From aa30e16976da452db37de988fdc6f62b64ebc8c0 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Fri, 26 Jul 2024 10:52:50 +0200 Subject: [PATCH 01/61] Forked version of the ispyb-database project --- .github/workflows/update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 31da589..4ce4166 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -50,7 +50,7 @@ jobs: password=password database=ispyb_build EOF - wget https://github.com/ispyb/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz + wget https://github.com/hormiai76/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz tar xfz v${SCHEMA_VERSION}.tar.gz ls cd ispyb-database-${SCHEMA_VERSION} From 92bcb131f4fc3ce954ed4858c5ebe66a5fca84a1 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 12:08:54 +0200 Subject: [PATCH 02/61] hormiai76 database repo set --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index e602c3e..e74c8e0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -22,7 +22,7 @@ keywords = ISPyB database SQLAlchemy -url = https://github.com/ispyb/ispyb-models +url = https://github.com/hormiai76/ispyb-models [options] include_package_data = True From a515fadec51519d3f0e60872e6b9a16bde6df9b4 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 12:09:18 +0200 Subject: [PATCH 03/61] =?UTF-8?q?Bump=20version:=201.1.0=20=E2=86=92=201.2?= =?UTF-8?q?.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 3a89be3..114ac43 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.1.0 +current_version = 1.2.0 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index e74c8e0..5dff044 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models -version = 1.1.0 +version = 1.2.0 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 32e5efe..54ca58b 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.1.0" +__version__ = "1.2.0" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From f29dccf9b459a7f172e0bcc2665d863696ed3701 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 12:09:31 +0200 Subject: [PATCH 04/61] =?UTF-8?q?Bump=20version:=201.2.0=20=E2=86=92=201.2?= =?UTF-8?q?.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 5dff044..76bb1cf 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models -version = 1.2.0 +version = version = 1.2.0 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 54ca58b..d9cb93a 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.0" +__version__ = "__version__ = "1.2.0"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 27154769a333ad317733c9d00414a798659bd135 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:07:39 +0200 Subject: [PATCH 05/61] Revert "Forked version of the ispyb-database project" This reverts commit aa30e16976da452db37de988fdc6f62b64ebc8c0. --- .github/workflows/update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 4ce4166..31da589 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -50,7 +50,7 @@ jobs: password=password database=ispyb_build EOF - wget https://github.com/hormiai76/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz + wget https://github.com/ispyb/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz tar xfz v${SCHEMA_VERSION}.tar.gz ls cd ispyb-database-${SCHEMA_VERSION} From 765843eb6832b942b7c7ecae44bd8c6d9e66bade Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:08:19 +0200 Subject: [PATCH 06/61] Revert "Revert "Forked version of the ispyb-database project"" This reverts commit 27154769a333ad317733c9d00414a798659bd135. --- .github/workflows/update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 31da589..4ce4166 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -50,7 +50,7 @@ jobs: password=password database=ispyb_build EOF - wget https://github.com/ispyb/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz + wget https://github.com/hormiai76/ispyb-database/archive/refs/tags/v${SCHEMA_VERSION}.tar.gz tar xfz v${SCHEMA_VERSION}.tar.gz ls cd ispyb-database-${SCHEMA_VERSION} From 8aff012d39286522a7058d5da7e75a2540b824cd Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:08:20 +0200 Subject: [PATCH 07/61] =?UTF-8?q?Revert=20"Bump=20version:=201.2.0=20?= =?UTF-8?q?=E2=86=92=201.2.0"?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This reverts commit f29dccf9b459a7f172e0bcc2665d863696ed3701. --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 76bb1cf..5dff044 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models -version = version = 1.2.0 +version = 1.2.0 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index d9cb93a..54ca58b 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.0"" +__version__ = "1.2.0" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 0c06680c2a016acdfafd3d013ea4b4fda816cae2 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 29 Jul 2024 14:09:52 +0200 Subject: [PATCH 08/61] Update update.yml --- .github/workflows/update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 4ce4166..36bb0ff 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -21,7 +21,7 @@ jobs: name: Get latest release uses: pozetroninc/github-action-get-latest-release@master with: - repository: ispyb/ispyb-database + repository: hormiai76/ispyb-database - uses: actions/checkout@v3 - name: Check if update required run: | From d14ca2e75754fa1bc4e5ce25c845fc03aa52fb37 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 29 Jul 2024 12:15:53 +0000 Subject: [PATCH 09/61] Update models to schema version 1.2.1 --- src/ispyb/models/_auto_db_schema.py | 63 ++++++++++++++++++++++++++++- 1 file changed, 62 insertions(+), 1 deletion(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 3ffaae2..4bd2868 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -3956,8 +3956,8 @@ class Component(Base): class LabContact(Base): __tablename__ = "LabContact" __table_args__ = ( - Index("cardNameAndProposal", "cardName", "proposalId", unique=True), Index("personAndProposal", "personId", "proposalId", unique=True), + Index("cardNameAndProposal", "cardName", "proposalId", unique=True), ) labContactId = Column(INTEGER(10), primary_key=True) @@ -6361,6 +6361,34 @@ class SSXDataCollection(Base): DataCollection = relationship("DataCollection", uselist=False) +class SSXProcessingResult(Base): + __tablename__ = "SSXProcessingResult" + __table_args__ = {"comment": "Processing Results table for SSX experiments."} + + ssxProcessingResultId = Column(INTEGER(11), primary_key=True, comment="Primary key") + dataCollectionId = Column( + ForeignKey( + "DataCollection.dataCollectionId", ondelete="CASCADE", onupdate="CASCADE" + ), + index=True, + ) + hitRate = Column(Float) + indexingRate = Column(Float) + indexingType = Column(Enum("Preliminary", "Final")) + status = Column(Enum("Running", "Failed", "Success")) + createdTimeStamp = Column( + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + ) + lastUpdate = Column( + TIMESTAMP, + nullable=False, + server_default=text("'0000-00-00 00:00:00'"), + comment="last update timestamp", + ) + + DataCollection = relationship("DataCollection") + + class XRFFluorescenceMapping(Base): __tablename__ = "XRFFluorescenceMapping" @@ -6587,6 +6615,39 @@ class PDBEntry(Base): AutoProcProgram = relationship("AutoProcProgram") +class SSXProcessingResultAttachment(Base): + __tablename__ = "SSXProcessingResultAttachment" + __table_args__ = { + "comment": "Processing Results attachments table for SSX experiments." + } + + ssxProcessingResultAttachmentId = Column( + INTEGER(11), primary_key=True, comment="Primary key" + ) + ssxProcessingResultId = Column( + ForeignKey( + "SSXProcessingResult.ssxProcessingResultId", + ondelete="CASCADE", + onupdate="CASCADE", + ), + index=True, + ) + fileName = Column(String(255), nullable=False) + filePath = Column(String(255), nullable=False) + fileType = Column(Enum("Result", "Log", "Graph"), nullable=False) + createdTimeStamp = Column( + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + ) + lastUpdate = Column( + TIMESTAMP, + nullable=False, + server_default=text("'0000-00-00 00:00:00'"), + comment="last update timestamp", + ) + + SSXProcessingResult = relationship("SSXProcessingResult") + + class WorkflowMesh(Base): __tablename__ = "WorkflowMesh" From e2e120b19d7f083978e4e7146e81f6b1ffa37eb3 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:17:44 +0200 Subject: [PATCH 10/61] =?UTF-8?q?Bump=20version:=201.2.0=20=E2=86=92=201.2?= =?UTF-8?q?.1?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 114ac43..3ad4215 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.0 +current_version = 1.2.1 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index 76bb1cf..e09a82d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models -version = version = 1.2.0 +version = version = 1.2.1 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index d9cb93a..64154ff 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.0"" +__version__ = "__version__ = "1.2.1"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 087ecab0cbca9c4d95c0f0cadfb2485696ce3521 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:21:06 +0200 Subject: [PATCH 11/61] fix quotes in init file --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 64154ff..c493f86 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.1"" +__version__ = "__version__ = '1.2.1'" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 595178e1aac67d8870420c4f5f88400b35e731fd Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:29:27 +0200 Subject: [PATCH 12/61] fix version number --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index e09a82d..bc26ead 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [metadata] -name = ispyb-models +name = ispyb-models-pyispyb version = version = 1.2.1 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index c493f86..1073dcb 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = '1.2.1'" +__version__ = "1.2.1" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 595e53d41ec50cb8579491d9fa14abbe2cd1456b Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 29 Jul 2024 14:31:59 +0200 Subject: [PATCH 13/61] fix version number --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index bc26ead..40eb2f9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.1 +version = 1.2.1 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown From 54a4094175a31a9ff8f4dcfaaa8fd827ad169c69 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 29 Jul 2024 14:43:15 +0200 Subject: [PATCH 14/61] Update publish.yml --- .github/workflows/publish.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 824dd3a..2112caf 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -11,6 +11,8 @@ jobs: # if: ${{ github.event.workflow_run.conclusion == 'success' }} name: Build and publish Python 🐍 distributions 📦 to PyPI runs-on: ubuntu-latest + permissions: + id-token: write steps: - uses: actions/checkout@master - name: Set up Python 3.10 From 5982656c33ae659864cb21684dc967ab0fdddb23 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 29 Jul 2024 14:59:41 +0200 Subject: [PATCH 15/61] Update publish.yml --- .github/workflows/publish.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 2112caf..52256bb 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -13,6 +13,7 @@ jobs: runs-on: ubuntu-latest permissions: id-token: write + environment: hormiai76 steps: - uses: actions/checkout@master - name: Set up Python 3.10 From 885cad8b1cc786cee72798564c4d9b4013c901e7 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 13 Sep 2024 12:07:41 +0200 Subject: [PATCH 16/61] new version to update SSX models --- .bumpversion.cfg | 2 +- .github/workflows/publish.yml | 3 ++ .github/workflows/update.yml | 2 +- setup.cfg | 4 +- src/ispyb/models/__init__.py | 2 +- src/ispyb/models/_auto_db_schema.py | 63 ++++++++++++++++++++++++++++- 6 files changed, 70 insertions(+), 6 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 114ac43..3ad4215 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.0 +current_version = 1.2.1 commit = True tag = True diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 824dd3a..52256bb 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -11,6 +11,9 @@ jobs: # if: ${{ github.event.workflow_run.conclusion == 'success' }} name: Build and publish Python 🐍 distributions 📦 to PyPI runs-on: ubuntu-latest + permissions: + id-token: write + environment: hormiai76 steps: - uses: actions/checkout@master - name: Set up Python 3.10 diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml index 4ce4166..36bb0ff 100644 --- a/.github/workflows/update.yml +++ b/.github/workflows/update.yml @@ -21,7 +21,7 @@ jobs: name: Get latest release uses: pozetroninc/github-action-get-latest-release@master with: - repository: ispyb/ispyb-database + repository: hormiai76/ispyb-database - uses: actions/checkout@v3 - name: Check if update required run: | diff --git a/setup.cfg b/setup.cfg index 5dff044..5a6ed2d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] -name = ispyb-models -version = 1.2.0 +name = ispyb-models-pyispyb +version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 54ca58b..f2a129c 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.0" +__version__ = "1.2.2" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 3ffaae2..4bd2868 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -3956,8 +3956,8 @@ class Component(Base): class LabContact(Base): __tablename__ = "LabContact" __table_args__ = ( - Index("cardNameAndProposal", "cardName", "proposalId", unique=True), Index("personAndProposal", "personId", "proposalId", unique=True), + Index("cardNameAndProposal", "cardName", "proposalId", unique=True), ) labContactId = Column(INTEGER(10), primary_key=True) @@ -6361,6 +6361,34 @@ class SSXDataCollection(Base): DataCollection = relationship("DataCollection", uselist=False) +class SSXProcessingResult(Base): + __tablename__ = "SSXProcessingResult" + __table_args__ = {"comment": "Processing Results table for SSX experiments."} + + ssxProcessingResultId = Column(INTEGER(11), primary_key=True, comment="Primary key") + dataCollectionId = Column( + ForeignKey( + "DataCollection.dataCollectionId", ondelete="CASCADE", onupdate="CASCADE" + ), + index=True, + ) + hitRate = Column(Float) + indexingRate = Column(Float) + indexingType = Column(Enum("Preliminary", "Final")) + status = Column(Enum("Running", "Failed", "Success")) + createdTimeStamp = Column( + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + ) + lastUpdate = Column( + TIMESTAMP, + nullable=False, + server_default=text("'0000-00-00 00:00:00'"), + comment="last update timestamp", + ) + + DataCollection = relationship("DataCollection") + + class XRFFluorescenceMapping(Base): __tablename__ = "XRFFluorescenceMapping" @@ -6587,6 +6615,39 @@ class PDBEntry(Base): AutoProcProgram = relationship("AutoProcProgram") +class SSXProcessingResultAttachment(Base): + __tablename__ = "SSXProcessingResultAttachment" + __table_args__ = { + "comment": "Processing Results attachments table for SSX experiments." + } + + ssxProcessingResultAttachmentId = Column( + INTEGER(11), primary_key=True, comment="Primary key" + ) + ssxProcessingResultId = Column( + ForeignKey( + "SSXProcessingResult.ssxProcessingResultId", + ondelete="CASCADE", + onupdate="CASCADE", + ), + index=True, + ) + fileName = Column(String(255), nullable=False) + filePath = Column(String(255), nullable=False) + fileType = Column(Enum("Result", "Log", "Graph"), nullable=False) + createdTimeStamp = Column( + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + ) + lastUpdate = Column( + TIMESTAMP, + nullable=False, + server_default=text("'0000-00-00 00:00:00'"), + comment="last update timestamp", + ) + + SSXProcessingResult = relationship("SSXProcessingResult") + + class WorkflowMesh(Base): __tablename__ = "WorkflowMesh" From ce46b61549558aa768792c2e5cd094bd85c22482 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Fri, 13 Sep 2024 10:21:01 +0000 Subject: [PATCH 17/61] Update models to schema version 1.2.2 --- src/ispyb/models/_auto_db_schema.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 4bd2868..8a01f87 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -6385,6 +6385,7 @@ class SSXProcessingResult(Base): server_default=text("'0000-00-00 00:00:00'"), comment="last update timestamp", ) + comments = Column(String(100)) DataCollection = relationship("DataCollection") From e856058076e792a6f6b8c70b4487d608d9b0522c Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 8 Nov 2024 08:44:11 +0100 Subject: [PATCH 18/61] add LineScan as new exp type --- src/ispyb/models/_auto_db_schema.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 3ffaae2..e6dc41c 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -1348,7 +1348,9 @@ class XRFFluorescenceMappingROI(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ), + ), Column("DataCollectionGroup_startTime", DateTime), Column("DataCollectionGroup_endTime", DateTime), @@ -1693,6 +1695,7 @@ class XRFFluorescenceMappingROI(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ), ), Column("DataCollectionGroup_startTime", DateTime), @@ -5319,6 +5322,7 @@ class DataCollectionGroup(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ) ) startTime = Column(DateTime, comment="Start time of the dataCollectionGroup") From 512188194e581e4564d5c2ffd2a30b37ef7ffe86 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 8 Nov 2024 08:44:11 +0100 Subject: [PATCH 19/61] add LineScan as new exp type --- src/ispyb/models/_auto_db_schema.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 8a01f87..7e1d5f3 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -1348,7 +1348,9 @@ class XRFFluorescenceMappingROI(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ), + ), Column("DataCollectionGroup_startTime", DateTime), Column("DataCollectionGroup_endTime", DateTime), @@ -1693,6 +1695,7 @@ class XRFFluorescenceMappingROI(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ), ), Column("DataCollectionGroup_startTime", DateTime), @@ -5319,6 +5322,7 @@ class DataCollectionGroup(Base): "Still", "SSX-Chip", "SSX-Jet", + "LineScan", ) ) startTime = Column(DateTime, comment="Start time of the dataCollectionGroup") From e86a91ed964bfc010fb847873f74f1e7b138c0b0 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 8 Nov 2024 08:47:48 +0100 Subject: [PATCH 20/61] new version for LineScan exp type --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 5a6ed2d..06e6bbb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.2 +version = 1.2.3 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown From 45fa404d8a2e394a0966ac9df1ece42db55628fd Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 8 Nov 2024 08:53:32 +0100 Subject: [PATCH 21/61] new version for LineScan exp type --- src/ispyb/models/_auto_db_schema.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 7e1d5f3..f7af471 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -1350,7 +1350,6 @@ class XRFFluorescenceMappingROI(Base): "SSX-Jet", "LineScan", ), - ), Column("DataCollectionGroup_startTime", DateTime), Column("DataCollectionGroup_endTime", DateTime), From f059e44700283eee9bf358e52d34ed6d7e83bcca Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Fri, 8 Nov 2024 09:39:13 +0100 Subject: [PATCH 22/61] update history --- HISTORY.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index 4759434..eab6f78 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,6 +2,20 @@ ## Unreleased / main + +## v1.2.2 (08/11/2024) + +Add LineScan to DataCollectionGroup.experimentType + + +## v1.2.2 (13/09/2024) + +Create new tables + +- SSXProcessingResult +- SSXProcessingResultAttachment + + ## v1.1.0 (17/01/2023) Create new tables: From ac3f66ea30621a3c372b82189ac48963bde66959 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 12:15:40 +0100 Subject: [PATCH 23/61] new GphNative experimentkind --- generate_models.sh | 0 requirements.txt | 2 + src/ispyb/models/_auto_db_schema.py | 243 ++++++++++++++-------------- 3 files changed, 126 insertions(+), 119 deletions(-) mode change 100644 => 100755 generate_models.sh diff --git a/generate_models.sh b/generate_models.sh old mode 100644 new mode 100755 diff --git a/requirements.txt b/requirements.txt index a680c96..cc0f06f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,5 @@ sqlalchemy mysql-connector-python==8.0.29 pytest +black +sqlacodegen diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index f7af471..33a3c52 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -149,7 +149,7 @@ class BeamLineSetup(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -185,7 +185,7 @@ class CTF(Base): estimatedBfactor = Column(String(45)) logFilePath = Column(String(512)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) @@ -206,7 +206,7 @@ class ComponentSubType(Base): componentSubTypeId = Column(INTEGER(10), primary_key=True) name = Column(String(31), nullable=False) - hasPh = Column(TINYINT(1), server_default=text("0")) + hasPh = Column(TINYINT(1), server_default=text("'0'")) class ComponentType(Base): @@ -264,7 +264,7 @@ class DatamatrixInSampleChanger(Base): datamatrixInSampleChangerId = Column(INTEGER(10), primary_key=True) proposalId = Column( - INTEGER(10), nullable=False, index=True, server_default=text("0") + INTEGER(10), nullable=False, index=True, server_default=text("'0'") ) beamLineName = Column(String(45)) datamatrixCode = Column(String(45)) @@ -384,9 +384,9 @@ class DiffractionPlan(Base): aimedIOverSigmaAtHighestRes = Column(Float(asdecimal=True)) aimedMultiplicity = Column(Float(asdecimal=True)) aimedResolution = Column(Float(asdecimal=True)) - anomalousData = Column(TINYINT(1), server_default=text("0")) + anomalousData = Column(TINYINT(1), server_default=text("'0'")) complexity = Column(String(45)) - estimateRadiationDamage = Column(TINYINT(1), server_default=text("0")) + estimateRadiationDamage = Column(TINYINT(1), server_default=text("'0'")) forcedSpaceGroup = Column(String(45)) requiredCompleteness = Column(Float(asdecimal=True)) requiredMultiplicity = Column(Float(asdecimal=True)) @@ -406,7 +406,7 @@ class DiffractionPlan(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) diffractionPlanUUID = Column(String(1000)) @@ -468,7 +468,7 @@ class Frame(Base): filePath = Column(String(255), index=True) comments = Column(String(45)) creationDate = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) frameSetId = Column(INTEGER(10)) @@ -547,7 +547,7 @@ class IspybAutoProcAttachment(Base): fileCategory = Column( Enum("input", "output", "log", "correction"), server_default=text("'output'") ) - hasGraph = Column(TINYINT(1), nullable=False, server_default=text("0")) + hasGraph = Column(TINYINT(1), nullable=False, server_default=text("'0'")) class IspybCrystalClass(Base): @@ -599,7 +599,7 @@ class Laboratory(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) laboratoryExtPk = Column(INTEGER(11)) @@ -680,7 +680,7 @@ class MotorPosition(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -737,7 +737,7 @@ class PhasingProgramRun(Base): phasingDirectory = Column(String(255), comment="Directory of execution") recordTimeStamp = Column( TIMESTAMP, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -852,7 +852,7 @@ class SchemaStatus(Base): scriptName = Column(String(100), nullable=False, unique=True) schemaStatus = Column(String(10)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) @@ -912,7 +912,7 @@ class UserGroup(Base): Column("lastPointUsed", String(45)), Column("I0", String(45)), Column("isagregated", String(45)), - Column("subtractionId", INTEGER(11)), + Column("subtractionId", BIGINT(11)), Column("rgGnom", String(45)), Column("total", String(45)), Column("dmax", String(45)), @@ -920,30 +920,30 @@ class UserGroup(Base): Column("i0stdev", String(45)), Column("quality", String(45)), Column("substractionCreationTime", DateTime), - Column("bufferBeforeMeasurementId", INTEGER(11)), - Column("bufferAfterMeasurementId", INTEGER(11)), + Column("bufferBeforeMeasurementId", BIGINT(11)), + Column("bufferAfterMeasurementId", BIGINT(11)), Column("bufferBeforeFramesMerged", String(45)), - Column("bufferBeforeMergeId", INTEGER(11)), + Column("bufferBeforeMergeId", BIGINT(11)), Column("bufferBeforeAverageFilePath", String(255)), - Column("sampleMeasurementId", INTEGER(11)), - Column("sampleMergeId", INTEGER(11)), + Column("sampleMeasurementId", BIGINT(11)), + Column("sampleMergeId", BIGINT(11)), Column("averageFilePath", String(255)), Column("framesMerge", String(45)), Column("framesCount", String(45)), Column("bufferAfterFramesMerged", String(45)), - Column("bufferAfterMergeId", INTEGER(11)), + Column("bufferAfterMergeId", BIGINT(11)), Column("bufferAfterAverageFilePath", String(255)), - Column("modelListId1", INTEGER(11)), + Column("modelListId1", BIGINT(11)), Column("nsdFilePath", String(255)), - Column("modelListId2", INTEGER(11)), + Column("modelListId2", BIGINT(11)), Column("chi2RgFilePath", String(255)), Column("averagedModel", String(255)), - Column("averagedModelId", INTEGER(11)), + Column("averagedModelId", BIGINT(11)), Column("rapidShapeDeterminationModel", String(255)), - Column("rapidShapeDeterminationModelId", INTEGER(11)), + Column("rapidShapeDeterminationModelId", BIGINT(11)), Column("shapeDeterminationModel", String(255)), - Column("shapeDeterminationModelId", INTEGER(11)), - Column("abInitioModelId", INTEGER(11)), + Column("shapeDeterminationModelId", BIGINT(11)), + Column("abInitioModelId", BIGINT(11)), Column("comments", String(512)), ) @@ -1349,6 +1349,7 @@ class XRFFluorescenceMappingROI(Base): "SSX-Chip", "SSX-Jet", "LineScan", + "GphNative", ), ), Column("DataCollectionGroup_startTime", DateTime), @@ -1695,6 +1696,7 @@ class XRFFluorescenceMappingROI(Base): "SSX-Chip", "SSX-Jet", "LineScan", + "GphNative", ), ), Column("DataCollectionGroup_startTime", DateTime), @@ -2074,7 +2076,7 @@ class XRFFluorescenceMappingROI(Base): Column( "Movie_createdTimeStamp", TIMESTAMP, - server_default=text("'current_timestamp()'"), + server_default=text("'0000-00-00 00:00:00'"), ), Column( "MotionCorrection_motionCorrectionId", INTEGER(11), server_default=text("'0'") @@ -2104,7 +2106,7 @@ class XRFFluorescenceMappingROI(Base): Column("CTF_estimatedBfactor", String(45)), Column("CTF_logFilePath", String(512)), Column( - "CTF_createdTimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'") + "CTF_createdTimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'") ), Column("Proposal_proposalId", INTEGER(10), server_default=text("'0'")), Column("BLSession_sessionId", INTEGER(10), server_default=text("'0'")), @@ -2119,7 +2121,7 @@ class XRFFluorescenceMappingROI(Base): Column("imageDirectory", String(255)), Column("movieId", INTEGER(11), server_default=text("'0'")), Column("movieNumber", INTEGER(11)), - Column("createdTimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'")), + Column("createdTimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'")), Column("motionCorrectionId", INTEGER(11), server_default=text("'0'")), Column("dataCollectionId", INTEGER(10), server_default=text("'0'")), Column("totalMotion", String(45)), @@ -2318,7 +2320,7 @@ class XRFFluorescenceMappingROI(Base): Column( "BLSample_recordTimeStamp", TIMESTAMP, - server_default=text("'current_timestamp()'"), + server_default=text("'0000-00-00 00:00:00'"), ), Column("BLSample_SMILES", String(400)), Column("Protein_proteinId", INTEGER(10), server_default=text("'0'")), @@ -2412,7 +2414,7 @@ class XRFFluorescenceMappingROI(Base): Column( "PhasingStep_recordTimeStamp", TIMESTAMP, - server_default=text("'current_timestamp()'"), + server_default=text("'0000-00-00 00:00:00'"), ), Column("DataCollection_dataCollectionId", INTEGER(10), server_default=text("'0'")), Column("DataCollection_dataCollectionGroupId", INTEGER(11)), @@ -2484,11 +2486,7 @@ class XRFFluorescenceMappingROI(Base): Column("PhasingProgramRun_phasingEndTime", DateTime), Column("PhasingProgramRun_phasingEnvironment", String(255)), Column("PhasingProgramRun_phasingDirectory", String(255)), - Column( - "PhasingProgramRun_recordTimeStamp", - TIMESTAMP, - server_default=text("'current_timestamp()'"), - ), + Column("PhasingProgramRun_recordTimeStamp", TIMESTAMP), Column("Protein_proteinId", INTEGER(10), server_default=text("'0'")), Column("BLSession_sessionId", INTEGER(10), server_default=text("'0'")), Column("BLSession_proposalId", INTEGER(10), server_default=text("'0'")), @@ -2703,7 +2701,7 @@ class XRFFluorescenceMappingROI(Base): Column("comments", String(2000)), Column("beamLineOperator", String(255)), Column("visit_number", INTEGER(10), server_default=text("'0'")), - Column("bltimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'")), + Column("bltimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'")), Column("usedFlag", TINYINT(1)), Column("sessionTitle", String(255)), Column("structureDeterminations", Float), @@ -2931,7 +2929,7 @@ class Buffer(Base): __tablename__ = "Buffer" bufferId = Column(INTEGER(11), primary_key=True) - proposalId = Column(INTEGER(11), nullable=False, server_default=text("-1")) + proposalId = Column(INTEGER(11), nullable=False, server_default=text("'-1'")) safetyLevelId = Column( ForeignKey("SafetyLevel.safetyLevelId", ondelete="CASCADE"), index=True ) @@ -3099,7 +3097,7 @@ class Person(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) externalId = Column(BINARY(16)) @@ -3148,7 +3146,7 @@ class PhasingProgramAttachment(Base): input = Column(TINYINT(1)) recordTimeStamp = Column( TIMESTAMP, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -3224,7 +3222,7 @@ class SpaceGroup(Base): MX_used = Column( TINYINT(1), nullable=False, - server_default=text("0"), + server_default=text("'0'"), comment="1 if used in the crystal form", ) @@ -3286,7 +3284,7 @@ class WorkflowDehydration(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -3371,7 +3369,9 @@ class AutoProcScalingStatistics(Base): anomalousMultiplicity = Column(Float, comment="Anomalous multiplicity") recordTimeStamp = Column(DateTime, comment="Creation or last update date/time") anomalous = Column( - TINYINT(1), server_default=text("0"), comment="boolean type:0 noanoum - 1 anoum" + TINYINT(1), + server_default=text("'0'"), + comment="boolean type:0 noanoum - 1 anoum", ) ccHalf = Column(Float, comment="information from XDS") ccAno = Column(Float) @@ -3453,7 +3453,7 @@ class MXMRRun(Base): ) success = Column( TINYINT(1), - server_default=text("0"), + server_default=text("'0'"), comment="Indicates whether the program completed. 1 for success, 0 for failure.", ) message = Column( @@ -3569,7 +3569,7 @@ class Phasing(Base): lowRes = Column(Float(asdecimal=True)) highRes = Column(Float(asdecimal=True)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) PhasingAnalysis = relationship("PhasingAnalysis") @@ -3610,7 +3610,7 @@ class PhasingStep(Base): highRes = Column(String(45)) groupName = Column(String(45)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) AutoProcScaling = relationship("AutoProcScaling") @@ -3645,7 +3645,7 @@ class PhasingHasScaling(Base): comment="serial number of the dataset and always reserve 0 for the reference", ) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) AutoProcScaling = relationship("AutoProcScaling") @@ -3719,14 +3719,14 @@ class Proposal(Base): ForeignKey("Person.personId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) title = Column(VARCHAR(200)) proposalCode = Column(String(45)) proposalNumber = Column(String(45)) proposalType = Column(String(2), comment="Proposal type: MX, BX") bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) externalId = Column(BINARY(16)) state = Column(Enum("Open", "Closed", "Cancelled"), server_default=text("'Open'")) @@ -3738,7 +3738,7 @@ class StockSolution(Base): __tablename__ = "StockSolution" stockSolutionId = Column(INTEGER(11), primary_key=True) - proposalId = Column(INTEGER(11), nullable=False, server_default=text("-1")) + proposalId = Column(INTEGER(11), nullable=False, server_default=text("'-1'")) bufferId = Column( ForeignKey("Buffer.bufferId", ondelete="CASCADE"), nullable=False, index=True ) @@ -3893,7 +3893,7 @@ class BLSession(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) projectCode = Column(String(45)) startDate = Column(DateTime, index=True) @@ -3903,9 +3903,9 @@ class BLSession(Base): nbShifts = Column(INTEGER(10), index=True) comments = Column(String(2000)) beamLineOperator = Column(String(255)) - visit_number = Column(INTEGER(10), server_default=text("0")) + visit_number = Column(INTEGER(10), server_default=text("'0'")) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) usedFlag = Column( TINYINT(1), @@ -3958,8 +3958,8 @@ class Component(Base): class LabContact(Base): __tablename__ = "LabContact" __table_args__ = ( - Index("personAndProposal", "personId", "proposalId", unique=True), Index("cardNameAndProposal", "cardName", "proposalId", unique=True), + Index("personAndProposal", "personId", "proposalId", unique=True), ) labContactId = Column(INTEGER(10), primary_key=True) @@ -3973,14 +3973,16 @@ class LabContact(Base): defaultCourrierCompany = Column(String(45)) courierAccount = Column(String(45)) billingReference = Column(String(45)) - dewarAvgCustomsValue = Column(INTEGER(10), nullable=False, server_default=text("0")) + dewarAvgCustomsValue = Column( + INTEGER(10), nullable=False, server_default=text("'0'") + ) dewarAvgTransportValue = Column( - INTEGER(10), nullable=False, server_default=text("0") + INTEGER(10), nullable=False, server_default=text("'0'") ) recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -4064,7 +4066,7 @@ class PhasingStatistics(Base): nReflections = Column(INTEGER(11)) recordTimeStamp = Column( TIMESTAMP, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -4136,7 +4138,7 @@ class Protein(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) name = Column(VARCHAR(255)) acronym = Column(String(45), index=True) @@ -4146,13 +4148,13 @@ class Protein(Base): hazardGroup = Column( TINYINT(3), nullable=False, - server_default=text("1"), + server_default=text("'1'"), comment="A.k.a. risk group", ) containmentLevel = Column( TINYINT(3), nullable=False, - server_default=text("1"), + server_default=text("'1'"), comment="A.k.a. biosafety level, which indicates the level of containment required", ) safetyLevel = Column(Enum("GREEN", "YELLOW", "RED")) @@ -4161,9 +4163,9 @@ class Protein(Base): sequence = Column(Text) personId = Column(INTEGER(10), index=True) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) - isCreatedBySampleSheet = Column(TINYINT(1), server_default=text("0")) + isCreatedBySampleSheet = Column(TINYINT(1), server_default=text("'0'")) externalId = Column(BINARY(16)) componentTypeId = Column( ForeignKey( @@ -4173,7 +4175,7 @@ class Protein(Base): ) modId = Column(String(20)) concentrationTypeId = Column(INTEGER(10)) - _global = Column("global", TINYINT(1), server_default=text("0")) + _global = Column("global", TINYINT(1), server_default=text("'0'")) ComponentType = relationship("ComponentType") Proposal = relationship("Proposal") @@ -4196,7 +4198,7 @@ class SWOnceToken(Base): ) validity = Column(String(200)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) Person = relationship("Person") @@ -4298,7 +4300,7 @@ class BeamlineAction(Base): startTimestamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp() ON UPDATE current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), ) endTimestamp = Column( TIMESTAMP, nullable=False, server_default=text("'0000-00-00 00:00:00'") @@ -4351,7 +4353,7 @@ class Crystal(Base): ForeignKey("Protein.proteinId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) crystalUUID = Column(String(45)) name = Column(String(255)) @@ -4373,7 +4375,7 @@ class Crystal(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) abundance = Column(Float) @@ -4397,7 +4399,7 @@ class DewarRegistry(Base): ) purchaseDate = Column(DateTime) bltimestamp = Column( - DateTime, nullable=False, server_default=text("current_timestamp()") + DateTime, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) LabContact = relationship("LabContact") @@ -4529,14 +4531,14 @@ class SessionHasPerson(Base): primary_key=True, nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) personId = Column( ForeignKey("Person.personId", ondelete="CASCADE", onupdate="CASCADE"), primary_key=True, nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) role = Column( Enum( @@ -4549,7 +4551,7 @@ class SessionHasPerson(Base): "Alternate Contact", ) ) - remote = Column(TINYINT(1), server_default=text("0")) + remote = Column(TINYINT(1), server_default=text("'0'")) Person = relationship("Person") BLSession = relationship("BLSession") @@ -4563,7 +4565,7 @@ class Shipping(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) shippingName = Column(String(45), index=True) deliveryAgent_agentName = Column(String(45)) @@ -4574,7 +4576,7 @@ class Shipping(Base): shippingStatus = Column(String(45), index=True) bltimeStamp = Column(DateTime) laboratoryId = Column(INTEGER(10), index=True) - isStorageShipping = Column(TINYINT(1), server_default=text("0")) + isStorageShipping = Column(TINYINT(1), server_default=text("'0'")) creationDate = Column(DateTime, index=True) comments = Column(String(255)) sendingLabContactId = Column( @@ -4672,8 +4674,8 @@ class Dewar(Base): comments = Column(TINYTEXT) storageLocation = Column(String(45)) dewarStatus = Column(String(45), index=True) - bltimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) - isStorageDewar = Column(TINYINT(1), server_default=text("0")) + bltimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) + isStorageDewar = Column(TINYINT(1), server_default=text("'0'")) barCode = Column(String(45), unique=True) firstExperimentId = Column( ForeignKey("BLSession.sessionId", ondelete="CASCADE", onupdate="CASCADE"), @@ -4689,7 +4691,7 @@ class Dewar(Base): ) isReimbursed = Column( TINYINT(1), - server_default=text("0"), + server_default=text("'0'"), comment="set this dewar as reimbursed by the user office", ) @@ -4715,7 +4717,7 @@ class DewarRegistryHasProposal(Base): index=True, comment="Person registering the dewar", ) - recordTimestamp = Column(DateTime, server_default=text("current_timestamp()")) + recordTimestamp = Column(DateTime, server_default=text("CURRENT_TIMESTAMP")) labContactId = Column( ForeignKey("LabContact.labContactId", ondelete="CASCADE", onupdate="CASCADE"), index=True, @@ -4856,7 +4858,7 @@ class Container(Base): requestedImagerId = Column(INTEGER(10)) requestedReturn = Column( TINYINT(1), - server_default=text("0"), + server_default=text("'0'"), comment="True for requesting return, False means container will be disposed", ) comments = Column(String(255)) @@ -4963,7 +4965,7 @@ class BFAutomationFault(Base): stacktrace = Column(Text) resolved = Column(TINYINT(1)) faultTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) BF_automationError = relationship("BFAutomationError") @@ -5007,7 +5009,7 @@ class BLSample(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) SMILES = Column( @@ -5047,7 +5049,7 @@ class ContainerHistory(Base): ) location = Column(String(45)) blTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) status = Column(String(45)) @@ -5100,7 +5102,7 @@ class ContainerQueue(Base): index=True, ) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) completedTimeStamp = Column(TIMESTAMP) @@ -5257,7 +5259,7 @@ class BLSubSample(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) motorPositionId = Column( @@ -5322,6 +5324,7 @@ class DataCollectionGroup(Base): "SSX-Chip", "SSX-Jet", "LineScan", + "GphNative", ) ) startTime = Column(DateTime, comment="Start time of the dataCollectionGroup") @@ -5425,7 +5428,7 @@ class RobotAction(Base): startTimestamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp() ON UPDATE current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), ) endTimestamp = Column( TIMESTAMP, nullable=False, server_default=text("'0000-00-00 00:00:00'") @@ -5514,7 +5517,7 @@ class BLSampleImageAnalysis(Base): goodnessOfFit = Column(Float) scaleFactor = Column(Float) resultCode = Column(String(15)) - matchStartTimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) + matchStartTimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) matchEndTimeStamp = Column(TIMESTAMP) BLSampleImage = relationship("BLSampleImage") @@ -5693,7 +5696,7 @@ class Screening(Base): ) dataCollectionId = Column(INTEGER(10)) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) programVersion = Column(String(45)) comments = Column(String(255)) @@ -5752,13 +5755,13 @@ class BLSampleHasEnergyScan(Base): ForeignKey("BLSample.blSampleId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) energyScanId = Column( ForeignKey("EnergyScan.energyScanId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) blSampleHasEnergyScanId = Column(INTEGER(11), primary_key=True) @@ -5838,7 +5841,7 @@ class ScreeningInput(Base): ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) diffractionPlanId = Column(INTEGER(11), comment="references DiffractionPlan table") beamX = Column(Float) @@ -5860,7 +5863,7 @@ class ScreeningOutput(Base): ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) statusDescription = Column(String(1024)) rejectedReflections = Column(INTEGER(10)) @@ -5875,8 +5878,8 @@ class ScreeningOutput(Base): mosaicity = Column(Float) iOverSigma = Column(Float) diffractionRings = Column(TINYINT(1)) - strategySuccess = Column(TINYINT(1), nullable=False, server_default=text("0")) - mosaicityEstimated = Column(TINYINT(1), nullable=False, server_default=text("0")) + strategySuccess = Column(TINYINT(1), nullable=False, server_default=text("'0'")) + mosaicityEstimated = Column(TINYINT(1), nullable=False, server_default=text("'0'")) rankingResolution = Column(Float(asdecimal=True)) program = Column(String(45)) doseTotal = Column(Float(asdecimal=True)) @@ -5884,8 +5887,8 @@ class ScreeningOutput(Base): totalRotationRange = Column(Float(asdecimal=True)) totalNumberOfImages = Column(INTEGER(11)) rFriedel = Column(Float(asdecimal=True)) - indexingSuccess = Column(TINYINT(1), nullable=False, server_default=text("0")) - screeningSuccess = Column(TINYINT(1), server_default=text("0")) + indexingSuccess = Column(TINYINT(1), nullable=False, server_default=text("'0'")) + screeningSuccess = Column(TINYINT(1), server_default=text("'0'")) Screening = relationship("Screening") @@ -5902,13 +5905,13 @@ class ScreeningRank(Base): ), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) screeningId = Column( ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) rankValue = Column(Float) rankInformation = Column(String(1024)) @@ -5927,7 +5930,7 @@ class ScreeningOutputLattice(Base): ), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) spaceGroup = Column(String(45)) pointGroup = Column(String(45)) @@ -5947,8 +5950,8 @@ class ScreeningOutputLattice(Base): unitCell_alpha = Column(Float) unitCell_beta = Column(Float) unitCell_gamma = Column(Float) - bltimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) - labelitIndexing = Column(TINYINT(1), server_default=text("0")) + bltimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) + labelitIndexing = Column(TINYINT(1), server_default=text("'0'")) ScreeningOutput = relationship("ScreeningOutput") @@ -5963,7 +5966,7 @@ class ScreeningStrategy(Base): ), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) phiStart = Column(Float) phiEnd = Column(Float) @@ -5972,7 +5975,7 @@ class ScreeningStrategy(Base): resolution = Column(Float) completeness = Column(Float) multiplicity = Column(Float) - anomalous = Column(TINYINT(1), nullable=False, server_default=text("0")) + anomalous = Column(TINYINT(1), nullable=False, server_default=text("'0'")) program = Column(String(45)) rankingResolution = Column(Float) transmission = Column( @@ -6111,7 +6114,7 @@ class DataCollection(Base): xBeamPix = Column(Float, comment="Beam size in pixels") yBeamPix = Column(Float, comment="Beam size in pixels") comments = Column(String(1024)) - printableForReport = Column(TINYINT(3), server_default=text("1")) + printableForReport = Column(TINYINT(3), server_default=text("'1'")) slitGapVertical = Column(Float) slitGapHorizontal = Column(Float) transmission = Column(Float) @@ -6144,7 +6147,7 @@ class DataCollection(Base): imageQualityIndicatorsPlotPath = Column(String(512)) imageQualityIndicatorsCSVPath = Column(String(512)) blSampleId = Column(INTEGER(10)) - sessionId = Column(INTEGER(10), server_default=text("0")) + sessionId = Column(INTEGER(10), server_default=text("'0'")) experimentType = Column(String(24)) crystalClass = Column(String(20)) chiStart = Column(Float) @@ -6164,7 +6167,7 @@ class DataCollection(Base): magnification = Column(INTEGER(11), comment="Unit: X") binning = Column( TINYINT(1), - server_default=text("1"), + server_default=text("'1'"), comment="1 or 2. Number of pixels to process as 1. (Use mean value.)", ) particleDiameter = Column(Float, comment="Unit: nm") @@ -6235,7 +6238,7 @@ class DataCollectionFileAttachment(Base): comment="snapshot: image file, usually of the sample. \\r\\nlog: a text file with logging info. \\r\\nxy: x and y data in text format. \\r\\nrecip: a compressed csv file with reciprocal space coordinates.", ) createTime = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) DataCollection = relationship("DataCollection") @@ -6264,13 +6267,13 @@ class Image(Base): imageId = Column(INTEGER(10), primary_key=True) dataCollectionId = Column( - ForeignKey("DataCollection.dataCollectionId", ondelete="CASCADE"), ForeignKey( "DataCollection.dataCollectionId", ondelete="CASCADE", onupdate="CASCADE" ), + ForeignKey("DataCollection.dataCollectionId", ondelete="CASCADE"), nullable=False, index=True, - server_default=text("0"), + server_default=text("'0'"), ) motorPositionId = Column(INTEGER(10), index=True) imageNumber = Column(INTEGER(10), index=True) @@ -6287,7 +6290,7 @@ class Image(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -6313,7 +6316,7 @@ class Movie(Base): xmlMetaDataFullPath = Column(String(255)) dosePerImage = Column(String(45)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) DataCollection = relationship("DataCollection") @@ -6380,12 +6383,12 @@ class SSXProcessingResult(Base): indexingType = Column(Enum("Preliminary", "Final")) status = Column(Enum("Running", "Failed", "Success")) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) lastUpdate = Column( TIMESTAMP, nullable=False, - server_default=text("'0000-00-00 00:00:00'"), + server_default=text("CURRENT_TIMESTAMP"), comment="last update timestamp", ) comments = Column(String(100)) @@ -6462,7 +6465,9 @@ class AutoProcIntegration(Base): cell_gamma = Column(Float, comment="Unit cell") recordTimeStamp = Column(DateTime, comment="Creation or last update date/time") anomalous = Column( - TINYINT(1), server_default=text("0"), comment="boolean type:0 noanoum - 1 anoum" + TINYINT(1), + server_default=text("'0'"), + comment="boolean type:0 noanoum - 1 anoum", ) AutoProcProgram = relationship("AutoProcProgram") @@ -6584,7 +6589,7 @@ class MotionCorrection(Base): patchesUsed = Column(String(45)) logFileFullPath = Column(String(512)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) Movie = relationship("Movie") @@ -6640,12 +6645,12 @@ class SSXProcessingResultAttachment(Base): filePath = Column(String(255), nullable=False) fileType = Column(Enum("Result", "Log", "Graph"), nullable=False) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) lastUpdate = Column( TIMESTAMP, nullable=False, - server_default=text("'0000-00-00 00:00:00'"), + server_default=text("CURRENT_TIMESTAMP"), comment="last update timestamp", ) @@ -6676,7 +6681,7 @@ class WorkflowMesh(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) @@ -6750,7 +6755,7 @@ class AutoProcStatus(Base): ) comments = Column(String(1024), comment="comments") bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("current_timestamp()") + TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") ) AutoProcIntegration = relationship("AutoProcIntegration") @@ -6778,7 +6783,7 @@ class GridInfo(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("current_timestamp()"), + server_default=text("CURRENT_TIMESTAMP"), comment="Creation or last update date/time", ) orientation = Column( From 2583cdd1ac592fd2e70b023e0baa9cafe53c4391 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:06:21 +0100 Subject: [PATCH 24/61] init current version to 1.2.1 --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 5a6ed2d..40eb2f9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.2 +version = 1.2.1 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index f2a129c..1073dcb 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.2" +__version__ = "1.2.1" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From dc71a8204508d91110e120f48abc5f72cbc50245 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:07:20 +0100 Subject: [PATCH 25/61] =?UTF-8?q?Bump=20version:=201.2.1=20=E2=86=92=201.2?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 3ad4215..b5cf7a8 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.1 +current_version = 1.2.2 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index 40eb2f9..5a6ed2d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.1 +version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 1073dcb..f2a129c 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.1" +__version__ = "1.2.2" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From d3212b36c21b64d95189ddbbaf7175996a305302 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:07:55 +0100 Subject: [PATCH 26/61] =?UTF-8?q?Bump=20version:=201.2.2=20=E2=86=92=201.2?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 5a6ed2d..a7357f8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.2 +version = version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index f2a129c..7f9a665 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.2" +__version__ = "__version__ = "1.2.2"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From c3d74ef4fd6d6e964c18f7af75e0beb807781318 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:09:36 +0100 Subject: [PATCH 27/61] init current version to 1.2.1 --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index b5cf7a8..3ad4215 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.2 +current_version = 1.2.1 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index a7357f8..bc26ead 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.2 +version = version = 1.2.1 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 7f9a665..fe88953 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.2"" +__version__ = "__version__ = 1.2.1" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 98f0e52346af4d9223a9e6e4d6622abb5777436c Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:10:38 +0100 Subject: [PATCH 28/61] new verison 1.2.2 --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index fe88953..76689ca 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = 1.2.1" +__version__ = "__version__ = 1.2.2" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 31daf1b7f28371ee8420680f2c527473589fc39b Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:11:26 +0100 Subject: [PATCH 29/61] init current version to 1.2.1 --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 76689ca..fe88953 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = 1.2.2" +__version__ = "__version__ = 1.2.1" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From b12d1d07115f1f942f322c2b3a7b76bb215052d8 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:13:00 +0100 Subject: [PATCH 30/61] init current version to 1.2.1 --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index fe88953..50e4225 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = 1.2.1" +__version__ = '__version__ = "1.2.1"' DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 391c586f70e3ff5ad8a44f090ca66dc1dbb9188e Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:13:08 +0100 Subject: [PATCH 31/61] =?UTF-8?q?Bump=20version:=201.2.1=20=E2=86=92=201.2?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 3ad4215..b5cf7a8 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.1 +current_version = 1.2.2 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index bc26ead..a7357f8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.1 +version = version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 50e4225..eb5324e 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = '__version__ = "1.2.1"' +__version__ = '__version__ = "1.2.2"' DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 72c440a06b36b134a81ca0b35a616eb12e757c5b Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:14:12 +0100 Subject: [PATCH 32/61] =?UTF-8?q?Bump=20version:=201.2.2=20=E2=86=92=201.2?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index a7357f8..2ec185d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.2 +version = version = version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index eb5324e..2b012bb 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = '__version__ = "1.2.2"' +__version__ = '__version__ = "__version__ = "1.2.2""' DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 5256413dff8990c94cfed3fbe844ba27e436442a Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:16:01 +0100 Subject: [PATCH 33/61] =?UTF-8?q?Bump=20version:=201.2.2=20=E2=86=92=201.2?= =?UTF-8?q?.2?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 2ec185d..b5d4387 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = version = 1.2.2 +version = version = version = version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 2b012bb..1211949 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = '__version__ = "__version__ = "1.2.2""' +__version__ = '__version__ = "__version__ = "__version__ = "1.2.2"""' DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From c73f321f44125f622315f159aa74e1714b3ff4cf Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:18:06 +0100 Subject: [PATCH 34/61] new tag 1.2.2 --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 1211949..eb5324e 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = '__version__ = "__version__ = "__version__ = "1.2.2"""' +__version__ = '__version__ = "1.2.2"' DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 775fee3fc5ae2f4878c7faa2a0ce826c9ab5af87 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:19:22 +0100 Subject: [PATCH 35/61] new tag 1.2.2 --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index b5d4387..5a6ed2d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = version = version = 1.2.2 +version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown From 7985f4f6d20f563743def35f2dc1f55eb686aa75 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 13:20:05 +0100 Subject: [PATCH 36/61] new tag 1.2.2 --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index eb5324e..f2a129c 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = '__version__ = "1.2.2"' +__version__ = "1.2.2" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 8107d122cc53fe945a56b0e9e3cc49e96e024f3d Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 11 Nov 2024 14:17:26 +0100 Subject: [PATCH 37/61] Update setup.cfg --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 06e6bbb..5a6ed2d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.3 +version = 1.2.2 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown From 1e916d0ee9d4b63bfdaaf3f624d74d51d91d82d9 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 15:27:35 +0100 Subject: [PATCH 38/61] new version --- src/ispyb/models/__init__.py | 2 +- src/ispyb/models/_auto_db_schema.py | 238 ++++++++++++++-------------- 2 files changed, 119 insertions(+), 121 deletions(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index f2a129c..51290c9 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.2" +__version__ = "1.2.3" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 33a3c52..bf2c09c 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -149,7 +149,7 @@ class BeamLineSetup(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -185,7 +185,7 @@ class CTF(Base): estimatedBfactor = Column(String(45)) logFilePath = Column(String(512)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) @@ -206,7 +206,7 @@ class ComponentSubType(Base): componentSubTypeId = Column(INTEGER(10), primary_key=True) name = Column(String(31), nullable=False) - hasPh = Column(TINYINT(1), server_default=text("'0'")) + hasPh = Column(TINYINT(1), server_default=text("0")) class ComponentType(Base): @@ -264,7 +264,7 @@ class DatamatrixInSampleChanger(Base): datamatrixInSampleChangerId = Column(INTEGER(10), primary_key=True) proposalId = Column( - INTEGER(10), nullable=False, index=True, server_default=text("'0'") + INTEGER(10), nullable=False, index=True, server_default=text("0") ) beamLineName = Column(String(45)) datamatrixCode = Column(String(45)) @@ -384,9 +384,9 @@ class DiffractionPlan(Base): aimedIOverSigmaAtHighestRes = Column(Float(asdecimal=True)) aimedMultiplicity = Column(Float(asdecimal=True)) aimedResolution = Column(Float(asdecimal=True)) - anomalousData = Column(TINYINT(1), server_default=text("'0'")) + anomalousData = Column(TINYINT(1), server_default=text("0")) complexity = Column(String(45)) - estimateRadiationDamage = Column(TINYINT(1), server_default=text("'0'")) + estimateRadiationDamage = Column(TINYINT(1), server_default=text("0")) forcedSpaceGroup = Column(String(45)) requiredCompleteness = Column(Float(asdecimal=True)) requiredMultiplicity = Column(Float(asdecimal=True)) @@ -406,7 +406,7 @@ class DiffractionPlan(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) diffractionPlanUUID = Column(String(1000)) @@ -468,7 +468,7 @@ class Frame(Base): filePath = Column(String(255), index=True) comments = Column(String(45)) creationDate = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) frameSetId = Column(INTEGER(10)) @@ -547,7 +547,7 @@ class IspybAutoProcAttachment(Base): fileCategory = Column( Enum("input", "output", "log", "correction"), server_default=text("'output'") ) - hasGraph = Column(TINYINT(1), nullable=False, server_default=text("'0'")) + hasGraph = Column(TINYINT(1), nullable=False, server_default=text("0")) class IspybCrystalClass(Base): @@ -599,7 +599,7 @@ class Laboratory(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) laboratoryExtPk = Column(INTEGER(11)) @@ -680,7 +680,7 @@ class MotorPosition(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -737,7 +737,7 @@ class PhasingProgramRun(Base): phasingDirectory = Column(String(255), comment="Directory of execution") recordTimeStamp = Column( TIMESTAMP, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -852,7 +852,7 @@ class SchemaStatus(Base): scriptName = Column(String(100), nullable=False, unique=True) schemaStatus = Column(String(10)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) @@ -912,7 +912,7 @@ class UserGroup(Base): Column("lastPointUsed", String(45)), Column("I0", String(45)), Column("isagregated", String(45)), - Column("subtractionId", BIGINT(11)), + Column("subtractionId", INTEGER(11)), Column("rgGnom", String(45)), Column("total", String(45)), Column("dmax", String(45)), @@ -920,30 +920,30 @@ class UserGroup(Base): Column("i0stdev", String(45)), Column("quality", String(45)), Column("substractionCreationTime", DateTime), - Column("bufferBeforeMeasurementId", BIGINT(11)), - Column("bufferAfterMeasurementId", BIGINT(11)), + Column("bufferBeforeMeasurementId", INTEGER(11)), + Column("bufferAfterMeasurementId", INTEGER(11)), Column("bufferBeforeFramesMerged", String(45)), - Column("bufferBeforeMergeId", BIGINT(11)), + Column("bufferBeforeMergeId", INTEGER(11)), Column("bufferBeforeAverageFilePath", String(255)), - Column("sampleMeasurementId", BIGINT(11)), - Column("sampleMergeId", BIGINT(11)), + Column("sampleMeasurementId", INTEGER(11)), + Column("sampleMergeId", INTEGER(11)), Column("averageFilePath", String(255)), Column("framesMerge", String(45)), Column("framesCount", String(45)), Column("bufferAfterFramesMerged", String(45)), - Column("bufferAfterMergeId", BIGINT(11)), + Column("bufferAfterMergeId", INTEGER(11)), Column("bufferAfterAverageFilePath", String(255)), - Column("modelListId1", BIGINT(11)), + Column("modelListId1", INTEGER(11)), Column("nsdFilePath", String(255)), - Column("modelListId2", BIGINT(11)), + Column("modelListId2", INTEGER(11)), Column("chi2RgFilePath", String(255)), Column("averagedModel", String(255)), - Column("averagedModelId", BIGINT(11)), + Column("averagedModelId", INTEGER(11)), Column("rapidShapeDeterminationModel", String(255)), - Column("rapidShapeDeterminationModelId", BIGINT(11)), + Column("rapidShapeDeterminationModelId", INTEGER(11)), Column("shapeDeterminationModel", String(255)), - Column("shapeDeterminationModelId", BIGINT(11)), - Column("abInitioModelId", BIGINT(11)), + Column("shapeDeterminationModelId", INTEGER(11)), + Column("abInitioModelId", INTEGER(11)), Column("comments", String(512)), ) @@ -2076,7 +2076,7 @@ class XRFFluorescenceMappingROI(Base): Column( "Movie_createdTimeStamp", TIMESTAMP, - server_default=text("'0000-00-00 00:00:00'"), + server_default=text("'current_timestamp()'"), ), Column( "MotionCorrection_motionCorrectionId", INTEGER(11), server_default=text("'0'") @@ -2106,7 +2106,7 @@ class XRFFluorescenceMappingROI(Base): Column("CTF_estimatedBfactor", String(45)), Column("CTF_logFilePath", String(512)), Column( - "CTF_createdTimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'") + "CTF_createdTimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'") ), Column("Proposal_proposalId", INTEGER(10), server_default=text("'0'")), Column("BLSession_sessionId", INTEGER(10), server_default=text("'0'")), @@ -2121,7 +2121,7 @@ class XRFFluorescenceMappingROI(Base): Column("imageDirectory", String(255)), Column("movieId", INTEGER(11), server_default=text("'0'")), Column("movieNumber", INTEGER(11)), - Column("createdTimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'")), + Column("createdTimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'")), Column("motionCorrectionId", INTEGER(11), server_default=text("'0'")), Column("dataCollectionId", INTEGER(10), server_default=text("'0'")), Column("totalMotion", String(45)), @@ -2320,7 +2320,7 @@ class XRFFluorescenceMappingROI(Base): Column( "BLSample_recordTimeStamp", TIMESTAMP, - server_default=text("'0000-00-00 00:00:00'"), + server_default=text("'current_timestamp()'"), ), Column("BLSample_SMILES", String(400)), Column("Protein_proteinId", INTEGER(10), server_default=text("'0'")), @@ -2414,7 +2414,7 @@ class XRFFluorescenceMappingROI(Base): Column( "PhasingStep_recordTimeStamp", TIMESTAMP, - server_default=text("'0000-00-00 00:00:00'"), + server_default=text("'current_timestamp()'"), ), Column("DataCollection_dataCollectionId", INTEGER(10), server_default=text("'0'")), Column("DataCollection_dataCollectionGroupId", INTEGER(11)), @@ -2486,7 +2486,11 @@ class XRFFluorescenceMappingROI(Base): Column("PhasingProgramRun_phasingEndTime", DateTime), Column("PhasingProgramRun_phasingEnvironment", String(255)), Column("PhasingProgramRun_phasingDirectory", String(255)), - Column("PhasingProgramRun_recordTimeStamp", TIMESTAMP), + Column( + "PhasingProgramRun_recordTimeStamp", + TIMESTAMP, + server_default=text("'current_timestamp()'"), + ), Column("Protein_proteinId", INTEGER(10), server_default=text("'0'")), Column("BLSession_sessionId", INTEGER(10), server_default=text("'0'")), Column("BLSession_proposalId", INTEGER(10), server_default=text("'0'")), @@ -2701,7 +2705,7 @@ class XRFFluorescenceMappingROI(Base): Column("comments", String(2000)), Column("beamLineOperator", String(255)), Column("visit_number", INTEGER(10), server_default=text("'0'")), - Column("bltimeStamp", TIMESTAMP, server_default=text("'0000-00-00 00:00:00'")), + Column("bltimeStamp", TIMESTAMP, server_default=text("'current_timestamp()'")), Column("usedFlag", TINYINT(1)), Column("sessionTitle", String(255)), Column("structureDeterminations", Float), @@ -2929,7 +2933,7 @@ class Buffer(Base): __tablename__ = "Buffer" bufferId = Column(INTEGER(11), primary_key=True) - proposalId = Column(INTEGER(11), nullable=False, server_default=text("'-1'")) + proposalId = Column(INTEGER(11), nullable=False, server_default=text("-1")) safetyLevelId = Column( ForeignKey("SafetyLevel.safetyLevelId", ondelete="CASCADE"), index=True ) @@ -3097,7 +3101,7 @@ class Person(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) externalId = Column(BINARY(16)) @@ -3146,7 +3150,7 @@ class PhasingProgramAttachment(Base): input = Column(TINYINT(1)) recordTimeStamp = Column( TIMESTAMP, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -3222,7 +3226,7 @@ class SpaceGroup(Base): MX_used = Column( TINYINT(1), nullable=False, - server_default=text("'0'"), + server_default=text("0"), comment="1 if used in the crystal form", ) @@ -3284,7 +3288,7 @@ class WorkflowDehydration(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -3369,9 +3373,7 @@ class AutoProcScalingStatistics(Base): anomalousMultiplicity = Column(Float, comment="Anomalous multiplicity") recordTimeStamp = Column(DateTime, comment="Creation or last update date/time") anomalous = Column( - TINYINT(1), - server_default=text("'0'"), - comment="boolean type:0 noanoum - 1 anoum", + TINYINT(1), server_default=text("0"), comment="boolean type:0 noanoum - 1 anoum" ) ccHalf = Column(Float, comment="information from XDS") ccAno = Column(Float) @@ -3453,7 +3455,7 @@ class MXMRRun(Base): ) success = Column( TINYINT(1), - server_default=text("'0'"), + server_default=text("0"), comment="Indicates whether the program completed. 1 for success, 0 for failure.", ) message = Column( @@ -3569,7 +3571,7 @@ class Phasing(Base): lowRes = Column(Float(asdecimal=True)) highRes = Column(Float(asdecimal=True)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) PhasingAnalysis = relationship("PhasingAnalysis") @@ -3610,7 +3612,7 @@ class PhasingStep(Base): highRes = Column(String(45)) groupName = Column(String(45)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) AutoProcScaling = relationship("AutoProcScaling") @@ -3645,7 +3647,7 @@ class PhasingHasScaling(Base): comment="serial number of the dataset and always reserve 0 for the reference", ) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) AutoProcScaling = relationship("AutoProcScaling") @@ -3719,14 +3721,14 @@ class Proposal(Base): ForeignKey("Person.personId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) title = Column(VARCHAR(200)) proposalCode = Column(String(45)) proposalNumber = Column(String(45)) proposalType = Column(String(2), comment="Proposal type: MX, BX") bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) externalId = Column(BINARY(16)) state = Column(Enum("Open", "Closed", "Cancelled"), server_default=text("'Open'")) @@ -3738,7 +3740,7 @@ class StockSolution(Base): __tablename__ = "StockSolution" stockSolutionId = Column(INTEGER(11), primary_key=True) - proposalId = Column(INTEGER(11), nullable=False, server_default=text("'-1'")) + proposalId = Column(INTEGER(11), nullable=False, server_default=text("-1")) bufferId = Column( ForeignKey("Buffer.bufferId", ondelete="CASCADE"), nullable=False, index=True ) @@ -3893,7 +3895,7 @@ class BLSession(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) projectCode = Column(String(45)) startDate = Column(DateTime, index=True) @@ -3903,9 +3905,9 @@ class BLSession(Base): nbShifts = Column(INTEGER(10), index=True) comments = Column(String(2000)) beamLineOperator = Column(String(255)) - visit_number = Column(INTEGER(10), server_default=text("'0'")) + visit_number = Column(INTEGER(10), server_default=text("0")) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) usedFlag = Column( TINYINT(1), @@ -3973,16 +3975,14 @@ class LabContact(Base): defaultCourrierCompany = Column(String(45)) courierAccount = Column(String(45)) billingReference = Column(String(45)) - dewarAvgCustomsValue = Column( - INTEGER(10), nullable=False, server_default=text("'0'") - ) + dewarAvgCustomsValue = Column(INTEGER(10), nullable=False, server_default=text("0")) dewarAvgTransportValue = Column( - INTEGER(10), nullable=False, server_default=text("'0'") + INTEGER(10), nullable=False, server_default=text("0") ) recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -4066,7 +4066,7 @@ class PhasingStatistics(Base): nReflections = Column(INTEGER(11)) recordTimeStamp = Column( TIMESTAMP, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -4138,7 +4138,7 @@ class Protein(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) name = Column(VARCHAR(255)) acronym = Column(String(45), index=True) @@ -4148,13 +4148,13 @@ class Protein(Base): hazardGroup = Column( TINYINT(3), nullable=False, - server_default=text("'1'"), + server_default=text("1"), comment="A.k.a. risk group", ) containmentLevel = Column( TINYINT(3), nullable=False, - server_default=text("'1'"), + server_default=text("1"), comment="A.k.a. biosafety level, which indicates the level of containment required", ) safetyLevel = Column(Enum("GREEN", "YELLOW", "RED")) @@ -4163,9 +4163,9 @@ class Protein(Base): sequence = Column(Text) personId = Column(INTEGER(10), index=True) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) - isCreatedBySampleSheet = Column(TINYINT(1), server_default=text("'0'")) + isCreatedBySampleSheet = Column(TINYINT(1), server_default=text("0")) externalId = Column(BINARY(16)) componentTypeId = Column( ForeignKey( @@ -4175,7 +4175,7 @@ class Protein(Base): ) modId = Column(String(20)) concentrationTypeId = Column(INTEGER(10)) - _global = Column("global", TINYINT(1), server_default=text("'0'")) + _global = Column("global", TINYINT(1), server_default=text("0")) ComponentType = relationship("ComponentType") Proposal = relationship("Proposal") @@ -4198,7 +4198,7 @@ class SWOnceToken(Base): ) validity = Column(String(200)) recordTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) Person = relationship("Person") @@ -4300,7 +4300,7 @@ class BeamlineAction(Base): startTimestamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), + server_default=text("current_timestamp() ON UPDATE current_timestamp()"), ) endTimestamp = Column( TIMESTAMP, nullable=False, server_default=text("'0000-00-00 00:00:00'") @@ -4353,7 +4353,7 @@ class Crystal(Base): ForeignKey("Protein.proteinId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) crystalUUID = Column(String(45)) name = Column(String(255)) @@ -4375,7 +4375,7 @@ class Crystal(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) abundance = Column(Float) @@ -4399,7 +4399,7 @@ class DewarRegistry(Base): ) purchaseDate = Column(DateTime) bltimestamp = Column( - DateTime, nullable=False, server_default=text("CURRENT_TIMESTAMP") + DateTime, nullable=False, server_default=text("current_timestamp()") ) LabContact = relationship("LabContact") @@ -4531,14 +4531,14 @@ class SessionHasPerson(Base): primary_key=True, nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) personId = Column( ForeignKey("Person.personId", ondelete="CASCADE", onupdate="CASCADE"), primary_key=True, nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) role = Column( Enum( @@ -4551,7 +4551,7 @@ class SessionHasPerson(Base): "Alternate Contact", ) ) - remote = Column(TINYINT(1), server_default=text("'0'")) + remote = Column(TINYINT(1), server_default=text("0")) Person = relationship("Person") BLSession = relationship("BLSession") @@ -4565,7 +4565,7 @@ class Shipping(Base): ForeignKey("Proposal.proposalId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) shippingName = Column(String(45), index=True) deliveryAgent_agentName = Column(String(45)) @@ -4576,7 +4576,7 @@ class Shipping(Base): shippingStatus = Column(String(45), index=True) bltimeStamp = Column(DateTime) laboratoryId = Column(INTEGER(10), index=True) - isStorageShipping = Column(TINYINT(1), server_default=text("'0'")) + isStorageShipping = Column(TINYINT(1), server_default=text("0")) creationDate = Column(DateTime, index=True) comments = Column(String(255)) sendingLabContactId = Column( @@ -4674,8 +4674,8 @@ class Dewar(Base): comments = Column(TINYTEXT) storageLocation = Column(String(45)) dewarStatus = Column(String(45), index=True) - bltimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) - isStorageDewar = Column(TINYINT(1), server_default=text("'0'")) + bltimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) + isStorageDewar = Column(TINYINT(1), server_default=text("0")) barCode = Column(String(45), unique=True) firstExperimentId = Column( ForeignKey("BLSession.sessionId", ondelete="CASCADE", onupdate="CASCADE"), @@ -4691,7 +4691,7 @@ class Dewar(Base): ) isReimbursed = Column( TINYINT(1), - server_default=text("'0'"), + server_default=text("0"), comment="set this dewar as reimbursed by the user office", ) @@ -4717,7 +4717,7 @@ class DewarRegistryHasProposal(Base): index=True, comment="Person registering the dewar", ) - recordTimestamp = Column(DateTime, server_default=text("CURRENT_TIMESTAMP")) + recordTimestamp = Column(DateTime, server_default=text("current_timestamp()")) labContactId = Column( ForeignKey("LabContact.labContactId", ondelete="CASCADE", onupdate="CASCADE"), index=True, @@ -4858,7 +4858,7 @@ class Container(Base): requestedImagerId = Column(INTEGER(10)) requestedReturn = Column( TINYINT(1), - server_default=text("'0'"), + server_default=text("0"), comment="True for requesting return, False means container will be disposed", ) comments = Column(String(255)) @@ -4965,7 +4965,7 @@ class BFAutomationFault(Base): stacktrace = Column(Text) resolved = Column(TINYINT(1)) faultTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) BF_automationError = relationship("BFAutomationError") @@ -5009,7 +5009,7 @@ class BLSample(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) SMILES = Column( @@ -5049,7 +5049,7 @@ class ContainerHistory(Base): ) location = Column(String(45)) blTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) status = Column(String(45)) @@ -5102,7 +5102,7 @@ class ContainerQueue(Base): index=True, ) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) completedTimeStamp = Column(TIMESTAMP) @@ -5259,7 +5259,7 @@ class BLSubSample(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) motorPositionId = Column( @@ -5428,7 +5428,7 @@ class RobotAction(Base): startTimestamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP"), + server_default=text("current_timestamp() ON UPDATE current_timestamp()"), ) endTimestamp = Column( TIMESTAMP, nullable=False, server_default=text("'0000-00-00 00:00:00'") @@ -5517,7 +5517,7 @@ class BLSampleImageAnalysis(Base): goodnessOfFit = Column(Float) scaleFactor = Column(Float) resultCode = Column(String(15)) - matchStartTimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) + matchStartTimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) matchEndTimeStamp = Column(TIMESTAMP) BLSampleImage = relationship("BLSampleImage") @@ -5696,7 +5696,7 @@ class Screening(Base): ) dataCollectionId = Column(INTEGER(10)) bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) programVersion = Column(String(45)) comments = Column(String(255)) @@ -5755,13 +5755,13 @@ class BLSampleHasEnergyScan(Base): ForeignKey("BLSample.blSampleId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) energyScanId = Column( ForeignKey("EnergyScan.energyScanId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) blSampleHasEnergyScanId = Column(INTEGER(11), primary_key=True) @@ -5841,7 +5841,7 @@ class ScreeningInput(Base): ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) diffractionPlanId = Column(INTEGER(11), comment="references DiffractionPlan table") beamX = Column(Float) @@ -5863,7 +5863,7 @@ class ScreeningOutput(Base): ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) statusDescription = Column(String(1024)) rejectedReflections = Column(INTEGER(10)) @@ -5878,8 +5878,8 @@ class ScreeningOutput(Base): mosaicity = Column(Float) iOverSigma = Column(Float) diffractionRings = Column(TINYINT(1)) - strategySuccess = Column(TINYINT(1), nullable=False, server_default=text("'0'")) - mosaicityEstimated = Column(TINYINT(1), nullable=False, server_default=text("'0'")) + strategySuccess = Column(TINYINT(1), nullable=False, server_default=text("0")) + mosaicityEstimated = Column(TINYINT(1), nullable=False, server_default=text("0")) rankingResolution = Column(Float(asdecimal=True)) program = Column(String(45)) doseTotal = Column(Float(asdecimal=True)) @@ -5887,8 +5887,8 @@ class ScreeningOutput(Base): totalRotationRange = Column(Float(asdecimal=True)) totalNumberOfImages = Column(INTEGER(11)) rFriedel = Column(Float(asdecimal=True)) - indexingSuccess = Column(TINYINT(1), nullable=False, server_default=text("'0'")) - screeningSuccess = Column(TINYINT(1), server_default=text("'0'")) + indexingSuccess = Column(TINYINT(1), nullable=False, server_default=text("0")) + screeningSuccess = Column(TINYINT(1), server_default=text("0")) Screening = relationship("Screening") @@ -5905,13 +5905,13 @@ class ScreeningRank(Base): ), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) screeningId = Column( ForeignKey("Screening.screeningId", ondelete="CASCADE", onupdate="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) rankValue = Column(Float) rankInformation = Column(String(1024)) @@ -5930,7 +5930,7 @@ class ScreeningOutputLattice(Base): ), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) spaceGroup = Column(String(45)) pointGroup = Column(String(45)) @@ -5950,8 +5950,8 @@ class ScreeningOutputLattice(Base): unitCell_alpha = Column(Float) unitCell_beta = Column(Float) unitCell_gamma = Column(Float) - bltimeStamp = Column(TIMESTAMP, server_default=text("CURRENT_TIMESTAMP")) - labelitIndexing = Column(TINYINT(1), server_default=text("'0'")) + bltimeStamp = Column(TIMESTAMP, server_default=text("current_timestamp()")) + labelitIndexing = Column(TINYINT(1), server_default=text("0")) ScreeningOutput = relationship("ScreeningOutput") @@ -5966,7 +5966,7 @@ class ScreeningStrategy(Base): ), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) phiStart = Column(Float) phiEnd = Column(Float) @@ -5975,7 +5975,7 @@ class ScreeningStrategy(Base): resolution = Column(Float) completeness = Column(Float) multiplicity = Column(Float) - anomalous = Column(TINYINT(1), nullable=False, server_default=text("'0'")) + anomalous = Column(TINYINT(1), nullable=False, server_default=text("0")) program = Column(String(45)) rankingResolution = Column(Float) transmission = Column( @@ -6114,7 +6114,7 @@ class DataCollection(Base): xBeamPix = Column(Float, comment="Beam size in pixels") yBeamPix = Column(Float, comment="Beam size in pixels") comments = Column(String(1024)) - printableForReport = Column(TINYINT(3), server_default=text("'1'")) + printableForReport = Column(TINYINT(3), server_default=text("1")) slitGapVertical = Column(Float) slitGapHorizontal = Column(Float) transmission = Column(Float) @@ -6147,7 +6147,7 @@ class DataCollection(Base): imageQualityIndicatorsPlotPath = Column(String(512)) imageQualityIndicatorsCSVPath = Column(String(512)) blSampleId = Column(INTEGER(10)) - sessionId = Column(INTEGER(10), server_default=text("'0'")) + sessionId = Column(INTEGER(10), server_default=text("0")) experimentType = Column(String(24)) crystalClass = Column(String(20)) chiStart = Column(Float) @@ -6167,7 +6167,7 @@ class DataCollection(Base): magnification = Column(INTEGER(11), comment="Unit: X") binning = Column( TINYINT(1), - server_default=text("'1'"), + server_default=text("1"), comment="1 or 2. Number of pixels to process as 1. (Use mean value.)", ) particleDiameter = Column(Float, comment="Unit: nm") @@ -6238,7 +6238,7 @@ class DataCollectionFileAttachment(Base): comment="snapshot: image file, usually of the sample. \\r\\nlog: a text file with logging info. \\r\\nxy: x and y data in text format. \\r\\nrecip: a compressed csv file with reciprocal space coordinates.", ) createTime = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) DataCollection = relationship("DataCollection") @@ -6267,13 +6267,13 @@ class Image(Base): imageId = Column(INTEGER(10), primary_key=True) dataCollectionId = Column( + ForeignKey("DataCollection.dataCollectionId", ondelete="CASCADE"), ForeignKey( "DataCollection.dataCollectionId", ondelete="CASCADE", onupdate="CASCADE" ), - ForeignKey("DataCollection.dataCollectionId", ondelete="CASCADE"), nullable=False, index=True, - server_default=text("'0'"), + server_default=text("0"), ) motorPositionId = Column(INTEGER(10), index=True) imageNumber = Column(INTEGER(10), index=True) @@ -6290,7 +6290,7 @@ class Image(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -6316,7 +6316,7 @@ class Movie(Base): xmlMetaDataFullPath = Column(String(255)) dosePerImage = Column(String(45)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) DataCollection = relationship("DataCollection") @@ -6383,12 +6383,12 @@ class SSXProcessingResult(Base): indexingType = Column(Enum("Preliminary", "Final")) status = Column(Enum("Running", "Failed", "Success")) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) lastUpdate = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="last update timestamp", ) comments = Column(String(100)) @@ -6465,9 +6465,7 @@ class AutoProcIntegration(Base): cell_gamma = Column(Float, comment="Unit cell") recordTimeStamp = Column(DateTime, comment="Creation or last update date/time") anomalous = Column( - TINYINT(1), - server_default=text("'0'"), - comment="boolean type:0 noanoum - 1 anoum", + TINYINT(1), server_default=text("0"), comment="boolean type:0 noanoum - 1 anoum" ) AutoProcProgram = relationship("AutoProcProgram") @@ -6589,7 +6587,7 @@ class MotionCorrection(Base): patchesUsed = Column(String(45)) logFileFullPath = Column(String(512)) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) Movie = relationship("Movie") @@ -6645,12 +6643,12 @@ class SSXProcessingResultAttachment(Base): filePath = Column(String(255), nullable=False) fileType = Column(Enum("Result", "Log", "Graph"), nullable=False) createdTimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) lastUpdate = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="last update timestamp", ) @@ -6681,7 +6679,7 @@ class WorkflowMesh(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) @@ -6755,7 +6753,7 @@ class AutoProcStatus(Base): ) comments = Column(String(1024), comment="comments") bltimeStamp = Column( - TIMESTAMP, nullable=False, server_default=text("CURRENT_TIMESTAMP") + TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) AutoProcIntegration = relationship("AutoProcIntegration") @@ -6783,7 +6781,7 @@ class GridInfo(Base): recordTimeStamp = Column( TIMESTAMP, nullable=False, - server_default=text("CURRENT_TIMESTAMP"), + server_default=text("current_timestamp()"), comment="Creation or last update date/time", ) orientation = Column( From 13d64d14bd95c3799830cbd4bd83657b37e914f4 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 15:28:15 +0100 Subject: [PATCH 39/61] new version --- HISTORY.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/HISTORY.md b/HISTORY.md index eab6f78..54a808d 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -3,7 +3,7 @@ ## Unreleased / main -## v1.2.2 (08/11/2024) +## v1.2.3 (11/11/2024) Add LineScan to DataCollectionGroup.experimentType From fe3144da21a052f92bedd2fd39d399ced75dae1f Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 15:49:28 +0100 Subject: [PATCH 40/61] new version --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 51290c9..f2a129c 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.3" +__version__ = "1.2.2" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 4cfd12d39d0890c32997179835c6221c609c7d5c Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 15:49:37 +0100 Subject: [PATCH 41/61] =?UTF-8?q?Bump=20version:=201.2.2=20=E2=86=92=201.2?= =?UTF-8?q?.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index b5cf7a8..2f0ca86 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.2 +current_version = 1.2.3 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index 5a6ed2d..06e6bbb 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.2 +version = 1.2.3 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index f2a129c..51290c9 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.2" +__version__ = "1.2.3" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 72308f53f63510b1c1153ef4249e7714181df431 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Mon, 11 Nov 2024 14:57:18 +0000 Subject: [PATCH 42/61] Update models to schema version 1.2.3 --- src/ispyb/models/_auto_db_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index bf2c09c..f735456 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -3960,8 +3960,8 @@ class Component(Base): class LabContact(Base): __tablename__ = "LabContact" __table_args__ = ( - Index("cardNameAndProposal", "cardName", "proposalId", unique=True), Index("personAndProposal", "personId", "proposalId", unique=True), + Index("cardNameAndProposal", "cardName", "proposalId", unique=True), ) labContactId = Column(INTEGER(10), primary_key=True) From 3553bcd553c06f4397639df5b4bc612ae81eab23 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Mon, 11 Nov 2024 16:00:33 +0100 Subject: [PATCH 43/61] update history file --- HISTORY.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 54a808d..4aa6a44 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -5,7 +5,7 @@ ## v1.2.3 (11/11/2024) -Add LineScan to DataCollectionGroup.experimentType +Add `LineScan` and `GphNative` to `DataCollectionGroup.experimentType`. ## v1.2.2 (13/09/2024) @@ -28,7 +28,7 @@ Create new tables: - EventType - Event -Add SSX-Chip and SSX-Jet to DataCollectionGroup.experimentType. +Add `SSX-Chip` and `SSX-Jet` to `DataCollectionGroup.experimentType`. ## v1.0.0 (20/07/2022) From 43abdb67e77305ebbc33e9af72642a148390e480 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Wed, 13 Nov 2024 15:30:40 +0000 Subject: [PATCH 44/61] Update models to schema version 1.2.4 --- src/ispyb/models/_auto_db_schema.py | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index f735456..7b73682 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -6392,6 +6392,7 @@ class SSXProcessingResult(Base): comment="last update timestamp", ) comments = Column(String(100)) + nbCrystals = Column(INTEGER(11), comment="Number of crystals") DataCollection = relationship("DataCollection") From e52f972982563e1dc174c44c45bf2305332ee391 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 16:56:38 +0100 Subject: [PATCH 45/61] update history file --- HISTORY.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index 4aa6a44..4089aa9 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,6 +2,9 @@ ## Unreleased / main +## v1.2.4 (13/11/2024) + +Add `nbCrystals` to `SSXProcessingResult` table. ## v1.2.3 (11/11/2024) From 21e8e5754c488fea2728dbfba5558daa302ea2f6 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 16:56:57 +0100 Subject: [PATCH 46/61] =?UTF-8?q?Bump=20version:=201.2.3=20=E2=86=92=201.2?= =?UTF-8?q?.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 06e6bbb..05847a9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.3 +version = version = 1.2.3 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 51290c9..321e3a4 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.3" +__version__ = "__version__ = "1.2.3"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 01586cf8cbefae8bc1a3517cab24d41ecb27155b Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 16:57:12 +0100 Subject: [PATCH 47/61] =?UTF-8?q?Bump=20version:=201.2.3=20=E2=86=92=201.2?= =?UTF-8?q?.4?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 2f0ca86..5b86553 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.3 +current_version = 1.2.4 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index 05847a9..1f79d78 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.3 +version = version = 1.2.4 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 321e3a4..ebaa01d 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.3"" +__version__ = "__version__ = "1.2.4"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From e74804594b97d7ee27c595e63f894e34c36d9b37 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 16:59:40 +0100 Subject: [PATCH 48/61] fix init file --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index ebaa01d..9dd5207 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.4"" +__version__ = "1.2.4" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 47610ec030ef486ff5abe790c358fc3080fb0aeb Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 17:03:20 +0100 Subject: [PATCH 49/61] =?UTF-8?q?Bump=20version:=201.2.4=20=E2=86=92=201.2?= =?UTF-8?q?.4?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.cfg b/setup.cfg index 1f79d78..47dac70 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = 1.2.4 +version = version = version = 1.2.4 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 9dd5207..ebaa01d 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.4" +__version__ = "__version__ = "1.2.4"" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From aa45b0804d01af0d006521fbac83f5f3f13eb7f6 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 17:04:05 +0100 Subject: [PATCH 50/61] fix init file --- src/ispyb/models/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index ebaa01d..9dd5207 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "__version__ = "1.2.4"" +__version__ = "1.2.4" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From 61fb63a2036788c31ad33809970bbd3932b37b27 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 13 Nov 2024 17:07:25 +0100 Subject: [PATCH 51/61] fix init file --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 47dac70..6d0c4c2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = version = version = 1.2.4 +version = 1.2.4 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown From 04dd1f656919a50d74234a8b3525758a75e3d772 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Wed, 27 Nov 2024 09:36:36 +0000 Subject: [PATCH 52/61] Update models to schema version 1.2.5 --- src/ispyb/models/_auto_db_schema.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 7b73682..1f40b58 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -3960,8 +3960,8 @@ class Component(Base): class LabContact(Base): __tablename__ = "LabContact" __table_args__ = ( - Index("personAndProposal", "personId", "proposalId", unique=True), Index("cardNameAndProposal", "cardName", "proposalId", unique=True), + Index("personAndProposal", "personId", "proposalId", unique=True), ) labContactId = Column(INTEGER(10), primary_key=True) @@ -6376,6 +6376,7 @@ class SSXProcessingResult(Base): ForeignKey( "DataCollection.dataCollectionId", ondelete="CASCADE", onupdate="CASCADE" ), + nullable=False, index=True, ) hitRate = Column(Float) From 54b7cfe04434fdfead5c8ba68fcd0904e98b7661 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 27 Nov 2024 10:42:52 +0100 Subject: [PATCH 53/61] history file updated --- HISTORY.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index 4089aa9..a858915 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,6 +2,11 @@ ## Unreleased / main +## v1.2.5 (26/11/2024) + +Make `dataCollectionId` mandatory in the `SSXProcessingResult` table. +Create a new entry in the `Permission` table to be used by beamine service accounts. + ## v1.2.4 (13/11/2024) Add `nbCrystals` to `SSXProcessingResult` table. From 610077ef0831bf1ad160a712b9a0a8d0d3c6ab64 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 27 Nov 2024 10:44:50 +0100 Subject: [PATCH 54/61] =?UTF-8?q?Bump=20version:=201.2.4=20=E2=86=92=201.2?= =?UTF-8?q?.5?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 5b86553..1ac4e9d 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.4 +current_version = 1.2.5 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index 6d0c4c2..aadadb2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.4 +version = 1.2.5 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index 9dd5207..ea4eeb7 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.4" +__version__ = "1.2.5" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From e65159daccd30ff6962470a325b1d26d2123dad8 Mon Sep 17 00:00:00 2001 From: hormiai76 Date: Wed, 27 Nov 2024 12:59:17 +0000 Subject: [PATCH 55/61] Update models to schema version 1.2.6 --- src/ispyb/models/_auto_db_schema.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 1f40b58..34fa924 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -6643,7 +6643,9 @@ class SSXProcessingResultAttachment(Base): ) fileName = Column(String(255), nullable=False) filePath = Column(String(255), nullable=False) - fileType = Column(Enum("Result", "Log", "Graph"), nullable=False) + fileType = Column( + Enum("Real-time processing results", "Processing results"), nullable=False + ) createdTimeStamp = Column( TIMESTAMP, nullable=False, server_default=text("current_timestamp()") ) From 28d99f13db8a85e49e4190dc8c63f833650bc29e Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 27 Nov 2024 14:18:22 +0100 Subject: [PATCH 56/61] history file updated --- HISTORY.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/HISTORY.md b/HISTORY.md index a858915..c5b4690 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,6 +2,11 @@ ## Unreleased / main +## v1.2.5 (26/11/2024) + +Update `fyleType` Enum values in the `SSXProcessingResultAttachment` table. + + ## v1.2.5 (26/11/2024) Make `dataCollectionId` mandatory in the `SSXProcessingResult` table. From dc764a93d78dfa3351ee8635ccc0b479e1c90b1b Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 27 Nov 2024 14:19:58 +0100 Subject: [PATCH 57/61] =?UTF-8?q?Bump=20version:=201.2.5=20=E2=86=92=201.2?= =?UTF-8?q?.6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .bumpversion.cfg | 2 +- setup.cfg | 2 +- src/ispyb/models/__init__.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 1ac4e9d..2c89678 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.5 +current_version = 1.2.6 commit = True tag = True diff --git a/setup.cfg b/setup.cfg index aadadb2..ad260d7 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.5 +version = 1.2.6 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/__init__.py b/src/ispyb/models/__init__.py index ea4eeb7..2dd8c35 100644 --- a/src/ispyb/models/__init__.py +++ b/src/ispyb/models/__init__.py @@ -30,7 +30,7 @@ EventChain, ) -__version__ = "1.2.5" +__version__ = "1.2.6" DataCollection.GridInfo = relationship( "GridInfo", secondary="DataCollectionGroup", back_populates="DataCollection" From b188f847b5c0b8bce0aa0a37d3aee21ddb60d16f Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 3 Jun 2026 11:11:42 +0200 Subject: [PATCH 58/61] feat: new dewar type --- src/ispyb/models/_auto_db_schema.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 34fa924..44c0503 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -2006,7 +2006,7 @@ class XRFFluorescenceMappingROI(Base): Column("transportValue", INTEGER(10)), Column("trackingNumberToSynchrotron", String(30)), Column("trackingNumberFromSynchrotron", String(30)), - Column("type", Enum("Dewar", "Toolbox"), server_default=text("'Dewar'")), + Column("type", Enum("Dewar", "Toolbox", "Other"), server_default=text("'Dewar'")), Column("isReimbursed", TINYINT(1), server_default=text("'0'")), Column("sessionId", INTEGER(10), server_default=text("'0'")), Column("beamlineName", String(45)), @@ -2739,7 +2739,7 @@ class XRFFluorescenceMappingROI(Base): Column("Dewar_firstExperimentId", INTEGER(10)), Column("Dewar_trackingNumberToSynchrotron", String(30)), Column("Dewar_trackingNumberFromSynchrotron", String(30)), - Column("Dewar_type", Enum("Dewar", "Toolbox"), server_default=text("'Dewar'")), + Column("Dewar_type", Enum("Dewar", "Toolbox", "Other"), server_default=text("'Dewar'")), Column("Shipping_shippingId", INTEGER(10), server_default=text("'0'")), Column("Shipping_proposalId", INTEGER(10), server_default=text("'0'")), Column("Shipping_shippingName", String(45)), @@ -4687,7 +4687,7 @@ class Dewar(Base): trackingNumberFromSynchrotron = Column(String(30)) facilityCode = Column(String(20), comment="Unique barcode assigned to each dewar") type = Column( - Enum("Dewar", "Toolbox"), nullable=False, server_default=text("'Dewar'") + Enum("Dewar", "Toolbox", "Other"), nullable=False, server_default=text("'Dewar'") ) isReimbursed = Column( TINYINT(1), From fc2ea36aa1d9add8731bfb85d80ee886fba9d6ac Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 3 Jun 2026 11:23:56 +0200 Subject: [PATCH 59/61] feat: new dewar type --- .bumpversion.cfg | 2 +- HISTORY.md | 7 ++++++- setup.cfg | 2 +- src/ispyb/models/_auto_db_schema.py | 9 ++++++--- 4 files changed, 14 insertions(+), 6 deletions(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 2c89678..b98cb7f 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.2.6 +current_version = 1.2.7 commit = True tag = True diff --git a/HISTORY.md b/HISTORY.md index c5b4690..c6304d1 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -2,7 +2,12 @@ ## Unreleased / main -## v1.2.5 (26/11/2024) +## v1.2.7 (03/06/2026) + +Update `type` Enum values in the `Dewar` table. + + +## v1.2.6 (26/11/2024) Update `fyleType` Enum values in the `SSXProcessingResultAttachment` table. diff --git a/setup.cfg b/setup.cfg index ad260d7..8eff894 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,6 +1,6 @@ [metadata] name = ispyb-models-pyispyb -version = 1.2.6 +version = 1.2.7 description = SQLAlchemy ORM models for the ISPyB database long_description = file: README.md long_description_content_type = text/markdown diff --git a/src/ispyb/models/_auto_db_schema.py b/src/ispyb/models/_auto_db_schema.py index 44c0503..a18ea24 100644 --- a/src/ispyb/models/_auto_db_schema.py +++ b/src/ispyb/models/_auto_db_schema.py @@ -31,7 +31,6 @@ from .base import CustomBase - Base = declarative_base(cls=CustomBase) metadata = Base.metadata @@ -2739,7 +2738,9 @@ class XRFFluorescenceMappingROI(Base): Column("Dewar_firstExperimentId", INTEGER(10)), Column("Dewar_trackingNumberToSynchrotron", String(30)), Column("Dewar_trackingNumberFromSynchrotron", String(30)), - Column("Dewar_type", Enum("Dewar", "Toolbox", "Other"), server_default=text("'Dewar'")), + Column( + "Dewar_type", Enum("Dewar", "Toolbox", "Other"), server_default=text("'Dewar'") + ), Column("Shipping_shippingId", INTEGER(10), server_default=text("'0'")), Column("Shipping_proposalId", INTEGER(10), server_default=text("'0'")), Column("Shipping_shippingName", String(45)), @@ -4687,7 +4688,9 @@ class Dewar(Base): trackingNumberFromSynchrotron = Column(String(30)) facilityCode = Column(String(20), comment="Unique barcode assigned to each dewar") type = Column( - Enum("Dewar", "Toolbox", "Other"), nullable=False, server_default=text("'Dewar'") + Enum("Dewar", "Toolbox", "Other"), + nullable=False, + server_default=text("'Dewar'"), ) isReimbursed = Column( TINYINT(1), From 0858fe298304f30b00823e2fd51d46cfca2640c7 Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 3 Jun 2026 11:28:38 +0200 Subject: [PATCH 60/61] feat: new dewar type --- tests/conftest.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/conftest.py b/tests/conftest.py index ae46a07..8754102 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -6,7 +6,6 @@ import sqlalchemy.orm import sqlalchemy.schema - engine = sqlalchemy.create_engine( url=os.environ["SQLALCHEMY_DATABASE_URI"], connect_args={"use_pure": True}, From c6a5bfab0fca78da176383c54a8d39385ac7c97c Mon Sep 17 00:00:00 2001 From: Alberto Nardella Date: Wed, 3 Jun 2026 14:09:12 +0200 Subject: [PATCH 61/61] remove tests --- .github/workflows/{test.yml => test.yml.old} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{test.yml => test.yml.old} (100%) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml.old similarity index 100% rename from .github/workflows/test.yml rename to .github/workflows/test.yml.old