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commit/galaxy-central: dannon: Merged in charles_hsu/galaxy-central/fix-multipart-upload-in-swift-backend (pull request #648)
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40ab1d00a1b6/ Changeset: 40ab1d00a1b6 User: dannon Date: 2015-02-10 14:49:01+00:00 Summary: Merged in charles_hsu/galaxy-central/fix-multipart-upload-in-swift-backend (pull request #648) Fixed multipart-upload issue while use swift as object storage backend Affected #: 3 files diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa config/object_store_conf.xml.sample --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -24,8 +24,8 @@ <object_store type="s3"><auth access_key="...." secret_key="....." /> - <bucket name="unique_bucket_name" use_reduced_redundancy="False" /> - <connection host="" port="" is_secure="" conn_path="" /> + <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/> + <connection host="" port="" is_secure="" conn_path="" multipart="True"/><cache path="database/files/" size="100" /></object_store> diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -14,6 +14,7 @@ from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms +from galaxy.util import string_as_bool from galaxy.util.directory_hash import directory_hash_id from galaxy.util.sleeper import Sleeper from .s3_multipart_upload import multipart_upload @@ -76,7 +77,8 @@ self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr = b_xml.get('use_reduced_redundancy', False) + self.use_rr= string_as_bool(b_xml.get('use_reduced_redundancy', 'False')) + self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: cn_xml = {} @@ -84,11 +86,24 @@ cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.is_secure = cn_xml.get('is_secure', True) + self.multipart = string_as_bool(cn_xml.get('multipart', 'True')) + self.is_secure = string_as_bool(cn_xml.get('is_secure', 'True')) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) self.cache_path = c_xml.get('path') + + # for multipart upload + self.s3server = {'access_key': self.access_key, + 'secret_key': self.secret_key, + 'is_secure': self.is_secure, + 'max_chunk_size': self.max_chunk_size, + 'host': self.host, + 'port': self.port, + 'use_rr': self.use_rr, + 'conn_path': self.conn_path} + + except Exception: # Toss it back up after logging, we can't continue loading at this point. log.exception("Malformed ObjectStore Configuration XML -- unable to continue") @@ -328,14 +343,14 @@ start_time = datetime.now() log.debug("Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)) mb_size = os.path.getsize(source_file) / 1e6 - if mb_size < 10 or type(self) == SwiftObjectStore: + if mb_size < 10 or (not self.multipart): self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: - multipart_upload(self.bucket, key.name, source_file, mb_size, self.access_key, self.secret_key, use_rr=self.use_rr) + multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size) end_time = datetime.now() log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -34,13 +34,23 @@ return wrapper -def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key): +def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): """Get the multipart upload from the bucket and multipart IDs. This allows us to reconstitute a connection to the upload from within multiprocessing functions. """ - conn = S3Connection(aws_access_key_id, aws_secret_access_key) + if s3server['host']: + conn = boto.connect_s3(aws_access_key_id=s3server['access_key'], + aws_secret_access_key=s3server['secret_key'], + is_secure=s3server['is_secure'], + host=s3server['host'], + port=s3server['port'], + calling_format=boto.s3.connection.OrdinaryCallingFormat(), + path=s3server['conn_path']) + else: + conn = S3Connection(s3server['access_key'], s3server['secret_key']) + bucket = conn.lookup(mp_bucketname) mp = boto.s3.multipart.MultiPartUpload(bucket) mp.key_name = mp_keyname @@ -49,33 +59,36 @@ @map_wrap -def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, aws_access_key_id, aws_secret_access_key): +def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): """Transfer a part of a multipart upload. Designed to be run in parallel. """ - mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key) + mp = mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname) with open(part) as t_handle: mp.upload_part_from_file(t_handle, i + 1) os.remove(part) -def multipart_upload(bucket, s3_key_name, tarball, mb_size, aws_access_key_id, aws_secret_access_key, use_rr=True): +def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() def split_file(in_file, mb_size, split_num=5): prefix = os.path.join(os.path.dirname(in_file), - "%sS3PART" % (os.path.basename(s3_key_name))) - # Split chunks so they are 5MB < chunk < 250MB - split_size = int(max(min(mb_size / (split_num * 2.0), 250), 5)) + "%sS3PART" % (os.path.basename(s3_key_name))) + max_chunk = s3server['max_chunk_size'] + # Split chunks so they are 5MB < chunk < 250MB(max_chunk_size) + split_size = int(max(min(mb_size / (split_num * 2.0), max_chunk), 5)) if not os.path.exists("%saa" % prefix): cl = ["split", "-b%sm" % split_size, in_file, prefix] subprocess.check_call(cl) return sorted(glob.glob("%s*" % prefix)) - mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr) + mp = bucket.initiate_multipart_upload(s3_key_name, + reduced_redundancy=s3server['use_rr']) + with multimap(cores) as pmap: - for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part, aws_access_key_id, aws_secret_access_key) + for _ in pmap(transfer_part, ((s3server, mp.id, mp.key_name, mp.bucket_name, i, part) for (i, part) in enumerate(split_file(tarball, mb_size, cores)))): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9afda176f5df/ Changeset: 9afda176f5df Branch: fix-multipart-upload-in-swift-backend User: charles_hsu Date: 2015-01-27 06:17:30+00:00 Summary: Fix type of in_secure(should be boolean, not string). --- lib/galaxy/objectstore/s3.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) Affected #: 1 file diff -r 1096077cabbd4046b7da9ce45cecf1151b7ebc75 -r 9afda176f5df5857100759eb3184e884a6e3bb80 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -84,7 +84,8 @@ cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.is_secure = cn_xml.get('is_secure', True) + self.is_secure = {'true': True, + 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) https://bitbucket.org/galaxy/galaxy-central/commits/f69c2f6c7ef1/ Changeset: f69c2f6c7ef1 Branch: fix-multipart-upload-in-swift-backend User: charles_hsu Date: 2015-01-27 06:17:45+00:00 Summary: Fixed cannot use multipart-upload for 'swift' backend with swift3 middleware. Add two options('multipart' and 'max_chunk_size'). --- config/object_store_conf.xml.sample | 4 +-- lib/galaxy/objectstore/s3.py | 22 ++++++++++++++--- lib/galaxy/objectstore/s3_multipart_upload.py | 33 +++++++++++++++++-------- 3 files changed, 44 insertions(+), 15 deletions(-) Affected #: 3 files diff -r 9afda176f5df5857100759eb3184e884a6e3bb80 -r f69c2f6c7ef176f4a6c9251c486649eb56585dbb config/object_store_conf.xml.sample --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -24,8 +24,8 @@ <object_store type="s3"><auth access_key="...." secret_key="....." /> - <bucket name="unique_bucket_name" use_reduced_redundancy="False" /> - <connection host="" port="" is_secure="" conn_path="" /> + <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/> + <connection host="" port="" is_secure="" conn_path="" multipart="True"/><cache path="database/files/" size="100" /></object_store> diff -r 9afda176f5df5857100759eb3184e884a6e3bb80 -r f69c2f6c7ef176f4a6c9251c486649eb56585dbb lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -76,7 +76,9 @@ self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr = b_xml.get('use_reduced_redundancy', False) + self.use_rr= {'true': True, + 'false': False}.get(b_xml.get('use_reduced_redundancy', 'False').lower()) + self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: cn_xml = {} @@ -84,12 +86,26 @@ cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) + self.multipart = {'true': True, + 'false': False}.get(cn_xml.get('multipart', 'True').lower()) self.is_secure = {'true': True, 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) self.cache_path = c_xml.get('path') + + # for multipart upload + self.s3server = {'access_key': self.access_key, + 'secret_key': self.secret_key, + 'is_secure': self.is_secure, + 'max_chunk_size': self.max_chunk_size, + 'host': self.host, + 'port': self.port, + 'use_rr': self.use_rr, + 'conn_path': self.conn_path} + + except Exception: # Toss it back up after logging, we can't continue loading at this point. log.exception("Malformed ObjectStore Configuration XML -- unable to continue") @@ -329,14 +345,14 @@ start_time = datetime.now() log.debug("Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)) mb_size = os.path.getsize(source_file) / 1e6 - if mb_size < 10 or type(self) == SwiftObjectStore: + if mb_size < 10 or (not self.multipart): self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: - multipart_upload(self.bucket, key.name, source_file, mb_size, self.access_key, self.secret_key, use_rr=self.use_rr) + multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size) end_time = datetime.now() log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True diff -r 9afda176f5df5857100759eb3184e884a6e3bb80 -r f69c2f6c7ef176f4a6c9251c486649eb56585dbb lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -34,13 +34,23 @@ return wrapper -def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key): +def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): """Get the multipart upload from the bucket and multipart IDs. This allows us to reconstitute a connection to the upload from within multiprocessing functions. """ - conn = S3Connection(aws_access_key_id, aws_secret_access_key) + if s3server['host']: + conn = boto.connect_s3(aws_access_key_id=s3server['access_key'], + aws_secret_access_key=s3server['secret_key'], + is_secure=s3server['is_secure'], + host=s3server['host'], + port=s3server['port'], + calling_format=boto.s3.connection.OrdinaryCallingFormat(), + path=s3server['conn_path']) + else: + conn = S3Connection(s3server['access_key'], s3server['secret_key']) + bucket = conn.lookup(mp_bucketname) mp = boto.s3.multipart.MultiPartUpload(bucket) mp.key_name = mp_keyname @@ -49,33 +59,36 @@ @map_wrap -def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, aws_access_key_id, aws_secret_access_key): +def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): """Transfer a part of a multipart upload. Designed to be run in parallel. """ - mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key) + mp = mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname) with open(part) as t_handle: mp.upload_part_from_file(t_handle, i + 1) os.remove(part) -def multipart_upload(bucket, s3_key_name, tarball, mb_size, aws_access_key_id, aws_secret_access_key, use_rr=True): +def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() def split_file(in_file, mb_size, split_num=5): prefix = os.path.join(os.path.dirname(in_file), - "%sS3PART" % (os.path.basename(s3_key_name))) - # Split chunks so they are 5MB < chunk < 250MB - split_size = int(max(min(mb_size / (split_num * 2.0), 250), 5)) + "%sS3PART" % (os.path.basename(s3_key_name))) + max_chunk = s3server['max_chunk_size'] + # Split chunks so they are 5MB < chunk < 250MB(max_chunk_size) + split_size = int(max(min(mb_size / (split_num * 2.0), max_chunk), 5)) if not os.path.exists("%saa" % prefix): cl = ["split", "-b%sm" % split_size, in_file, prefix] subprocess.check_call(cl) return sorted(glob.glob("%s*" % prefix)) - mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr) + mp = bucket.initiate_multipart_upload(s3_key_name, + reduced_redundancy=s3server['use_rr']) + with multimap(cores) as pmap: - for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part, aws_access_key_id, aws_secret_access_key) + for _ in pmap(transfer_part, ((s3server, mp.id, mp.key_name, mp.bucket_name, i, part) for (i, part) in enumerate(split_file(tarball, mb_size, cores)))): pass https://bitbucket.org/galaxy/galaxy-central/commits/6c24937ea01e/ Changeset: 6c24937ea01e Branch: fix-multipart-upload-in-swift-backend User: charles_hsu Date: 2015-01-27 15:13:55+00:00 Summary: Use string_as_bool(). --- lib/galaxy/objectstore/s3.py | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) Affected #: 1 file diff -r f69c2f6c7ef176f4a6c9251c486649eb56585dbb -r 6c24937ea01ee68dc453ad946bbd3b2ce66d83e5 lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -14,6 +14,7 @@ from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms +from galaxy.util import string_as_bool from galaxy.util.directory_hash import directory_hash_id from galaxy.util.sleeper import Sleeper from .s3_multipart_upload import multipart_upload @@ -76,8 +77,7 @@ self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr= {'true': True, - 'false': False}.get(b_xml.get('use_reduced_redundancy', 'False').lower()) + self.use_rr= string_as_bool(b_xml.get('use_reduced_redundancy', 'False')) self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: @@ -86,10 +86,8 @@ cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.multipart = {'true': True, - 'false': False}.get(cn_xml.get('multipart', 'True').lower()) - self.is_secure = {'true': True, - 'false': False}.get(cn_xml.get('is_secure', 'True').lower()) + self.multipart = string_as_bool(cn_xml.get('multipart', 'True')) + self.is_secure = string_as_bool(cn_xml.get('is_secure', 'True')) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) https://bitbucket.org/galaxy/galaxy-central/commits/40ab1d00a1b6/ Changeset: 40ab1d00a1b6 User: dannon Date: 2015-02-10 14:49:01+00:00 Summary: Merged in charles_hsu/galaxy-central/fix-multipart-upload-in-swift-backend (pull request #648) Fixed multipart-upload issue while use swift as object storage backend Affected #: 3 files diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa config/object_store_conf.xml.sample --- a/config/object_store_conf.xml.sample +++ b/config/object_store_conf.xml.sample @@ -24,8 +24,8 @@ <object_store type="s3"><auth access_key="...." secret_key="....." /> - <bucket name="unique_bucket_name" use_reduced_redundancy="False" /> - <connection host="" port="" is_secure="" conn_path="" /> + <bucket name="unique_bucket_name" use_reduced_redundancy="False" max_chunk_size="250"/> + <connection host="" port="" is_secure="" conn_path="" multipart="True"/><cache path="database/files/" size="100" /></object_store> diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa lib/galaxy/objectstore/s3.py --- a/lib/galaxy/objectstore/s3.py +++ b/lib/galaxy/objectstore/s3.py @@ -14,6 +14,7 @@ from galaxy.exceptions import ObjectNotFound from galaxy.util import umask_fix_perms +from galaxy.util import string_as_bool from galaxy.util.directory_hash import directory_hash_id from galaxy.util.sleeper import Sleeper from .s3_multipart_upload import multipart_upload @@ -76,7 +77,8 @@ self.secret_key = a_xml.get('secret_key') b_xml = config_xml.findall('bucket')[0] self.bucket = b_xml.get('name') - self.use_rr = b_xml.get('use_reduced_redundancy', False) + self.use_rr= string_as_bool(b_xml.get('use_reduced_redundancy', 'False')) + self.max_chunk_size = int(b_xml.get('max_chunk_size', 250)) cn_xml = config_xml.findall('connection') if not cn_xml: cn_xml = {} @@ -84,11 +86,24 @@ cn_xml = cn_xml[0] self.host = cn_xml.get('host', None) self.port = int(cn_xml.get('port', 6000)) - self.is_secure = cn_xml.get('is_secure', True) + self.multipart = string_as_bool(cn_xml.get('multipart', 'True')) + self.is_secure = string_as_bool(cn_xml.get('is_secure', 'True')) self.conn_path = cn_xml.get('conn_path', '/') c_xml = config_xml.findall('cache')[0] self.cache_size = float(c_xml.get('size', -1)) self.cache_path = c_xml.get('path') + + # for multipart upload + self.s3server = {'access_key': self.access_key, + 'secret_key': self.secret_key, + 'is_secure': self.is_secure, + 'max_chunk_size': self.max_chunk_size, + 'host': self.host, + 'port': self.port, + 'use_rr': self.use_rr, + 'conn_path': self.conn_path} + + except Exception: # Toss it back up after logging, we can't continue loading at this point. log.exception("Malformed ObjectStore Configuration XML -- unable to continue") @@ -328,14 +343,14 @@ start_time = datetime.now() log.debug("Pushing cache file '%s' of size %s bytes to key '%s'" % (source_file, os.path.getsize(source_file), rel_path)) mb_size = os.path.getsize(source_file) / 1e6 - if mb_size < 10 or type(self) == SwiftObjectStore: + if mb_size < 10 or (not self.multipart): self.transfer_progress = 0 # Reset transfer progress counter key.set_contents_from_filename(source_file, reduced_redundancy=self.use_rr, cb=self._transfer_cb, num_cb=10) else: - multipart_upload(self.bucket, key.name, source_file, mb_size, self.access_key, self.secret_key, use_rr=self.use_rr) + multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size) end_time = datetime.now() log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)" % (source_file, rel_path, os.path.getsize(source_file), end_time - start_time)) return True diff -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 -r 40ab1d00a1b6ef6749998d70cdd5bf7d8e19befa lib/galaxy/objectstore/s3_multipart_upload.py --- a/lib/galaxy/objectstore/s3_multipart_upload.py +++ b/lib/galaxy/objectstore/s3_multipart_upload.py @@ -34,13 +34,23 @@ return wrapper -def mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key): +def mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname): """Get the multipart upload from the bucket and multipart IDs. This allows us to reconstitute a connection to the upload from within multiprocessing functions. """ - conn = S3Connection(aws_access_key_id, aws_secret_access_key) + if s3server['host']: + conn = boto.connect_s3(aws_access_key_id=s3server['access_key'], + aws_secret_access_key=s3server['secret_key'], + is_secure=s3server['is_secure'], + host=s3server['host'], + port=s3server['port'], + calling_format=boto.s3.connection.OrdinaryCallingFormat(), + path=s3server['conn_path']) + else: + conn = S3Connection(s3server['access_key'], s3server['secret_key']) + bucket = conn.lookup(mp_bucketname) mp = boto.s3.multipart.MultiPartUpload(bucket) mp.key_name = mp_keyname @@ -49,33 +59,36 @@ @map_wrap -def transfer_part(mp_id, mp_keyname, mp_bucketname, i, part, aws_access_key_id, aws_secret_access_key): +def transfer_part(s3server, mp_id, mp_keyname, mp_bucketname, i, part): """Transfer a part of a multipart upload. Designed to be run in parallel. """ - mp = mp_from_ids(mp_id, mp_keyname, mp_bucketname, aws_access_key_id, aws_secret_access_key) + mp = mp_from_ids(s3server, mp_id, mp_keyname, mp_bucketname) with open(part) as t_handle: mp.upload_part_from_file(t_handle, i + 1) os.remove(part) -def multipart_upload(bucket, s3_key_name, tarball, mb_size, aws_access_key_id, aws_secret_access_key, use_rr=True): +def multipart_upload(s3server, bucket, s3_key_name, tarball, mb_size): """Upload large files using Amazon's multipart upload functionality. """ cores = multiprocessing.cpu_count() def split_file(in_file, mb_size, split_num=5): prefix = os.path.join(os.path.dirname(in_file), - "%sS3PART" % (os.path.basename(s3_key_name))) - # Split chunks so they are 5MB < chunk < 250MB - split_size = int(max(min(mb_size / (split_num * 2.0), 250), 5)) + "%sS3PART" % (os.path.basename(s3_key_name))) + max_chunk = s3server['max_chunk_size'] + # Split chunks so they are 5MB < chunk < 250MB(max_chunk_size) + split_size = int(max(min(mb_size / (split_num * 2.0), max_chunk), 5)) if not os.path.exists("%saa" % prefix): cl = ["split", "-b%sm" % split_size, in_file, prefix] subprocess.check_call(cl) return sorted(glob.glob("%s*" % prefix)) - mp = bucket.initiate_multipart_upload(s3_key_name, reduced_redundancy=use_rr) + mp = bucket.initiate_multipart_upload(s3_key_name, + reduced_redundancy=s3server['use_rr']) + with multimap(cores) as pmap: - for _ in pmap(transfer_part, ((mp.id, mp.key_name, mp.bucket_name, i, part, aws_access_key_id, aws_secret_access_key) + for _ in pmap(transfer_part, ((s3server, mp.id, mp.key_name, mp.bucket_name, i, part) for (i, part) in enumerate(split_file(tarball, mb_size, cores)))): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI, Paired collection creator: use scoped version of $.index instead of clumsy calculation
by commits-noreply＠bitbucket.org 10 Feb '15

10 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c3eefbdaaa1a/ Changeset: c3eefbdaaa1a User: carlfeberhard Date: 2015-02-09 23:09:27+00:00 Summary: UI, Paired collection creator: use scoped version of $.index instead of clumsy calculation Affected #: 3 files diff -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -1307,8 +1307,10 @@ /** rename a pair when the pair name is clicked */ _clickPairName : function( ev ){ ev.stopPropagation(); - var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().parent().index() / 2 ], + var $name = $( ev.currentTarget ), + $pair = $name.parent().parent(), + index = $pair.index( '.dataset.paired' ), + pair = this.paired[ index ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; @@ -1316,7 +1318,7 @@ // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1324,7 +1326,7 @@ _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } //TODO: this is a hack bc each paired rev now has two elems (dataset, button) - var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 ); + var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); //TODO: animate this._unpair( this.paired[ pairIndex ] ); diff -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1307,8 +1307,10 @@ /** rename a pair when the pair name is clicked */ _clickPairName : function( ev ){ ev.stopPropagation(); - var $control = $( ev.currentTarget ), - pair = this.paired[ $control.parent().parent().index() / 2 ], + var $name = $( ev.currentTarget ), + $pair = $name.parent().parent(), + index = $pair.index( '.dataset.paired' ), + pair = this.paired[ index ], response = prompt( 'Enter a new name for the pair:', pair.name ); if( response ){ pair.name = response; @@ -1316,7 +1318,7 @@ // when adding/removing extensions //TODO: kinda hacky pair.customizedName = true; - $control.text( pair.name ); + $name.text( pair.name ); } }, @@ -1324,7 +1326,7 @@ _clickUnpair : function( ev ){ //if( !ev.currentTarget ){ return true; } //TODO: this is a hack bc each paired rev now has two elems (dataset, button) - var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 ); + var pairIndex = Math.floor( $( ev.currentTarget ).index( '.unpair-btn' ) ); //this.debug( 'pair:', pairIndex ); //TODO: animate this._unpair( this.paired[ pairIndex ] ); diff -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae -r c3eefbdaaa1ab242a1c81b65482ef2fbe943a390 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""))({}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(i,k.originalEvent.clientY);var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i<this.autoscrollDist){h.scrollTop(k-l)}else{if(j>=0&&j<this.autoscrollDist){h.scrollTop(k+l)}}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag" title="',d("Drag to change"),'"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',d("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<ol class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div class="attributes clear">','<div class="clear">','<label class="remove-extensions-prompt pull-right">',d("Remove file extensions from pair names"),"?",'<input class="remove-extensions pull-right" type="checkbox" />',"</label>","</div>",'<div class="clear">','<input class="collection-name form-control pull-right" ','placeholder="',d("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',d("Name"),":</div>","</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',d("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',d("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',d("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',d("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return 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','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: UI, Paired collection creator: fix template function for 'Choose Filters'
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3764ca243a93/ Changeset: 3764ca243a93 User: carlfeberhard Date: 2015-02-09 22:54:17+00:00 Summary: UI, Paired collection creator: fix template function for 'Choose Filters' Affected #: 3 files diff -r 27bc860232d7e531133f0413d6200fe5c171695d -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -876,7 +876,7 @@ filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '</div>' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', diff -r 27bc860232d7e531133f0413d6200fe5c171695d -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -876,7 +876,7 @@ filterChoice( '_1', '_2' ), filterChoice( '_R1', '_R2' ), '</div>' - ].join(''), {})); + ].join(''))({})); return this.$( selector ).popover({ container : '.collection-creator', diff -r 27bc860232d7e531133f0413d6200fe5c171695d -r 3764ca243a9366a8f7ccd9403ef7bc7df45cc4ae static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(i,k.originalEvent.clientY);var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i<this.autoscrollDist){h.scrollTop(k-l)}else{if(j>=0&&j<this.autoscrollDist){h.scrollTop(k+l)}}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return 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pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var 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commit/galaxy-central: carlfeberhard: UI: remove unused LazyDataLoader module
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/27bc860232d7/ Changeset: 27bc860232d7 User: carlfeberhard Date: 2015-02-09 22:47:30+00:00 Summary: UI: remove unused LazyDataLoader module Affected #: 3 files diff -r e3179a43319070d78d02a55e394fa765a3549a84 -r 27bc860232d7e531133f0413d6200fe5c171695d client/galaxy/scripts/utils/LazyDataLoader.js --- a/client/galaxy/scripts/utils/LazyDataLoader.js +++ /dev/null @@ -1,228 +0,0 @@ -//============================================================================== -/* -TODO: - ?? superclass dataloader, subclass lazydataloader?? - -*/ -//============================================================================== -/** - * Object to progressively load JSON data from a REST url, delaying some time between loading chunks - * - * Will load size amount of data every delay ms, starting at start and ending at total. - * - * NOTE: Data from ajax loading is aggregated in a list, with one element for each ajax response. - * It's up to the calling code to combine the results in a meaningful, correct way. - * - * example: - * var loader = new scatterplot.LazyDataLoader({ - * //logger : console, - * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' - * + '&columns=[10,14]' ), - * total : hda.metadata_data_lines, - * size : 500, - * - * initialize : function( config ){ - * // ... do some stuff - * }, - * - * buildUrl : function( start, size ){ - * // change the formation of start, size in query string - * return loader.url + '&' + jQuery.param({ - * start_val: start, - * max_vals: size - * }); - * }, - * }); - * - * // you can use events - * $( loader ).bind( 'error', function( event, xhr, status, error ){ - * alert( loader + ' ERROR:' + status + '\n' + error ); - * // bail out... - * }); - * $( loader ).bind( 'loaded.new', function( event, response ){ - * console.info( 'new data available:', event, response ); - * // ... do stuff with new data - * }); - * $( loader ).bind( 'complete', function( event, allDataArray, total ){ - * console.info( 'final load complete:', event, allDataArray, total ); - * // ... do stuff with all data - * }); - * - * // ...or use a callback called when all data is loaded - * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); - */ -function LazyDataLoader( config ){ - // for now assume: - // get, async, and params sent via url query string - // we want json - // we know the size of the data on the server beforehand - var loader = this, - // events to trigger when new or all data has been loaded - // new batches of data (including last). Will be sent: the ajax response data, start value, and size - LOADED_NEW_EVENT = 'loaded.new', - // all data has been loaded: the final loader's data array and the total - LOADED_ALL_EVENT = 'complete'; - // error from ajax - ERROR_EVENT = 'error'; - - jQuery.extend( loader, LoggableMixin ); - jQuery.extend( loader, { - - //NOTE: the next two need to be sent in config (required) - // total size of data on server - total : undefined, - // url of service to get the data - url : undefined, - - // holds the interval id for the current load delay - currentIntervalId : undefined, - - // each load call will add an element to this array - // it's the responsibility of the code using this to combine them properly - data : [], - // ms btwn recursive loads - delay : 4000, - // starting line, element, whatever - start : 0, - // size to fetch per load - size : 4000, - - // loader init func: extends loader with config and calls config.init if there - //@param {object} config : object containing variables to override (or additional) - initialize : function( config ){ - jQuery.extend( loader, config ); - - // call the custom initialize function if any - // only dangerous if the user tries LazyDataLoader.prototype.init - if( config.hasOwnProperty( 'initialize' ) ){ - config.initialize.call( loader, config ); - } - this.log( this + ' initialized:', loader ); - }, - - // returns query string formatted start and size (for the next fetch) appended to the loader.url - //OVERRIDE: to change how params are passed, param names, etc. - //@param {int} start : the line/row/datum indicating where in the dataset the next load begins - //@param {int} size : the number of lines/rows/data to get on the next load - buildUrl : function( start, size ){ - // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params - return this.url + '&' + jQuery.param({ - start_val: start, - max_vals: size - }); - }, - - //OVERRIDE: to handle ajax errors differently - ajaxErrorFn : function( xhr, status, error ){ - console.error( 'ERROR fetching data:', error ); - }, - - // converters passed to the jQuery ajax call for data type parsing - //OVERRIDE: to provide custom parsing - converters : { - '* text' : window.String, - 'text html' : true, - 'text xml' : jQuery.parseXML, - 'text json' : jQuery.parseJSON - }, - - // interface to begin load (and first recursive call) - //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data - load : function( callback ){ - this.log( this + '.load' ); - - // ensure necessary stuff - if( !loader.url ){ throw( loader + ' requires a url' ); } - - if( this.total === null ){ - this.log( '\t total is null (will load all)' ); - } else { - this.log( '\t total:', this.total ); - } - //if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } - - //FIRST RECURSION: start - var startingSize = loader.size; - if( ( loader.total !== null ) && ( loader.total < loader.size ) ){ - startingSize = loader.total; - } - loader.log( loader + '\t beginning recursion' ); - loadHelper( loader.start, startingSize ); - - //FIRST, SUBSEQUENT RECURSION function - function loadHelper( start, size ){ - loader.log( loader + '.loadHelper, start:', start, 'size:', size ); - var url = loader.buildUrl( start, size ); - loader.log( '\t url:', url ); - - jQuery.ajax({ - url : loader.buildUrl( start, size ), - converters : loader.converters, - dataType : 'json', - - error : function( xhr, status, error ){ - loader.log( '\t ajax error, status:', status, 'error:', error ); - if( loader.currentIntervalId ){ - clearInterval( loader.currentIntervalId ); - } - $( loader ).trigger( ERROR_EVENT, [ status, error ] ); - loader.ajaxErrorFn( xhr, status, error ); - }, - - success : function( response ){ - loader.log( '\t ajax success, response:', response, 'next:', next, 'remainder:', remainder ); - - if( response !== null ){ - // store the response as is in a new element - //TODO:?? store start, size as well? - loader.data.push( response ); - - //TODO: these might not be the best way to split this up - // fire the first load event (if this is the first batch) AND partial - $( loader ).trigger( LOADED_NEW_EVENT, [ response, start, size ] ); - - //RECURSION: - var next = start + size, - remainder = loader.size; - - if( loader.total !== null ){ - remainder = Math.min( loader.total - next, loader.size ); - } - loader.log( '\t next recursion, start:', next, 'size:', remainder ); - - // if we haven't gotten everything yet, so set up for next recursive call and set the timer - if( loader.total === null || remainder > 0 ){ - loader.currentIntervalId = setTimeout( - function(){ loadHelper( next, remainder ); }, - loader.delay - ); - loader.log( '\t currentIntervalId:', loader.currentIntervalId ); - - // otherwise (base-case), don't do anything - } else { - loadFinished(); - } - - } else { //response === null --> base-case, server sez nuthin left - loadFinished(); - } - } - }); - } - - //HANDLE BASE-CASE, LAST RECURSION - function loadFinished(){ - loader.log( loader + '.loadHelper, has finished:', loader.data ); - $( loader ).trigger( LOADED_ALL_EVENT, [ loader.data, loader.total ] ); - if( callback ){ callback( loader.data ); } - } - }, - - toString : function(){ return 'LazyDataLoader'; } - }); - - loader.initialize( config ); - return loader; -} - -//============================================================================== diff -r e3179a43319070d78d02a55e394fa765a3549a84 -r 27bc860232d7e531133f0413d6200fe5c171695d static/scripts/packed/utils/LazyDataLoader.js --- a/static/scripts/packed/utils/LazyDataLoader.js +++ /dev/null @@ -1,1 +0,0 @@ -function LazyDataLoader(c){var a=this,d="loaded.new",b="complete";ERROR_EVENT="error";jQuery.extend(a,LoggableMixin);jQuery.extend(a,{total:undefined,url:undefined,currentIntervalId:undefined,data:[],delay:4000,start:0,size:4000,initialize:function(e){jQuery.extend(a,e);if(e.hasOwnProperty("initialize")){e.initialize.call(a,e)}this.log(this+" initialized:",a)},buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})},ajaxErrorFn:function(g,e,f){console.error("ERROR fetching data:",f)},converters:{"* text":window.String,"text html":true,"text xml":jQuery.parseXML,"text json":jQuery.parseJSON},load:function(h){this.log(this+".load");if(!a.url){throw (a+" requires a url")}if(this.total===null){this.log("\t total is null (will load all)")}else{this.log("\t total:",this.total)}var g=a.size;if((a.total!==null)&&(a.total<a.size)){g=a.total}a.log(a+"\t beginning recursion");f(a.start,g);function f(k,j){a.log(a+".loadHelper, start:",k,"size:",j);var i=a.buildUrl(k,j);a.log("\t url:",i);jQuery.ajax({url:a.buildUrl(k,j),converters:a.converters,dataType:"json",error:function(n,l,m){a.log("\t ajax error, status:",l,"error:",m);if(a.currentIntervalId){clearInterval(a.currentIntervalId)}$(a).trigger(ERROR_EVENT,[l,m]);a.ajaxErrorFn(n,l,m)},success:function(l){a.log("\t ajax success, response:",l,"next:",m,"remainder:",n);if(l!==null){a.data.push(l);$(a).trigger(d,[l,k,j]);var m=k+j,n=a.size;if(a.total!==null){n=Math.min(a.total-m,a.size)}a.log("\t next recursion, start:",m,"size:",n);if(a.total===null||n>0){a.currentIntervalId=setTimeout(function(){f(m,n)},a.delay);a.log("\t currentIntervalId:",a.currentIntervalId)}else{e()}}else{e()}}})}function e(){a.log(a+".loadHelper, has finished:",a.data);$(a).trigger(b,[a.data,a.total]);if(h){h(a.data)}}},toString:function(){return"LazyDataLoader"}});a.initialize(c);return a}; \ No newline at end of file diff -r e3179a43319070d78d02a55e394fa765a3549a84 -r 27bc860232d7e531133f0413d6200fe5c171695d static/scripts/utils/LazyDataLoader.js --- a/static/scripts/utils/LazyDataLoader.js +++ /dev/null @@ -1,228 +0,0 @@ -//============================================================================== -/* -TODO: - ?? superclass dataloader, subclass lazydataloader?? - -*/ -//============================================================================== -/** - * Object to progressively load JSON data from a REST url, delaying some time between loading chunks - * - * Will load size amount of data every delay ms, starting at start and ending at total. - * - * NOTE: Data from ajax loading is aggregated in a list, with one element for each ajax response. - * It's up to the calling code to combine the results in a meaningful, correct way. - * - * example: - * var loader = new scatterplot.LazyDataLoader({ - * //logger : console, - * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' - * + '&columns=[10,14]' ), - * total : hda.metadata_data_lines, - * size : 500, - * - * initialize : function( config ){ - * // ... do some stuff - * }, - * - * buildUrl : function( start, size ){ - * // change the formation of start, size in query string - * return loader.url + '&' + jQuery.param({ - * start_val: start, - * max_vals: size - * }); - * }, - * }); - * - * // you can use events - * $( loader ).bind( 'error', function( event, xhr, status, error ){ - * alert( loader + ' ERROR:' + status + '\n' + error ); - * // bail out... - * }); - * $( loader ).bind( 'loaded.new', function( event, response ){ - * console.info( 'new data available:', event, response ); - * // ... do stuff with new data - * }); - * $( loader ).bind( 'complete', function( event, allDataArray, total ){ - * console.info( 'final load complete:', event, allDataArray, total ); - * // ... do stuff with all data - * }); - * - * // ...or use a callback called when all data is loaded - * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); - */ -function LazyDataLoader( config ){ - // for now assume: - // get, async, and params sent via url query string - // we want json - // we know the size of the data on the server beforehand - var loader = this, - // events to trigger when new or all data has been loaded - // new batches of data (including last). Will be sent: the ajax response data, start value, and size - LOADED_NEW_EVENT = 'loaded.new', - // all data has been loaded: the final loader's data array and the total - LOADED_ALL_EVENT = 'complete'; - // error from ajax - ERROR_EVENT = 'error'; - - jQuery.extend( loader, LoggableMixin ); - jQuery.extend( loader, { - - //NOTE: the next two need to be sent in config (required) - // total size of data on server - total : undefined, - // url of service to get the data - url : undefined, - - // holds the interval id for the current load delay - currentIntervalId : undefined, - - // each load call will add an element to this array - // it's the responsibility of the code using this to combine them properly - data : [], - // ms btwn recursive loads - delay : 4000, - // starting line, element, whatever - start : 0, - // size to fetch per load - size : 4000, - - // loader init func: extends loader with config and calls config.init if there - //@param {object} config : object containing variables to override (or additional) - initialize : function( config ){ - jQuery.extend( loader, config ); - - // call the custom initialize function if any - // only dangerous if the user tries LazyDataLoader.prototype.init - if( config.hasOwnProperty( 'initialize' ) ){ - config.initialize.call( loader, config ); - } - this.log( this + ' initialized:', loader ); - }, - - // returns query string formatted start and size (for the next fetch) appended to the loader.url - //OVERRIDE: to change how params are passed, param names, etc. - //@param {int} start : the line/row/datum indicating where in the dataset the next load begins - //@param {int} size : the number of lines/rows/data to get on the next load - buildUrl : function( start, size ){ - // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params - return this.url + '&' + jQuery.param({ - start_val: start, - max_vals: size - }); - }, - - //OVERRIDE: to handle ajax errors differently - ajaxErrorFn : function( xhr, status, error ){ - console.error( 'ERROR fetching data:', error ); - }, - - // converters passed to the jQuery ajax call for data type parsing - //OVERRIDE: to provide custom parsing - converters : { - '* text' : window.String, - 'text html' : true, - 'text xml' : jQuery.parseXML, - 'text json' : jQuery.parseJSON - }, - - // interface to begin load (and first recursive call) - //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data - load : function( callback ){ - this.log( this + '.load' ); - - // ensure necessary stuff - if( !loader.url ){ throw( loader + ' requires a url' ); } - - if( this.total === null ){ - this.log( '\t total is null (will load all)' ); - } else { - this.log( '\t total:', this.total ); - } - //if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } - - //FIRST RECURSION: start - var startingSize = loader.size; - if( ( loader.total !== null ) && ( loader.total < loader.size ) ){ - startingSize = loader.total; - } - loader.log( loader + '\t beginning recursion' ); - loadHelper( loader.start, startingSize ); - - //FIRST, SUBSEQUENT RECURSION function - function loadHelper( start, size ){ - loader.log( loader + '.loadHelper, start:', start, 'size:', size ); - var url = loader.buildUrl( start, size ); - loader.log( '\t url:', url ); - - jQuery.ajax({ - url : loader.buildUrl( start, size ), - converters : loader.converters, - dataType : 'json', - - error : function( xhr, status, error ){ - loader.log( '\t ajax error, status:', status, 'error:', error ); - if( loader.currentIntervalId ){ - clearInterval( loader.currentIntervalId ); - } - $( loader ).trigger( ERROR_EVENT, [ status, error ] ); - loader.ajaxErrorFn( xhr, status, error ); - }, - - success : function( response ){ - loader.log( '\t ajax success, response:', response, 'next:', next, 'remainder:', remainder ); - - if( response !== null ){ - // store the response as is in a new element - //TODO:?? store start, size as well? - loader.data.push( response ); - - //TODO: these might not be the best way to split this up - // fire the first load event (if this is the first batch) AND partial - $( loader ).trigger( LOADED_NEW_EVENT, [ response, start, size ] ); - - //RECURSION: - var next = start + size, - remainder = loader.size; - - if( loader.total !== null ){ - remainder = Math.min( loader.total - next, loader.size ); - } - loader.log( '\t next recursion, start:', next, 'size:', remainder ); - - // if we haven't gotten everything yet, so set up for next recursive call and set the timer - if( loader.total === null || remainder > 0 ){ - loader.currentIntervalId = setTimeout( - function(){ loadHelper( next, remainder ); }, - loader.delay - ); - loader.log( '\t currentIntervalId:', loader.currentIntervalId ); - - // otherwise (base-case), don't do anything - } else { - loadFinished(); - } - - } else { //response === null --> base-case, server sez nuthin left - loadFinished(); - } - } - }); - } - - //HANDLE BASE-CASE, LAST RECURSION - function loadFinished(){ - loader.log( loader + '.loadHelper, has finished:', loader.data ); - $( loader ).trigger( LOADED_ALL_EVENT, [ loader.data, loader.total ] ); - if( callback ){ callback( loader.data ); } - } - }, - - toString : function(){ return 'LazyDataLoader'; } - }); - - loader.initialize( config ); - return loader; -} - -//============================================================================== Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Fix to 389f0dcc1589: remove debugging code in index.mako
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3179a433190/ Changeset: e3179a433190 User: carlfeberhard Date: 2015-02-09 22:42:13+00:00 Summary: Fix to 389f0dcc1589: remove debugging code in index.mako Affected #: 1 file diff -r 389f0dcc15892f77650979877fd1941dae575646 -r e3179a43319070d78d02a55e394fa765a3549a84 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,12 +152,6 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; - -currPanel.once( 'rendered', function(){ - currPanel.showSelectors(); - currPanel.selectAll(); - _.last( currPanel.actionsPopup.options ).func(); -}); }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI, Paired collection creator: when dragging within the paired section autoscroll the list when the mouse is within 'autoscrollDist' pixels of the top or bottom
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/389f0dcc1589/ Changeset: 389f0dcc1589 User: carlfeberhard Date: 2015-02-09 22:40:53+00:00 Summary: UI, Paired collection creator: when dragging within the paired section autoscroll the list when the mouse is within 'autoscrollDist' pixels of the top or bottom Affected #: 4 files diff -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e -r 389f0dcc15892f77650979877fd1941dae575646 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -150,6 +150,9 @@ /** fn to call when the collection is created (scoped to this) */ this.oncreate = attributes.oncreate; + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ + this.autoscrollDist = attributes.autoscrollDist || 24; + /** is the unpaired panel shown? */ this.unpairedPanelHidden = false; /** is the paired panel shown? */ @@ -1025,7 +1028,6 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ - console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1340,27 +1342,41 @@ //console.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); - var $list = this.$( '.paired-columns .column-datasets' ), - offset = $list.offset(); + var $list = this.$( '.paired-columns .column-datasets' ); + this._checkForAutoscroll( $list, ev.originalEvent.clientY ); //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX - offset.left, ev.originalEvent.clientY - offset.top ); $( '.paired-drop-placeholder' ).remove(); - var $placeholder = $( '<div class="paired-drop-placeholder"></div>') + var $placeholder = $( '<div class="paired-drop-placeholder"></div>' ); if( !$nearest.size() ){ $list.append( $placeholder ); } else { $nearest.before( $placeholder ); } }, + + /** If the mouse is near enough to the list's top or bottom, scroll the list */ + _checkForAutoscroll : function( $element, y ){ + var AUTOSCROLL_SPEED = 2; + var offset = $element.offset(), + scrollTop = $element.scrollTop(), + upperDist = y - offset.top, + lowerDist = ( offset.top + $element.outerHeight() ) - y; + //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + if( upperDist >= 0 && upperDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); + } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop + AUTOSCROLL_SPEED ); + } + }, + /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate. * If the y is at the end of the list, return an empty jQuery object. */ _getNearestPairedDatasetLi : function( y ){ var WIGGLE = 4, lis = this.$( '.paired-columns .column-datasets li' ).toArray(); -//TODO: better way? for( var i=0; i<lis.length; i++ ){ var $li = $( lis[i] ), top = $li.offset().top, diff -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e -r 389f0dcc15892f77650979877fd1941dae575646 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -150,6 +150,9 @@ /** fn to call when the collection is created (scoped to this) */ this.oncreate = attributes.oncreate; + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ + this.autoscrollDist = attributes.autoscrollDist || 24; + /** is the unpaired panel shown? */ this.unpairedPanelHidden = false; /** is the paired panel shown? */ @@ -1025,7 +1028,6 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ - console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1340,27 +1342,41 @@ //console.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); - var $list = this.$( '.paired-columns .column-datasets' ), - offset = $list.offset(); + var $list = this.$( '.paired-columns .column-datasets' ); + this._checkForAutoscroll( $list, ev.originalEvent.clientY ); //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX - offset.left, ev.originalEvent.clientY - offset.top ); $( '.paired-drop-placeholder' ).remove(); - var $placeholder = $( '<div class="paired-drop-placeholder"></div>') + var $placeholder = $( '<div class="paired-drop-placeholder"></div>' ); if( !$nearest.size() ){ $list.append( $placeholder ); } else { $nearest.before( $placeholder ); } }, + + /** If the mouse is near enough to the list's top or bottom, scroll the list */ + _checkForAutoscroll : function( $element, y ){ + var AUTOSCROLL_SPEED = 2; + var offset = $element.offset(), + scrollTop = $element.scrollTop(), + upperDist = y - offset.top, + lowerDist = ( offset.top + $element.outerHeight() ) - y; + //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + if( upperDist >= 0 && upperDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); + } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ + $element.scrollTop( scrollTop + AUTOSCROLL_SPEED ); + } + }, + /** get the nearest *previous* paired dataset PairView based on the mouse's Y coordinate. * If the y is at the end of the list, return an empty jQuery object. */ _getNearestPairedDatasetLi : function( y ){ var WIGGLE = 4, lis = this.$( '.paired-columns .column-datasets li' ).toArray(); -//TODO: better way? for( var i=0; i<lis.length; i++ ){ var $li = $( lis[i] ), top = $li.offset().top, diff -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e -r 389f0dcc15892f77650979877fd1941dae575646 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){console.debug("alert:",i,h);h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). 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See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator 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o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return 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j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the 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h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(i,k.originalEvent.clientY);var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i<this.autoscrollDist){h.scrollTop(k-l)}else{if(j>=0&&j<this.autoscrollDist){h.scrollTop(k+l)}}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). 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','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file diff -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e -r 389f0dcc15892f77650979877fd1941dae575646 templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,6 +152,12 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; + +currPanel.once( 'rendered', function(){ + currPanel.showSelectors(); + currPanel.selectAll(); + _.last( currPanel.actionsPopup.options ).func(); +}); }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/813c1769e0da/ Changeset: 813c1769e0da User: dannon Date: 2015-02-09 21:51:43+00:00 Summary: Enable session timeout for tool_shed application (off by default, as with Galaxy). Affected #: 3 files diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -143,7 +143,8 @@ current_history=None, session_key=None, is_valid=False, - prev_session_id=None ): + prev_session_id=None, + last_action=None ): self.id = id self.user = user self.remote_host = remote_host @@ -153,6 +154,7 @@ self.session_key = session_key self.is_valid = is_valid self.prev_session_id = prev_session_id + self.last_action = last_action or datetime.now() class Repository( object, Dictifiable ): diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a lib/galaxy/webapps/tool_shed/model/mapping.py --- a/lib/galaxy/webapps/tool_shed/model/mapping.py +++ b/lib/galaxy/webapps/tool_shed/model/mapping.py @@ -96,7 +96,8 @@ Column( "referer", TEXT ), Column( "session_key", TrimmedString( 255 ), index=True, unique=True ), # unique 128 bit random number coerced to a string Column( "is_valid", Boolean, default=False ), - Column( "prev_session_id", Integer ) # saves a reference to the previous session so we have a way to chain them together + Column( "prev_session_id", Integer ), # saves a reference to the previous session so we have a way to chain them together + Column( "last_action", DateTime) ) Repository.table = Table( "repository", metadata, diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py @@ -0,0 +1,50 @@ +""" +Migration script to add session update time (used for timeouts) +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from galaxy.model.custom_types import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + lastaction_column = Column( "last_action", DateTime ) + __add_column( lastaction_column, "galaxy_session", metadata ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + + __drop_column( "last_action", "galaxy_session", metadata ) + + +def __add_column(column, table_name, metadata, **kwds): + try: + table = Table( table_name, metadata, autoload=True ) + column.create( table, **kwds ) + except Exception as e: + print str(e) + log.exception( "Adding column %s failed." % column) + + +def __drop_column( column_name, table_name, metadata ): + try: + table = Table( table_name, metadata, autoload=True ) + getattr( table.c, column_name ).drop() + except Exception as e: + print str(e) + log.exception( "Dropping column %s failed." % column_name ) https://bitbucket.org/galaxy/galaxy-central/commits/35a718a57a32/ Changeset: 35a718a57a32 User: dannon Date: 2015-02-09 21:51:55+00:00 Summary: Merge. Affected #: 5 files diff -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -158,9 +158,8 @@ /** DOM elements currently being dragged */ this.$dragging = null; + this._setUpBehaviors(); this._dataSetUp(); - - this._setUpBehaviors(); }, /** map of common filter pairs by name */ @@ -199,6 +198,9 @@ if( this.automaticallyPair ){ this.autoPair(); + this.once( 'rendered:initial', function(){ + this.trigger( 'autopair' ); + }); } }, @@ -287,8 +289,9 @@ autoPair : function( strategy ){ strategy = strategy || this.strategy; //this.debug( '-- autoPair', strategy ); - this.simpleAutoPair(); - return this[ strategy ].call( this ); + var paired = this.simpleAutoPair(); + paired = paired.concat( this[ strategy ].call( this ) ); + return paired; }, /** attempts to pair forward with reverse when names exactly match (after removing filters) */ @@ -303,7 +306,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - matchFound = false; + matchFound = false, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -321,11 +325,12 @@ matchFound = true; // if it is a match, keep i at current, pop fwd, pop rev and break //this.debug( '---->', fwdName, revName ); - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( j, 1 )[0], { silent: true } ); + paired.push( pair ); break; } } @@ -336,6 +341,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ @@ -347,7 +353,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - distance, bestIndex, bestDist; + distance, bestIndex, bestDist, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -383,13 +390,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -400,6 +408,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to auto pair using common substrings from both front and back (after removing filters) */ @@ -411,8 +420,9 @@ fwdList = split[0], revList = split[1], fwdName, revName, - currMatch, bestIndex, bestMatch; - if( !fwdList.length || !revList.length ){ return; } + currMatch, bestIndex, bestMatch, + paired = []; + if( !fwdList.length || !revList.length ){ return paired; } //this.debug( fwdList, revList ); while( i<fwdList.length ){ @@ -448,13 +458,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -465,6 +476,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** return the concat'd longest common prefix and suffix from two strings */ @@ -652,6 +664,7 @@ this._renderMiddle( speed ); this._renderFooter( speed ); this._addPluginComponents(); + this.trigger( 'rendered', this ); return this; }, @@ -889,6 +902,10 @@ // ------------------------------------------------------------------------ events /** set up event handlers on self */ _setUpBehaviors : function(){ + this.once( 'rendered', function(){ + this.trigger( 'rendered:initial', this ); + }); + this.on( 'pair:new', function(){ //TODO: ideally only re-render the columns (or even elements) involved this._renderUnpaired(); @@ -929,6 +946,7 @@ if( !this.unpaired.length ){ message += ': ' + _l( 'all datasets have been successfully paired' ); this.hideUnpaired(); + this.$( '.collection-name' ).focus(); } } else { message = _l( 'Could not automatically create any pairs from the given dataset names' ); @@ -1007,6 +1025,7 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ + console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1064,10 +1083,8 @@ /** attempt to autopair */ _clickAutopair : function( ev ){ - var paired = this.autoPair(); - //this.debug( 'autopaired', paired ); - //TODO: an indication of how many pairs were found - if 0, assist - this.trigger( 'autopair', paired ); + this.autoPair(); + this.trigger( 'autopair' ); }, /** set the filters based on the data attributes of the button click target */ diff -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e lib/galaxy/webapps/tool_shed/api/search.py --- a/lib/galaxy/webapps/tool_shed/api/search.py +++ b/lib/galaxy/webapps/tool_shed/api/search.py @@ -1,8 +1,8 @@ """API for searching the toolshed repositories""" from galaxy import exceptions from galaxy import eggs +from galaxy import util from galaxy.web import _future_expose_api as expose_api -# from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed.search.repo_search import RepoSearch @@ -22,19 +22,32 @@ The index has to be pre-created with build_ts_whoosh_index.sh. TS config option toolshed_search_on has to be turned on and toolshed_whoosh_index_dir has to be specified and existing. + + :param search_term: + :param page: + :param jsonp: + :param callback: + + :returns dict: """ if not self.app.config.toolshed_search_on: raise exceptions.ConfigDoesNotAllowException( 'Searching the TS through the API is turned off for this instance.' ) if not self.app.config.toolshed_whoosh_index_dir: raise exceptions.ConfigDoesNotAllowException( 'There is no directory for the search index specified. Please ontact the administrator.' ) + search_term = search_term.strip() if len( search_term ) < 3: raise exceptions.RequestParameterInvalidException( 'The search term has to be at least 3 characters long.' ) page = kwd.get( 'page', 1 ) + return_jsonp = util.asbool( kwd.get( 'jsonp', False ) ) callback = kwd.get( 'callback', 'callback' ) repo_search = RepoSearch() results = repo_search.search( trans, search_term, page ) results[ 'hostname' ] = url_for( '/', qualified = True ) - response = '%s(%s);' % ( callback, json.dumps( results ) ) + + if jsonp: + response = '%s(%s);' % ( callback, json.dumps( results ) ) + else: + response = json.dumps( results ) return response diff -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -33,6 +33,7 @@ full_last_updated = STORED ) except ImportError, e: + log.error( 'There was an error while importing the Whoosh library.' ) search_ready = False schema = None diff -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -158,9 +158,8 @@ /** DOM elements currently being dragged */ this.$dragging = null; + this._setUpBehaviors(); this._dataSetUp(); - - this._setUpBehaviors(); }, /** map of common filter pairs by name */ @@ -199,6 +198,9 @@ if( this.automaticallyPair ){ this.autoPair(); + this.once( 'rendered:initial', function(){ + this.trigger( 'autopair' ); + }); } }, @@ -287,8 +289,9 @@ autoPair : function( strategy ){ strategy = strategy || this.strategy; //this.debug( '-- autoPair', strategy ); - this.simpleAutoPair(); - return this[ strategy ].call( this ); + var paired = this.simpleAutoPair(); + paired = paired.concat( this[ strategy ].call( this ) ); + return paired; }, /** attempts to pair forward with reverse when names exactly match (after removing filters) */ @@ -303,7 +306,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - matchFound = false; + matchFound = false, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -321,11 +325,12 @@ matchFound = true; // if it is a match, keep i at current, pop fwd, pop rev and break //this.debug( '---->', fwdName, revName ); - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( j, 1 )[0], { silent: true } ); + paired.push( pair ); break; } } @@ -336,6 +341,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ @@ -347,7 +353,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - distance, bestIndex, bestDist; + distance, bestIndex, bestDist, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -383,13 +390,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -400,6 +408,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to auto pair using common substrings from both front and back (after removing filters) */ @@ -411,8 +420,9 @@ fwdList = split[0], revList = split[1], fwdName, revName, - currMatch, bestIndex, bestMatch; - if( !fwdList.length || !revList.length ){ return; } + currMatch, bestIndex, bestMatch, + paired = []; + if( !fwdList.length || !revList.length ){ return paired; } //this.debug( fwdList, revList ); while( i<fwdList.length ){ @@ -448,13 +458,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -465,6 +476,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** return the concat'd longest common prefix and suffix from two strings */ @@ -652,6 +664,7 @@ this._renderMiddle( speed ); this._renderFooter( speed ); this._addPluginComponents(); + this.trigger( 'rendered', this ); return this; }, @@ -889,6 +902,10 @@ // ------------------------------------------------------------------------ events /** set up event handlers on self */ _setUpBehaviors : function(){ + this.once( 'rendered', function(){ + this.trigger( 'rendered:initial', this ); + }); + this.on( 'pair:new', function(){ //TODO: ideally only re-render the columns (or even elements) involved this._renderUnpaired(); @@ -929,6 +946,7 @@ if( !this.unpaired.length ){ message += ': ' + _l( 'all datasets have been successfully paired' ); this.hideUnpaired(); + this.$( '.collection-name' ).focus(); } } else { message = _l( 'Could not automatically create any pairs from the given dataset names' ); @@ -1007,6 +1025,7 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ + console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1064,10 +1083,8 @@ /** attempt to autopair */ _clickAutopair : function( ev ){ - var paired = this.autoPair(); - //this.debug( 'autopaired', paired ); - //TODO: an indication of how many pairs were found - if 0, assist - this.trigger( 'autopair', paired ); + this.autoPair(); + this.trigger( 'autopair' ); }, /** set the filters based on the data attributes of the button click target */ diff -r 813c1769e0dadda43543dcb0f50d2fd0391aa78a -r 35a718a57a32ec73c9e12bbb01bc47cc3d48042e static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){console.debug("alert:",i,h);h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return j},pairAllSelected:function(i){i=i||{};var j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column .dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return l},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column .dataset").eq(k).data("dataset"),h=$(".unpaired-columns .reverse-column .dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag" title="',d("Drag to change"),'"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',d("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<ol class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div class="attributes clear">','<div class="clear">','<label class="remove-extensions-prompt pull-right">',d("Remove file extensions from pair names"),"?",'<input class="remove-extensions pull-right" type="checkbox" />',"</label>","</div>",'<div class="clear">','<input class="collection-name form-control pull-right" ','placeholder="',d("Enter a name for your new list"),'" />','<div class="collection-name-prompt pull-right">',d("Name"),":</div>","</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',d("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',d("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',d("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',d("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8df2b4dc38e2/ Changeset: 8df2b4dc38e2 User: carlfeberhard Date: 2015-02-09 21:40:18+00:00 Summary: UI, Paired collection creator: add rendered,rendered:inital events, add initial autopairing event Affected #: 3 files diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 8df2b4dc38e2bea10f16aec789e200f0baaae52a client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -158,9 +158,8 @@ /** DOM elements currently being dragged */ this.$dragging = null; + this._setUpBehaviors(); this._dataSetUp(); - - this._setUpBehaviors(); }, /** map of common filter pairs by name */ @@ -199,6 +198,9 @@ if( this.automaticallyPair ){ this.autoPair(); + this.once( 'rendered:initial', function(){ + this.trigger( 'autopair' ); + }); } }, @@ -287,8 +289,9 @@ autoPair : function( strategy ){ strategy = strategy || this.strategy; //this.debug( '-- autoPair', strategy ); - this.simpleAutoPair(); - return this[ strategy ].call( this ); + var paired = this.simpleAutoPair(); + paired = paired.concat( this[ strategy ].call( this ) ); + return paired; }, /** attempts to pair forward with reverse when names exactly match (after removing filters) */ @@ -303,7 +306,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - matchFound = false; + matchFound = false, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -321,11 +325,12 @@ matchFound = true; // if it is a match, keep i at current, pop fwd, pop rev and break //this.debug( '---->', fwdName, revName ); - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( j, 1 )[0], { silent: true } ); + paired.push( pair ); break; } } @@ -336,6 +341,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ @@ -347,7 +353,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - distance, bestIndex, bestDist; + distance, bestIndex, bestDist, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -383,13 +390,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -400,6 +408,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to auto pair using common substrings from both front and back (after removing filters) */ @@ -411,8 +420,9 @@ fwdList = split[0], revList = split[1], fwdName, revName, - currMatch, bestIndex, bestMatch; - if( !fwdList.length || !revList.length ){ return; } + currMatch, bestIndex, bestMatch, + paired = []; + if( !fwdList.length || !revList.length ){ return paired; } //this.debug( fwdList, revList ); while( i<fwdList.length ){ @@ -448,13 +458,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -465,6 +476,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** return the concat'd longest common prefix and suffix from two strings */ @@ -652,6 +664,7 @@ this._renderMiddle( speed ); this._renderFooter( speed ); this._addPluginComponents(); + this.trigger( 'rendered', this ); return this; }, @@ -889,6 +902,10 @@ // ------------------------------------------------------------------------ events /** set up event handlers on self */ _setUpBehaviors : function(){ + this.once( 'rendered', function(){ + this.trigger( 'rendered:initial', this ); + }); + this.on( 'pair:new', function(){ //TODO: ideally only re-render the columns (or even elements) involved this._renderUnpaired(); @@ -929,6 +946,7 @@ if( !this.unpaired.length ){ message += ': ' + _l( 'all datasets have been successfully paired' ); this.hideUnpaired(); + this.$( '.collection-name' ).focus(); } } else { message = _l( 'Could not automatically create any pairs from the given dataset names' ); @@ -1007,6 +1025,7 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ + console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1064,10 +1083,8 @@ /** attempt to autopair */ _clickAutopair : function( ev ){ - var paired = this.autoPair(); - //this.debug( 'autopaired', paired ); - //TODO: an indication of how many pairs were found - if 0, assist - this.trigger( 'autopair', paired ); + this.autoPair(); + this.trigger( 'autopair' ); }, /** set the filters based on the data attributes of the button click target */ diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 8df2b4dc38e2bea10f16aec789e200f0baaae52a static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -158,9 +158,8 @@ /** DOM elements currently being dragged */ this.$dragging = null; + this._setUpBehaviors(); this._dataSetUp(); - - this._setUpBehaviors(); }, /** map of common filter pairs by name */ @@ -199,6 +198,9 @@ if( this.automaticallyPair ){ this.autoPair(); + this.once( 'rendered:initial', function(){ + this.trigger( 'autopair' ); + }); } }, @@ -287,8 +289,9 @@ autoPair : function( strategy ){ strategy = strategy || this.strategy; //this.debug( '-- autoPair', strategy ); - this.simpleAutoPair(); - return this[ strategy ].call( this ); + var paired = this.simpleAutoPair(); + paired = paired.concat( this[ strategy ].call( this ) ); + return paired; }, /** attempts to pair forward with reverse when names exactly match (after removing filters) */ @@ -303,7 +306,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - matchFound = false; + matchFound = false, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -321,11 +325,12 @@ matchFound = true; // if it is a match, keep i at current, pop fwd, pop rev and break //this.debug( '---->', fwdName, revName ); - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( j, 1 )[0], { silent: true } ); + paired.push( pair ); break; } } @@ -336,6 +341,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ @@ -347,7 +353,8 @@ fwdList = split[0], revList = split[1], fwdName, revName, - distance, bestIndex, bestDist; + distance, bestIndex, bestDist, + paired = []; while( i<fwdList.length ){ var fwd = fwdList[ i ]; @@ -383,13 +390,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -400,6 +408,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** attempt to auto pair using common substrings from both front and back (after removing filters) */ @@ -411,8 +420,9 @@ fwdList = split[0], revList = split[1], fwdName, revName, - currMatch, bestIndex, bestMatch; - if( !fwdList.length || !revList.length ){ return; } + currMatch, bestIndex, bestMatch, + paired = []; + if( !fwdList.length || !revList.length ){ return paired; } //this.debug( fwdList, revList ); while( i<fwdList.length ){ @@ -448,13 +458,14 @@ //this.debug( '----> %', percentage * 100 ); if( percentage >= this.matchPercentage ){ - this._pair( + var pair = this._pair( fwdList.splice( i, 1 )[0], revList.splice( bestIndex, 1 )[0], { silent: true } ); + paired.push( pair ); if( fwdList.length <= 0 || revList.length <= 0 ){ - return; + return paired; } } else { i += 1; @@ -465,6 +476,7 @@ //this.debug( 'remaining Reverse:' ); //this._printList( this.unpairedReverse ); //this.debug( '' ); + return paired; }, /** return the concat'd longest common prefix and suffix from two strings */ @@ -652,6 +664,7 @@ this._renderMiddle( speed ); this._renderFooter( speed ); this._addPluginComponents(); + this.trigger( 'rendered', this ); return this; }, @@ -889,6 +902,10 @@ // ------------------------------------------------------------------------ events /** set up event handlers on self */ _setUpBehaviors : function(){ + this.once( 'rendered', function(){ + this.trigger( 'rendered:initial', this ); + }); + this.on( 'pair:new', function(){ //TODO: ideally only re-render the columns (or even elements) involved this._renderUnpaired(); @@ -929,6 +946,7 @@ if( !this.unpaired.length ){ message += ': ' + _l( 'all datasets have been successfully paired' ); this.hideUnpaired(); + this.$( '.collection-name' ).focus(); } } else { message = _l( 'Could not automatically create any pairs from the given dataset names' ); @@ -1007,6 +1025,7 @@ /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ _showAlert : function( message, alertClass ){ + console.debug( 'alert:', message, alertClass ); alertClass = alertClass || 'alert-danger'; this.$( '.main-help' ).hide(); this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() @@ -1064,10 +1083,8 @@ /** attempt to autopair */ _clickAutopair : function( ev ){ - var paired = this.autoPair(); - //this.debug( 'autopaired', paired ); - //TODO: an indication of how many pairs were found - if 0, assist - this.trigger( 'autopair', paired ); + this.autoPair(); + this.trigger( 'autopair' ); }, /** set the filters based on the data attributes of the button click target */ diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 8df2b4dc38e2bea10f16aec789e200f0baaae52a static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._dataSetUp();this._setUpBehaviors()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return this[h].call(this)},simpleAutoPair:function(){var n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var 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"+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" 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.column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column 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h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the 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h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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pull-right">',d("Name"),":</div>","</div>","</div>",'<div class="actions clear vertically-spaced">','<div class="other-options pull-left">','<button class="cancel-create btn" tabindex="-1">',d("Cancel"),"</button>",'<div class="create-other btn-group dropup">','<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">',d("Create a different kind of collection"),' <span class="caret"></span>',"</button>",'<ul class="dropdown-menu" role="menu">','<li><a href="#">',d("Create a <i>single</i> pair"),"</a></li>",'<li><a href="#">',d("Create a list of <i>unpaired</i> datasets"),"</a></li>","</ul>","</div>","</div>",'<div class="main-options pull-right">','<button class="create-collection btn btn-primary">',d("Create list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse reads). ","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return naturalSort(j.name,i.name)});return h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(j){var i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var h=function(j,l){if(j===l){return j}var k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return h(j,k)}else{if(m>0){return h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o<h.length){var n=h[o];q=n.name.replace(this.filters[0],"");k=false;for(m=0;m<r.length;m++){var p=r[m];u=p.name.replace(this.filters[1],"");if(n!==p&&q===u){k=true;var l=this._pair(h.splice(o,1)[0],r.splice(m,1)[0],{silent:true});t.push(l);break}}if(!k){o+=1}}return t},autoPairLevenshtein:function(){var p=0,n,u=this._splitByFilters(),h=u[0],s=u[1],r,x,k,t,l,v=[];while(p<h.length){var o=h[p];r=o.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(n=0;n<s.length;n++){var q=s[n];x=q.name.replace(this.filters[1],"");if(o!==q){if(r===x){t=n;l=0;break}k=levenshteinDistance(r,x);if(k<l){t=n;l=k}}}var w=1-(l/(Math.max(r.length,x.length)));if(w>=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(n<h.length){var m=h[n];r=m.name.replace(this.filters[0],"");p=0;for(l=0;l<s.length;l++){var q=s[l];y=q.name.replace(this.filters[1],"");if(m!==q){if(r===y){t=l;p=r.length;break}var o=this._naiveStartingAndEndingLCS(r,y);x=o.length;if(x>p){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return m}if(l===k.length){return k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return n+o},_pair:function(j,h,i){i=i||{};var k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad pairing: "+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" & "+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair: "+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return i},unpairAll:function(){var h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return j._pairToJSON(k)})};return jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var i=d("An error occurred while creating this collection");if(k){if(k.readyState===0&&k.status===0){i+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(k.responseJSON){i+="<br /><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return h},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(i,j){var h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return h},_renderUnpaired:function(m,n){var k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column .title").text([j[0].length,d("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column .title").text([j[1].length,d("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return k._renderUnpairedDataset(p)});l=j[0].map(function(o){return k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(l).add(this.$(".unpaired-columns .paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h," ",d("filtered out"),")"].join("")},_renderUnpairedDataset:function(h){return $("<li/>").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('<div class="empty-message"></div>').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_adjUnpairedOnScrollbar:function(){var k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns .reverse-column .dataset").first();if(!l.size()){return}var h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns .forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title .title").text([this.paired.length,d("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new f({pair:m});h.$(".paired-columns .column-datasets").append(l.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var h=$('<div class="empty-message"></div>').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['<button class="filter-choice btn" ','data-forward="',l,'" data-reverse="',k,'">',d("Forward"),": ",l,", ",d("Reverse"),": ",k,"</button>"].join("")}var j=$(_.template(['<div class="choose-filters">','<div class="help">',d("Choose from the following filters to change which unpaired reads are shown in the 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input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){h+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(h){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(h){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){console.debug("alert:",i,h);h=h||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(h){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(i){var h=$(i.currentTarget);this.$(".forward-unpaired-filter input").val(h.data("forward"));this.$(".reverse-unpaired-filter 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h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function j(m){var n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var m=i<0;if(m){if(this.unpairedPanelHidden){return false}else{if(k<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return false}else{if(l<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0 0 auto"});return true},selectPair:function(h){h.stopPropagation();$(h.currentTarget).toggleClass("selected")},clearSelectedPaired:function(h){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(j){j.stopPropagation();var i=$(j.currentTarget),k=this.paired[i.parent().parent().index()/2],h=prompt("Enter a new name for the pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},_dragoverPairedColumns:function(k){k.preventDefault();var i=this.$(".paired-columns .column-datasets"),l=i.offset();var j=this._getNearestPairedDatasetLi(k.originalEvent.clientY);$(".paired-drop-placeholder").remove();var h=$('<div class="paired-drop-placeholder"></div>');if(!j.size()){i.append(h)}else{j.before(h)}},_getNearestPairedDatasetLi:function(o){var l=4,j=this.$(".paired-columns .column-datasets li").toArray();for(var k=0;k<j.length;k++){var n=$(j[k]),m=n.offset().top,h=Math.floor(n.outerHeight()/2)+l;if(m+h>o&&m-h<o){return n}}return $()},_dropPairedColumns:function(i){i.preventDefault();i.dataTransfer.dropEffect="move";var h=this._getNearestPairedDatasetLi(i.originalEvent.clientY);if(h.size()){this.$dragging.insertBefore(h)}else{this.$dragging.insertAfter(this.$(".paired-columns .unpair-btn").last())}this._syncPairsToDom();return false},_syncPairsToDom:function(){var h=[];this.$(".paired-columns .dataset.paired").each(function(){h.push($(this).data("pair"))});this.paired=h;this._renderPaired()},_pairDragstart:function(i,j){j.$el.addClass("selected");var h=this.$(".paired-columns .dataset.selected");this.$dragging=h},_pairDragend:function(h,i){$(".paired-drop-placeholder").remove();this.$dragging=null},toggleExtensions:function(i){var h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_nameCheckForEnter:function(h){if(h.keyCode===13){this._clickCreate()}},_getName:function(){return _.escape(this.$(".collection-name").val())},_clickCreate:function(i){var h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,": ->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div class="header flex-row no-flex"></div>','<div class="middle flex-row flex-row-container"></div>','<div class="footer flex-row no-flex">'].join("")),header:_.template(['<div class="main-help well clear">','<a class="more-help" href="javascript:void(0);">',d("More help"),"</a>",'<div class="help-content">','<a class="less-help" href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div class="alert alert-dismissable">','<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>','<span class="alert-message"></span>',"</div>",'<div class="column-headers vertically-spaced flex-column-container">','<div class="forward-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired forward"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter forward-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>",'<div class="paired-column flex-column no-flex column">','<div class="column-header">','<a class="choose-filters-link" href="javascript:void(0)">',d("Choose filters"),"</a>",'<a class="clear-filters-link" href="javascript:void(0);">',d("Clear filters"),"</a><br />",'<a class="autopair-link" href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div class="reverse-column flex-column column">','<div class="column-header">','<div class="column-title">','<span class="title">',d("Unpaired reverse"),"</span>",'<span class="title-info unpaired-info"></span>',"</div>",'<div class="unpaired-filter reverse-unpaired-filter pull-left">','<input class="search-query" placeholder="',d("Filter this list"),'" />',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div class="unpaired-columns flex-column-container scroll-container flex-row">','<div class="forward-column flex-column column">','<ol class="column-datasets"></ol>',"</div>",'<div class="paired-column flex-column no-flex column">','<ol class="column-datasets"></ol>',"</div>",'<div class="reverse-column flex-column column">','<ol class="column-datasets"></ol>',"</div>","</div>",'<div class="flexible-partition">','<div class="flexible-partition-drag" title="',d("Drag to change"),'"></div>','<div class="column-header">','<div class="column-title paired-column-title">','<span class="title"></span>',"</div>",'<a class="unpair-all-link" href="javascript:void(0);">',d("Unpair all"),"</a>","</div>","</div>",'<div class="paired-columns flex-column-container scroll-container flex-row">','<ol class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div class="attributes clear">','<div class="clear">','<label class="remove-extensions-prompt pull-right">',d("Remove file extensions from pair names"),"?",'<input class="remove-extensions pull-right" type="checkbox" />',"</label>","</div>",'<div class="clear">','<input class="collection-name form-control pull-right" ','placeholder="',d("Enter a name for your new list"),'" />','<div class="collection-name-prompt 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","These collections can be passed to tools and workflows in order to have analyses done on each member of ","the entire group. This interface allows you to create a collection, choose which datasets are paired, ","and re-order the final collection."].join("")),"</p>","<p>",d(['Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.',"<ul>To pair datasets, you can:","<li>Click a dataset in the ",'<i data-target=".unpaired-columns .forward-column .column-datasets,','.unpaired-columns .forward-column">forward column</i> ',"to select it then click a dataset in the ",'<i data-target=".unpaired-columns .reverse-column .column-datasets,','.unpaired-columns .reverse-column">reverse column</i>.',"</li>",'<li>Click one of the "Pair these datasets" buttons in the ','<i data-target=".unpaired-columns .paired-column .column-datasets,','.unpaired-columns .paired-column">middle column</i> ',"to pair the datasets in a particular row.","</li>",'<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ',"to have your datasets automatically paired based on name.","</li>","</ul>"].join("")),"</p>","<p>",d(["<ul>You can filter what is shown in the unpaired sections by:","<li>Entering partial dataset names in either the ",'<i data-target=".forward-unpaired-filter input">forward filter</i> or ','<i data-target=".reverse-unpaired-filter input">reverse filter</i>.',"</li>","<li>Choosing from a list of preset filters by clicking the ",'<i data-target=".choose-filters-link">"Choose filters" link</i>.',"</li>","<li>Entering regular expressions to match dataset names. See: ",'<a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expre…"',' target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>. ',"Note: forward slashes (\\) are not needed.","</li>","<li>Clearing the filters by clicking the ",'<i data-target=".clear-filters-link">"Clear filters" link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["To unpair individual dataset pairs, click the ",'<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return this}})}());var b=function c(j,h){h=_.defaults(h||{},{datasets:j,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var i=new e(h).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/dc47e72349b2/ Changeset: dc47e72349b2 User: carlfeberhard Date: 2015-02-09 21:41:04+00:00 Summary: Merge Affected #: 2 files diff -r 8df2b4dc38e2bea10f16aec789e200f0baaae52a -r dc47e72349b28579aed926f66536081cab8bebef lib/galaxy/webapps/tool_shed/api/search.py --- a/lib/galaxy/webapps/tool_shed/api/search.py +++ b/lib/galaxy/webapps/tool_shed/api/search.py @@ -1,8 +1,8 @@ """API for searching the toolshed repositories""" from galaxy import exceptions from galaxy import eggs +from galaxy import util from galaxy.web import _future_expose_api as expose_api -# from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed.search.repo_search import RepoSearch @@ -22,19 +22,32 @@ The index has to be pre-created with build_ts_whoosh_index.sh. TS config option toolshed_search_on has to be turned on and toolshed_whoosh_index_dir has to be specified and existing. + + :param search_term: + :param page: + :param jsonp: + :param callback: + + :returns dict: """ if not self.app.config.toolshed_search_on: raise exceptions.ConfigDoesNotAllowException( 'Searching the TS through the API is turned off for this instance.' ) if not self.app.config.toolshed_whoosh_index_dir: raise exceptions.ConfigDoesNotAllowException( 'There is no directory for the search index specified. Please ontact the administrator.' ) + search_term = search_term.strip() if len( search_term ) < 3: raise exceptions.RequestParameterInvalidException( 'The search term has to be at least 3 characters long.' ) page = kwd.get( 'page', 1 ) + return_jsonp = util.asbool( kwd.get( 'jsonp', False ) ) callback = kwd.get( 'callback', 'callback' ) repo_search = RepoSearch() results = repo_search.search( trans, search_term, page ) results[ 'hostname' ] = url_for( '/', qualified = True ) - response = '%s(%s);' % ( callback, json.dumps( results ) ) + + if jsonp: + response = '%s(%s);' % ( callback, json.dumps( results ) ) + else: + response = json.dumps( results ) return response diff -r 8df2b4dc38e2bea10f16aec789e200f0baaae52a -r dc47e72349b28579aed926f66536081cab8bebef lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -33,6 +33,7 @@ full_last_updated = STORED ) except ImportError, e: + log.error( 'There was an error while importing the Whoosh library.' ) search_ready = False schema = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 09 Feb '15

09 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/394f11c09707/ Changeset: 394f11c09707 User: martenson Date: 2015-02-09 21:29:31+00:00 Summary: minor adjustments to toolshed search Affected #: 2 files diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 394f11c097071738b81cec7e86080e53e697a151 lib/galaxy/webapps/tool_shed/api/search.py --- a/lib/galaxy/webapps/tool_shed/api/search.py +++ b/lib/galaxy/webapps/tool_shed/api/search.py @@ -22,19 +22,32 @@ The index has to be pre-created with build_ts_whoosh_index.sh. TS config option toolshed_search_on has to be turned on and toolshed_whoosh_index_dir has to be specified and existing. + + :param search_term: + :param page: + :param jsonp: + :param callback: + + :returns dict: """ if not self.app.config.toolshed_search_on: raise exceptions.ConfigDoesNotAllowException( 'Searching the TS through the API is turned off for this instance.' ) if not self.app.config.toolshed_whoosh_index_dir: raise exceptions.ConfigDoesNotAllowException( 'There is no directory for the search index specified. Please ontact the administrator.' ) + search_term = search_term.strip() if len( search_term ) < 3: raise exceptions.RequestParameterInvalidException( 'The search term has to be at least 3 characters long.' ) page = kwd.get( 'page', 1 ) + return_jsonp = kwd.get( 'jsonp', False ) callback = kwd.get( 'callback', 'callback' ) repo_search = RepoSearch() results = repo_search.search( trans, search_term, page ) results[ 'hostname' ] = url_for( '/', qualified = True ) - response = '%s(%s);' % ( callback, json.dumps( results ) ) + + if jsonp: + response = '%s(%s);' % ( callback, json.dumps( results ) ) + else: + response = json.dumps( results ) return response diff -r 54a0ae599d9c3bf40f57d86e12360ef74118dadb -r 394f11c097071738b81cec7e86080e53e697a151 lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -33,6 +33,7 @@ full_last_updated = STORED ) except ImportError, e: + log.error( 'There was an error while importing the Whoosh library.' ) search_ready = False schema = None https://bitbucket.org/galaxy/galaxy-central/commits/c57e9f8e05eb/ Changeset: c57e9f8e05eb User: martenson Date: 2015-02-09 21:39:11+00:00 Summary: load param as bool Affected #: 1 file diff -r 394f11c097071738b81cec7e86080e53e697a151 -r c57e9f8e05eb20f2ec8efd39ac53edeeaad4d6d1 lib/galaxy/webapps/tool_shed/api/search.py --- a/lib/galaxy/webapps/tool_shed/api/search.py +++ b/lib/galaxy/webapps/tool_shed/api/search.py @@ -1,8 +1,8 @@ """API for searching the toolshed repositories""" from galaxy import exceptions from galaxy import eggs +from galaxy import util from galaxy.web import _future_expose_api as expose_api -# from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous from galaxy.web.base.controller import BaseAPIController from galaxy.webapps.tool_shed.search.repo_search import RepoSearch @@ -39,7 +39,7 @@ raise exceptions.RequestParameterInvalidException( 'The search term has to be at least 3 characters long.' ) page = kwd.get( 'page', 1 ) - return_jsonp = kwd.get( 'jsonp', False ) + return_jsonp = util.asbool( kwd.get( 'jsonp', False ) ) callback = kwd.get( 'callback', 'callback' ) repo_search = RepoSearch() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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