Metadata fbc3 group #988

Hemant27031999 · 2020-08-15T13:00:49Z

Description of Features

Metadata Classes: A separate directory for handling metadata information is made inside cobra/core directory. Every object derived from SBase can have meta information like annotation (CVTerms), notes, history attached to it.

The Notes class is holding a simple string containing notes data (XHTML string) and a dictionary, synchronized with the notes string, storing key-value pair of the form <p> key : value </p> present in the notes string. One can only modify this key-value pair data, he can't add new key-value pairs inside notes because notes are not a right place to store these key-value pairs.
The CVTerms class for storing externally linked resources to each component derived from SBase. This class is maintaining the new format annotation as well as old format annotation simultaneously, and both are kept synchronized with each other. Changing one will modify the other accordingly. This new class for annotation can handle any type of annotation data (be it the case of nested annotation or alternative annotation). It can read the old format as well as the new format annotation data from JSON and other formats. At the time of writing back the model, the new data format is used because it contains the complete data organized in the same way as SBML.
The History class used for storing the history, validating dates, etc, is now attached to each component derived from SBase.
The KeyValuePair class for storing key-value pairs, defined by fbc-v3.

The last three metadata objects (i.e CVTerms, History, KeyValuePair) are present inside a single attribute of SBase (Object) class and can be accessed via object.annotation.cvterms, object.annotation.history and object.annotation.key_value_data attributes. Calling simply the annotation attribute (object.annotation) will return the annotation data in old format (making it backward compatible).

Group to JSON: The support of the group package is extended to JSON.
JSON schema v2: The version2 of JSON schema has been added which defines the new format annotation, history, key-value pair, notes, group package data, user-defined constraints data and basic SBML info.

Issues Fixed

fixes issue Discussion for Group feature in COBRApy #954: The support of group package has been extended to JSON and other formats.
fixes issue JSON format does not support -inf/inf bounds #856: The infinity values are also enabled for storing bounds.
fixes issue Store SBML meta information (level, version, packages, provenance) #810: The sbml_info storing basic information of SBML is written to JSON to store the basic SBML document information like packages, level, version, notes, annotation attached to the SBML component etc.
fixes issue Cannot export SBML when annotation is a list of lists #736: If annotation is present in the form of list of list, it is first modified and then data is read.
fixes issue Consistent output multiple-value elements as array of string in JSON/Yaml format. #706: Single annotation resource are now put into a string. While reading from JSON also, if a single resource attribute is in the form of string, it is first fixed to list and then read into the model.
fixes issue Import/export of SBML <notes> #695: The notes data is now read into a string and this string is synchronized with a dictionary storing key-value pairs present inside notes string.
fixes issue Update storage of annotations #684: The complete metadata structure (CVTerms, Notes, History) has been redesigned with backward compatibility. Old format data is read, fixed and then written in new format metadata structures. The fbc-v3 "KeyValuePair" class is also a part of this new format annotation. Its corresponding class and its support to JSON and other format has been added. However, the SBML parser for it has to be updated when libsbml adds support for fbc-v3.
fixes issue Loss of relation elements in annotation when writing a SBML model again. #937: The annotation format has been updated, which is backward compatible too.
JSON schema v1: The JSON schema version 1 is modified to resolve some pre-existing issues.

Tests

Tests for all the newly implemented features are added to check the functionalities. A few old tests are also modified accordingly. Some tests which were initially marked 'xfail' are now working dew to modified formats.

codecov-commenter · 2020-08-26T09:24:37Z

Codecov Report

Merging #988 into devel will decrease coverage by 1.31%.
The diff coverage is 75.92%.

@@            Coverage Diff             @@
##            devel     #988      +/-   ##
==========================================
- Coverage   84.45%   83.13%   -1.32%     
==========================================
  Files          58       64       +6     
  Lines        5036     5888     +852     
  Branches     1092     1276     +184     
==========================================
+ Hits         4253     4895     +642     
- Misses        508      660     +152     
- Partials      275      333      +58

Impacted Files	Coverage Δ
src/cobra/core/formula.py	`25.00% <ø> (ø)`
src/cobra/core/metabolite.py	`70.65% <ø> (ø)`
src/cobra/core/reaction.py	`88.02% <ø> (ø)`
src/cobra/flux_analysis/deletion.py	`93.33% <ø> (ø)`
src/cobra/flux_analysis/loopless.py	`91.11% <ø> (ø)`
src/cobra/flux_analysis/variability.py	`92.78% <ø> (ø)`
src/cobra/sampling/achr.py	`100.00% <ø> (ø)`
src/cobra/sampling/optgp.py	`96.92% <ø> (ø)`
src/cobra/summary/metabolite_summary.py	`89.65% <ø> (ø)`
src/cobra/summary/model_summary.py	`86.66% <ø> (ø)`
... and 28 more

Continue to review full report at Codecov.

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matthiaskoenig · 2020-08-26T23:53:03Z

@Hemant27031999 I went over most of the code and cleaned it up. Was much more work then expected but most of the metadata is now pretty clean and neat. I also updated to the latest develop code.

Could you

add the cvterms.to_dict method which will handle the serialization of the cvterms. I added the similar methods on the other metadata objects. You can currently see in the two failing tests where this is still missing
can you update the `metadata.ipynb I started for the the documentation of the metadata features. Here you should add the common use cases, i.e., adding CVTerms, adding ModelHistory, modifying notes, storying information as Key-Value pairs, ...

Hemant27031999 · 2020-08-27T10:19:44Z

@matthiaskoenig I have made the requested changes. All tests are passing now.

Hemant27031999 · 2020-08-28T06:00:44Z

Hey people, metadata and UserDefinedConstraints are two separate functionalities. So I have removed UserDefinedConstraint from this branch, it now majorly includes metadata and some JSON serialization. I shall link another PR for Constraint class.

draeger · 2020-08-20T09:42:41Z

src/cobra/io/dict.py

+    cvterms = data["cvterms"] if "cvterms" in data else None
+    history = data["history"] if "history" in data else None
+    keyValueDict = data["history"] if "key_value_data" in data else None


Would it be possible to define String literals as constants? Using such literal expressions repeatedly belongs to a possible source of error (because of typos) that can be relatively easily eliminated.

draeger · 2020-08-20T09:43:40Z

src/cobra/io/dict.py

+    if "sbo" in data:
+        annotation["sbo"] = [data["sbo"]]


Here also: Please avoid using String literals repeatedly.

draeger · 2020-08-20T09:44:24Z

src/cobra/io/dict.py

@@ -180,7 +186,7 @@ def _update_optional(cobra_object, new_dict, optional_attribute_dict,
 def metabolite_to_dict(metabolite):
    new_met = OrderedDict()
    for key in _REQUIRED_METABOLITE_ATTRIBUTES:
-        if key == 'id':
+        if key == "id":


Again... Define as a String constant if possible.

draeger · 2020-08-20T09:45:56Z

src/cobra/io/dict.py

                    cobra_members.append(cobra_obj)
                elif member["type"] == "Gene":
                    cobra_obj = model.genes.get_by_id(
-                        F_REPLACE["F_GENE"](member["idRef"]))
+                        F_REPLACE["F_GENE"](member["idRef"])


I just notice that there are many String literals all over the source code. I will not add further remarks about it. If possible, please go through the source code, identify String literals and replace them with constant expressions (constant variables).

draeger · 2020-08-20T10:12:30Z

src/cobra/core/user_defined_constraints.py

@@ -295,7 +295,7 @@ def constraint_from_expression(id=None, expression: 'str' = '',
        tree = ast.parse(source=expression, mode='eval')
        compute_nodes = UserDefinedConstraint.ComputeNumericNodes()
        tree = compute_nodes.visit(tree)
-        print(ast.dump(tree))
+        print((ast.dump(tree)))


Why are additional parentheses needed?

I am not sure if I added them or the code formatter. By the way, I will update it. This file is actually a part of other the PR now. It's no longer on this branch.

draeger · 2020-08-20T10:13:30Z

src/cobra/core/user_defined_constraints.py

+                    result = Num(n=node.left.n + node.right.n)
+                    return copy_location(result, node)
+                elif isinstance(node.op, Sub):
+                    result = Num(n=node.left.n - node.right.n)
+                    return copy_location(result, node)
+                elif isinstance(node.op, Mult):
+                    result = Num(n=node.left.n * node.right.n)
+                    return copy_location(result, node)
+                elif isinstance(node.op, Div):
+                    result = Num(n=node.left.n / node.right.n)
+                    return copy_location(result, node)
+                elif isinstance(node.op, Mod):
+                    result = Num(n=node.left.n % node.right.n)


Please add blanks between variables and operators, e.g., change n=xyz to n = xyz.

The python code format tool "black" doesn't allow spaces between the variable and operator when passed as arguments.

draeger · 2020-08-20T10:19:26Z

src/cobra/core/formula.py

+    "P": 30.973761,
+    "S": 32.065000,
+    "Cl": 35.453000,
+    "Ar": 39.948000,
+    "K": 39.098300,
+    "Ca": 40.078000,
+    "Sc": 44.955910,
+    "Ti": 47.867000,
+    "V": 50.941500,
+    "Cr": 51.996100,
+    "Mn": 54.938049,
+    "Fe": 55.845000,
+    "Co": 58.933200,
+    "Ni": 58.693400,
+    "Cu": 63.546000,
+    "Zn": 65.409000,
+    "Ga": 69.723000,
+    "Ge": 72.640000,
+    "As": 74.921600,
+    "Se": 78.960000,
+    "Br": 79.904000,
+    "Kr": 83.798000,
+    "Rb": 85.467800,
+    "Sr": 87.620000,
+    "Y": 88.905850,
+    "Zr": 91.224000,
+    "Nb": 92.906380,
+    "Mo": 95.940000,
+    "Tc": 98.000000,
+    "Ru": 101.070000,
+    "Rh": 102.905500,
+    "Pd": 106.420000,
+    "Ag": 107.868200,
+    "Cd": 112.411000,
+    "In": 114.818000,
+    "Sn": 118.710000,
+    "Sb": 121.760000,
+    "Te": 127.600000,
+    "I": 126.904470,
+    "Xe": 131.293000,
+    "Cs": 132.905450,
+    "Ba": 137.327000,
+    "La": 138.905500,
+    "Ce": 140.116000,
+    "Pr": 140.907650,
+    "Nd": 144.240000,
+    "Pm": 145.000000,
+    "Sm": 150.360000,
+    "Eu": 151.964000,
+    "Gd": 157.250000,
+    "Tb": 158.925340,
+    "Dy": 162.500000,
+    "Ho": 164.930320,
+    "Er": 167.259000,
+    "Tm": 168.934210,
+    "Yb": 173.040000,
+    "Lu": 174.967000,
+    "Hf": 178.490000,
+    "Ta": 180.947900,
+    "W": 183.840000,
+    "Re": 186.207000,
+    "Os": 190.230000,
+    "Ir": 192.217000,
+    "Pt": 195.078000,
+    "Au": 196.966550,
+    "Hg": 200.590000,
+    "Tl": 204.383300,
+    "Pb": 207.200000,
+    "Bi": 208.980380,
+    "Po": 209.000000,
+    "At": 210.000000,
+    "Rn": 222.000000,
+    "Fr": 223.000000,
+    "Ra": 226.000000,
+    "Ac": 227.000000,
+    "Th": 232.038100,
+    "Pa": 231.035880,
+    "U": 238.028910,
+    "Np": 237.000000,
+    "Pu": 244.000000,
+    "Am": 243.000000,
+    "Cm": 247.000000,
+    "Bk": 247.000000,
+    "Cf": 251.000000,
+    "Es": 252.000000,
+    "Fm": 257.000000,
+    "Md": 258.000000,
+    "No": 259.000000,
+    "Lr": 262.000000,
+    "Rf": 261.000000,
+    "Db": 262.000000,
+    "Sg": 266.000000,
+    "Bh": 264.000000,
+    "Hs": 277.000000,
+    "Mt": 268.000000,
+    "Ds": 281.000000,
+    "Rg": 272.000000,
+    "Cn": 285.000000,
+    "Uuq": 289.000000,
+    "Uuh": 292.000000,


Please note that elements naturally occur in different isotopes. Please indicate if these values are the average or the most likely molecular weight in form of a user-readable description. Better could be to use a dictionary whose values are lists of values for the different isotopes.

Members, please provide review. I haven't updated it. It's been reformatted by "black" itself by adding double quotes in place of single quotes.

draeger · 2020-08-20T10:37:53Z

cobra/core/annotation.py

+QUALIFIER_TYPES = (
+    "is", "hasPart", "isPartOf", "isVersionOf", "hasVersion",
+    "isHomologTo", "isDescribedBy", "isEncodedBy", "encodes",
+    "occursIn", "hasProperty", "isPropertyOf", "hasTaxon",
+    "unknown", "bqm_is", "bqm_isDescribedBy", "bqm_isDerivedFrom",
+    "bqm_isInstanceOf", "bqm_hasInstance", "bqm_unknown",
+)


Please add a documentation comment here where to find the most recent list of qualifiers to ease later updats.

Hemant27031999 and others added 30 commits June 4, 2020 22:14

added annotation class

782b645

made some modifications

9709974

made the complete metadata package

a7af772

modified meta_data classes

a191413

modified classes to look exactly like dictionaries and lists

4ea5b3e

modified imports and incorporated SBO term in metadata

7795ea6

made the classed to inherit from MutableSequence and MutableMapping

02345bb

adding backward compatibility

4c6c1ca

added instance

ff72c55

work on annotation structure

989ffe4

adding json example

a4eb840

fixed instance2

cf38e02

work on cvterms

7d490a4

made backward compatible

024c980

code review metadata

ff440fb

cleaned the metadata class by putting code in respective classes

e4ad484

new annotation format supported for SBML to cobra model

2508ac3

added io for json and other formats

d5fc54c

added tests for new annotation format

c9e904b

updated history

a6e2f8a

fixing broken tests

23f9699

commented a few methods

2f55bbf

added equal method inisde metadata classes

5aae1b0

modified directories paths

d467a14

fixed imports and tox tests

e4cc72b

solved the problem of annotation copy

32a81da

new notes format

a07ccaf

code refactoring

f69a55c

modified history, keyvaluepair and notes

e4ab40b

modified tests and imports

8dc96cf

modified notes return type

66dd463

matthiaskoenig added 9 commits August 26, 2020 15:46

adding dependency for json validation

479c2b2

added .idea files

543d1f8

merged latest devel

65e48f1

refactored and cleanup of history

564a51a

Intermediate refactoring, breaking changes

a6aefc5

refactored keyvaluepairs

42f4838

cleanup of datetimes

b3e26cc

cleanup metadata

ca9ef48

cleanup dict methods

093f799

Hemant27031999 added 2 commits August 27, 2020 14:48

added to_dict for CVTerm and fixed models

b5f7516

added metadata.ipynb

c8b850a

fixed imports

67d3af1

Hemant27031999 force-pushed the metadata_fbc3_group branch from e77f9ab to 67d3af1 Compare August 27, 2020 11:36

Hemant27031999 and others added 4 commits August 27, 2020 17:37

Merge branch 'devel' into metadata_fbc3_group

b951dbd

smaller fix to_dict usage

e5b3fba

modified to_dict for cvterms

8b2d6dc

separated UserDefinedConstraint

010bb44

Hemant27031999 mentioned this pull request Aug 28, 2020

User defined constraints #996

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draeger suggested changes Aug 28, 2020

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cdiener added the stale The issue or pull request lacks activity. label Sep 1, 2021

Midnighter mentioned this pull request May 11, 2022

Import/export of SBML <notes> #695

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akaviaLab mentioned this pull request May 29, 2022

Metadata fbc3 group #1225

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cdiener mentioned this pull request Jun 6, 2022

User defined constraints #1228

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akaviaLab pushed a commit to akaviaLab/cobrapy that referenced this pull request Jun 19, 2022

merged devel into opencobra#988 and updated it to current code

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Metadata fbc3 group #988

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Hemant27031999 commented Aug 15, 2020 •

edited

codecov-commenter commented Aug 26, 2020 •

edited

matthiaskoenig commented Aug 26, 2020

Hemant27031999 commented Aug 27, 2020

Hemant27031999 commented Aug 28, 2020

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draeger Aug 20, 2020

Metadata fbc3 group #988

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Metadata fbc3 group #988

Conversation

Hemant27031999 commented Aug 15, 2020 • edited

Description of Features

Issues Fixed

Tests

codecov-commenter commented Aug 26, 2020 • edited

Codecov Report

matthiaskoenig commented Aug 26, 2020

Hemant27031999 commented Aug 27, 2020

Hemant27031999 commented Aug 28, 2020

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Hemant27031999 commented Aug 15, 2020 •

edited

codecov-commenter commented Aug 26, 2020 •

edited