Db 0 0.01 delta

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