Db 0 0.01 delta

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These are detailed notes on changes made between 0 and bioperl-db-release-0-01.

Bio::DB::Annotation
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
Bio::DB::BasicUpdateableDB
Ensembl-lite now really works with an ensembl db with extra feature tables
Committing mid-way through writing. create schema loads. Started on adaptor work
Bio::DB::BioDatabasePSeqStream
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Got biocorba bindings to work well
Bio::DB::BioSQL::AbstractQuery
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Bio::DB::BioSQL::BaseAdaptor
Committing mid-way through writing. create schema loads. Started on adaptor work
Minor tweaks
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Proper array test - errant ','
Bio::DB::BioSQL::BioDatabaseAdaptor
More fixes. started on feature table (schema - objects coming)
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Added missing modules
Got biocorba bindings to work well
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
Seq description fixes
Uber commit to try and get tests back to normal. Skipping most marker related tests, due to schema change awaiting code change and decisions. In DBTestHarness removed the need to connect to the mysql database. This breaks the test on setups where a user is allowed to create databases but not allowed to access the mysql mysql database directly, as in ensembl machines. Minor fixes to MapAdaptor due to simple schema changes in the map table Catching exception in BioDatabaseAdaptor->fetch_by_name_store_if_needed to get the method to work
Remove and clean-up methods: first release
Bio::DB::BioSQL::BioQuery
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Bio::DB::BioSQL::CommentAdaptor
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Bio::DB::BioSQL::DBAdaptor
Committing mid-way through writing. create schema loads. Started on adaptor work
Added simple seq/primary seq store and fetch; no feature table; no annotation; not good enough scripts. But a start
More fixes. started on feature table (schema - objects coming)
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
Adding tiny BUGS comments, removing one offending line from genbank
Bio::DB::BioSQL::DBLinkAdaptor
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Remove and clean-up methods: first release
Bio::DB::BioSQL::PrimarySeqAdaptor
Committing mid-way through writing. create schema loads. Started on adaptor work
Added simple seq/primary seq store and fetch; no feature table; no annotation; not good enough scripts. But a start
Got biocorba bindings to work well
Added molecule and division storing/fetching, (bioentry division and biosequence molecule)
Changed molecule stuff in EMBL parsing in bioperl, less messy in boperl-db
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
Bio::DB::BioSQL::QueryConstraint
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Bio::DB::BioSQL::ReferenceAdaptor
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
Fixed bug in comment writing rank always 1, reminds of me exon_transcript Ewan.. ;), and modified reference because one reference (medline) can be used by more than one bioentry
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Remove and clean-up methods: first release
Bio::DB::BioSQL::SeqAdaptor
Added missing modules
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Added molecule and division storing/fetching, (bioentry division and biosequence molecule)
Changed molecule stuff in EMBL parsing in bioperl, less messy in boperl-db
Added support for fetching/storing dates
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
Fixed bug in comment writing rank always 1, reminds of me exon_transcript Ewan.. ;), and modified reference because one reference (medline) can be used by more than one bioentry
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Added embl keywords to biopeperl db schema
Added seqids, replace select last_insert_id for sth mysqlinsertid
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Seq description fixes
Remove and clean-up methods: first release
Fixed bug with seqfeature rank not being incremented in SeqAdaptor->store()
Bio::DB::BioSQL::SeqFeatureAdaptor
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Added seqids, replace select last_insert_id for sth mysqlinsertid
Remove and clean-up methods: first release
Bio::DB::BioSQL::SeqFeatureKeyAdaptor
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Remove and clean-up methods: first release
Bio::DB::BioSQL::SeqFeatureQualifierAdaptor
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
Remove and clean-up methods: first release
Bio::DB::BioSQL::SeqFeatureSourceAdaptor
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
Remove and clean-up methods: first release
Bio::DB::BioSQL::SeqLocationAdaptor
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
Half commit, remote locations get stored
Remote locations go in and our of the db
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
Minor tweaks
Remove and clean-up methods: first release
Bio::DB::BioSQL::SpeciesAdaptor
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Bio::DB::BioSQL::SqlQuery
Basic framework for rich / complex queries added SeqAdaptor->fetch_by_query() added genetic methods for query resolution to BaseAdaptor modified no existing methods new classes for representing queries
Bio::DB::BioSeqDatabase
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Added missing modules
Got biocorba bindings to work well
Adding tiny BUGS comments, removing one offending line from genbank
Bio::DB::CacheServer::SeqDB
Forgot to add the actual CacheServer object. Doh!
Bio::DB::PrimarySeq
Forgot PrimarySeq business object
Added simple seq/primary seq store and fetch; no feature table; no annotation; not good enough scripts. But a start
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Added molecule and division storing/fetching, (bioentry division and biosequence molecule)
Bio::DB::Seq
Added missing modules
Got biocorba bindings to work well
Added molecule and division storing/fetching, (bioentry division and biosequence molecule)
Changed molecule stuff in EMBL parsing in bioperl, less messy in boperl-db
Added support for fetching/storing dates
Added support for dumping the SV line (seq_version method)
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Added embl keywords to biopeperl db schema
Added seqids, replace select last_insert_id for sth mysqlinsertid
Proper perl 5.6.0 syntax for arrays
Seq description fixes
Makefile.PL
Initial commit
Preparing for 0.01 release
PWD.basic
Revised to handle new ensembl schema
Remove cruft
TODO
Added TODO file
Accounted for new ensembl schema
Cruft begone!
model/bioperl-maps.dia
Added initial model of the maps objects, Lincoln to help refactor to better model
Updated to reflect schema changes
scripts/bioentry2flat.pl
Added simple db to flatfile dumping script
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Added seqids, replace select last_insert_id for sth mysqlinsertid
scripts/bioenv_server.pl
Got biocorba bindings to work well
scripts/caching_corba_server.pl
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
scripts/download_marker_data.pl
Automagic downloading of all the necessary data sets w/ cmd line args to be specific
Work for genemap99 now
scripts/load_genemap99_markers.pl
Load genemap99 markers
scripts/load_genethon_data.pl
Initial commit of script to load genethon markers and genethon map into db - may be better way to get marshfield marker info anyways
Added -online flag, -debug flag handle duplicated markers by merging information into existing marker
scripts/load_marshfield_map.pl
Script to import marshfield map
Smarted script only reads in huge STS file still have 435 out of 15583 markers that have map positions but no pcr primers in dbSTS (because of naming issues as they have info in GDB)
Bug cleanup
Handle updates and auto-find markers based on primers
Added -online flag, -debug flag handle duplicated markers by merging information into existing marker
scripts/load_seqdatabase.pl
Added simple seq/primary seq store and fetch; no feature table; no annotation; not good enough scripts. But a start
More fixes. started on feature table (schema - objects coming)
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Added embl keywords to biopeperl db schema
Remote locations go in and our of the db
scripts/load_whitehead_markers.pl
Initial script to load whitehead sts markers
Handle updates and auto-find markers based on primers
Added -online flag, -debug flag handle duplicated markers by merging information into existing marker
scripts/test_bioenv.pl
Got biocorba bindings to work well
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
scripts/validate_whitehead_markers.pl
Validation script for whitehead markers where there appears to be cruft giving 2 markers with same primers different RH positions in what should be the same map?
sql/basicseqdb-mysql.sql
Initial sql commit
Ensembl-lite now really works with an ensembl db with extra feature tables
Committing mid-way through writing. create schema loads. Started on adaptor work
Added simple seq/primary seq store and fetch; no feature table; no annotation; not good enough scripts. But a start
More fixes. started on feature table (schema - objects coming)
Started SeqFeature work. Quite alot of Adaptors - does make sense if a little repetitive in there. <<sigh>>. Done all the components of the seqfeature - just got to finish it off - tomorrow I guess
All singing, all dancing, features, location (no remote locations, no fuzzy handling) annotation (no references, but comments and dblinks) and Bio::DB::SeqI support database. Mucho fun
Had to add some NOT NULLS for fields which had been defined as UNIQUE or indexes.... Ewan to comment on this, looking at the scheam it seemed the right thing to do compared to dropping the index
Tried bioperl_db with real data, lots of it, and found that most fields need a substitution of \' with \\', to let mysql swallow them
Added molecule and division storing/fetching, (bioentry division and biosequence molecule)
Added support for fetching/storing dates
Added all the code needed to fetch and store references, not stored twice if same medline, checked embl entry going in and out basically identical, no info missing
Fixed bug in comment writing rank always 1, reminds of me exon_transcript Ewan.. ;), and modified reference because one reference (medline) can be used by more than one bioentry
GRRRRRRR..... one finds out after about 120000 entries that people use the same reference twice in an entry.... anyway fixed bug, ref start and end should not be in reference table...
Added embl keywords to biopeperl db schema
Made caching server - corba round trip now works; put in RichSeqI tests for RichSeq specific pieces - elia - can you make sure we test for the right interface if you need to put any more richness into the system
Changing unique key in bioentry, adding biodatabase, makes sense, well spotted by Alex Zelensky
sql/bibliography-mysql.sql
Expanded version of genetic mapping schema to support a variety of mapping studies
sql/ensembl-lite-mysql-addon.sql
Initial sql commit
Commented #'s
Ensembl-lite now really works with an ensembl db with extra feature tables
Marker adaptor and map adaptor started, not functional
sql/ensembl-lite-mysql.sql
Initial sql commit
Accounted for new ensembl schema
Marker adaptor and map adaptor started, not functional
sql/ensembl-lite-sybase.sql
Initial sql commit
Marker adaptor and map adaptor started, not functional
sql/markerdb-mysql.sql
Let's go ahead and label this with db specific name
Named keys and corrected name of map
Expanded version of genetic mapping schema to support a variety of mapping studies
Uber commit to try and get tests back to normal. Skipping most marker related tests, due to schema change awaiting code change and decisions. In DBTestHarness removed the need to connect to the mysql database. This breaks the test on setups where a user is allowed to create databases but not allowed to access the mysql mysql database directly, as in ensembl machines. Minor fixes to MapAdaptor due to simple schema changes in the map table Catching exception in BioDatabaseAdaptor->fetch_by_name_store_if_needed to get the method to work
sql/markerdb.sql
Marker adaptor and map adaptor started, not functional
Adaptors work more correctly now added functionality for get/delete/write/update markers added functionality for get/delete/write maps added foreign keys, temporary table support to SQL
Allow pcrprimers/length to be null so that we can store ALL markers with a map position
Remove old version
sql/rawdata-mysql.sql
Expanded version of genetic mapping schema to support a variety of mapping studies
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