0e9/3.json test-data/dataset_1_files/data/names/83f/8.json test-data/dataset_1_files/data/names/92c/2.json test-data/dataset_1_files/data/names/cf0/e.json test-data/dataset_1_files/data/names/f26/8.json test-data/dataset_1_files/data/names/meta.json test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz.tbi test-data/dataset_1_files/data/seq/genome.fasta test-data/dataset_1_files/data/seq/genome.fasta.fai test-data/dataset_1_files/data/seq/refSeqs.json test-data/dataset_1_files/data/trackList.json test-data/dataset_1_files/data/tracks.conf test-data/dataset_1_files/galaxy.xml test-data/dataset_1_files/jbrowse.conf test-data/dataset_1_files/jbrowse_conf.json test-data/export/cdna.fa test-data/export/cds.fa test-data/export/out.vcf test-data/export/pep.fa test-data/load_gff3/output.tsv test-data/merlin.gff test-data/org_remote.tar.gz |
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removed:
test-data/bad-model.gff3 test-data/good-model.gff3 |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 README.rst --- a/README.rst Mon Jul 29 10:09:19 2019 -0400 +++ b/README.rst Mon Dec 02 05:44:41 2019 -0500 |
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| @@ -1,27 +1,13 @@ Galaxy-apollo ============= -Galaxy tools to interface with Apollo The webapollo.py file is also -`separately -available <https://github.com/galaxy-genome-annotation/python-apollo>`__ -as a pip-installable package. - -Dependencies ------------- - -You will need to install some python modules in the Galaxy virtualenv for these -tools to be fully functional: - -.. code:: bash - - . /path/to/galaxy/.venv/bin/activate - pip install six biopython bcbio-gff - deactivate +Galaxy tools to interface with Apollo. +Uses `python-apollo <https://github.com/galaxy-genome-annotation/python-apollo>`__ for most of it. Environment ----------- -The following environment variables must be set: +The following environment variables can be set: +--------------------------------+-----------------------------------------------------------+ | ENV | Use | @@ -34,15 +20,22 @@ | | | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. | -| | | -| | | ++--------------------------------+-----------------------------------------------------------+ +| ``$ARROW_GLOBAL_CONFIG_PATH`` | Path to a python-apollo/arrow conf file. Use in place of | +| | ``$GALAXY_WEBAPOLLO_URL``, ``$GALAXY_WEBAPOLLO_USER`` | +| | and ``$GALAXY_WEBAPOLLO_PASSWORD``. | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. | | | The external URL at which Apollo is accessible to end | | | users. | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to | -| | exchange JBrowse instances. | +| | exchange JBrowse instances. If not set, JBrowse data will | +| | be zipped and sent to the remote server. | ++--------------------------------+-----------------------------------------------------------+ +| ``$GALAXY_APOLLO_ORG_SUFFIX`` | Set to 'id' if you want organism names to be suffixed | +| | with user id to avoid name collisions. Set to 'email' to | +| | use user email as suffix. Leave empty for no suffix. | +--------------------------------+-----------------------------------------------------------+ License |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 create_account.py --- a/create_account.py Mon Jul 29 10:09:19 2019 -0400 +++ b/create_account.py Mon Dec 02 05:44:41 2019 -0500 |
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| @@ -4,35 +4,30 @@ import argparse import time -from six.moves.builtins import str - -from webapollo import PasswordGenerator, WAAuth, WebApolloInstance +from arrow.apollo import get_apollo_instance if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to add an account via web services') - WAAuth(parser) - parser.add_argument('email', help='User Email') parser.add_argument('--first', help='First Name', default='Jane') parser.add_argument('--last', help='Last Name', default='Aggie') args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() - password = PasswordGenerator(12) + password = wa.users._password_generator(12) time.sleep(1) - users = wa.users.loadUsers() + users = wa.users.get_users() user = [u for u in users - if u.username == args.email] + if u['username'] == args.email] if len(user) == 1: # Update name, regen password if the user ran it again - userObj = user[0] - returnData = wa.users.updateUser(userObj, args.email, args.first, args.last, password) + returnData = wa.users.update_user(args.email, args.first, args.last, password) print('Updated User\nUsername: %s\nPassword: %s' % (args.email, password)) else: - returnData = wa.users.createUser(args.email, args.first, args.last, password, role='user') + returnData = wa.users.create_user(args.email, args.first, args.last, password, role='user') print('Created User\nUsername: %s\nPassword: %s' % (args.email, password)) print("Return data: " + str(returnData)) |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 create_features_from_gff3.py --- a/create_features_from_gff3.py Mon Jul 29 10:09:19 2019 -0400 +++ b/create_features_from_gff3.py Mon Dec 02 05:44:41 2019 -0500 |
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| b'@@ -1,21 +1,19 @@\n #!/usr/bin/env python\n import argparse\n import logging\n-import sys\n-import time\n+\n+from apollo import accessible_organisms\n+from apollo.util import GuessOrg, OrgOrGuess\n \n-from BCBio import GFF\n+from arrow.apollo import get_apollo_instance\n \n-from six.moves.builtins import str\n-\n-from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry\n+from webapollo import UserObj, handle_credentials\n logging.basicConfig(level=logging.INFO)\n log = logging.getLogger(__name__)\n \n \n if __name__ == \'__main__\':\n parser = argparse.ArgumentParser(description=\'Sample script to add an attribute to a feature via web services\')\n- WAAuth(parser)\n parser.add_argument(\'email\', help=\'User Email\')\n parser.add_argument(\'--source\', help=\'URL where the input dataset can be found.\')\n OrgOrGuess(parser)\n@@ -23,165 +21,25 @@\n parser.add_argument(\'gff3\', type=argparse.FileType(\'r\'), help=\'GFF3 file\')\n args = parser.parse_args()\n \n- wa = WebApolloInstance(args.apollo, args.username, args.password)\n+ wa = get_apollo_instance()\n # User must have an account\n- gx_user = wa.users.assertOrCreateUser(args.email)\n+ gx_user = UserObj(**wa.users._assert_or_create_user(args.email))\n+ handle_credentials(gx_user)\n \n # Get organism\n org_cn = GuessOrg(args, wa)\n if isinstance(org_cn, list):\n org_cn = org_cn[0]\n \n- if not PermissionCheck(gx_user, org_cn, "WRITE"):\n- raise Exception("Action not permitted")\n- org = wa.organisms.findOrganismByCn(org_cn)\n-\n- bad_quals = [\'date_creation\', \'source\', \'owner\', \'date_last_modified\', \'Name\', \'ID\']\n-\n- sys.stdout.write(\'# \')\n- sys.stdout.write(\'\\t\'.join([\'Feature ID\', \'Apollo ID\', \'Success\', \'Messages\']))\n- sys.stdout.write(\'\\n\')\n- # print(wa.annotations.getFeatures())\n- for rec in GFF.parse(args.gff3):\n- wa.annotations.setSequence(rec.id, org[\'id\'])\n- for feature in rec.features:\n- # We can only handle genes right now\n- if feature.type not in (\'gene\', \'terminator\'):\n- continue\n- # Convert the feature into a presentation that Apollo will accept\n- featureData = featuresToFeatureSchema([feature])\n- if \'children\' in featureData[0] and any([child[\'type\'][\'name\'] == \'tRNA\' for child in featureData[0][\'children\']]):\n- # We\'re experiencing a (transient?) problem where gene_001 to\n- # gene_025 will be rejected. Thus, hardcode to a known working\n- # gene name and update later.\n-\n- featureData[0][\'name\'] = \'tRNA_000\'\n- tRNA_sf = [child for child in feature.sub_features if child.type == \'tRNA\'][0]\n- tRNA_type = \'tRNA-\' + tRNA_sf.qualifiers.get(\'Codon\', ["Unk"])[0]\n-\n- if \'Name\' in feature.qualifiers:\n- if feature.qualifiers[\'Name\'][0].startswith(\'tRNA-\'):\n- tRNA_type = feature.qualifiers[\'Name\'][0]\n-\n- newfeature = wa.annotations.addFeature(featureData, trustme=True)\n-\n- def func0():\n- wa.annotations.setName(\n- newfeature[\'features\'][0][\'uniquename\'],\n- tRNA_type,\n- )\n- retry(func0)\n-\n- if args.source:\n- gene_id = newfeature[\'features\'][0][\'parent_id\']\n-\n- def setSource():\n- wa.annotations.addAttributes(gene_id, {\'DatasetSource\': [args.source]})\n- retry(setSource)\n-\n- sys.stdout.write(\'\\t\'.join([\n- feature.id,\n- newfeature[\'features\'][0][\'uniquename\'],\n- \'success\',\n- ]))\n- elif featureData[0][\'type\'][\'name\'] == \'terminator\':\n- # We\'re experiencing a (transient?) problem where gene_001 to\n- # gene_025 will'..b'eature.id,\n- newfeature[\'features\'][0][\'uniquename\'],\n- \'success\',\n- ]))\n- else:\n- try:\n- # We\'re experiencing a (transient?) problem where gene_001 to\n- # gene_025 will be rejected. Thus, hardcode to a known working\n- # gene name and update later.\n- featureData[0][\'name\'] = \'gene_000\'\n- # Extract CDS feature from the feature data, this will be used\n- # to set the CDS location correctly (apollo currently screwing\n- # this up (2.0.6))\n- CDS = featureData[0][\'children\'][0][\'children\']\n- CDS = [x for x in CDS if x[\'type\'][\'name\'] == \'CDS\'][0][\'location\']\n- # Create the new feature\n- newfeature = wa.annotations.addFeature(featureData, trustme=True)\n- # Extract the UUIDs that apollo returns to us\n- mrna_id = newfeature[\'features\'][0][\'uniquename\']\n- gene_id = newfeature[\'features\'][0][\'parent_id\']\n- # Sleep to give it time to actually persist the feature. Apollo\n- # is terrible about writing + immediately reading back written\n- # data.\n- time.sleep(1)\n- # Correct the translation start, but with strand specific log\n- if CDS[\'strand\'] == 1:\n- wa.annotations.setTranslationStart(mrna_id, min(CDS[\'fmin\'], CDS[\'fmax\']))\n- else:\n- wa.annotations.setTranslationStart(mrna_id, max(CDS[\'fmin\'], CDS[\'fmax\']) - 1)\n-\n- # Finally we set the name, this should be correct.\n- time.sleep(0.5)\n- wa.annotations.setName(mrna_id, feature.qualifiers.get(\'product\', feature.qualifiers.get(\'Name\', ["Unknown"]))[0])\n- time.sleep(0.5)\n-\n- def func():\n- wa.annotations.setName(gene_id, feature.qualifiers.get(\'product\', feature.qualifiers.get(\'Name\', ["Unknown"]))[0])\n- retry(func)\n+ orgs = accessible_organisms(gx_user, [org_cn], \'WRITE\')\n+ if not orgs:\n+ raise Exception("You do not have write permission on this organism")\n \n- if args.source:\n- gene_id = newfeature[\'features\'][0][\'parent_id\']\n-\n- def setSource():\n- wa.annotations.addAttributes(gene_id, {\'DatasetSource\': [args.source]})\n- retry(setSource)\n- extra_attr = {}\n- for (key, values) in feature.qualifiers.items():\n- if key in bad_quals:\n- continue\n-\n- if key == \'Note\':\n- def func2():\n- wa.annotations.addComments(gene_id, values)\n- retry(func2)\n- else:\n- extra_attr[key] = values\n-\n- def func3():\n- wa.annotations.addAttributes(gene_id, extra_attr)\n- retry(func3)\n-\n- sys.stdout.write(\'\\t\'.join([\n- feature.id,\n- gene_id,\n- \'success\',\n- ]))\n- except Exception as e:\n- msg = str(e)\n- if \'\\n\' in msg:\n- msg = msg[0:msg.index(\'\\n\')]\n- sys.stdout.write(\'\\t\'.join([\n- feature.id,\n- \'\',\n- \'ERROR\',\n- msg\n- ]))\n- sys.stdout.write(\'\\n\')\n- sys.stdout.flush()\n+ wa.annotations.load_gff3(org_cn, args.gff3, args.source)\n' |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 create_or_update_organism.py --- a/create_or_update_organism.py Mon Jul 29 10:09:19 2019 -0400 +++ b/create_or_update_organism.py Mon Dec 02 05:44:41 2019 -0500 |
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| b'@@ -2,17 +2,25 @@\n from __future__ import print_function\n \n import argparse\n+import glob\n import json\n import logging\n import os\n import shutil\n+import stat\n import subprocess\n import sys\n+import tarfile\n import tempfile\n import time\n \n+from apollo import accessible_organisms\n+from apollo.util import GuessOrg, OrgOrGuess\n \n-from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance\n+from arrow.apollo import get_apollo_instance\n+\n+from webapollo import UserObj, handle_credentials\n+\n logging.basicConfig(level=logging.INFO)\n log = logging.getLogger(__name__)\n \n@@ -27,11 +35,24 @@\n return False\n \n \n+def IsOrgCNSuffixEnabled():\n+ if \'GALAXY_APOLLO_ORG_SUFFIX\' not in os.environ:\n+ return False\n+ value = os.environ[\'GALAXY_APOLLO_ORG_SUFFIX\'].lower()\n+ if value in (\'id\', \'email\'):\n+ return value\n+\n+ return False\n+\n+\n+def IsRemote():\n+ return \'GALAXY_SHARED_DIR\' not in os.environ or len(os.environ[\'GALAXY_SHARED_DIR\'].lower().strip()) == 0\n+\n+\n if __name__ == \'__main__\':\n parser = argparse.ArgumentParser(description=\'Create or update an organism in an Apollo instance\')\n- WAAuth(parser)\n- parser.add_argument(\'jbrowse_src\', help=\'Old JBrowse Data Directory\')\n- parser.add_argument(\'jbrowse\', help=\'JBrowse Data Directory\')\n+ parser.add_argument(\'jbrowse_src\', help=\'Source JBrowse Data Directory\')\n+ parser.add_argument(\'jbrowse\', help=\'Destination JBrowse Data Directory\')\n parser.add_argument(\'email\', help=\'User Email\')\n OrgOrGuess(parser)\n parser.add_argument(\'--genus\', help=\'Organism Genus\')\n@@ -39,94 +60,158 @@\n parser.add_argument(\'--public\', action=\'store_true\', help=\'Make organism public\')\n parser.add_argument(\'--group\', help=\'Give access to a user group\')\n parser.add_argument(\'--remove_old_directory\', action=\'store_true\', help=\'Remove old directory\')\n+ parser.add_argument(\'--no_reload_sequences\', action=\'store_true\', help=\'Disable update genome sequence\')\n+ parser.add_argument(\'--userid\', help=\'User unique id\')\n args = parser.parse_args()\n CHUNK_SIZE = 2**20\n blat_db = None\n \n+ path_fasta = args.jbrowse_src + \'/seq/genome.fasta\'\n+\n # Cleanup if existing\n- if(os.path.exists(args.jbrowse)):\n- shutil.rmtree(args.jbrowse)\n- # Copy files\n- shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)\n+ if not IsRemote():\n+ if(os.path.exists(args.jbrowse)):\n+ shutil.rmtree(args.jbrowse)\n+ # Copy files\n+ shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)\n \n- path_fasta = args.jbrowse + \'/seq/genome.fasta\'\n- path_2bit = args.jbrowse + \'/seq/genome.2bit\'\n+ path_2bit = args.jbrowse + \'/seq/genome.2bit\'\n+ else:\n+ twobittemp = tempfile.NamedTemporaryFile(prefix="genome.2bit")\n+ path_2bit = twobittemp.name\n+ os.chmod(path_2bit, stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IROTH)\n \n # Convert fasta if existing\n- if(IsBlatEnabled() and os.path.exists(path_fasta)):\n+ if IsBlatEnabled() and os.path.exists(path_fasta):\n arg = [\'faToTwoBit\', path_fasta, path_2bit]\n- tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr")\n- proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno())\n- return_code = proc.wait()\n- if return_code:\n- tmp_stderr.flush()\n- tmp_stderr.seek(0)\n+ proc = subprocess.Popen(args=arg, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)\n+ out, err = proc.communicate()\n+ if proc.returncode:\n print("Error building index:", file=sys.stderr)\n- while True:\n- chunk = tmp_stderr.read(CHUNK_SIZE)\n- if not chunk:\n- break\n- sys.stderr.write(chunk)\n- sys.exit(return_code)\n- blat_db = path_2bit\n- tmp_stderr.close()\n+ sys.stderr.write(er'..b' blatdb=blat_db,\n+ genus=args.genus,\n+ species=args.species,\n+ public=args.public,\n+ no_reload_sequences=args.no_reload_sequences\n+ )\n+ else:\n+ data = wa.organisms.update_organism(\n+ org[\'id\'],\n+ org_cn,\n+ args.jbrowse,\n+ # mandatory\n+ genus=args.genus,\n+ species=args.species,\n+ public=args.public,\n+ blatdb=blat_db,\n+ no_reload_sequences=args.no_reload_sequences\n+ )\n time.sleep(2)\n- if args.remove_old_directory and args.jbrowse != old_directory:\n+\n+ if not IsRemote() and args.remove_old_directory and args.jbrowse != old_directory:\n shutil.rmtree(old_directory)\n \n- data = [wa.organisms.findOrganismById(org[\'id\'])]\n+ data = wa.organisms.show_organism(org_cn)\n \n else:\n # New organism\n log.info("\\tAdding Organism")\n- data = wa.organisms.addOrganism(\n- org_cn,\n- args.jbrowse,\n- genus=args.genus,\n- species=args.species,\n- public=args.public,\n- blatdb=blat_db\n- )\n+\n+ if IsRemote():\n+ with tempfile.NamedTemporaryFile(suffix=\'.tar.gz\') as archive:\n+ with tarfile.open(archive.name, mode="w:gz") as tar:\n+ dataset_data_dir = args.jbrowse_src\n+ for file in glob.glob(dataset_data_dir):\n+ tar.add(file, arcname=file.replace(dataset_data_dir, \'./\'))\n+ if IsBlatEnabled():\n+ with tempfile.TemporaryDirectory() as empty_dir:\n+ os.chmod(empty_dir, stat.S_IRUSR | stat.S_IXUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)\n+ tar.add(empty_dir, arcname="./searchDatabaseData/")\n+ tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")\n+ data = wa.remote.add_organism(\n+ org_cn,\n+ archive,\n+ blatdb=blat_db,\n+ genus=args.genus,\n+ species=args.species,\n+ public=args.public,\n+ metadata=None\n+ )\n+ if isinstance(data, list) and len(data) > 0:\n+ data = data[0]\n+ else:\n+ data = wa.organisms.add_organism(\n+ org_cn,\n+ args.jbrowse,\n+ blatdb=blat_db,\n+ genus=args.genus,\n+ species=args.species,\n+ public=args.public,\n+ metadata=None\n+ )\n \n # Must sleep before we\'re ready to handle\n time.sleep(2)\n log.info("Updating permissions for %s on %s", gx_user, org_cn)\n- wa.users.updateOrganismPermission(\n- gx_user, org_cn,\n+ wa.users.update_organism_permissions(\n+ gx_user.username,\n+ org_cn,\n write=True,\n export=True,\n read=True,\n@@ -134,10 +219,9 @@\n \n # Group access\n if args.group:\n- group = wa.groups.loadGroupByName(name=args.group)\n- res = wa.groups.updateOrganismPermission(group, org_cn,\n- administrate=False, write=True, read=True,\n- export=True)\n+ group = wa.groups.get_groups(name=args.group)[0]\n+ res = wa.groups.update_organism_permissions(group[\'name\'], org_cn,\n+ administrate=False, write=True, read=True,\n+ export=True)\n \n- data = [o for o in data if o[\'commonName\'] == org_cn]\n print(json.dumps(data, indent=2))\n' |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 delete_features.py --- a/delete_features.py Mon Jul 29 10:09:19 2019 -0400 +++ b/delete_features.py Mon Dec 02 05:44:41 2019 -0500 |
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| @@ -5,40 +5,54 @@ import logging import random -from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance, retry +from apollo import accessible_organisms +from apollo.util import GuessOrg, OrgOrGuess, retry + +from arrow.apollo import get_apollo_instance + +from webapollo import UserObj, handle_credentials + logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Sample script to delete all features from an organism') - WAAuth(parser) + parser = argparse.ArgumentParser(description='Script to delete all features from an organism') parser.add_argument('email', help='User Email') parser.add_argument('--type', help='Feature type filter') OrgOrGuess(parser) args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() # User must have an account - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] - if not PermissionCheck(gx_user, org_cn, "WRITE"): - raise Exception("Action not permitted") - org = wa.organisms.findOrganismByCn(org_cn) + all_orgs = wa.organisms.get_organisms() + if 'error' in all_orgs: + all_orgs = [] + all_orgs = [org['commonName'] for org in all_orgs] + if org_cn not in all_orgs: + raise Exception("Could not find organism %s" % org_cn) - sequences = wa.organisms.getSequencesForOrganism(org['id']) + orgs = accessible_organisms(gx_user, [org_cn], 'WRITE') + if not orgs: + raise Exception("You do not have write permission on this organism") + org = wa.organisms.show_organism(org_cn) + + sequences = wa.organisms.get_sequences(org['id']) for sequence in sequences['sequences']: log.info("Processing %s %s", org['commonName'], sequence['name']) # Call setSequence to tell apollo which organism we're working with - wa.annotations.setSequence(sequence['name'], org['id']) + wa.annotations.set_sequence(org['id'], sequence['name']) # Then get a list of features. - features = wa.annotations.getFeatures() + features = wa.annotations.get_features() # For each feature in the features for feature in sorted(features['features'], key=lambda x: random.random()): if args.type: @@ -60,7 +74,7 @@ # We see that deleteFeatures wants a uniqueName, and so we pass # is the uniquename field in the feature. def fn(): - wa.annotations.deleteFeatures([feature['uniquename']]) + wa.annotations.delete_feature(feature['uniquename']) print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name'])) if not retry(fn, limit=3): |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 delete_features.xml --- a/delete_features.xml Mon Jul 29 10:09:19 2019 -0400 +++ b/delete_features.xml Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -7,29 +7,32 @@ <expand macro="requirements"/> <code file="webapollo.py"/> <command detect_errors="aggressive"><![CDATA[ +@AUTH@ + #if str($ask_one) == "yes": ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. - python $__tool_directory__/export.py - @ADMIN_AUTH@ + python '$__tool_directory__/export.py' @ORG_OR_GUESS@ - --gff "$gff_out" - --fasta "$fasta_out" - --json "$json_out" - "$__user_email__" + --gff '$gff_out' + --fasta_pep '$fasta_pep' + --fasta_cds '$fasta_cds' + --fasta_cdna '$fasta_cdna' + --vcf '$vcf_out' + --json '$json_out' + '$__user_email__' && ## Now we delete - python $__tool_directory__/delete_features.py - @ADMIN_AUTH@ + python '$__tool_directory__/delete_features.py' @ORG_OR_GUESS@ - "$__user_email__" + '$__user_email__' #if str($filter) != "all" --type $filter #end if - > $output; + > '$output'; #else - echo "Nothing to do" > $output; + echo "Nothing to do" > '$output'; #end if ]]></command> <inputs> @@ -43,23 +46,49 @@ <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/> </inputs> <outputs> - <data format="tabular" name="output" label="Process and Error Log"> + <data format="txt" name="output" label="Process and Error Log"> <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" visible="true"/> </data> - <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> - <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> - <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> + <data format="gff3" name="gff_out" label="Annotations from Apollo"/> + <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/> + <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/> + <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/> + <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/> + <data format="json" name="json_out" label="Metadata from Apollo"/> </outputs> <tests> - <test expect_failure="true"> + <test> <conditional name="org_source"> <param name="source_select" value="direct"/> - <param name="org_raw" value="Test org" /> + <param name="org_raw" value="org4" /> </conditional> <param name="filter" value="all"/> <param name="ask_one" value="yes"/> - <expand macro="test_result" /> + + <output name="gff_out"> + <assert_contents> + <has_text text="##sequence-region Merlin 1 172788" /> + <has_text text="owner=admin@local.host;" /> + <has_text text="Name=cds-not-under-exon" /> + </assert_contents> + </output> + <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/> + <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/> + <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/> + <output name="vcf_out" file="export/out.vcf" lines_diff="4"/> + <output name="json_out"> + <assert_contents> + <has_text text="org4" /> + <has_text text="apollo_shared_dir/org4" /> + </assert_contents> + </output> + <output name="output"> + <assert_contents> + <has_text text="Deleted" /> + <has_text text="[type=mRNA]" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 delete_organism.py --- a/delete_organism.py Mon Jul 29 10:09:19 2019 -0400 +++ b/delete_organism.py Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -3,41 +3,56 @@ import argparse import logging +import os -from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance +from apollo import accessible_organisms +from apollo.util import GuessOrg, OrgOrGuess + +from arrow.apollo import get_apollo_instance + +from webapollo import UserObj, handle_credentials + logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) +def IsRemote(): + return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0 + + if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Sample script to completely delete an organism') - WAAuth(parser) + parser = argparse.ArgumentParser(description='Script to completely delete an organism') parser.add_argument('email', help='User Email') OrgOrGuess(parser) args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() + # User must have an account - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] - if not PermissionCheck(gx_user, org_cn, "WRITE"): - raise Exception("You do not have write permission on this organism") - org = wa.organisms.findOrganismByCn(org_cn) + all_orgs = wa.organisms.get_organisms() + if 'error' in all_orgs: + all_orgs = [] + all_orgs = [org['commonName'] for org in all_orgs] + if org_cn not in all_orgs: + raise Exception("Could not find organism %s" % org_cn) - # Call setSequence to tell apollo which organism we're working with - wa.annotations.setSequence(org['commonName'], org['id']) - # Then get a list of features. - features = wa.annotations.getFeatures() - # For each feature in the features - # If it exists - if 'features' in features: - for feature in features['features']: - # We see that deleteFeatures wants a uniqueName, and so we pass - # is the uniquename field in the feature. - print(wa.annotations.deleteFeatures([feature['uniquename']])) + orgs = accessible_organisms(gx_user, [org_cn], 'WRITE') + if not orgs: + raise Exception("You do not have write permission on this organism") + org = wa.organisms.show_organism(org_cn) + + wa.organisms.delete_features(org['id']) + + if IsRemote(): + print(wa.remote.delete_organism(org['commonName'])) + else: + print(wa.organisms.delete_organism(org['id'])) |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 export.py --- a/export.py Mon Jul 29 10:09:19 2019 -0400 +++ b/export.py Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -3,89 +3,86 @@ import argparse import json -import sys - -from BCBio import GFF - -from Bio import SeqIO - -from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance - -try: - import StringIO as io -except ImportError: - import io - - -def export(org_cn, seqs): - org_data = wa.organisms.findOrganismByCn(org_cn) - - data = io.StringIO() - - kwargs = dict( - exportType='GFF3', - seqType='genomic', - exportGff3Fasta=True, - output="text", - exportFormat="text", - organism=org_cn, - ) +import time - if len(seqs) > 0: - data.write(wa.io.write( - exportAllSequences=False, - sequences=seqs, - **kwargs - ).encode('utf-8')) - else: - data.write(wa.io.write( - exportAllSequences=True, - sequences=[], - **kwargs - ).encode('utf-8')) - - # Seek back to start - data.seek(0) +from apollo import accessible_organisms +from apollo.util import CnOrGuess, GuessCn - records = list(GFF.parse(data)) - if len(records) == 0: - print("Could not find any sequences or annotations for this organism + reference sequence") - sys.exit(2) - else: - for record in records: - record.annotations = {} - record.features = sorted(record.features, key=lambda x: x.location.start) - if args.gff: - GFF.write([record], args.gff) - record.description = "" - if args.fasta: - SeqIO.write([record], args.fasta, 'fasta') +from arrow.apollo import get_apollo_instance - return org_data - +from webapollo import UserObj, handle_credentials if __name__ == '__main__': - parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') - WAAuth(parser) + parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services') CnOrGuess(parser) parser.add_argument('--gff', type=argparse.FileType('w')) - parser.add_argument('--fasta', type=argparse.FileType('w')) + parser.add_argument('--fasta_pep', type=argparse.FileType('w')) + parser.add_argument('--fasta_cds', type=argparse.FileType('w')) + parser.add_argument('--fasta_cdna', type=argparse.FileType('w')) + parser.add_argument('--vcf', type=argparse.FileType('w')) parser.add_argument('--json', type=argparse.FileType('w')) parser.add_argument('email', help='User Email') args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) - - org_cn_list, seqs = GuessCn(args, wa) + wa = get_apollo_instance() # User must have an apollo account, if not, create it - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) + + org_cns, seqs = GuessCn(args, wa) + if not isinstance(org_cns, list): + org_cns = [org_cns] + + all_orgs = wa.organisms.get_organisms() + if 'error' in all_orgs: + all_orgs = [] + all_orgs = [org['commonName'] for org in all_orgs] org_data = [] - for org_cn in org_cn_list: - # User must have read permission on organism - if not PermissionCheck(gx_user, org_cn, "READ"): - continue - indiv_org_data = export(org_cn, seqs) - org_data.append(indiv_org_data) + for org_cn in org_cns: + if org_cn not in all_orgs: + raise Exception("Could not find organism %s" % org_cn) + + orgs = accessible_organisms(gx_user, [org_cn], 'READ') + if not orgs: + raise Exception("You do not have read permission on organism %s" % org_cn) + + org = wa.organisms.show_organism(org_cn) + + uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs) + if 'error' in uuid_gff or 'uuid' not in uuid_gff: + raise Exception("Apollo failed to prepare the file for download: %s" % uuid_gff) + args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text")) + + time.sleep(1) + + uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs) + if 'error' in uuid_vcf or 'uuid' not in uuid_vcf: + raise Exception("Apollo failed to prepare the file for download: %s" % uuid_vcf) + args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text")) + + time.sleep(1) + + uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna') + if 'error' in uuid_fa or 'uuid' not in uuid_fa: + raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa) + args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text")) + + time.sleep(1) + + uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds') + if 'error' in uuid_fa or 'uuid' not in uuid_fa: + raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa) + args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text")) + + time.sleep(1) + + uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide') + if 'error' in uuid_fa or 'uuid' not in uuid_fa: + raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa) + args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text")) + + org_data.append(org) + args.json.write(json.dumps(org_data, indent=2)) |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 fetch_organism_jbrowse.py --- a/fetch_organism_jbrowse.py Mon Jul 29 10:09:19 2019 -0400 +++ b/fetch_organism_jbrowse.py Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -9,7 +9,13 @@ import sys import time -from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance +from apollo import accessible_organisms +from apollo.util import GuessOrg, OrgOrGuess + +from arrow.apollo import get_apollo_instance + +from webapollo import UserObj, handle_credentials + logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) @@ -52,27 +58,34 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services') - WAAuth(parser) OrgOrGuess(parser) parser.add_argument('target_dir', help='Target directory') parser.add_argument('email', help='User Email') args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() # User must have an account org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] - org = wa.organisms.findOrganismByCn(org_cn) # User must have an account, if not, create it - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) + + all_orgs = wa.organisms.get_organisms() + if 'error' in all_orgs: + all_orgs = [] + all_orgs = [org['commonName'] for org in all_orgs] + if org_cn not in all_orgs: + raise Exception("Could not find organism %s" % org_cn) # User must have READ access - - if not PermissionCheck(gx_user, org_cn, "READ"): - raise Exception("READ permissions are required for this action") + orgs = accessible_organisms(gx_user, [org_cn], 'READ') + if not orgs: + raise Exception("You do not have write permission on this organism") + org = wa.organisms.show_organism(org_cn) if not os.path.exists(args.target_dir): os.makedirs(args.target_dir) @@ -94,7 +107,7 @@ # files / folders before and after. sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') - sys.stderr.write(subprocess.check_output(cmd)) + sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/')), os.path.join(args.target_dir, 'data') @@ -104,7 +117,7 @@ sys.stderr.write('\n') sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') - sys.stderr.write(subprocess.check_output(cmd)) + sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/'), 'data'), os.path.join(args.target_dir, 'data') @@ -113,7 +126,7 @@ sys.stderr.write('\n') sys.stderr.write(' '.join(cmd)) sys.stderr.write('\n') - sys.stderr.write(subprocess.check_output(cmd)) + sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding)) if not are_dir_trees_equal( os.path.join(org['directory'].rstrip('/'), 'data'), os.path.join(args.target_dir, 'data') |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 list_organisms.py --- a/list_organisms.py Mon Jul 29 10:09:19 2019 -0400 +++ b/list_organisms.py Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -4,19 +4,23 @@ import argparse import json -from webapollo import WAAuth, WebApolloInstance, accessible_organisms +from apollo import accessible_organisms + +from arrow.apollo import get_apollo_instance + +from webapollo import UserObj, handle_credentials if __name__ == '__main__': parser = argparse.ArgumentParser(description='List all organisms available in an Apollo instance') - WAAuth(parser) parser.add_argument('email', help='User Email') args = parser.parse_args() - wa = WebApolloInstance(args.apollo, args.username, args.password) + wa = get_apollo_instance() - gx_user = wa.users.assertOrCreateUser(args.email) + gx_user = UserObj(**wa.users._assert_or_create_user(args.email)) + handle_credentials(gx_user) - all_orgs = wa.organisms.findAllOrganisms() + all_orgs = wa.organisms.get_organisms() orgs = accessible_organisms(gx_user, all_orgs) |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 macros.xml --- a/macros.xml Mon Jul 29 10:09:19 2019 -0400 +++ b/macros.xml Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -1,14 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">4.0.0</token> + <token name="@WRAPPER_VERSION@">4.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> - <requirement type="package" version="2.12.4">requests</requirement> - <requirement type="package" version="1.11.0">six</requirement> + <requirement type="package" version="4.1">apollo</requirement> <yield/> </requirements> </xml> @@ -19,20 +15,27 @@ <token name="@URL@"> "\$GALAXY_WEBAPOLLO_URL" </token> - <token name="@ADMIN_AUTH@"> -"\$GALAXY_WEBAPOLLO_URL" -"\$GALAXY_WEBAPOLLO_USER" -"\$GALAXY_WEBAPOLLO_PASSWORD" - </token> + + <token name="@AUTH@"><![CDATA[ + if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then + echo "__default: local" > '.auth.yml' && + echo "local:" >> '.auth.yml' && + echo " url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' && + echo " username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' && + echo " password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' && + + export ARROW_GLOBAL_CONFIG_PATH='.auth.yml' + ; fi && + ]]></token> <token name="@ORG_OR_GUESS@"> <![CDATA[ #if $org_source.source_select == "auto_json": - --org_json "${org_source.org_file}" + --org_json '${org_source.org_file}' #elif $org_source.source_select == "select": - --org_id "${org_source.org_select}" + --org_id '${org_source.org_select}' #else: - --org_raw "${org_source.org_raw}" + --org_raw '${org_source.org_raw}' #end if ]]> </token> @@ -42,13 +45,13 @@ #if $cn_source.source_select == "auto": #if str($cn_source.cn_file) != "None": - --seq_fasta $cn_source.cn_file + --seq_fasta '$cn_source.cn_file' #end if #else #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0: --seq_raw #for $item in $cn_source.refseqs: - "${item.refseq}" + '${item.refseq}' #end for #end if #end if @@ -93,12 +96,6 @@ </conditional> </xml> - <xml name="test_result"> - <assert_stderr> - <has_text text="MissingSchema" /> - </assert_stderr> - </xml> - <xml name="citations"> <citations> <citation type="doi">10.1371/journal.pcbi.1006790</citation> @@ -109,12 +106,12 @@ </xml> <token name="@GENOME_SELECTOR_PRE@"> #if $reference_genome.reference_genome_source == 'history': - ln -s $reference_genome.genome_fasta genomeref.fa; + ln -s '$reference_genome.genome_fasta' genomeref.fa; #end if </token> <token name="@GENOME_SELECTOR@"> #if $reference_genome.reference_genome_source == 'cached': - "${reference_genome.fasta_indexes.fields.path}" + '${reference_genome.fasta_indexes.fields.path}' #elif $reference_genome.reference_genome_source == 'history': genomeref.fa #end if |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/arrow.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arrow.yml Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,5 @@ +__default: local +local: + url: "http://localhost:8888" + username: "admin@local.host" + password: "password" |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/bad-model.gff3 --- a/test-data/bad-model.gff3 Mon Jul 29 10:09:19 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -##gff-version 3 -##sequence-region Maroon_JMcDermott 1 144762 -Maroon_JMcDermott . gene 14488 14805 . + . Name=gene_26;date_creation=2016-02-17;owner=jmc_texas@tamu.edu;ID=707c88b7-36d1-44e3-93e6-d1d4f1219d57;date_last_modified=2016-02-17 -Maroon_JMcDermott . mRNA 14488 14805 . + . Name=gene_26-00001;date_creation=2016-02-17;Parent=707c88b7-36d1-44e3-93e6-d1d4f1219d57;owner=jmc_texas@tamu.edu;ID=8760695d-b88c-41c0-857b-540e6db81fe8;date_last_modified=2016-02-17 -Maroon_JMcDermott . CDS 14707 14805 . + 0 Name=94abf796-4c8d-45f4-916b-4d279616565e-CDS;Parent=8760695d-b88c-41c0-857b-540e6db81fe8;ID=94abf796-4c8d-45f4-916b-4d279616565e -Maroon_JMcDermott . exon 14497 14805 . + . Name=d2ebd8d0-6558-4674-a38f-346f88256340-exon;Parent=8760695d-b88c-41c0-857b-540e6db81fe8;ID=d2ebd8d0-6558-4674-a38f-346f88256340 -Maroon_JMcDermott . exon 14488 14491 . + . Name=2e4119f9-3220-4502-8ddd-4821c872e0d6-exon;Parent=8760695d-b88c-41c0-857b-540e6db81fe8;ID=2e4119f9-3220-4502-8ddd-4821c872e0d6 -Maroon_JMcDermott . non_canonical_five_prime_splice_site 14494 14494 . + . Name=8760695d-b88c-41c0-857b-540e6db81fe8-non_canonical_five_prime_splice_site-14493;Parent=8760695d-b88c-41c0-857b-540e6db81fe8;ID=8760695d-b88c-41c0-857b-540e6db81fe8-non_canonical_five_prime_splice_site-14493 -Maroon_JMcDermott . non_canonical_three_prime_splice_site 14497 14497 . + . Name=8760695d-b88c-41c0-857b-540e6db81fe8-non_canonical_three_prive_splice_site-14496;Parent=8760695d-b88c-41c0-857b-540e6db81fe8;ID=8760695d-b88c-41c0-857b-540e6db81fe8-non_canonical_three_prive_splice_site-14496 |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/create_org/output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/create_org/output.json Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +{ + "commonName": "Test org", + "blatdb": "/data/temporary/apollo_data/1384-Test_org/searchDatabaseData/genome.2bit", + "metadata": "{\"creator\":\"20\"}", + "annotationCount": 0, + "currentOrganism": true, + "obsolete": false, + "sequences": 1, + "directory": "/XX/apollo_shared_dir/1", + "publicMode": false, + "valid": true, + "genus": "genus", + "species": null, + "id": 23, + "nonDefaultTranslationTable": null +} |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/create_org/output2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/create_org/output2.json Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +{ + "commonName": "Test org", + "blatdb": "/data/temporary/apollo_data/1384-Test_org/searchDatabaseData/genome.2bit", + "metadata": "{\"creator\":\"20\"}", + "annotationCount": 0, + "currentOrganism": true, + "obsolete": false, + "sequences": 1, + "directory": "/XX/apollo_shared_dir/3", + "publicMode": false, + "valid": true, + "genus": "genus2", + "species": "sp", + "id": 23, + "nonDefaultTranslationTable": null +} |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1.dat Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,44 @@ +<!DOCTYPE html> +<html> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> + <title>JBrowse</title> + + <link rel="apple-touch-icon" sizes="180x180" href="img/favicons/apple-touch-icon.png"> + <link rel="icon" type="image/png" sizes="32x32" href="img/favicons/favicon-32x32.png"> + <link rel="icon" type="image/png" sizes="16x16" href="img/favicons/favicon-16x16.png"> + <link rel="manifest" href="site.webmanifest"> + <link rel="mask-icon" href="img/favicons/safari-pinned-tab.svg" color="#5bbad5"> + <meta name="msapplication-TileColor" content="#2d89ef"> + <meta name="theme-color" content="#ffffff"> + + <script type="text/javascript"> + window.onerror=function(msg){ + if( document.body ) + document.body.setAttribute("JSError",msg); + } + if(window.process&&process.versions&&process.versions.electron) { + window.electronRequire = require; + delete window.require; + } + </script> + <style> + html, body, div.jbrowse { + margin: 0; + padding: 0; + height: 100%; + width: 100%; + } + </style> + <script type="text/javascript" src="dist/main.bundle.js" charset="utf-8"></script> + </head> + + <body> + <div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": false, "cacheBuster": true'> + <div id="LoadingScreen" style="padding: 50px;"> + <h1>Loading...</h1> + </div> + </div> + <div style="display: none">JBrowseDefaultMainPage</div> + </body> +</html> |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/.htaccess --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/.htaccess Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +# This Apache .htaccess file is generated by JBrowse (GenomeDB) for +# allowing cross-origin requests as defined by the Cross-Origin +# Resource Sharing working draft from the W3C +# (http://www.w3.org/TR/cors/). In order for Apache to pay attention +# to this, it must have mod_headers enabled, and its AllowOverride +# configuration directive must allow FileInfo overrides. +<IfModule mod_headers.c> + Header onsuccess set Access-Control-Allow-Origin * + Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range +</IfModule> |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/02b/9.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/02b/9.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"merli":{"exact":[],"prefix":["Merlin"]}} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/0e9/3.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/0e9/3.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"mer":{"prefix":["Merlin"],"exact":[]}} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/83f/8.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/83f/8.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"merlin":{"prefix":[],"exact":[["Merlin",null,"Merlin",null,0,172788,null]]}} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/92c/2.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/92c/2.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"me":{"prefix":["Merlin"],"exact":[]}} \ No newline at end of file |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/cf0/e.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/cf0/e.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"merl":{"prefix":["Merlin"],"exact":[]}} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/f26/8.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/f26/8.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"m":{"exact":[],"prefix":["Merlin"]}} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/names/meta.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/names/meta.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +{"compress":0,"track_names":[],"format":"json","lowercase_keys":1,"hash_bits":16} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz |
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| Binary file test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz has changed |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz.tbi |
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| Binary file test-data/dataset_1_files/data/raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz.tbi has changed |
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| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/seq/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/seq/genome.fasta Mon Dec 02 05:44:41 2019 -0500 |
| b |
| b'@@ -0,0 +1,2881 @@\n+>Merlin\n+TCGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGA\n+GCATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCC\n+TCTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTA\n+TACTGCTGAGACGCCTGATGATTATAATCGTTTCGCAAACCCAGAAGATATAATTGATAT\n+TGGCGCTACTCAAAAAGACTCATTTGACGATAACAATAATGATGGAACATCTATTAATAT\n+CGGCAAACAAGTTAATTTAGGATTCGTTATTTCCGGTGCTGAAAATGTTCGAGTTATTGT\n+TCCAGGTTCTTTAACTGAATATCCAGAAGAAGCGGAAGTTATTCTGCCTCGTGGTACTCT\n+TTTGAAGATCAATAAAATCACTACTCAAGTAGATAAACGCTCGAATAAGTTCATGGTTGA\n+AGGTTCAATCGTTCCGCCTTCTGAGCAAATTGATGAATCTGTTGAGATTTATGACGGTGA\n+TCTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGA\n+ATCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGA\n+CATTGATGACATGCCACGTAAGTTCCGCTAGCCGTTTACATCCACATGGAAGTGGATTAT\n+AATGGCTCTACGTTAACAAGAGGAAAACAACATGAAATCAATTTTTCGTATCAACGGTGT\n+AGAAATTGTAGTTGAAGATGTAGTTCCTATGTCTTATGAATTCAATGAAGTTGTTTTCAA\n+AGAGCTTAAGAAAATTTTAGGCGATAAGAAGCTTCAAAGTACTCCAATTGGACGTTTTGG\n+AATGAAAGAAAACGTTGATACTTATATTGAAAGTGTAGTGACAGGGCAGTTAGAAGGTGA\n+ATTTTCTGTAGCAGTTCAAACTGTAGAAAATGATGAAGTTATTTTAACTTTACCAGCTTT\n+CGTAATTTTCCGCAAATAAAACAATGGGGAGCTATGCTCCCCATTTTTACAATCCAAGTA\n+TTTTCGAAGTAGAGTTTCGGGTCGAATTAATGACGTGAGACAACCCTCCAGCAGCTCCTC\n+CAAGTCTAGATAATCTACTTAAACTTCCATTAAGAGACATTTCACTATTAATTCCAGTTA\n+TAGAATTAACAGCTCTATCTTCAATCCAATCAAGAGCAGCTTGACGTCCAACAGCACCCG\n+TTTGCATTACTCTGTAAGCAAATGTAACATCGAAAACCGCAATTTGGTTATCTCCTTCAT\n+ATGTAAGCTCAGGAGCTCCACACGCAACAGGAACACAACCTGTGAACATTATCACAGTAT\n+GAGGTAATCCATTTCGAGCATGAAGGTTAACCTGAATGTCAGCTTCGACGTCAGTTGGTA\n+ATGCTCGCAATCCAGTAACCGGGTCTTGAACGGAGTTCACCCAATCTTGCATTGCACGAT\n+AGTTACTTGCTTCGGGATCCATTCTGAATGATATAGTTAACGGATCGAGTTCACGTCCAG\n+TTATTCTAATATTCGGTGAGTTATGGTTGAAATCCATTTCATGAGACAATCTGTTCTCTG\n+GAATTTTGACCGAATAAATCATCAATCCAGATTGCGGATAAGCCATGTTAAAGAAGTCTA\n+ACAAATAAGTTCCGACTTCAAATTCACCTAATAAAGACTGAACAACACGATTGCTCATTG\n+CTCCAATAAGATATTTCGATACACCAGACTTTCTTACCAGCTGTTGAGTACCGGCAGTGA\n+TAATTGAGGTGAGTCCTGATGTGAACTCACCTTGTGTTAATCCAAGCCAGTCATTATTCA\n+ACGGAAGGTTATTAAAGAGCATACCGCCAAATTGATCGAGTAATTGTTGAGACTTTGCTG\n+ACGGAGTAGTTGCAAATACACAACTAAACATATTAGTACGCTGAAAGTCTATATTACCCG\n+CTTGGTTTTTAAATTCATCTAAAGTTAGCATCAGAATCCTTCCGCATATACTGAAGCTCG\n+GTTCAATGTCAAGATTTCACGCATAGTAATTTCTAATGTGAATGTACTTGGCAGGTTTGG\n+AGCTATAGCTAAACCGTTAAAGTTTCCATTTGGAGTTTTATCAAAACGGATACTCTGAAT\n+TTGACATGGACCGAATACTTCAGCACGTCCATCGAATTTACTTGTGGTTCCAAAGTTTCT\n+GACGAACCACACAGTAGGGTTACTTACAACAATAACATTACTTAAGAATGAAGTTATTTT\n+CTCAAAAACAGTGTCATTTTTATTAGCTTCATCTGGAGTTAATGTATCAAGGAAAGTTGA\n+TTTATACCATTCATCTAATTGAGACTTAACTTCTTTTGCATAAGTAGACGTTCCCGTTTC\n+GCCATAACTATAGTAGTTAAAGTATTCATAGATCTCGATAATAGCAATAAGATCTTGTAC\n+TGATCGAGGAGTTAAATCCCACGTGAATACCTTCGTACGGTTATCTGCGCCGCCATACAT\n+TGATCGAGCAGTGTTATAGATCTGCTCGTTATGGTCAGCCATTAATCCTTGAGTCAATGA\n+CTCTAATCCGCCAAAGACAGCAGTAGATGCAACGTTACTTAATACCCCTGTAGCAGTACC\n+GCCGCCACGAGAAATAAGTGAATCTCCAACGTCATTAAATTTATGAGAAACTGATTCAAC\n+ATCTGATTTCGAGCGTGGAAGTAAAATATTCACTACTGGAATTTTATCAACTTTATTAGT\n+ATTTGTTCCAGTGATTGATTTCACTACACTATTTGCAGTACGTTTCATTTCACCTAAACG\n+CATGCTACGCATATCACCGGTTGTACGAGAATTCATATCATACGCAGTGAACAACAACCC\n+GTTCTTATAAAGATCATGAACTCGTAAAGAACCAGATGTGTCATTACCAGCTGAACGTTC\n+AGACGGATATTGCGCAGTTATAGTGGATTTTATTTTTGCTGATTGTGAACTTTGACCAGC\n+GGAGGTTTTAACTCCGCTAATTAAAGCATCAGTCTTATCATCTAATTCTCTGACTTTAAT\n+GCTCATTAATTAACTCCTGTTGCCCCGAATACTCCAGGAGCTGGAGTAGCCGTGACTGTT\n+TGAACCTGGTGAATAGTCTTACTATTATTTACGTTATTAACCTGAGTGTTAGCAACATTC\n+ATATCACCGGTTGATTTTTTAGATTGCTCTTTAGCATTTTCAGCTTTTTGAATATTTTGA\n+ACTCGTTGATTATCTTCCGAAGTAGCTGGAGCCGCAGGCTTCGGAGTGTTATCTTCTTTG\n+AGCTTCTGATACTTGGATTCTACTCGTTGGAATCTTTTATCGAGTTCCTTTTTAGTAGCT\n+GGTTGATCACTTATAGCAGAATCACTAATAGACTTTTTGGCACTGTTATATGCCTTCTCT\n+AAAGATTGCATATTAGTTGGATTCTCTGGATCAACATCACCAATATATTTTTCTAAACGC\n+TGAACAGCTGCACGAGCTTCGTTTTGTTTGATCAGTGTTTCTTCGCGTTTTTCAGGAGCC\n+ATTGCTTTAAGATTCTGAGTCTCTTGATCACGGTCAGATGCTTGTGTAGAATCGATTTTA\n+TTCTCTCTTCCTAGTACCCAATCAAATGCACGAGTTTTAAATTCGCCAGCTTTATCAATA\n+ATTCCAGGACCTTCTTCAATACGCTTACTCTGATATTTAGCCAAAGCTTTTTGATCATCT\n+TCAGACAATGAATTACCAGTGCGTTCCTGGAATCCTTCTAGTGCTGAACCACGAATAGTA\n+GTTGCTGCATTTTCAAAGCCAAGTGCATCGAGTATAGAAGCAGATATCTTTGAAATTCCC\n+AA'..b'ATTTCCATGAGGTTACTGGGTTATGAGTTATAAAATTCTTTT\n+AGAAGTTACCGTGATGTCTTCGACTGGACATGTGGCGGTTAGTACTGAACAGCTGGATTT\n+TTATAGCTGGGATAATGCTAATATGTATTATGAAGCAGTAGAAGTTTATGAAGAAACGCC\n+AGATATTAAAGTATGGCGTCAAGTAACAAAACTTTATTAAAGCCCTTCGGGGCTTTTGTT\n+GTCTATAAATATAGTAAACTATAGAGGACTTTTTATGATCGAATTAAATGAAGTCTTCGA\n+TGAAGGGAAAGAACGTCTAGCAGTTACGAACCTTTATCCGAAGCTCAAGATTCCACAAAT\n+TTTTGCAATAGACAACACTAAAGTAGCTTATCGTATGTGCTCATATACTGGTGGTGGAGA\n+TGCAAATAAAAACATCAAACCCGGTGATAAAATGATGCATGTCATTGCATTAGGAGTTAC\n+TGATAAAGGCCTTGGTCAACTTAAGACCTTAGGTGATAATCCAATTGCTGTTATTGATAC\n+AATCTTTAACCACGTAATGGGTATCATGAAGTTTTATCGTTTTGACGCTGCTTTATTTCG\n+TGTTAAAAAGAATAAAACTGGTGGAGCAGGTCGCCAGATGCAAGTTATTGTTGATCGTCT\n+AATCAAGAAGAAAGGCGGTGGCAAATTCGTTATGCTTAAAGAGTTGTATGATTTTGATAA\n+GAAATACAACTACATTTTAGTATACAAGAAGAATGCTGATCTTGTCAATATCCCTGGAAT\n+GACTGAGATCATGGACTCAATTTATAAGAAAGTAGACACTGATGTAGGTGATGCTTATAT\n+CAACGTTGAGACCGGCAAACAAGTATCTAAGCTTGAAGCTATCGCGGGTTCAATCGCAGC\n+AGAAAATGATAAACGCTCAGACCAGGCGGTTGCGTCTCGAGCTAAAATATCTCGTCGTGC\n+TTTAATGGCTTCTCAATATTCAATCCAAGTGGGATTTGATACTCGTAAAGATGCGGTAGA\n+ACATGATAAGCGATTAGATGTAATTAACTCTAAACCTCCGGTTTATTTGACAGATAAGTC\n+TTCTGACCAAGTATCGAATATTCAAATGGCTATTGATAATTTCAGAAATGATTCTCAATC\n+AATTGCTAAAACCGGCGAAGCGTTTAAGACATTTGACCCGTCATGGAAAATGGATGATGA\n+TCGTCATTCTACTGGTACAATGAAAGCCCAAGAACTTGTTCTAAGGCTCACTAATATATT\n+AACCAGTGGAACAGTAGACGATTTCAGTCAACATCCTACTGATAGAAGAGAAGCATTTAA\n+AACATTAGCGGTCAGAGACATTTATCGTATTGGTGAAGCCTGGTCTAAATTAGAGCCTAA\n+TGACTATTATGGTGCTATTAAAGAACTTACTCGAGTCGCAATGGAAGACAAAGAATGGTC\n+TTCTGATGCAAATCGTGAATACGCAGTAAAAGAGATTGTAGAATTAATTTCTAAACAGTT\n+CTCTGATTTAGCAGCTAGCATGTACAAAAATACATCAGATGTGGATCGTTATACTCCGGT\n+ACAATTGTCAGGTTTACATGCTTACGTCGGTTCATCTTATAAGTACATCAACGACTATCT\n+TTTAGGCCTTGATGATTATGGCAAAGAAACTGTTGAAAAATGGATTGAGTCTATCGATTC\n+TGCGTTTGAAAATGGTGTTCGTCTTCCGAAGGGAACTAAGCTATTTCGAGGTCAACATAC\n+TAAGCGCGAAGCTATTGAAGTTAGTTTAGAAAACAAGCACTTCTATTTCAAGAATTATGT\n+GTCAACTTCAATGGCTCCTATTATCTTTGGTGGATATGGACGAGCATATGATGCAATGGA\n+CCCCGCTGCATTGAACACAGATACATCGACTCCTAAAGAAGTGCTTGACTCTGTTTCAAC\n+TGTTCGGCCTGATAGTATTACTAACTCTGAAATGGGTGAATTGCGTTTAGCGTTCGTTAT\n+TTCTGGCGCAGAGAAAATAAAGACTATCGTAACCAATGCTGGAATCTCAGGATTGTCATT\n+TGAAGCTGAAGTTATTCTTCCTCGTGGTACTGTTCTTAGAATTGATAAAATGTATGGAAC\n+AGCTCAGAAACTTCAAGCTAATGACTACACAGCATCAAAGAGTGTTCTTATGGAATGCAC\n+TGTAGTATCTCCAGAACAATTATCTGAAACTACAATTTATGATGGCGATAAATTGTTAGA\n+AGGTGAATTGGTTGAATCTGATTATTCGTTCAGTTCTTTTATTGGTCAATTAAATGAAGC\n+TAAAGTTGAAACACCAGATTGGTTAGGTGAAGCTCTAGCATCATTTGTTGACATAAATAA\n+TTTACCAGAACGATTCATAAATTAATATTTTCACATGGACGTGAATTCAGAGAGGGCTTT\n+ATGGAAATTTTAAACGAAGTACTAGACGAAAGTAAACTGGATTTACCAGTTACGAACCTT\n+TATCCAAAGACGAAAATTCCACAAATTTTTGCTATTCAAACTAACTCCGAGGGTTCACTG\n+CCAGCATTCAGGATGTGTTCATATACATCTGGCGGTGATACCAATAAGAACGTTAAACCT\n+GGCGACAAAATGATTCATGTTGTTATGCTATCATTGAGCGAAAAAGGATCATTAGTTAAG\n+CTTAAAAACTTAGGCGGCGATCCAATTGGTGTTATCTCTACTACGTTCAATATCGTTTAT\n+TCAACGATGAAGCAGTATAAAATGGACGCATGCTTGTTCCGAATGGCCAAAAGCAAAATC\n+GGTGGACAAGCTCGTCAGATGCAGGTTATTATGGACCGACTCGTACGTTCTCGTACTGGT\n+GGTAAATTTGTTATCCTGAAAGAACTCTGGGATTATGATAAGAAGTACGCATATATTCTT\n+ATTCATCGTAAAAATGTTGATCTCTCAACCATCCCTGGCGTCCCAGAGATTGATACTGGA\n+CTGTTCACTGCAGTTGAAACTAAAGTTGGTGAAGTTTATGTTGAAAAGAAATCAGGTCAA\n+CAAGTAACTAAAGCCCAAGCCGTTGCTGCTTCTATTGCAGTCGAAAACGATAAGCGTTCA\n+GATCAAAACGTTATTTCTCGTGCTAAGATAAATCGTCGTCAAGCTATTGCTGCTCAGTAT\n+TCTGTTGATGCATCTAGCATCCAAGGCGATGATCGTGCTGCTGAAGAATTTAAACGCTTA\n+GAAGCTAAAGTTCCAGTTAAAAGCTCTAAAGGCGCTGAGTCATCAGACATGGTAGCAAAA\n+GTTAATACCATCGCTGACCGTCAAGGAAATGAGTATATCGGCAAAGTACTAAACTTCATC\n+ACTAATCCTGAAACATCTCAGGACACAGATGGTAAAGCATTGACTGCACGAATAGGTCAA\n+TTGCGCCAGTTATCTAAAATGCCTAAAGGTGCCATGTTATCAGGTGGATTTGAAACTGGT\n+GGTATGAAGTACTACATGGAAAACCAAAAAGAAATGTACAATGAAGTTCGTTCATTTGCT\n+CGATTGATAGCTGGGGTGAATACAACTAACTCCTTTCAGACGATGAAAGATTTAGTTAAA\n+ATGGCTTCAGCTGGAACTAGACCTGAAGATCGTGAACAGTTAATTGCAAATTTAATTGGA\n+TTAGCTTATAAAGAAATAAGTGCAATCATCAGAGATTCATACCAAACTGCAGCAAGTTTA\n+TCTAAAGAGAATGATCATTATTCTAAAGATGAAAAACAAGCTATCAGTGAATACTGCGCA\n+AACGCTTTCGAATACGTGAATATGTTCTTAATCGGTAAGCCGGAAGAAGGGTATTCAACT\n+TCTGATTCTCTCGAGATCATCGATAATATGGACTCTGCGTTTGAAAAAGGAACTCGTTTA\n+GACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACA\n' |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/seq/genome.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/seq/genome.fasta.fai Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,1 @@ +Merlin 172788 8 60 61 |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/seq/refSeqs.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/seq/refSeqs.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,1 @@ +[{"end":172788,"length":172788,"line_byte_length":"61","line_length":"60","name":"Merlin","offset":"8","start":0}] \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/data/trackList.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/data/trackList.json Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,170 @@ +{ + "formatVersion" : 1, + "hideGenomeOptions" : false, + "names" : { + "type" : "Hash", + "url" : "names/" + }, + "plugins" : [ + { + "location" : "https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/", + "name" : "BlastView" + } + ], + "refSeqs" : "seq/genome.fasta.fai", + "shareLink" : true, + "show_menu" : true, + "show_nav" : true, + "show_overview" : true, + "show_tracklist" : true, + "tracks" : [ + { + "category" : "Reference sequence", + "codonStarts" : [ + "TTG", + "CTG", + "ATG" + ], + "codonStops" : [ + "TAA", + "TAG", + "TGA" + ], + "codonTable" : { + "AAA" : "K", + "AAC" : "N", + "AAG" : "K", + "AAT" : "N", + "ACA" : "T", + "ACC" : "T", + "ACG" : "T", + "ACT" : "T", + "AGA" : "R", + "AGC" : "S", + "AGG" : "R", + "AGT" : "S", + "ATA" : "I", + "ATC" : "I", + "ATG" : "M", + "ATT" : "I", + "CAA" : "Q", + "CAC" : "H", + "CAG" : "Q", + "CAT" : "H", + "CCA" : "P", + "CCC" : "P", + "CCG" : "P", + "CCT" : "P", + "CGA" : "R", + "CGC" : "R", + "CGG" : "R", + "CGT" : "R", + "CTA" : "L", + "CTC" : "L", + "CTG" : "L", + "CTT" : "L", + "GAA" : "E", + "GAC" : "D", + "GAG" : "E", + "GAT" : "D", + "GCA" : "A", + "GCC" : "A", + "GCG" : "A", + "GCT" : "A", + "GGA" : "G", + "GGC" : "G", + "GGG" : "G", + "GGT" : "G", + "GTA" : "V", + "GTC" : "V", + "GTG" : "V", + "GTT" : "V", + "TAC" : "Y", + "TAT" : "Y", + "TCA" : "S", + "TCC" : "S", + "TCG" : "S", + "TCT" : "S", + "TGC" : "C", + "TGG" : "W", + "TGT" : "C", + "TTA" : "L", + "TTC" : "F", + "TTG" : "L", + "TTT" : "F" + }, + "faiUrlTemplate" : "seq/genome.fasta.fai", + "key" : "Reference sequence", + "label" : "DNA", + "metadata" : { + "dataset_edam_format" : "<a target=\"_blank\" href=\"http://edamontology.org/format_1929\">fasta</a>", + "dataset_file_ext" : "fasta", + "dataset_hid" : "1", + "dataset_id" : "7495a4247e72f5f1", + "dataset_size" : "171.6 KB", + "history_display_name" : "<a target=\"_blank\" href=\"http://localhost/history/view/d29e465b351a50c9\">Unnamed history</a>", + "history_id" : "d29e465b351a50c9", + "history_user_email" : "<a href=\"mailto:anthony.bretaudeau@irisa.fr\">anthony.bretaudeau@irisa.fr</a>", + "history_user_id" : "17", + "metadata_data_lines" : "2881", + "metadata_dbkey" : "?", + "metadata_sequences" : "1", + "tool_tool" : "<a target=\"_blank\" href=\"http://localhost/datasets/7495a4247e72f5f1/show_params\">upload1</a>", + "tool_tool_id" : "upload1", + "tool_tool_version" : "1.1.6" + }, + "seqType" : "dna", + "storeClass" : "JBrowse/Store/SeqFeature/IndexedFasta", + "type" : "SequenceTrack", + "urlTemplate" : "seq/genome.fasta", + "useAsRefSeqStore" : 1 + }, + { + "category" : "Default", + "key" : "merlin.gff", + "label" : "4ced49b280a72a29f1b922ae1a9664c8_0", + "maxHeight" : "600", + "menuTemplate" : [ + {}, + {}, + {}, + {} + ], + "metadata" : { + "dataset_edam_format" : "<a target=\"_blank\" href=\"http://edamontology.org/format_1975\">gff3</a>", + "dataset_file_ext" : "gff3", + "dataset_hid" : "2", + "dataset_id" : "b02ee2031011d9cf", + "dataset_size" : "110.3 KB", + "history_display_name" : "<a target=\"_blank\" href=\"http://localhost/history/view/d29e465b351a50c9\">Unnamed history</a>", + "history_id" : "d29e465b351a50c9", + "history_user_email" : "<a href=\"mailto:anthony.bretaudeau@irisa.fr\">anthony.bretaudeau@irisa.fr</a>", + "history_user_id" : "17", + "metadata_attributes" : "4", + "metadata_columns" : "9", + "metadata_comment_lines" : "2", + "metadata_data_lines" : "1228", + "metadata_dbkey" : "?", + "metadata_delimiter" : "__tc__", + "tool_tool" : "<a target=\"_blank\" href=\"http://localhost/datasets/b02ee2031011d9cf/show_params\">upload1</a>", + "tool_tool_id" : "upload1", + "tool_tool_version" : "1.1.6" + }, + "overrideDraggable" : false, + "overridePlugins" : false, + "storeClass" : "JBrowse/Store/SeqFeature/GFF3Tabix", + "style" : { + "className" : "feature", + "color" : "#a6cee3", + "description" : "note,description", + "label" : "product,name,id" + }, + "trackType" : "NeatHTMLFeatures/View/Track/NeatFeatures", + "type" : "NeatHTMLFeatures/View/Track/NeatFeatures", + "urlTemplate" : "raw/4ced49b280a72a29f1b922ae1a9664c8_0.gff.gz" + } + ], + "view" : { + "trackPadding" : 20 + } +} |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/galaxy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/galaxy.xml Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,106 @@ +<?xml version="1.0"?> +<root> + <metadata> + <gencode>1</gencode> + <genomes> + <genome path="/opt/galaxy-dist/database/files/002/188/dataset_2188862.dat"> + <metadata> + <dataset id="7495a4247e72f5f1" hid="1" + size="171.6 KB" + edam_format="format_1929" + file_ext="fasta" /> + <history id="d29e465b351a50c9" + user_email="anthony.bretaudeau@irisa.fr" + user_id="17" + display_name="Unnamed history"/> + <metadata + dbkey="?" + data_lines="2881" + sequences="1" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </genome> + </genomes> + <general> + <defaultLocation></defaultLocation> + <trackPadding>20</trackPadding> + + <shareLink>true</shareLink> + <aboutDescription></aboutDescription> + <show_tracklist>true</show_tracklist> + <show_nav>true</show_nav> + <show_overview>true</show_overview> + <show_menu>true</show_menu> + <hideGenomeOptions>false</hideGenomeOptions> + </general> + <galaxyUrl>http://localhost</galaxyUrl> + </metadata> + <tracks> + <track cat="Default" format="gene_calls" visibility="default_off"> + <files> + <trackFile path="/opt/galaxy-dist/database/files/002/188/dataset_2188863.dat" ext="gff3" label="merlin.gff"> + <metadata> + <dataset id="b02ee2031011d9cf" hid="2" + size="110.3 KB" + edam_format="format_1975" + file_ext="gff3" /> + <history id="d29e465b351a50c9" + user_email="anthony.bretaudeau@irisa.fr" + user_id="17" + display_name="Unnamed history"/> + <metadata + dbkey="?" + data_lines="1228" + comment_lines="2" + columns="9" + delimiter="__tc__" + attributes="4" + /> + <tool + tool_id="upload1" + tool_version="1.1.6" + /> + </metadata> + </trackFile> + </files> + + <options> + <style> + <overridePlugins>False</overridePlugins> + <overrideDraggable>False</overrideDraggable> + <className>feature</className> + <description>note,description</description> + <label>product,name,id</label> + <height>10px</height> + <maxHeight>600</maxHeight> + </style> + <scaling> + <method>ignore</method> + <scheme> + <color>__auto__</color> + </scheme> + </scaling> + <menus> + </menus> + <custom_config> + </custom_config> + + <gff> + <trackType>NeatHTMLFeatures/View/Track/NeatFeatures</trackType> + <index>false</index> + </gff> + </options> + </track> + </tracks> + <plugins + ComboTrackSelector="" + Bookmarks="" + GCContent="" + BlastView="True" + theme="" + /> +</root> |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/jbrowse.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/jbrowse.conf Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,110 @@ +#### JBrowse main configuration file + +## uncomment the section below to customize this browser's title and description +# [aboutThisBrowser] +# title = <i>Oryza sativa</i> +# description = Browser for O. sativa transcripts and RNA-seq data, +# produced by the Smith laboratory at Example State University. + +## uncomment and edit the example below to configure a faceted track selector +# [trackSelector] +# type = Faceted +# displayColumns = +# + label +# + key +# + organism +# + technique +## optionally sort the faceted track selector by column (use the names from displayColumns) +# initialSortColumn=label +## optionally give different names to some of the data facets using renameFacets +# [trackSelector.renameFacets] +# submission = Submission ID +# developmental-stage = Conditions +# cell-line = Cell Line +# key = Dataset +# label = Track + +## uncomment this section to get hierarchical trackselector options +# [trackSelector] +## optionally turn off sorting for the hierarchical track selector +# sortHierarchical = false +## set collapsed categories for the hierarchical track selector +# collapsedCategories = Reference sequence,Quantitative / XY Plot +## set category ordering in the hierarchical track selector +# categoryOrder = BAM, Transcripts, Quantitative/Density, VCF + +## configure where to get metadata about tracks. always indexes the +## `metadata` part of each track config, but this can be used to load +## additional metadata from CSV or JSON urls +# [trackMetadata] +# sources = data/trackMetadata.csv + + +[GENERAL] + + +## add a document.domain to set the same-origin policy +# documentDomain=foobar.com + +## use classic jbrowse menu with file instead of track and genome +#classicMenu = true + +## hide open genome option +#hideGenomeOptions = true + +## enable or disable high resolution rendering for canvas features. set to auto, disabled, or numerical scaling factor. default: 2 +# highResolutionMode=auto + +## uncomment to change the default sort order of the reference +## sequence dropdown +# refSeqOrder = length descending + +## Uncomment to prevent HTML tracks from displaying gene subfeatures (enabled by default) +# inferHTMLSubfeatures = false + +## to set a default data directory other than 'data', uncomment and +## edit the line below +# dataRoot = data + +## optionally add more include statements to load and merge in more +## configuration files +include = {dataRoot}/trackList.json +include += {dataRoot}/tracks.conf +# include += ../url/of/my/other/config.json +# include += another_config.conf + +## uncomment and edit the example below to enable one or more +## JBrowse plugins +# [ plugins.MyPlugin ] +# location = plugins/MyPlugin +# [ plugins.AnotherPlugin ] +# location = ../plugin/dir/someplace/else + +## edit the datasets list below to add datasets to the jbrowse dataset +## selector + +# [datasets.volvox] +# url = ?data=sample_data/json/volvox +# name = Volvox Example + +# [datasets.modencode] +# url = ?data=sample_data/json/modencode +# name = MODEncode Example + +# [datasets.yeast] +# url = ?data=sample_data/json/yeast +# name = Yeast Example +[ plugins.BlastView ] +location = ../plugin/BlastView/ +[ plugins.GCContent ] +location = ../plugin/GCContent/ +[ plugins.ComboTrackSelector ] +location = ../plugin/ComboTrackSelector/ +[ plugins.MultiBigWig ] +location = ../plugin/MultiBigWig/ +[ plugins.bookmarks ] +location = ../plugin/bookmarks/ +[ plugins.NeatCanvasFeatures ] +location = ../plugin/NeatCanvasFeatures/ +[ plugins.NeatHTMLFeatures ] +location = ../plugin/NeatHTMLFeatures/ |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/dataset_1_files/jbrowse_conf.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_1_files/jbrowse_conf.json Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,9 @@ +// top-level JBrowse configuration file. Treated the same as +// jbrowse.conf, but this one is in JSON format. +// +// Unless generating configuration from scripts, most users will +// prefer to add variables to jbrowse.conf instead of this file, since +// jbrowse.conf is much easier to hand-edit. +{ + +} \ No newline at end of file |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/export/cdna.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export/cdna.fa Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,103 @@ +>ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 690 residues [Merlin:2-691 + strand] [cdna] name=Unknown +CGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGAG +CATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCCT +CTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTAT +ACTGCTGAGACGCCTGATGATTATAATCGTTTCGCAAACCCAGAAGATATAATTGATATT +GGCGCTACTCAAAAAGACTCATTTGACGATAACAATAATGATGGAACATCTATTAATATC +GGCAAACAAGTTAATTTAGGATTCGTTATTTCCGGTGCTGAAAATGTTCGAGTTATTGTT +CCAGGTTCTTTAACTGAATATCCAGAAGAAGCGGAAGTTATTCTGCCTCGTGGTACTCTT +TTGAAGATCAATAAAATCACTACTCAAGTAGATAAACGCTCGAATAAGTTCATGGTTGAA +GGTTCAATCGTTCCGCCTTCTGAGCAAATTGATGAATCTGTTGAGATTTATGACGGTGAT +CTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGAA +TCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGAC +ATTGATGACATGCCACGTAAGTTCCGCTAG +>f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 288 residues [Merlin:752-1039 + strand] [cdna] name=Unknown +ATGAAATCAATTTTTCGTATCAACGGTGTAGAAATTGTAGTTGAAGATGTAGTTCCTATG +TCTTATGAATTCAATGAAGTTGTTTTCAAAGAGCTTAAGAAAATTTTAGGCGATAAGAAG +CTTCAAAGTACTCCAATTGGACGTTTTGGAATGAAAGAAAACGTTGATACTTATATTGAA +AGTGTAGTGACAGGGCAGTTAGAAGGTGAATTTTCTGTAGCAGTTCAAACTGTAGAAAAT +GATGAAGTTATTTTAACTTTACCAGCTTTCGTAATTTTCCGCAAATAA +>12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 945 residues [Merlin:1067-2011 - strand] [cdna] name=Unknown +ATGCTAACTTTAGATGAATTTAAAAACCAAGCGGGTAATATAGACTTTCAGCGTACTAAT +ATGTTTAGTTGTGTATTTGCAACTACTCCGTCAGCAAAGTCTCAACAATTACTCGATCAA +TTTGGCGGTATGCTCTTTAATAACCTTCCGTTGAATAATGACTGGCTTGGATTAACACAA +GGTGAGTTCACATCAGGACTCACCTCAATTATCACTGCCGGTACTCAACAGCTGGTAAGA +AAGTCTGGTGTATCGAAATATCTTATTGGAGCAATGAGCAATCGTGTTGTTCAGTCTTTA +TTAGGTGAATTTGAAGTCGGAACTTATTTGTTAGACTTCTTTAACATGGCTTATCCGCAA +TCTGGATTGATGATTTATTCGGTCAAAATTCCAGAGAACAGATTGTCTCATGAAATGGAT +TTCAACCATAACTCACCGAATATTAGAATAACTGGACGTGAACTCGATCCGTTAACTATA +TCATTCAGAATGGATCCCGAAGCAAGTAACTATCGTGCAATGCAAGATTGGGTGAACTCC +GTTCAAGACCCGGTTACTGGATTGCGAGCATTACCAACTGACGTCGAAGCTGACATTCAG +GTTAACCTTCATGCTCGAAATGGATTACCTCATACTGTGATAATGTTCACAGGTTGTGTT +CCTGTTGCGTGTGGAGCTCCTGAGCTTACATATGAAGGAGATAACCAAATTGCGGTTTTC +GATGTTACATTTGCTTACAGAGTAATGCAAACGGGTGCTGTTGGACGTCAAGCTGCTCTT +GATTGGATTGAAGATAGAGCTGTTAATTCTATAACTGGAATTAATAGTGAAATGTCTCTT +AATGGAAGTTTAAGTAGATTATCTAGACTTGGAGGAGCTGCTGGAGGGTTGTCTCACGTC +ATTAATTCGACCCGAAACTCTACTTCGAAAATACTTGGATTGTAA +>58fc8255-95ed-4417-a373-238f826810ac (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cdna] name=Unknown +ATGAGCATTAAAGTCAGAGAATTAGATGATAAGACTGATGCTTTAATTAGCGGAGTTAAA +ACCTCCGCTGGTCAAAGTTCACAATCAGCAAAAATAAAATCCACTATAACTGCGCAATAT +CCGTCTGAACGTTCAGCTGGTAATGACACATCTGGTTCTTTACGAGTTCATGATCTTTAT +AAGAACGGGTTGTTGTTCACTGCGTATGATATGAATTCTCGTACAACCGGTGATATGCGT +AGCATGCGTTTAGGTGAAATGAAACGTACTGCAAATAGTGTAGTGAAATCAATCACTGGA +ACAAATACTAATAAAGTTGATAAAATTCCAGTAGTGAATATTTTACTTCCACGCTCGAAA +TCAGATGTTGAATCAGTTTCTCATAAATTTAATGACGTTGGAGATTCACTTATTTCTCGT +GGCGGCGGTACTGCTACAGGGGTATTAAGTAACGTTGCATCTACTGCTGTCTTTGGCGGA +TTAGAGTCATTGACTCAAGGATTAATGGCTGACCATAACGAGCAGATCTATAACACTGCT +CGATCAATGTATGGCGGCGCAGATAACCGTACGAAGGTATTCACGTGGGATTTAACTCCT +CGATCAGTACAAGATCTTATTGCTATTATCGAGATCTATGAATACTTTAACTACTATAGT +TATGGCGAAACGGGAACGTCTACTTATGCAAAAGAAGTTAAGTCTCAATTAGATGAATGG +TATAAATCAACTTTCCTTGATACATTAACTCCAGATGAAGCTAATAAAAATGACACTGTT +TTTGAGAAAATAACTTCATTCTTAAGTAATGTTATTGTTGTAAGTAACCCTACTGTGTGG +TTCGTCAGAAACTTTGGAACCACAAGTAAATTCGATGGACGTGCTGAAGTATTCGGTCCA +TGTCAAATTCAGAGTATCCGTTTTGATAAAACTCCAAATGGAAACTTTAACGGTTTAGCT +ATAGCTCCAAACCTGCCAAGTACATTCACATTAGAAATTACTATGCGTGAAATCTTGACA +TTGAACCGAGCTTCAGTATATGCGGAAGGATTCTGA +>c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cdna] name=multiexongene +ATGAAAAGCGAAAACATGTCCACAATGAGACGTCGTAAAGTTATCGCTGATTCAAAGGGT +GAAAGAGATGCAGCCTCGACTGCATCTGATCAAGTAGACTCTTTAGAATTAATCGGCCTT +AAACTTGATGATGTACAAAGCGCTAATGAACTAGTTGCTGAAGTAATTGAAGAAAAGGGC +AATAACTTAATTGATTCAGTTGATAACGTCGCTGAAGGTACTGAATTAGCTGCTGAAGCA +TCTGAACGAACTACTGAGTCTATCAAGACTCTTACTGGCGTAGCGTCAACAATCAGCGAC +AAATTAAGTAAACTCGCTTCGATGCTCGAGTCGAAGGTTCAGGCTGTGGAGCAAAAAGTA +CAAGAATCTGGTGCCTCAGCTTCAACTGGGCTGTCAGTGATAGAAGATAAGCTTCCAGAT +CCTGATGAGCCTTTCTTTCCACCTGTCCCTCAGGAACCCGAGAACAACAAGAAAGATCAA +AAGAAAGATGATAAGAAACCTACCGATATGTTAGGTGACTTGCTGAAGACTACGAAGGGC +GGATTTAAAGCTACGATATCAATCACTGATAAAATATCGTCTATGCTTTTCAAATACACC +GTAACAGCATTAGCTGAAGCTGCTAAAATGGCTGCTATGCTATTTGCATTAGTATTAGGC +ATAGATTTACTTCGTATTCATTTTAAGTATTGGACTGATAAATTCATGAGTAACTTCGAT +GAATTCAGTGCTGAAGCTGGTGAATGGGGTGGACTGCTTCAATCAATTTTTGGAATGTTA +GGAGATATTAAAAAGTTCTGGGAAGCTGGAGACTGGAGTGGATTAGCAGTAGCTATTGTC +AAAGGATTAGCTGATGTGATTTACAACCTGAGCGAAATAATGTCTTTGGGAATTTCAAAG +ATATCTGCTTCTATACTCGATGCACTTGGCTTTGAAAATGCAGCAACTACTATTCGTGGT +TCAGCACTAGAAGGATTCCAGGAACGCACTGGTAATTCATTGTCTGAAGATGATCAAAAA +GCTTTGGCTAAATATCAGAGTAAGCGTATTGAAGAAGGTCCTGGAATTATTGATAAAGCT +GGCGAATTTAAAACTCGTGCATTTGATTGGGTACTAGGAAGAGAGAATAAAATCGATTCT +ACACAAGCATCTGACCGTGATCAAGAGACTCAGAATCTTAAAGCAATGGCTCCTGAAAAA +CGCGAAGAAACACTGATCAAACAAAACGAAGCTCGTGCAGCTGTTCAGCGTTTAGAAAAA +TATATTGGTGATGTTGATCCAGAGAATCCAACTAATATGCAATCTTTAGAGAAGGCATAT +AACAGTGCCAAAAAGTCTATTAGTGATTCTGCTATAAGTGATCAACCAGCTACTAAAAAG +GAACTCGATAAAAGATTCCAACGAGTAGAATCCAAGTATCAGAAGCTCAAAGAAGATAAC +ACTCCGAAGCCTGCGGCTCCAGCTACTTCGGAAGATAATCAACGAGTTCAAAATATTCAA +AAAGCTGAAAATGCTAAAGAGCAATCTAAAAAATCAACCGGTGATATGAATGTTGCTAAC +ACTCAGGTTAATAACGTAAATAATAGTAAGACTATTCACCAGGTTCAAACAGTCACGGCT +ACTCCAGCTCCTGGAGTATTCGGGGCAACAGGAGTTAATTAA +>2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 1056 residues [Merlin:5011-6066 - strand] [cdna] name=cds-not-under-exon +CTTTAATGACGCTGGTGAATCAATAAAAGAGATGATCGGTGCAATTTATGAATCAAAACC +TCTTATAGCACCTGCGATGAACACAATCAACACATATGTTCCTCGAGTTCCATGGACGAG +TAACATAACTGAATACAAGAAATATGTTCGAGATGTTGCATTAGCAGTAGATAATGACCA +ATTCGTTTTTGTATGGGAAGATATCTATGGCTTGAACATGATGGATTATGACGCAATGAT +TAACCAAGAATCAATCAAGGTTATTGTCGGTGAACCACGCACAATAGGTCAATTTGTCGG +TGAGCTGGAATATAATCTCGCTTATGACTTCCAGTGGTTAACGAAGGCTAATGCCCATAC +ACGCGATCCTATTTTTAACGCTACAATCTATTCACACTCATTCTTGGATAATAACCTTCC +TAGAATAGTAACAGGTGATGGACAGAATAGCATCTTCGTTTCTCGCTCGGGTGCATATTC +TGAAATGACTTATCGAAATGGATATGAAGAAGCTATCAGGCTTCAGACTATGGCACAATA +CGACGGTTATGCAACTTGTAAAATGGTTGGAGACTTTGAAATGACTCCTGGAGATAAGAT +TAATTTCTTTGATCCAAAGAAACAATTCAAAGCTGATTTTTACATTGATGAAGTAATTCA +TGAAGTAAGTAATAACCAAAGCATAACTACACTTTATATGTTTACTAACTCTCGTAAGTT +GGAAACAGTAGAACCAATAAAGGTTAAAAATGAACTTAAATCTGATACTACCACTTAAGA +AAATACAAGTCAATGGCAAAACCATTTCTATTCCTAAGCTTGGCTTGAAGCATCACACGT +TGATTAAAGATGTTCGTGCAATGGATGAGAACATGGGAATTCTTTTGGACTCAATTCATC +CTGGGCTAAACGCTGCTGAATCAGATTTAGTGTCTATTCATTTGCTAGAGTTCAATGGCA +AGTTAAAATCAAGTGTCGTTAAAGATGGATACACTTACAATATCAATGACATTTATATTT +GCCAACGCCTTGAATTCCAGTTCCAAGGAAAGACAT |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/export/cds.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export/cds.fa Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,68 @@ +>ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 690 residues [Merlin:2-691 + strand] [cds] name=Unknown +CGTTTAGACAAAGGTACATTATTGTATCGTGGCCAAAAATTAGACCTTCCTACATTCGAG +CATAACGCAGAGAATAAGTTGTTCTATTTCAGAAACTACGTTTCAACTTCATTAAAGCCT +CTGATCTTTGGTGAATTTGGTCGTATGTTTATGGCACTAGATGACGATACTACAATTTAT +ACTGCTGAGACGCCTGATGATTATAATCGTTTCGCAAACCCAGAAGATATAATTGATATT +GGCGCTACTCAAAAAGACTCATTTGACGATAACAATAATGATGGAACATCTATTAATATC +GGCAAACAAGTTAATTTAGGATTCGTTATTTCCGGTGCTGAAAATGTTCGAGTTATTGTT +CCAGGTTCTTTAACTGAATATCCAGAAGAAGCGGAAGTTATTCTGCCTCGTGGTACTCTT +TTGAAGATCAATAAAATCACTACTCAAGTAGATAAACGCTCGAATAAGTTCATGGTTGAA +GGTTCAATCGTTCCGCCTTCTGAGCAAATTGATGAATCTGTTGAGATTTATGACGGTGAT +CTGTTCATGGAAACAGGTGAAGTAGTAAAACTGTCCGGATTCATGCAGTTCGTCAACGAA +TCTGCATACGATGAAGAGCAAAACCAGATGGCTGCTGAGATTCTGTCTGGATTCTTGGAC +ATTGATGACATGCCACGTAAGTTCCGCTAG +>f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 9 residues [Merlin:752-1039 + strand] [cds] name=Unknown +AAATTTTAG +>12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 108 residues [Merlin:1067-2011 - strand] [cds] name=Unknown +CACCTCAATTATCACTGCCGGTACTCAACAGCTGGTAAGAAAGTCTGGTGTATCGAAATA +TCTTATTGGAGCAATGAGCAATCGTGTTGTTCAGTCTTTATTAGGTGA +>58fc8255-95ed-4417-a373-238f826810ac (mRNA) 1056 residues [Merlin:2011-3066 - strand] [cds] name=Unknown +ATGAGCATTAAAGTCAGAGAATTAGATGATAAGACTGATGCTTTAATTAGCGGAGTTAAA +ACCTCCGCTGGTCAAAGTTCACAATCAGCAAAAATAAAATCCACTATAACTGCGCAATAT +CCGTCTGAACGTTCAGCTGGTAATGACACATCTGGTTCTTTACGAGTTCATGATCTTTAT +AAGAACGGGTTGTTGTTCACTGCGTATGATATGAATTCTCGTACAACCGGTGATATGCGT +AGCATGCGTTTAGGTGAAATGAAACGTACTGCAAATAGTGTAGTGAAATCAATCACTGGA +ACAAATACTAATAAAGTTGATAAAATTCCAGTAGTGAATATTTTACTTCCACGCTCGAAA +TCAGATGTTGAATCAGTTTCTCATAAATTTAATGACGTTGGAGATTCACTTATTTCTCGT +GGCGGCGGTACTGCTACAGGGGTATTAAGTAACGTTGCATCTACTGCTGTCTTTGGCGGA +TTAGAGTCATTGACTCAAGGATTAATGGCTGACCATAACGAGCAGATCTATAACACTGCT +CGATCAATGTATGGCGGCGCAGATAACCGTACGAAGGTATTCACGTGGGATTTAACTCCT +CGATCAGTACAAGATCTTATTGCTATTATCGAGATCTATGAATACTTTAACTACTATAGT +TATGGCGAAACGGGAACGTCTACTTATGCAAAAGAAGTTAAGTCTCAATTAGATGAATGG +TATAAATCAACTTTCCTTGATACATTAACTCCAGATGAAGCTAATAAAAATGACACTGTT +TTTGAGAAAATAACTTCATTCTTAAGTAATGTTATTGTTGTAAGTAACCCTACTGTGTGG +TTCGTCAGAAACTTTGGAACCACAAGTAAATTCGATGGACGTGCTGAAGTATTCGGTCCA +TGTCAAATTCAGAGTATCCGTTTTGATAAAACTCCAAATGGAAACTTTAACGGTTTAGCT +ATAGCTCCAAACCTGCCAAGTACATTCACATTAGAAATTACTATGCGTGAAATCTTGACA +TTGAACCGAGCTTCAGTATATGCGGAAGGATTCTGA +>c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 1662 residues [Merlin:3066-4796 - strand] [cds] name=multiexongene +ATGAAAAGCGAAAACATGTCCACAATGAGACGTCGTAAAGTTATCGCTGATTCAAAGGGT +GAAAGAGATGCAGCCTCGACTGCATCTGATCAAGTAGACTCTTTAGAATTAATCGGCCTT +AAACTTGATGATGTACAAAGCGCTAATGAACTAGTTGCTGAAGTAATTGAAGAAAAGGGC +AATAACTTAATTGATTCAGTTGATAACGTCGCTGAAGGTACTGAATTAGCTGCTGAAGCA +TCTGAACGAACTACTGAGTCTATCAAGACTCTTACTGGCGTAGCGTCAACAATCAGCGAC +AAATTAAGTAAACTCGCTTCGATGCTCGAGTCGAAGGTTCAGGCTGTGGAGCAAAAAGTA +CAAGAATCTGGTGCCTCAGCTTCAACTGGGCTGTCAGTGATAGAAGATAAGCTTCCAGAT +CCTGATGAGCCTTTCTTTCCACCTGTCCCTCAGGAACCCGAGAACAACAAGAAAGATCAA +AAGAAAGATGATAAGAAACCTACCGATATGTTAGGTGACTTGCTGAAGACTACGAAGGGC +GGATTTAAAGCTACGATATCAATCACTGATAAAATATCGTCTATGCTTTTCAAATACACC +GTAACAGCATTAGCTGAAGCTGCTAAAATGGCTGCTATGCTATTTGCATTAGTATTAGGC +ATAGATTTACTTCGTATTCATTTTAAGTATTGGACTGATAAATTCATGAGTAACTTCGAT +GAATTCAGTGCTGAAGCTGGTGAATGGGGTGGACTGCTTCAATCAATTTTTGGAATGTTA +GGAGATATTAAAAAGTTCTGGGAAGCTGGAGACTGGAGTGGATTAGCAGTAGCTATTGTC +AAAGGATTAGCTGATGTGATTTACAACCTGAGCGAAATAATGTCTTTGGGAATTTCAAAG +ATATCTGCTTCTATACTCGATGCACTTGGCTTTGAAAATGCAGCAACTACTATTCGTGGT +TCAGCACTAGAAGGATTCCAGGAACGCACTGGTAATTCATTGTCTGAAGATGATCAAAAA +GCTTTGGCTAAATATCAGAGTAAGCGTATTGAAGAAGGTCCTGGAATTATTGATAAAGCT +GGCGAATTTAAAACTCGTGCATTTGATTGGGTACTAGGAAGAGAGAATAAAATCGATTCT +ACACAAGCATCTGACCGTGATCAAGAGACTCAGAATCTTAAAGCAATGGCTCCTGAAAAA +CGCGAAGAAACACTGATCAAACAAAACGAAGCTCGTGCAGCTGTTCAGCGTTTAGAAAAA +TATATTGGTGATGTTGATCCAGAGAATCCAACTAATATGCAATCTTTAGAGAAGGCATAT +AACAGTGCCAAAAAGTCTATTAGTGATTCTGCTATAAGTGATCAACCAGCTACTAAAAAG +GAACTCGATAAAAGATTCCAACGAGTAGAATCCAAGTATCAGAAGCTCAAAGAAGATAAC +ACTCCGAAGCCTGCGGCTCCAGCTACTTCGGAAGATAATCAACGAGTTCAAAATATTCAA +AAAGCTGAAAATGCTAAAGAGCAATCTAAAAAATCAACCGGTGATATGAATGTTGCTAAC +ACTCAGGTTAATAACGTAAATAATAGTAAGACTATTCACCAGGTTCAAACAGTCACGGCT +ACTCCAGCTCCTGGAGTATTCGGGGCAACAGGAGTTAATTAA +>2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 6 residues [Merlin:5011-6066 - strand] [cds] name=cds-not-under-exon +CTTTAA |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/export/out.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export/out.vcf Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,5 @@ +##fileformat=VCFv4.2 +##fileDate=20191025XX +##source=. +##reference=/home/apollo_shared_dir/org2/seq/genome.fasta +#CHROM POS ID REF ALT QUAL FILTER INFO |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/export/pep.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/export/pep.fa Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| @@ -0,0 +1,29 @@ +>ff2fe902-7bab-431c-be82-30ed072915d1 (mRNA) 229 residues [Merlin:2-691 + strand] [peptide] name=Unknown +RLDKGTLLYRGQKLDLPTFEHNAENKLFYFRNYVSTSLKPLIFGEFGRMFMALDDDTTIY +TAETPDDYNRFANPEDIIDIGATQKDSFDDNNNDGTSINIGKQVNLGFVISGAENVRVIV +PGSLTEYPEEAEVILPRGTLLKINKITTQVDKRSNKFMVEGSIVPPSEQIDESVEIYDGD +LFMETGEVVKLSGFMQFVNESAYDEEQNQMAAEILSGFLDIDDMPRKFR +>f2e1909a-1d40-4a49-a67b-5fe2afdc4957 (mRNA) 2 residues [Merlin:752-1039 + strand] [peptide] name=Unknown +KF +>12fe0db6-c8e1-4bc9-b594-87c92c6c9669 (mRNA) 35 residues [Merlin:1067-2011 - strand] [peptide] name=Unknown +HLNYHCRYSTAGKKVWCIEISYWSNEQSCCSVFIR +>58fc8255-95ed-4417-a373-238f826810ac (mRNA) 351 residues [Merlin:2011-3066 - strand] [peptide] name=Unknown +MSIKVRELDDKTDALISGVKTSAGQSSQSAKIKSTITAQYPSERSAGNDTSGSLRVHDLY +KNGLLFTAYDMNSRTTGDMRSMRLGEMKRTANSVVKSITGTNTNKVDKIPVVNILLPRSK +SDVESVSHKFNDVGDSLISRGGGTATGVLSNVASTAVFGGLESLTQGLMADHNEQIYNTA +RSMYGGADNRTKVFTWDLTPRSVQDLIAIIEIYEYFNYYSYGETGTSTYAKEVKSQLDEW +YKSTFLDTLTPDEANKNDTVFEKITSFLSNVIVVSNPTVWFVRNFGTTSKFDGRAEVFGP +CQIQSIRFDKTPNGNFNGLAIAPNLPSTFTLEITMREILTLNRASVYAEGF +>c009dd7a-3284-4e7f-9ee1-3b56e2598e07 (mRNA) 553 residues [Merlin:3066-4796 - strand] [peptide] name=multiexongene +MKSENMSTMRRRKVIADSKGERDAASTASDQVDSLELIGLKLDDVQSANELVAEVIEEKG +NNLIDSVDNVAEGTELAAEASERTTESIKTLTGVASTISDKLSKLASMLESKVQAVEQKV +QESGASASTGLSVIEDKLPDPDEPFFPPVPQEPENNKKDQKKDDKKPTDMLGDLLKTTKG +GFKATISITDKISSMLFKYTVTALAEAAKMAAMLFALVLGIDLLRIHFKYWTDKFMSNFD +EFSAEAGEWGGLLQSIFGMLGDIKKFWEAGDWSGLAVAIVKGLADVIYNLSEIMSLGISK +ISASILDALGFENAATTIRGSALEGFQERTGNSLSEDDQKALAKYQSKRIEEGPGIIDKA +GEFKTRAFDWVLGRENKIDSTQASDRDQETQNLKAMAPEKREETLIKQNEARAAVQRLEK +YIGDVDPENPTNMQSLEKAYNSAKKSISDSAISDQPATKKELDKRFQRVESKYQKLKEDN +TPKPAAPATSEDNQRVQNIQKAENAKEQSKKSTGDMNVANTQVNNVNNSKTIHQVQTVTA +TPAPGVFGATGVN +>2706ea76-172a-48c1-b940-eb603996f082 (mRNA) 1 residues [Merlin:5011-6066 - strand] [peptide] name=cds-not-under-exon +L |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/good-model.gff3 --- a/test-data/good-model.gff3 Mon Jul 29 10:09:19 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -##gff-version 3 -##sequence-region Maroon_JMcDermott 1 14805 -Maroon_JMcDermott feature gene 14488 14805 . + . ID=707c88b7-36d1-44e3-93e6-d1d4f1219d57;Name=gene_26;date_creation=2016-02-17;date_last_modified=2016-02-17;owner=jmc_texas%40tamu.edu -Maroon_JMcDermott feature mRNA 14488 14805 . + . ID=8760695d-b88c-41c0-857b-540e6db81fe8;Name=gene_26-00001;Parent=707c88b7-36d1-44e3-93e6-d1d4f1219d57;date_creation=2016-02-17;date_last_modified=2016-02-17;owner=jmc_texas%40tamu.edu -Maroon_JMcDermott feature CDS 14707 14805 . + 0 ID=94abf796-4c8d-45f4-916b-4d279616565e;Name=94abf796-4c8d-45f4-916b-4d279616565e-CDS;Parent=8760695d-b88c-41c0-857b-540e6db81fe8 -Maroon_JMcDermott feature exon 14497 14805 . + . ID=d2ebd8d0-6558-4674-a38f-346f88256340;Name=d2ebd8d0-6558-4674-a38f-346f88256340-exon;Parent=8760695d-b88c-41c0-857b-540e6db81fe8 -Maroon_JMcDermott feature Shine_Dalgarno_sequence 14488 14491 . + . ID=2e4119f9-3220-4502-8ddd-4821c872e0d6;Name=2e4119f9-3220-4502-8ddd-4821c872e0d6-exon;Parent=8760695d-b88c-41c0-857b-540e6db81fe8 |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/load_gff3/output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/load_gff3/output.tsv Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +# Feature ID Apollo ID Success Messages +Merlin_1 a036ab4f-512d-45e3-b19e-1fe83984a185 success +Merlin_2 4a3f5c6b-03fc-43d1-8d6d-1a7075931cc6 success +Merlin_3 de819682-eb71-4b98-a532-032d59354b95 success +Merlin_4 423ca5cc-d570-4ae8-8527-6a52e0a6862b success +Merlin_5 f1b5327d-79ca-40f0-b4b3-90ea03d79a56 success +Merlin_42 3629a7fe-03bb-420d-85d3-f23e55430abd success |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/merlin.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merlin.gff Mon Dec 02 05:44:41 2019 -0500 |
| b |
| @@ -0,0 +1,28 @@ +##gff-version 3 +##sequence-region Merlin 1 172788 +Merlin GeneMark.hmm gene 2 691 -856.563659 + . ID=Merlin_1;seqid=Merlin +Merlin GeneMark.hmm mRNA 2 691 . + . ID=Merlin_1_mRNA;Parent=Merlin_1;seqid=Merlin;color=#00ff00 +Merlin GeneMark.hmm exon 2 691 . + . ID=Merlin_1_exon;Parent=Merlin_1_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 2 691 . + 0 ID=Merlin_1_CDS;Parent=Merlin_1_exon;seqid=Merlin +Merlin GeneMark.hmm gene 752 1039 -339.046618 + . ID=Merlin_2;seqid=Merlin +Merlin GeneMark.hmm mRNA 752 1039 . + . ID=Merlin_2_mRNA;Parent=Merlin_2;seqid=Merlin;Name=mrna-name +Merlin GeneMark.hmm exon 752 1039 . + . ID=Merlin_2_exon;Parent=Merlin_2_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 852 939 . + 0 ID=Merlin_2_CDS;Parent=Merlin_2_exon;seqid=Merlin +Merlin GeneMark.hmm gene 1067 2011 -1229.683915 - . ID=Merlin_3;seqid=Merlin +Merlin GeneMark.hmm mRNA 1067 2011 . - . ID=Merlin_3_mRNA;Parent=Merlin_3;seqid=Merlin +Merlin GeneMark.hmm exon 1067 2011 . - . ID=Merlin_3_exon;Parent=Merlin_3_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 1367 1811 . - 0 ID=Merlin_3_CDS;Parent=Merlin_3_exon;seqid=Merlin +Merlin GeneMark.hmm gene 2011 3066 -1335.034872 - . ID=Merlin_4;seqid=Merlin +Merlin GeneMark.hmm mRNA 2011 3066 . - . ID=Merlin_4_mRNA;Parent=Merlin_4;seqid=Merlin +Merlin GeneMark.hmm exon 2011 3066 . - . ID=Merlin_4_exon;Parent=Merlin_4_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 2011 3066 . - 0 ID=Merlin_4_CDS;Parent=Merlin_4_exon;seqid=Merlin +Merlin GeneMark.hmm gene 3066 4796 -2177.374893 - . ID=Merlin_5;seqid=Merlin;Name=multiexongene +Merlin GeneMark.hmm mRNA 3066 4796 . - . ID=Merlin_5_mRNA;Parent=Merlin_5;seqid=Merlin +Merlin GeneMark.hmm exon 3066 4296 . - . ID=Merlin_5_exon;Parent=Merlin_5_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 3066 4296 . - 0 ID=Merlin_5_CDS;Parent=Merlin_5_exon;seqid=Merlin +Merlin GeneMark.hmm exon 4366 4796 . - . ID=Merlin_5_exon2;Parent=Merlin_5_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 4366 4796 . - 0 ID=Merlin_5_CDS2;Parent=Merlin_5_exon2;seqid=Merlin +Merlin GeneMark.hmm gene 5011 6066 -1335.034872 - . ID=Merlin_42;seqid=Merlin;Name=cds-not-under-exon +Merlin GeneMark.hmm mRNA 5011 6066 . - . ID=Merlin_42_mRNA;Parent=Merlin_42;seqid=Merlin +Merlin GeneMark.hmm exon 5011 6066 . - . ID=Merlin_42_exon;Parent=Merlin_42_mRNA;seqid=Merlin +Merlin GeneMark.hmm CDS 5011 6066 . - 0 ID=Merlin_42_CDS;Parent=Merlin_42_mRNA;seqid=Merlin |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 test-data/org_remote.tar.gz |
| b |
| Binary file test-data/org_remote.tar.gz has changed |
| b |
| diff -r 2adc3aa47d15 -r df0e4eb2dfa5 webapollo.py --- a/webapollo.py Mon Jul 29 10:09:19 2019 -0400 +++ b/webapollo.py Mon Dec 02 05:44:41 2019 -0500 |
| [ |
| b'@@ -5,25 +5,16 @@\n import json\n import logging\n import os\n-import random\n import time\n from abc import abstractmethod\n \n-from BCBio import GFF\n-\n-from Bio import SeqIO\n-\n import requests\n \n from six.moves.builtins import next\n from six.moves.builtins import object\n-from six.moves.builtins import str\n-\n \n-try:\n- import StringIO as io\n-except BaseException:\n- import io\n+import yaml\n+\n logging.getLogger("requests").setLevel(logging.CRITICAL)\n log = logging.getLogger()\n \n@@ -431,38 +422,6 @@\n parser.add_argument(\'--seq_raw\', nargs=\'*\', help=\'Sequence Names\')\n \n \n-def GuessOrg(args, wa):\n- if args.org_json:\n- orgs = [x.get(\'commonName\', None)\n- for x in json.load(args.org_json)]\n- orgs = [x for x in orgs if x is not None]\n- return orgs\n- elif args.org_raw:\n- org = args.org_raw.strip()\n- if len(org) > 0:\n- return [org]\n- else:\n- raise Exception("Organism Common Name not provided")\n- elif args.org_id:\n- return [wa.organisms.findOrganismById(args.org_id).get(\'commonName\', None)]\n- else:\n- raise Exception("Organism Common Name not provided")\n-\n-\n-def GuessCn(args, wa):\n- org = GuessOrg(args, wa)\n- seqs = []\n- if args.seq_fasta:\n- # If we have a fasta, pull all rec ids from that.\n- for rec in SeqIO.parse(args.seq_fasta, \'fasta\'):\n- seqs.append(rec.id)\n- elif args.seq_raw:\n- # Otherwise raw list.\n- seqs = [x.strip() for x in args.seq_raw if len(x.strip()) > 0]\n-\n- return org, seqs\n-\n-\n def AssertUser(user_list):\n if len(user_list) == 0:\n raise UnknownUserException()\n@@ -472,50 +431,29 @@\n raise Exception("Too many users!")\n \n \n-def AssertAdmin(user):\n- if user.role == \'ADMIN\':\n- return True\n- else:\n- raise Exception("User is not an administrator. Permission denied")\n-\n-\n-def PermissionCheck(user, org_cn, permission_type):\n- return any(org["organism"] == org_cn and permission_type in org["permissions"] for org in user.organismPermissions)\n-\n-\n-def PasswordGenerator(length):\n- chars = list(\'qwrtpsdfghjklzxcvbnm\')\n- return \'\'.join(random.choice(chars) for _ in range(length))\n-\n-\n-def IsRemoteUser():\n- if \'GALAXY_WEBAPOLLO_REMOTE_USER\' not in os.environ:\n- return False\n- value = os.environ[\'GALAXY_WEBAPOLLO_REMOTE_USER\']\n- if value.lower() in (\'true\', \'t\', \'1\'):\n- return True\n- else:\n- return False\n-\n-\n class WebApolloInstance(object):\n \n- def __init__(self, url, username, password):\n- self.apollo_url = url\n- self.username = username\n- self.password = password\n+ def __init__(self):\n+\n+ if \'ARROW_GLOBAL_CONFIG_PATH\' in os.environ:\n \n- self.annotations = AnnotationsClient(self)\n+ with open(os.environ[\'ARROW_GLOBAL_CONFIG_PATH\'], \'r\') as config:\n+ conf = yaml.safe_load(config)\n+ try:\n+ instance_name = conf[\'__default\']\n+ except KeyError:\n+ raise Exception("Unknown Apollo instance and no __default provided")\n+ self.apollo_url = conf[instance_name][\'url\']\n+ self.username = conf[instance_name][\'username\']\n+ self.password = conf[instance_name][\'password\']\n+ else:\n+ self.apollo_url = os.environ[\'GALAXY_WEBAPOLLO_URL\']\n+ self.username = os.environ[\'GALAXY_WEBAPOLLO_USER\']\n+ self.password = os.environ[\'GALAXY_WEBAPOLLO_PASSWORD\']\n+\n self.groups = GroupsClient(self)\n- self.io = IOClient(self)\n self.organisms = OrganismsClient(self)\n self.users = UsersClient(self)\n- self.metrics = MetricsClient(self)\n- self.bio = RemoteRecord(self)\n- self.status = StatusClient(self)\n- self.canned_comments = CannedCommentsClient(self)\n- self.canned_keys = CannedKeysClient(self)\n- self.canned_values = CannedValuesClient(self)\n \n def '..b' # Key for cached data\n cacheKey = \'groups-\' + email\n@@ -1601,11 +658,7 @@\n \n def galaxy_list_orgs(trans, *args, **kwargs):\n email = trans.get_user().email\n- wa = WebApolloInstance(\n- os.environ[\'GALAXY_WEBAPOLLO_URL\'],\n- os.environ[\'GALAXY_WEBAPOLLO_USER\'],\n- os.environ[\'GALAXY_WEBAPOLLO_PASSWORD\']\n- )\n+ wa = WebApolloInstance()\n try:\n gx_user = wa.requireUser(email)\n except UnknownUserException:\n@@ -1635,53 +688,6 @@\n return orgs\n \n \n-def galaxy_list_users(trans, *args, **kwargs):\n- email = trans.get_user().email\n- wa = WebApolloInstance(\n- os.environ[\'GALAXY_WEBAPOLLO_URL\'],\n- os.environ[\'GALAXY_WEBAPOLLO_USER\'],\n- os.environ[\'GALAXY_WEBAPOLLO_PASSWORD\']\n- )\n- # Assert that the email exists in apollo\n- try:\n- gx_user = wa.requireUser(email)\n- except UnknownUserException:\n- return []\n-\n- # Key for cached data\n- cacheKey = \'users-\' + email\n- # We don\'t want to trust "if key in cache" because between asking and fetch\n- # it might through key error.\n- if cacheKey not in cache:\n- # However if it ISN\'T there, we know we\'re safe to fetch + put in\n- # there.\n- data = _galaxy_list_users(wa, gx_user, *args, **kwargs)\n- cache[cacheKey] = data\n- return data\n- try:\n- # The cache key may or may not be in the cache at this point, it\n- # /likely/ is. However we take no chances that it wasn\'t evicted between\n- # when we checked above and now, so we reference the object from the\n- # cache in preparation to return.\n- data = cache[cacheKey]\n- return data\n- except KeyError:\n- # If access fails due to eviction, we will fail over and can ensure that\n- # data is inserted.\n- data = _galaxy_list_users(wa, gx_user, *args, **kwargs)\n- cache[cacheKey] = data\n- return data\n-\n-\n-def _galaxy_list_users(wa, gx_user, *args, **kwargs):\n- # Fetch the users.\n- user_data = []\n- for user in wa.users.loadUsers():\n- # Reformat\n- user_data.append((user.username, user.username, False))\n- return user_data\n-\n-\n # This is all for implementing the command line interface for testing.\n class obj(object):\n pass\n@@ -1698,45 +704,14 @@\n return o\n \n \n-def retry(closure, sleep=1, limit=5):\n- """\n- Apollo has the bad habit of returning 500 errors if you call APIs\n- too quickly, largely because of the unholy things that happen in\n- grails.\n-\n- To deal with the fact that we cannot send an addComments call too\n- quickly after a createFeature call, we have this function that will\n- keep calling a closure until it works.\n- """\n- count = 0\n- while True:\n- count += 1\n-\n- if count >= limit:\n- return False\n- try:\n- # Try calling it\n- closure()\n- # If successful, exit\n- return True\n- except Exception as e:\n- log.info(str(e)[0:100])\n- time.sleep(sleep)\n-\n-\n if __name__ == \'__main__\':\n parser = argparse.ArgumentParser(description=\'Test access to apollo server\')\n parser.add_argument(\'email\', help=\'Email of user to test\')\n- parser.add_argument(\'--action\', choices=[\'org\', \'group\', \'users\'], default=\'org\', help=\'Data set to test, fetch a list of groups or users known to the requesting user.\')\n+ parser.add_argument(\'--action\', choices=[\'org\', \'group\'], default=\'org\', help=\'Data set to test, fetch a list of groups or orgs known to the requesting user.\')\n args = parser.parse_args()\n \n trans = fakeTrans(args.email)\n if args.action == \'org\':\n- for f in galaxy_list_orgs(trans):\n- print(f)\n+ print(galaxy_list_orgs(trans))\n elif args.action == \'group\':\n- for f in galaxy_list_groups(trans):\n- print(f)\n- else:\n- for f in galaxy_list_users(trans):\n- print(f)\n+ print(galaxy_list_groups(trans))\n' |